Kenneth A Feldmann

Interests

Teaching

Biotechnology

Research

Functional Genomics

Courses

Scholarly Contributions

Chapters

• Feldmann, K. A., & Goff, S. A. (2014). The first plant genome sequence; Arabidopsis thaliana. In Genomes of Herbaceous Land Plants.
• Goff, S. A., Feldmann, K. A., & Schnable, J. (2014). The evolution of plant gene and genome sequencing. In Genomes of Herbaceous Land Plants.

Journals/Publications

• Feldmann, K. A., Dyer, J., Tomasi, P., Lohrey, G., Weaver, J. M., & Jenks, M. (2018). Cuticular wax variants in a population of switchgrass (Panicum virgatum L.). Industrial Crops and Products, 117, 310-316. doi:https://doi.org/10.1016/j.indcrop.2018.02.081
• Chuang, M. a., Xin, M., Feldmann, K. A., & Wang, X. (2014). Machine learning-based differential network analysis: A study of stress-responsive transcriptomes in Arabidopsis. Plant Cell, 26(2), 520-537.
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  Abstract: Machine learning (ML) is an intelligent data mining technique that builds a prediction model based on the learning of prior knowledge to recognize patterns in large-scale data sets. We present an ML-based methodology for transcriptome analysis via comparison of gene coexpression networks, implemented as an R package called machine learning-based differential network analysis (mlDNA) and apply this method to reanalyze a set of abiotic stress expression data in Arabidopsis thaliana. The mlDNA first used a ML-based filtering process to remove nonexpressed, constitutively expressed, or non-stressresponsive "noninformative" genes prior to network construction, through learning the patterns of 32 expression characteristics of known stress-related genes. The retained "informative" genes were subsequently analyzed by ML-based network comparison to predict candidate stress-related genes showing expression and network differences between control and stress networks, based on 33 network topological characteristics. Comparative evaluation of the network-centric and gene-centric analytic methods showed that mlDNA substantially outperformed traditional statistical testing-based differential expression analysis at identifying stress-related genes, with markedly improved prediction accuracy. To experimentally validate the mlDNA predictions, we selected 89 candidates out of the 1784 predicted salt stress-related genes with available SALK T-DNA mutagenesis lines for phenotypic screening and identified two previously unreported genes, mutants of which showed salt-sensitive phenotypes. © 2014 American Society of Plant Biologists. All rights reserved.
• Weaver, J., Montes-Sujo, L., & Feldmann, K. A. (2014). A simplified technique for the propagation of shoots from nodes of Switchgrass (Panicum virgatum L.) genotypes. BioEnergy Research.
• White, J. W., Andrade-Sanchez, P., Gore, M. A., Bronson, K. F., Coffelt, T. A., Conley, M. M., Feldmann, K. A., French, A. N., Heun, J. T., Hunsaker, D. J., Jenks, M. A., Kimball, B. A., Roth, R. L., Strand, R. J., Thorp, K. R., Wall, G. W., & Wang, G. (2012). Field-based phenomics for plant genetics research. Field Crops Research, 133, 101-112.
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  Abstract: A major challenge for crop research in the 21st century is how to predict crop performance as a function of genetic architecture. Advances in " next generation" DNA sequencing have greatly improved genotyping efficiency and reduced genotyping costs. Methods for characterizing plant traits (phenotypes), however, have much progressed more slowly over the past 30 years, and constraints in phenotyping capability limit our ability to dissect the genetics of quantitative traits, especially those related to harvestable yield and stress tolerance. As a case in point, mapping populations for major crops may consist of 20 or more families, each represented by as many as 200 lines, necessitating field trials with over 20,000 plots at a single location. Investing in the resources and labor needed to quantify even a few agronomic traits for linkage with genetic markers in such massive populations is currently impractical for most breeding programs. Herein, we define key criteria, experimental approaches, equipment and data analysis tools required for robust, high-throughput field-based phenotyping (FBP). The focus is on simultaneous proximal sensing for spectral reflectance, canopy temperature, and plant architecture where a vehicle carrying replicated sets of sensors records data on multiple plots, with the potential to record data throughout the crop life cycle. The potential to assess traits, such as adaptations to water deficits or acute heat stress, several times during a single diurnal cycle is especially valuable for quantifying stress recovery. Simulation modeling and related tools can help estimate physiological traits such as canopy conductance and rooting capacity. Many of the underlying techniques and requisite instruments are available and in use for precision crop management. Further innovations are required to better integrate the functions of multiple instruments and to ensure efficient, robust analysis of the large volumes of data that are anticipated. A complement to the core proximal sensing is high-throughput phenotyping of specific traits such as nutrient status, seed composition, and other biochemical characteristics, as well as underground root architecture. The ability to " ground truth" results with conventional measurements is also necessary. The development of new sensors and imaging systems undoubtedly will continue to improve our ability to phenotype very large experiments or breeding nurseries, with the core FBP abilities achievable through strong interdisciplinary efforts that assemble and adapt existing technologies in novel ways. © 2012 .
• Wang, W., Yang, D., & Feldmann, K. A. (2011). EFO1 and EFO2, encoding putative WD-domain proteins, have overlapping and distinct roles in the regulation of vegetative development and flowering of Arabidopsis. Journal of Experimental Botany, 62(3), 1077-1088.
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  PMID: 21242318;Abstract: From screening a population of Arabidopsis overexpression lines, two Arabidopsis genes were identified, EFO1 (EARLY FLOWERING BY OVEREXPRESSION 1) and EFO2, that confer early flowering when overexpressed. The two genes encode putative WD-domain proteins which share high sequence similarity and constitute a small subfamily. Interestingly, the efo2-1 loss-of-function mutant also flowered earlier in short days and slightly earlier in long days than the wild type, while no flowering-time or morphological differences were observed in efo1-1 relative to the wild type. In addition, the efo2-1 mutation perturbed hypocotyl elongation, leaf expansion and formation, and stem elongation. EFO1 and EFO2 are both regulated by the circadian clock. Expression and genetic analyses revealed that EFO2 suppresses flowering largely through the action of CONSTANS (CO) and FLOWERING LOCUS T (FT), suggesting that EFO2 is a negative regulator of photoperiodic flowering. The growth defects in efo2-1 were augmented in efo1 efo2, but the induction of FT in the double mutant was comparable to that in efo2-1. Thus, while EFO2 acts as a floral repressor, EFO1 may not be directly involved in flowering, but the two genes do have overlapping roles in regulating other developmental processes. EFO1 and EFO2 may function collectively to serve as one of the converging points where the signals of growth and flowering intersect. © 2010 The Author(s).
• Tatarinova, T. V., Alexandrov, N. N., Bouck, J. B., & Feldmann, K. A. (2010). GC₃ biology in corn, rice, sorghum and other grasses. BMC Genomics, 11(1).
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  PMID: 20470436;PMCID: PMC2895627;Abstract: Background: The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates.Results: Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC3) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC3 content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC3 bimodality in grasses.Conclusions: Our findings suggest that high levels of GC3 typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation. © 2010 Tatarinova et al; licensee BioMed Central Ltd.
• Alexandrov, N. N., Brover, V. V., Freidin, S., Troukhan, M. E., Tatarinova, T. V., Zhang, H., Swaller, T. J., Lu, Y., Bouck, J., Flavell, R. B., & Feldmann, K. A. (2009). Insights into corn genes derived from large-scale cDNA sequencing. Plant Molecular Biology, 69(1-2), 179-194.
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  PMID: 18937034;PMCID: PMC2709227;Abstract: We present a large portion of the transcriptome of Zea mays, including ESTs representing 484,032 cDNA clones from 53 libraries and 36,565 fully sequenced cDNA clones, out of which 31,552 clones are non-redundant. These and other previously sequenced transcripts have been aligned with available genome sequences and have provided new insights into the characteristics of gene structures and promoters within this major crop species. We found that although the average number of introns per gene is about the same in corn and Arabidopsis, corn genes have more alternatively spliced isoforms. Examination of the nucleotide composition of coding regions reveals that corn genes, as well as genes of other Poaceae (Grass family), can be divided into two classes according to the GC content at the third position in the amino acid encoding codons. Many of the transcripts that have lower GC content at the third position have dicot homologs but the high GC content transcripts tend to be more specific to the grasses. The high GC content class is also enriched with intronless genes. Together this suggests that an identifiable class of genes in plants is associated with the Poaceae divergence. Furthermore, because many of these genes appear to be derived from ancestral genes that do not contain introns, this evolutionary divergence may be the result of horizontal gene transfer from species not only with different codon usage but possibly that did not have introns, perhaps outside of the plant kingdom. By comparing the cDNAs described herein with the non-redundant set of corn mRNAs in GenBank, we estimate that there are about 50,000 different protein coding genes in Zea. All of the sequence data from this study have been submitted to DDBJ/GenBank/EMBL under accession numbers EU940701-EU977132 (FLI cDNA) and FK944382-FL482108 (EST). © 2008 The Author(s).
• Wu, C., Trieu, A., Radhakrishnan, P., Kwok, S. F., Harris, S., Zhang, K., Wang, J., Wan, J., Zhai, H., Takatsuto, S., Matsumoto, S., Fujiok, S., Feldmann, K. A., & Pennell, R. I. (2008). Brassinosteroids regulate grain filling in rice. Plant Cell, 20(8), 2130-2145.
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  PMID: 18708477;PMCID: PMC2553602;Abstract: Genes controlling hormone levels have been used to increase grain yields in wheat (Triticum aestivum) and rice (Oryza sativa). We created transgenic rice plants expressing maize (Zea mays), rice, or Arabidopsis thaliana genes encoding sterol C-22 hydroxylases that control brassinosteroid (BR) hormone levels using a promoter that is active in only the stems, leaves, and roots. The transgenic plants produced more tillers and more seed than wild-type plants. The seed were heavier as well, especially the seed at the bases of the spikes that fill the least. These phenotypic changes brought about 15 to 44% increases in grain yield per plant relative to wild-type plants in greenhouse and field trials. Expression of the Arabidopsis C-22 hydroxylase in the embryos or endosperms themselves had no apparent effect on seed weight. These results suggested that BRs stimulate the flow of assimilate from the source to the sink. Microarray and photosynthesis analysis of transgenic plants revealed evidence of enhanced CO2 assimilation, enlarged glucose pools in the flag leaves, and increased assimilation of glucose to starch in the seed. These results further suggested that BRs stimulate the flow of assimilate. Plants have not been bred directly for seed filling traits, suggesting that genes that control seed filling could be used to further increase grain yield in crop plants. © 2008 American Society of Plant Biologists.
• Coury, D. A., Zhang, C., Ara, K. o., Skaggs, M. I., Christensen, C. A., Drews, G. N., Feldmann, K. A., & Yadegari, R. (2007). Segregation distortion in Arabidopsis gametophytic factor 1 (gfa1) mutants is caused by a deficiency of an essential RNA splicing factor. Sexual Plant Reproduction, 20(2), 87-97.
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  Abstract: The female and male gametophytes are critical components of the angiosperm life cycle and are essential for the reproductive process. The gametophytes share many essential cellular processes with each other and with the sporophyte generation. As a consequence, these processes can only be analyzed genetically in the gametophyte generation. Here, we report the characterization of the gametophytic factor 1 (gfa1) mutant. The gfa1 mutation exhibits reduced transmission through both the female and male gametophytes. Reduced transmission through the female gametophyte is due to an effect on female gametophyte development. By contrast, development of the pollen grain is not affected in gfa1; rather, reduced transmission is likely due to an effect on pollen tube growth. We have identified multiple T-DNA-insertion alleles of gfa1 in a gene encoding a protein with high similarity to Snu114/U5-116 kD proteins from yeast and animals required for normal pre-mRNA splicing. Consistent with its predicted function, the GFA1 gene (At1g06220) is expressed throughout the plant. Together, these data suggest that GFA1 functions in mRNA splicing during the plant life cycle. © 2007 Springer-Verlag.
• Alexandrov, N. N., Troukhan, M. E., Brover, V. V., Tatarinova, T., Flavell, R. B., & Feldmann, K. A. (2006). Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Molecular Biology, 60(1), 69-85.
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  PMID: 16463100;Abstract: Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5′-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3′-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5′-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper. © Springer 2006.
• Feldmann, K. A. (2006). Steroid regulation improves crop yield. Nature Biotechnology, 24(1), 46-47.
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  PMID: 16404394;Abstract: Slight decreases in brassinosteroid levels help rice plants make the most of daylight. © 2006 Nature Publishing Group.
• Goodwin, S. M., Rashotte, A. M., Rahman, M., Feldmann, K. A., & Jenks, M. A. (2005). Wax constituents on the inflorescence stems of double eceriferum mutants in Arabidopsis reveal complex gene interactions. Phytochemistry, 66(7), 771-780.
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  PMID: 15797603;Abstract: To shed new light on gene involvement in plant cuticular-wax production, 11 eceriferum (cer) mutants of Arabidopsis having dramatic alterations in wax composition of inflorescence stems were used to create 14 double cer mutants each with two homozygous recessive cer loci. A comprehensive analysis of stem waxes on these double mutants revealed unexpected CER gene interactions and new ideas about individual CER gene functions. Five of the 14 double cer mutants produced significantly more total wax than one of their respective cer parents, indicating from a genetic standpoint a partial bypassing (or complementation) of one cer mutation by the other. Eight of the 14 double cer mutants had alkane amounts lower than both respective cer parents, suggesting that most of these CER gene products play a major additive role in alkane synthesis. Other results suggested that some CER genes function in more than one step of the wax pathway, including those associated with sequential steps in acyl-CoA elongation. Surprisingly, complete epistasis was not observed for any of the cer gene combinations tested. Significant overlap or redundancy of genetic operations thus appears to be a central feature of wax metabolism. Future studies of CER gene product function, as well as the utilization of CER genes for crop improvement, must now account for the complex gene interactions described here. © 2005 Elsevier Ltd. All rights reserved.
• Kim, H. B., Schaller, H., Goh, C., Kwon, M., Choe, S., An, C. S., Durst, F., Feldmann, K. A., & Feyereisen, R. (2005). Arabidopsis cyp51 mutant shows postembryonic seedling lethality associated with lack of membrane integrity. Plant Physiology, 138(4), 2033-2047.
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  PMID: 16040657;PMCID: PMC1183393;Abstract: CYP51 exists in all organisms that synthesize sterols de novo. Plant CYP51 encodes an obtusifoliol 14α-demethylase involved in the postsqualene sterol biosynthetic pathway. According to the current gene annotation the Arabidopsis (Arabidopsis thaliana) genome contains two putative CYP51 genes, CYP51A1 and CYP51A2. Our studies revealed that CYP51A1 should be considered an expressed pseudogene. To study the functional importance of the CYP51A2 gene in plant growth and development, we isolated T-DNA knockout alleles for CYP51A2. Loss-of-function mutants for CYP51A2 showed multiple defects, such as stunted hypocotyls, short roots, reduced cell elongation, and seedling lethality. In contrast to other sterol mutants, such as fk/hydra2 and hydra1, the cyp51A2 mutant has only minor defects in early embryo genesis. Measurements of endogenous sterol levels in the cyp51A2 mutant revealed that it accumulates obtusifoliol, the substrate of CYP51, and a high proportion of 14α-methyl-Δ8-sterols, at the expense of campesterol and sitosterol. The cyp51A2 mutants have defects in membrane integrity and hypocotyl elongation. The defect in hypocotyl elongation was not rescued by the exogenous application of brassinolide, although the brassinosteroid-signaling cascade is apparently not affected in the mutants. Developmental defects in the cyp51A2 mutant were completely rescued by the ectopic expression of CYP51A2. Taken together, our results demonstrate that the Arabidopsis CYP51A2 gene encodes a functional obtusifoliol 14α-demethylase enzyme and plays an essential role in controlling plant growth and development by a sterol-specific pathway. © 2005 American Society of Plant Biologists.
• Schneeberger, R. G., Zhang, K., Tatarinova, T., Troukhan, M., Kwok, S. F., Drais, J., Klinger, K., Orejudos, F., Macy, K., Bhakta, A., Burns, J., Subramanian, G., Donson, J., Flavell, R., & Feldmann, K. A. (2005). Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions. Functional and Integrative Genomics, 5(4), 240-253.
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  PMID: 15744539;Abstract: Mobile insertion elements such as transposons and T-DNA generate useful genetic variation and are important tools for functional genomics studies in plants and animals. The spectrum of mutations obtained in different systems can be highly influenced by target site preferences inherent in the mechanism of DNA integration. We investigated the target site preferences of Agrobacterium T-DNA insertions in the chromosomes of the model plant Arabidopsis thaliana. The relative frequencies of insertions in genic and intergenic regions of the genome were calculated and DNA composition features associated with the insertion site flanking sequences were identified. Insertion frequencies across the genome indicate that T-strand integration is suppressed near centromeres and rDNA loci, progressively increases towards telomeres, and is highly correlated with gene density. At the gene level, T-DNA integration events show a statistically significant preference for insertion in the 5′ and 3′ flanking regions of protein coding sequences as well as the promoter region of RNA polymerase I transcribed rRNA gene repeats. The increased insertion frequencies in 5′ upstream regions compared to coding sequences are positively correlated with gene expression activity and DNA sequence composition. Analysis of the relationship between DNA sequence composition and gene activity further demonstrates that DNA sequences with high CG-skew ratios are consistently correlated with T-DNA insertion site preference and high gene expression. The results demonstrate genomic and gene-specific preferences for T-strand integration and suggest that DNA sequences with a pronounced transition in CG- and AT-skew ratios are preferred targets for T-DNA integration. © Springer-Verlag 2005.
• Feldmann, K., Rashotte, A. M., Jenks, M. A., Ross, A. S., & Feldmann, K. A. (2004). Novel eceriferum mutants in Arabidopsis thaliana. Planta, 219(1).
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  We conducted a novel non-visual screen for cuticular wax mutants in Arabidopsis thaliana (L.) Heynh. Using gas chromatography we screened over 1,200 ethyl methane sulfonate (EMS)-mutagenized lines for alterations in the major A. thaliana wild-type stem cuticular chemicals. Five lines showed distinct differences from the wild type and were further analyzed by gas chromatography and scanning electron microscopy. The five mutants were mapped to specific chromosome locations and tested for allelism with other wax mutant loci mapping to the same region. Toward this end, the mapping of the cuticular wax ( cer) mutants cer10 to cer20 was conducted to allow more efficient allelism tests with newly identified lines. From these five lines, we have identified three mutants defining novel genes that have been designated CER22, CER23, and CER24. Detailed stem and leaf chemistry has allowed us to place these novel mutants in specific steps of the cuticular wax biosynthetic pathway and to make hypotheses about the function of their gene products.
• Rashotte, A. M., Jenks, M. A., Ross, A. S., & Feldmann, K. A. (2004). Novel eceriferum mutants in Arabidopsis thaliana. Planta, 219(1), 5-13.
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  PMID: 14758476;Abstract: We conducted a novel non-visual screen for cuticular wax mutants in Arabidopsis thaliana (L.) Heynh. Using gas chromatography we screened over 1,200 ethyl methane sulfonate (EMS)-mutagenized lines for alterations in the major A. thaliana wild-type stem cuticular chemicals. Five lines showed distinct differences from the wild type and were further analyzed by gas chromatography and scanning electron microscopy. The five mutants were mapped to specific chromosome locations and tested for allelism with other wax mutant loci mapping to the same region. Toward this end, the mapping of the cuticular wax (cer) mutants cer10 to cer20 was conducted to allow more efficient allelism tests with newly identified lines. From these five lines, we have identified three mutants defining novel genes that have been designated CER22, CER23, and CER24. Detailed stem and leaf chemistry has allowed us to place these novel mutants in specific steps of the cuticular wax biosynthetic pathway and to make hypotheses about the function of their gene products. © Springer-Verlag 2004.
• Durfee, T., Roe, J. L., Sessions, R. A., Inouye, C., Serikawa, K., Feldmann, K. A., Weigel, D., & Zambryski, P. C. (2003). The F-box-containing protein UFO and agamous participate in antagonistic pathways governing early petal development in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 100(14), 8571-8576.
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  PMID: 12826617;PMCID: PMC166270;Abstract: The UNUSUAL FLORAL ORGANS (UFO) gene is required for multiple processes in the developing Arabidopsis flower, including the proper patterning and identity of both petals and stamens. The gene encodes an F-box-containing protein, UFO, which interacts physically and genetically with the Skp1 homolog, ASK1. In this report, we describe four ufo alleles characterized by the absence of petals, which uncover another role for UFO in promoting second whorl development. This UFO-dependent pathway is required regardless of the second whorl organ to be formed, arguing that it affects a basic process acting in parallel with those establishing organ identity. However, the pathway is dispensable in the absence of AGAMOUS (AG), a known inhibitor of petal development. In situ hybridization results argue that AG is not transcribed in the petal region, suggesting that it acts non-cell-autonomously to inhibit second whorl development in ufo mutants. These results are combined into a genetic model explaining early second whorl initiation/proliferation, in which UFO functions to inhibit an AG-dependent activity.
• Feldmann, K. A., Choe, S., Kim, H., & Park, J. (2002). Chapter Eight Functional genomics of cytochromes P450 in plants. Recent Advances in Phytochemistry, 36(C), 125-143.
• Haas, B. J., Volfovsky, N., Town, C. D., Troukhan, M., Alexandrov, N., Feldmann, K. A., Flavell, R. B., White, O., & Salzberg, S. L. (2002). Full-length messenger RNA sequences greatly improve genome annotation.. Genome biology, 3(6), RESEARCH0029.
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  PMID: 12093376;PMCID: PMC116726;Abstract: BACKGROUND: Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of genome sequence data now available, methods for accurate identification of large numbers of genes have become urgently needed. In an effort to create a set of very high-quality gene models, we used the sequence of 5,000 full-length gene transcripts from Arabidopsis to re-annotate its genome. We have mapped these transcripts to their exact chromosomal locations and, using alignment programs, have created gene models that provide a reference set for this organism. RESULTS: Approximately 35% of the transcripts indicated that previously annotated genes needed modification, and 5% of the transcripts represented newly discovered genes. We also discovered that multiple transcription initiation sites appear to be much more common than previously known, and we report numerous cases of alternative mRNA splicing. We include a comparison of different alignment software and an analysis of how the transcript data improved the previously published annotation. CONCLUSIONS: Our results demonstrate that sequencing of large numbers of full-length transcripts followed by computational mapping greatly improves identification of the complete exon structures of eukaryotic genes. In addition, we are able to find numerous introns in the untranslated regions of the genes.
• Park, J., Halitschke, R., Kim, H. B., Baldwin, I. T., Feldmann, K. A., & Feyereisen, R. (2002). A knock-out mutation in allene oxide synthase results in male sterility and defective wound signal transduction in Arabidopsis due to a block in jasmonic acid biosynthesis. Plant Journal, 31(1), 1-12.
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  PMID: 12100478;Abstract: Recent studies on jasmonic acid (JA) biosynthetic mutants have shown that jasmonates play essential roles in pollen maturation and dehiscence and wound-induced defence against biotic attacks. To better understand the biosynthetic mechanisms of this essential plant hormone, we isolated an Arabidopsis knock-out mutant defective in the JA biosynthetic gene CYP74A (allene oxide synthase, AOS) using reverse genetics screening methods. This enzyme catalyses dehydration of the hydroperoxide to an unstable allene oxide in the JA biosynthetic pathway. Endogenous JA levels, which increase 100-fold 1 h after wounding in wild-type plants, do not increase after wounding in the aos mutant. In addition, the mutant showed severe male sterility due to defects in anther and pollen development. The male-sterile phenotype was completely rescued by exogenous application of methyl jasomonate and by complementation with constitutive expression of the AOS gene. RT-PCR analysis showed that the induction of transcripts for vegetative storage protein and lipoxygenase genes, previously shown to be inducible by wound and jasmonate application in the wild-type, was absent in the aos mutant. In transgenic plants constitutively expressing AOS, wound-induced JA levels were 50-100% higher compared to wild-type plants. Taken together with JA deficiency in the aos mutant, our results show that AOS is critical for the biosynthesis of all biologically active jasmonates. Our results also suggest that AOS expression is limiting JA levels in wounded plants, but that the AOS hydroperoxide substrate levels, controlled by upstream enzymes (lipoxygenase and phospholipase), determine JA levels in unwounded plants.
• Choe, S., Fujioka, S., Noguchi, T., Takatsuto, S., Yoshida, S., & Feldmann, K. A. (2001). Overexpression of DWARF4 in the brassinosteroid biosynthetic pathway results in increased vegetative growth and seed yield in Arabidopsis. Plant Journal, 26(6), 573-582.
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  PMID: 11489171;Abstract: Plants unable to synthesize or perceive brassinosteroids (BRs) are dwarfs. Arabidopsis dwf4 was shown to be defective in a steroid 22α hydroxylase (CYP90B1) step that is the putative rate-limiting step in the BR biosynthetic pathway. To better understand the role of DWF4 in BR biosynthesis, transgenic Arabidopsis plants ectopically overexpressing DWF4 (AOD4) were generated, using the cauliflower mosaic virus 35S promoter, and their phenotypes were characterized. The hypocotyl length of both light-and dark-grown AOD4 seedlings was increased dramatically as compared to wild type. At maturity, inflorescence height increased >35% in AOD4 lines and >14% in tobacco DWF4 overexpressing lines (TOD4), relative to controls. The total number of branches and siliques increased more than twofold in AOD4 plants, leading to a 59% increase in the number of seeds produced. Analysis of endogenous BR levels in dwf4, Ws-2 and AOD4 revealed that dwf4 accumulated the precursors of the 22α-hydroxylation steps, whereas overexpression of DWF4 resulted in increased levels of downstream compounds relative to Ws-2, indicative of facilitated metabolic flow through the step. Both the levels of DWF4 transcripts and BR phenotypic effects were progressively increased in dwf4, wild-type and AOD4 plants, respectively. This suggests that it will be possible to control plant growth by engineering DWF4 transcription in plants.
• Feldmann, K. A. (2001). Cytochrome p450s as genes for crop improvement. Current Opinion in Plant Biology, 4(2), 162-167.
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  PMID: 11228441;Abstract: In the past year, several cytochrome P450 genes have been identified that will be important for generating crop protectants and natural medicinal products. Among these are the 2-hydroxyisoflavone synthase (CYP93C) and the indole-3-acetaldoxime N-hydroxylase (CYP83B1) genes, which catalyze the formation of isoflavones and glucosinolates, respectively.
• Rashotte, A. M., Jenks, M. A., & Feldmann, K. A. (2001). Cuticular waxes on eceriferum mutants of Arabidopsis thaliana. Phytochemistry, 57(1), 115-123.
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  PMID: 11336252;Abstract: We present cuticular wax chemical profiles for the leaves and stems of Arabidopsis wildtype Landsberg erecta and eleven isogenic eceriferum mutants: cer5, cer10 to cer15, and cer17 to cer20. These cer mutants have wax profiles that are different from those of wildtype in chemical chain length distribution, amount per chemical class, and/or total wax load. Analyses of detailed leaf and stem wax profiles for these cer mutants have allowed us to place some of these mutants at specific steps in wax production. The cer13 gene is predicted to affect release of the 30 carbon fatty acid from the elongation complex or the reduction of C30 fatty acid to C30 aldehyde. The CER19 gene product is predicted to be involved in C28 to C30 fatty acyl-CoA elongation. The CER20 gene is predicted to affect the oxidation of C29 alkane to C29 secondary alcohol. Several predicted gene products affect only stem specific steps in the wax pathway. © 2001 Elsevier Science Ltd.
• Rigas, S., Debrosses, G., Haralampidis, K., Vicente-Agullo, F., Feldmann, K. A., Grabov, A., Dolan, L., & Hatzopoulos, P. (2001). TRH1 encodes a potassium transporter required for tip growth in arabidopsis root hairs. Plant Cell, 13(1), 139-151.
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  PMID: 11158535;PMCID: PMC102205;Abstract: Root hair initiation involves the formation of a bulge at the basal end of the trichoblast by localized diffuse growth. Tip growth occurs subsequently at this initiation site and is accompanied by the establishment of a polarized cytoplasmic organization. Arabidopsis plants homozygous for a complete loss-of-function tiny root hair 1 (trh1) mutation were generated by means of the T-DNA-tagging method. Trichoblasts of trh1 plants form initiation sites but fail to undergo tip growth. A predicted primary structure of TRH1 indicates that it belongs to the AtKT/AtKUP/HAK K+ transporter family. The proposed function of TRH1 as a K+ transporter was confirmed in 86Rb uptake experiments, which demonstrated that trh1 plants are partially impaired in K+ transport. In line with these results, TRH1 was able to complement the trk1 potassium transporter mutant of Saccharomyces, which is defective in high-affinity K+ uptake. Surprisingly, the trh1 phenotype was not restored when mutant seedlings were grown at high external potassium concentrations. These data demonstrate that TRH1 mediates K+ transport in Arabidopsis roots and is responsible for specific K+ translocation, which is essential for root hair elongation.
• Feldmann, K. A. (1999). The greening of chimeric oligonucleotides. Nature Biotechnology, 17(9), 857-858.
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  PMID: 10471924;
• Azpiroz, R., Yewen, W. u., Locascio, J. C., & Feldmann, K. A. (1998). An Arabidopsis brassinosteroid-dependent mutant is blocked in cell elongation. Plant Cell, 10(2), 219-230.
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  PMID: 9490745;PMCID: PMC143978;Abstract: Cell elongation is a developmental process that is regulated by light and phytohormones and is of critical importance for plant growth. Mutants defective in their response to light and various hormones are often dwarfs. The dwarfed phenotype results because of a failure in normal cell elongation. Little is known, however, about the basis of dwarfism as a common element in these diverse signaling pathways and the nature of the cellular functions responsible for cell elongation. Here, we describe an Arabidopsis mutant, dwarf4 (dwf4), whose phenotype can be rescued with exogenously supplied brassinolide. dwf4 mutants display features of light-regulatory mutants, but the dwarfed phenotype is entirely and specifically brassinosteroid dependent; no other hormone can rescue dwf4 to a wild-type phenotype. Therefore, an intact brassinosteroid system is an absolute requirement for cell elongation.
• Choe, S., Dilkes, B. P., Fujioka, S., Takatsuto, S., Sakurai, A., & Feldmann, K. A. (1998). The DWF4 gene of Arabidopsis encodes a cytochrome P450 that mediates multiple 22α-hydroxylation steps in brassinosteroid biosynthesis. Plant Cell, 10(2), 231-243.
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  PMID: 9490746;PMCID: PMC143988;Abstract: dwarf4 (dwf4) mutants of Arabidopsis display a dwarfed phenotype due to a lack of cell elongation. Dwarfism could be rescued by the application of brassinolide, suggesting that DWF4 plays a role in brassinosteroid (BR) biosynthesis. The DWF4 locus is defined by four mutant alleles. One of these is the result of a T-DNA insertion. Plant DNA flanking the insertion site was cloned and used as a probe to isolate the entire DWF4 gene. Sequence analysis revealed that DWF4 encodes a cytochrome P450 monooxygenase with 43% identity to the putative Arabidopsis steroid hydroxylating enzyme CONSTITUTIVE PHOTOMORPHOGENESIS AND DWARFISM. Sequence analysis of two other mutant alleles revealed deletions or a premature stop codon, confirming that DWF4 had been cloned. This sequence similarity suggests that DWF4 functions in specific hydroxylation steps during BR biosynthesis. In fact, feeding studies utilizing BR intermediates showed that only 22α-hydroxylated BRs rescued the dwf4 phenotype, confirming that DWF4 acts as a 22α-hydroxylase.
• Dilkes, B. P., & Feldmann, K. A. (1998). Cloning genes from T-DNA tagged mutants.. Methods in molecular biology (Clifton, N.J.), 82, 339-351.
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  PMID: 9664437;
• Rashotte, A. M., & Feldmann, K. A. (1998). Correlations between epicuticular wax structures and chemical composition in Arabidopsis thaliana. International Journal of Plant Sciences, 159(5), 773-779.
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  Abstract: The epicuticular waxes of vascular plants are both chemically and structurally diverse. This investigation attempts to clarify the poorly understood relationships between epicuticular wax chemicals and structures by correlating the diversity of chemical compositions and structures in wildtype and epicuticular wax mutants of Arabidopsis thaliana. An expanded classification of A. thaliana epicuticular wax structures was conducted preceding their quantification on 24 genotypes of A. thaliana. Correlations between all A. thaliana stem epicuticular wax chemical and structural categories showed that 19 of the 26 epicuticular wax compounds were significantly correlated to at least one of the six structural types. The chain-length distribution of an epicuticular wax profile was also found to be correlated to structural type: short chain-length compounds to dendritic structures and long chain-length compounds to umbrella structures. The 29-carbon-length alkane, ketone, and secondary alcohol are each correlated to the same four structures: horizontal structures, rods, tubes, and vertical plates. In addition, these three 29-carbon wax components and four structures make up a majority of the chemical and structural constituents on 19 of the 20 genotypes that possess structures.
• Tokuhisa, J. G., Vijayan, P., Feldmann, K. A., & Browse, J. A. (1998). Chloroplast development at low temperatures requires a homolog of DIM1, a yeast gene encoding the 18S rRNA dimethylase. Plant Cell, 10(5), 699-711.
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  PMID: 9596631;PMCID: PMC144018;Abstract: Poikilothermic organisms require mechanisms that allow survival at chilling temperatures (2 to 15°C). We have isolated chilling-sensitive mutants of Arabidopsis, a plant that is very chilling resistant, and are characterizing them to understand the genes involved in chilling resistance. The T-DNA-tagged mutant paleface1 (pfc1) grows normally at 22°C but at 5°C exhibits a pattern of chilling-induced chlorosis consistent with a disruption of chloroplast development. Genomic DNA flanking the T-DNA was cloned and used to isolate wild-type genomic and cDNA clones. The PFC1 transcript is present at a low level in wild-type plants and was not detected in pfc1 plants. Wild-type Arabidopsis expressing antisense constructs of PFC1 grew normally at 22°C but showed chilling-induced chlorosis, confirming that the gene is essential for low-temperature development of chloroplasts. The deduced amino acid sequence of PFC1 has identity with rRNA methylases found in bacteria and yeast that modify specific adenosines of pre-rRNA transcripts. The pfc1 mutant does not have these modifications in the small subunit rRNA of the Plastid.
• Winkler, R. G., & Feldmann, K. A. (1998). PCR-based identification of T-DNA insertion mutants.. Methods in molecular biology (Clifton, N.J.), 82, 129-136.
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  PMID: 9664420;
• Azpiroz-Leehan, R., & Feldmann, K. A. (1997). T-DNA insertion mutagenesis in Arabidopsis: Going back and forth. Trends in Genetics, 13(4), 152-156.
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  PMID: 9097726;Abstract: T-DNA insertion mutagenesis in Arabidopsis has been instrumental in advancing our knowledge of the physiolagy, biochemistry and development of plants. In just a few years plant biology, the late starter of molecular genetics, has placed itself at the forefront of science in large measure as a result of the more than 20000 T-DNA transformants that have been generated in Arabidopsis. To date, approximately 4000 mutants have been identified and more than 40 genes have been isolated via the T-DNA tag. The large population of transformed lines is now being subjected to a PCR-based reverse genetics strategy to identify new insertion mutants in sequences of interest.
• Feldmann, K. A., Coury, D. A., & Christianson, M. L. (1997). Exceptional segregation of a selectable marker (Kan(R)) in arabidopsis identifies genes important for gametophytic growth and development. Genetics, 147(3), 1411-1422.
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  PMID: 9383081;PMCID: PMC1208262;Abstract: Genes transformed into plants are usually inherited in a regular Mendelian manner. There are, however, transformants in which the selectable trait fails to segregate as expected. Genetic analysis of the kanamycin- resistance (Kan(R)) trait in >900 independent transformants of Arabidopsis revealed that 9% produced progeny families with an enormous deficiency of Kan(R) individuals. Self-pollination of individual Kan(R) plants from these families revealed lines that continued to segregate for a deficiency of Kan(R) seedlings. In subsequent generations, the segregation ratio in these families stabilized at ~1 Kan(R): 3 Kan(S). Molecular analyses showed that the deficiency of Kan(R) individuals reflected the complete absence of the introduced DNA. Reciprocal backcrosses to untransformed plants showed unequal transmission of the Kan(R) trait through the gametes in these exceptional lines. In five cases, this was primarily a failure of transmission through the microgametophyte (pollen) and in the other two cases, primarily a failure of transmission through the megagametophyte (embryo sac or egg). The number of seeds per silique was reduced by 50% in the latter two lines. We conclude that our exceptional transformants contain T-DNA insertions that delete or disrupt genes essential for gametophytic growth and development.
• Grierson, C. S., Roberts, K., Feldmann, K. A., & Dolan, L. (1997). The COW1 locus of Arabidopsis acts after RHD2, and in parallel with RHD3 and TIP1, to determine the shape, rate of elongation, and number of root hairs produced from each site of hair formation. Plant Physiology, 115(3), 981-990.
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  PMID: 9390433;PMCID: PMC158561;Abstract: Two recessive mutant alleles at CAN OF WORMS1 (COW1), a new locus involved in root hair morphogenesis, have been identified in Arabidopsis thaliana L. Heynh. Root hairs on Cow1- mutants are short and wide and occasionally formed as pairs at a single site of hair formation. The COW1 locus maps to chromosome 4. Root hairs on Cow1- plants form in the usual positions, suggesting that the phenotype is not the result of abnormal positional signals. Root hairs on Cow1- roots begin hair formation normally, forming a small bulge, or root hair initiation site, of normal size and shape and in the usual position on the hair-forming cell. However, when Cow1- root hairs start to elongate by tip growth, abnormalities in the shape and elongation rate of the hairs become apparent. Genetic evidence from double-mutant analysis of cow1-1 and other loci involved in root hair development supports our conclusion that COW1 is required during root hair elongation.
• Oppenheimer, D. G., Pollock, M. A., Vacik, J., Szymanski, D. B., Ericson, B., Feldmann, K., & Marks, M. D. (1997). Essential role of a kinesin-like protein in Arabidopsis trichome morphogenesis. Proceedings of the National Academy of Sciences of the United States of America, 94(12), 6261-6266.
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  PMID: 9177205;PMCID: PMC21037;Abstract: Little is known about how cell shape is controlled. We are using the morphogenesis of trichomes (plant hairs) on the plant Arabidopsis thaliana as a model to study how cell shape is controlled. Wild-type Arabidopsis trichomes are large, single epidermal cells with a stalk and three or four branches, whereas in zwichel (zwi) mutants the trichomes have a shortened stalk and only two branches. To further understand the role of the ZWI gene in trichome morphogenesis we have cloned the wild-type ZWICHEL (ZWI) gene by T-DNA tagging, and report here that it encodes a member of the kinesin superfamily of microtubule motor proteins. Kinesin proteins transport diverse cellular materials in a directional manner along microtubules. Kinesin-like proteins are characterized by a highly conserved 'head' region that comprises the motor domain, and a nonconserved 'tail' region that is thought to participate in recognition and binding of the appropriate cargo.
• Paterson, A. H., Lan, T. -., Reischmann, K. P., Chang, C., Lin, Y. -., S.-, C. L., Burow, M. D., Kowalski, S. P., Katsar, C. S., DelMonte, T. A., Feldmann, K. A., Schertz, K. F., & Wendel, J. F. (1997). Erattum: Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence (Nature Genetics (1996) 14 (380-382)). Nature Genetics, 15(3), 322-.
• Rashotte, A. M., Jenks, M. A., Nguyen, T. D., & Feldmann, K. A. (1997). Epicuticular wax variation in ecotypes of Arabidopsis thaliana. Phytochemistry, 45(2), 251-255.
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  PMID: 9141716;Abstract: Quantification of the epicuticular wax from the stems of 40 ecotypes of Arabidopsis thailuna showed a two-fold range in total wax lead that was not correlated to known abiotic characteristics of the ecotype's origin of collection. Chemical analysis of these ecotypes revealed similar epicuticular wax profiles for all ecotypes except CT-1. In CT-1 the amount of 22 and 24 carbon length primary alcohols was increased by 16-and 8-fold, respectively, over that observed in the epicuticular wax averaged over all ecotypes.
• Sessions, A., Nemhauser, J. L., McColl, A., Roe, J. L., Feldmann, K. A., & Zambryski, P. C. (1997). ETTIN patterns the Arabidopsis floral meristem and reproductive organs. Development, 124(22), 4481-4491.
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  PMID: 9409666;Abstract: ettin (ett) mutations have pleiotropic effects on Arabidopsis flower development, causing increases in perianth organ number, decreases in stamen number and anther formation, and apical-basal patterning defects in the gynoecium. The ETTIN gene was cloned and encodes a protein with homology to DNA binding proteins which bind to auxin response elements. ETT transcript is expressed throughout stage 1 floral meristems and subsequently resolves to a complex pattern within petal, stamen and carpel primordia. The data suggest that ETT functions to impart regional identity in floral meristems that affects perianth organ number spacing, stamen formation, and regional differentiation in stamens and the gynoecium. During stage 5, ETT expression appears in a ring at the top of the floral meristem before morphological appearance of the gynoecium, consistent with the proposal that ETT is involved in prepatterning apical and basal boundaries in the gynoecium primordium. Double mutant analyses and expression studies show that although ETT transcriptional activation occurs independently of the meristem and organ identity genes LEAFY, APETELA1, APETELA2 and AGAMOUS, the functioning of these genes is necessary for ETT activity. Double mutant analyses also demonstrate that ETT functions independently of the 'b' class genes APETELA3 and PISTILLATA. Lastly, double mutant analyses suggest that ETT control of floral organ number acts independently of CLAVATA loci and redundantly with PERIANTHIA.
• Bennett, M. J., Marchant, A., Green, H. G., May, S. T., Ward, S. P., Millner, P. A., Walker, A. R., Schulz, B., & Feldmann, K. A. (1996). Arabidopsis AUX1 gene: A permease-like regulator of root gravitropism. Science, 273(5277), 948-950.
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  PMID: 8688077;Abstract: The plant hormone auxin regulates various developmental processes including root formation, vascular development, and gravitropism. Mutations within the AUX1 gene confer an auxin-resistant root growth phenotype and abolish root gravitropic curvature. Polypeptide sequence similarity to amino acid permeases suggests that AUX1 mediates the transport of an amino acid- like signaling molecule. Indole-3-acetic acid, the major form of auxin in higher plants, is structurally similar to tryptophan and is a likely substrate for the AUX1 gene product. The cloned AUX1 gene can restore the auxin-responsiveness of transgenic aux1 roots. Spatially, AUX1 is expressed in root apical tissues that regulate root gravitropic curvature.
• Jenks, M. A., Rashotte, A. M., Tuttle, H. A., & Feldmann, K. A. (1996). Mutants in Arabidopsis thaliana altered in epicuticular wax and leaf morphology. Plant Physiology, 110(2), 377-385.
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  Abstract: We report eight new mutants in Arabidopsis thaliana possessing altered leaf morphology and epicuticular wax. These were isolated from a T-DNA-mutagenized population using a visual screen for altered leaf reflectance, i.e. increased glaucousness or glossiness. The mutants were placed into three distinct classes based on alterations in overall plant morphology: knobhead (knb), bicentifolia (bcf), and wax. The four knb mutants formed callus-like growths in the axillary region of the rosette leaves and apical meristem, the two bcf mutants produced hundreds of narrow leaves, and the two wax mutants had leaves and stems that were more glossy than wild type and organs that fused during early development. Leaves of knb and bcf were more glaucous and abnormally shaped than wild type. Epicuticular wax crystals over knb and bcf leaf surfaces (where none were present on wild type) likely contributed to their more glaucous appearance. In contrast, the glossy appearance of the wax mutants was associated with a reduced epicuticular wax load on both leaves and stems. One representative from each phenotypic class was selected for detailed analyses of epicuticular wax chemistry. All three lines, knb1, bcf1, and wax1, had dramatic alterations in the total amounts and relative proportions of their leaf epicuticular wax constituents.
• Jenks, M. A., Tuttle, H. A., & Feldmann, K. A. (1996). Changes in epicuticular waxes on wildtype and eceriferum mutants in Arabidopsis during development. Phytochemistry, 42(1), 29-34.
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  Abstract: We analysed the leaf epicuticular wax chemical constituents on wildtype and eceriferum (cer; cer1, cer3 and cer4) mutants of Arabidopsis thaliana at 7, 15, 25 and 40 days after germination. Changes during development are described for the partitioning of epicuticular waxes into the five major chemical classes; free carboxylic fatty acids, aldehydes, alkanes, primary alcohols and wax esters. Changes are described for cumulative total epicuticular wax loads per leaf area, percentages of total constituents in each of the five major chemical classes and chain length distributions for the two major chemical classes: alkanes and primary alcohols. Stem epicuticular waxes on wildtype and cer mutants were analysed at 25 and 40 days and found to be similar. Copyright © 1996 Elsevier Science Ltd. All rights reserved.
• Laurenzio, L. D., Wysocka-Diller, J., Malamy, J. E., Pysh, L., Helariutta, Y., Freshour, G., Hahn, M. G., Feldmann, K. A., & Benfey, P. N. (1996). The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell, 86(3), 423-433.
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  PMID: 8756724;Abstract: In the Arabidopsis root meristem, initial cells undergo asymmetric divisions to generate the cell lineages of the root. The scarecrow mutation results in roots that are missing one cell layer owing to the disruption of an asymmetric division that normally generates cortex and endodermis. Tissue- specific markers indicate that a heterogeneous cell type is formed in the mutant. The deduced amino acid sequence of SCARECROW (SCR) suggests that it is a member of a novel family of putative transcription factors. SCR is expressed in the cortex/endodermal initial cells and in the endodermal cell lineage. Tissue-specific expression is regulated at the transcriptional level. These results indicate a key role for SCR in regulating the radial organization of the root.
• Liu, S. -., Kowalski, S. P., Lan, T. -., Feldmann, K. A., & Paterson, A. H. (1996). Erratum: Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model (Genetics (January, 1996) 142 (247- 258)). Genetics, 143(4), 1861-.
• Lui, S., Kowalski, S. P., Lan, T., Feldmann, K. A., & Paterson, A. H. (1996). Genome-wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model. Genetics, 142(1), 247-258.
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  PMID: 8770602;PMCID: PMC1206953;Abstract: We demonstrate a method for developing populations suitable for genome- wide high-resolution genetic linkage mapping, by recurrent intermating among F2 individuals derived from crosses between homozygous parents. Comparison of intermated progenies to F2 an 'recombinant inbred' (RI) populations from the same pedigree corroborate theoretical expectations that progenies intermated for four generations harbor about threefold more information for estimating recombination fraction between closely linked markers than either RI-selfed or F2 individuals (which are, in fact, equivalent in this regard). Although intermated populations are heterozygous, homozygous 'intermated recombinant inbred' (RI) populations can readily be generated, combining additional information afforded by intermating with the permanence of RI populations. Intermated populations permit fine-mapping of genetic markers throughout a genome, helping to bridge the gap between genetic map resolution and the DNA-carrying capacity of modern cloning vectors, thus facilitating merger of genetic and physical maps. Intermating can also facilitate high- resolution mapping of genes and QTLs, accelerating map-based cloning. Finally, intermated populations will facilitate investigation of other fundamental genetic questions requiring a genome-wide high-resolution analysis, such as comparative mapping of distantly related species, and the genetic basis of heterosis.
• Mandel, M. A., Feldmann, K. A., Herrera-Estrella, L., Rocha-Sosa, M., & León, P. (1996). CLA1, a novel gene required for chloroplast development, is highly conserved in evolution. Plant Journal, 9(5), 649-658.
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  PMID: 8653115;Abstract: An albino mutant designated cla1-1 (for 'cloroplastos alterados', or 'altered chloroplasts') has been isolated from a T-DNA-generated library of Arabidopsis thaliana. In cla1-1 plants, chloroplast development is arrested at an early stage. cla1-1 plants behave like wild-type in their capacity to etiolate and produce anthocyanins indicating that the light signal transduction pathway seems to be unaffected. Genetic and molecular analyses show that the disruption of a single gene, CLA1. by the T-DNA insertion is responsible for the mutant phenotype. RNA expression patterns indicate that CLA1 is positively regulated by light and that it has different effects on the steady-state RNA levels of some nuclear- and chloroplast-encoded photosynthetic genes. Although the specific function of the CLA1 gene is still unknown, it encodes a novel protein conserved in evolution between photosynthetic bacteria and plants which is essential for chloroplast development in Arabidopsis.
• Paterson, A. H., Lan, T. -., Reischmann, K. P., Chang, C., Lin, Y. -., S.-, C. L., Burow, M. D., Kowalski, S. P., Katsar, C. S., DelMonte, T. A., Feldmann, K. A., Schertz, K. F., & Wendel, J. F. (1996). Toward a unified genetic map of higher plants, transcending the monocot- dicot divergence. Nature Genetics, 14(4), 380-382.
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  PMID: 8944014;
• Peirson, B. N., Owen, H. A., Feldmann, K. A., & Makaroff, C. A. (1996). Characterization of three male-sterile mutants of Arabidopsis thaliana exhibiting alterations in meiosis. Sexual Plant Reproduction, 9(1), 1-16.
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  Abstract: Male-sterile mutants are being studied to deepen our understanding of the complex processes of microsporogenesis and microgametogenesis. Due to difficulties associated with isolating the mutated gene, there is currently very little molecular information on the defects responsible for male sterility. As a first step in utilizing male-sterile mutants to better understand the biochemical and molecular processes that control pollen development, we have characterized a number of Arabidopsis thaliana lines that were generated by seed transformation and exhibit male sterility. We report here the identification and characterization of three male- sterile A. thaliana lines, all of which are tagged with T-DNA and show aberrant meiosis. A detailed cytochemical study was conducted on these lines to better understand the timing and nature of each mutation and to investigate how these mutations affect subsequent steps of pollen development. All three mutants undergo apparently normal morphogenesis until the onset of meiosis. In one line (6492) the mutations is most notable at the tetrad stage when up to eight microspores can be seen in each callose-encased tetrad. The resulting mutant microspores are of variable sizes and contain different amounts of DNA. Two other mutants (7219 and 7593) possess many common features, including variable developmental pathways, failure to produce callose, production of vacuolate, coenocytic (multi-nucleate) cells that are surrounded by persistent microsporocyte walls, and asynchronous patterns of development. Unlike the situation in wild-type plants, where developmental stages are correlated with bud length, such correlations are almost impossible with these two mutants. The sporogenous tissue within all three of these mutant lines collapses to anthesis.
• Aeschbacher, R. A., Hauser, M. -., Feldmann, K. A., & Benfey, P. N. (1995). The SABRE gene is required for normal cell expansion in Arabidopsis. Genes and Development, 9(3), 330-340.
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  PMID: 7867930;Abstract: Regulated cell expansion is an important determinant of organ shape in higher plants. The sabre mutation results in abnormal cell expansion in Arabidopsis. There is a shift in the orientation of expansion evident primarily in root cortex cells. The SABRE gene has been cloned and found to encode a novel protein. Reduction of effective levels of the plant phytohormone ethylene through use of inhibitors and an insensitive mutant resulted in partial rescue of the sabre phenotype. This suggested that one of the roles of SABRE is to counter the action of ethylene in promoting radial expansion in plant cells.
• Jenks, M. A., Tuttle, H. A., Eigenbrode, S. D., & Feldmann, K. A. (1995). Leaf epicuticular waxes of the Eceriferum mutants in Arabidopsis. Plant Physiology, 108(1), 369-377.
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  Abstract: Wild-type Arabidopsis leaf epicuticular wax (EW) occurs as a smooth layer over the epidermal surface, whereas stem EW has a crystalline microstructure. Wild-type EW load was more than 10-fold lower on leaves than on stems. Compared with the EW on wild-type stems, EW on wild-type leaves had a much higher proportion of their total EW load in the form of alkanes and 1 -alcohols; a large reduction in secondary alcohols, ketones, and esters; and a chain-length distribution for major EW classes that was skewed toward longer lengths. The eceriferum (cer) mutations often differentially affected leaf and stem EW chemical compositions. For example, the cer2 mutant EW phenotype was expressed on the stem but not on the leaf. Compared to wild type, the amount of primary alcohols on cer9 mutants was reduced on leaves but elevated on stems, whereas an opposite differential effect for primary alcohols was observed on cer16 leaves and stems. Putative functions for CER gene products are discussed. The CER4 and CER6 gene products may be involved in fatty aldehyde reduction and C26 fatty acylcoenzyme A elongation, respectively. CFR1, CFR8, CER9, and CER16 gene products may be involved in EW substrate transfer. The CER3 gene product may be involved in release of fatty acids from elongase complexes. CER2 gene product may have regulatory functions.
• McKinney, E. C., Ali, N., Traut, A., Feldmann, K. A., Belostotsky, D. A., McDowell, J. M., & Meagher, R. B. (1995). Sequence-based identification of T-DNA insertion mutations in Arabidopsis: Actin mutants act2-7 and act4-1. Plant Journal, 8(4), 613-622.
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  PMID: 7496405;Abstract: A method is presented to facilitate the isolation of mutations in plant genes, which requires knowledge of the target gene or protein sequence, and is independent of mutant phenotype. The polymerase chain reaction was used to amplify the junctions between a T-DNA insert and the gene of interest from pools of mutant plant lines. The approach was used to identify mutations in Arabidopsis thaliana actin genes. The Arabidopsis genome encodes 10 actins in six ancient subclasses each with distinct expression patterns. Primers in the T-DNA border and highly degenerate actin primers, designed from conserved amino acid motifs, were used to prime the amplification. The PCR products were transferred to filters and probed for actin at low stringency. Thus, mutations in all 10 actin genes were screened for simultaneously. Mutations in the vegetative constitutive actin gene, ACT2, and the pollenspecific actin gene, ACT4, were identified in a population of 5300 lines containing approximately 1.5 T-DNA insertions per line. The screen was sensitive enough that actin insertion alleles were easily distinguished among pools of 100 plant lines. PCR techniques were used which accelerated the purification of mutant lines, and segregation, physical mapping, and sequencing of the act 2-1 and act 4-1 mutations. This strategy should be generally useful in screening mutant libraries made with a variety of plant insertion elements for mutations in any known sequence.
• Kowalski, S. P., Lan, T. -., Feldmann, K. A., & Paterson, A. H. (1994). Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics, 138(2), 499-510.
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  PMID: 7828831;PMCID: PMC1206166;Abstract: The chromosomes of Arabidopsis thaliana and Brassica oleracea have been extensively rearranged since the divergence of these species; however, conserved regions are evident. Eleven regions of conserved organization were detected, ranging from 3.7 to 49.6 cM in A. thaliana, spanning 158.2 cM (24.6%) of the A. thaliana genome, and 245 cM (29.9%) of the B. oleracea genome. At least 17 translocations and 9 inversions distinguish the genomes of A. thaliana and B. oleracea. In one case B. oleracea homoeologs show a common marker order, which is distinguished from the A. thaliana order by a rearrangement, indicating that the lineages of A. thaliana and B. oleracea diverged prior to chromosomal duplication in the Brassica lineage (for at least this chromosome). Some chromosomal segments in B. oleracea appear to be triplicated, indicating the need for reevaluation of a classical model for Brassica chromosome evolution by duplication. The distribution of duplicated loci mapped for about 13% of the DNA probes studied in A. thaliana suggests that ancient duplications may also have occurred in Arabidopsis. The degree of chromosomal divergence between A. thaliana and B. oleracea appears greater than that found in other confamilial species for which comparative maps are available.
• Kowalski, S. P., Lan, T., Feldmann, K. A., & Paterson, A. H. (1994). QTL mapping of naturally-occurring variation in flowering time of Arabidopsis thaliana. MGG Molecular & General Genetics, 245(5), 548-555.
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  PMID: 7808406;Abstract: A segregating F2 population of Arabidopsis thaliana derived from a cross between the late-flowering ecotype Hannover/Münden (HM) and the early-flowering ecotype Wassilewskija (WS) was analyzed for flowering time and other morphological traits. Two unlinked quantitative trait loci (QTLs) affecting days to first flower (DFF-a and DFF-b) mapped to chromosome 5. QTLs which affect node number (NN), leaf length at flowering (LLF), and leaf length at 35 days (LL35) also mapped to chromosome 5; LLF-a, LL35-a, NN-a map to the same region of chromosome 5 as DFF-a; LLF-b and LL35-bmap to the same region of chromosome 5 as DFF-b. Another QTL affecting leaf length at flowering (LLF-c) maps to chromosome 3. The proximity of DFF-a, LLF-a, LL35-a and NN-a, as well as the similarity in gene action among these QTLs (additivity), suggest that they may be pleiotropic consequences of a single gene at this locus. Similarly, LL35-b and LLF-b map near each other and both display recessive gene action, again suggesting the possibility of pleiotropy. DFF-b, which also maps near LL35-b and LLF-b, displays largely additive gene action (although recessive gene action could not be ruled out). This suggests that DFF-b may represent a different gene from LL35-b and/or LLF-b. DFF-a maps near two previously identified mutants: co (which also affects flowering time and displays gene action consistent with additivity) and flc. Similar map locations and gene actions of QTLs affecting the correlated traits DFF, LLF, LL35 and NN suggest that these genomic regions harbor naturally occurring allelic variants involved in the general transition of the plant from vegetative to reproductive growth. © 1994 Springer-Verlag.
• Lee, I., Aukerman, M. J., Gore, S. L., Lohman, K. N., Michaels, S. D., Weaver, L. M., John, M. C., Feldmann, K. A., & Amasino, R. M. (1994). Isolation of LUMINIDEPENDENS: A gene involved in the control of flowering time in arabidopsis. Plant Cell, 6(1), 75-83.
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  PMID: 7907507;PMCID: PMC160417;Abstract: Plants have evolved the ability to regulate flowering in response to environmental signals such as temperature and photoperiod. The physiology and genetics of floral induction have been studied extensively, but the molecular mechanisms that underlie this process are poorly understood. To study this process, we isolated a gene, LUMINIDEPENDENS (LD), that is involved in the timing of flowering in Arabidopsis. Mutations in this gene render Arabidopsis late flowering and appear to affect light perception. The late-flowering phenotype of the Id mutation was partially suppressed by vernalization. Genomic and cDNA clones of the LD gene were characterized. The predicted amino acid sequence of the LD protein contains 953 residues and includes two putative bipartite nuclear localization signals and a glutamine-rich region.
• Modrusan, Z., Reiser, L., Feldmann, K. A., Fischer, R. L., & Haughn, G. W. (1994). Homeotic transformation of ovules into carpel-like structures in arabidopsis. Plant Cell, 6(3), 333-349.
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  Abstract: Ovules are specialized reproductive organs that develop within the carpels of higher plants. In Arabidopsis, mutations in two genes, BELL1 (BEL1) and APETALA2 (AP2), disrupt ovule development. In Bel1 ovules, the inner integument fails to form, the outer integument develops abnormally, and the embryo sac arrests at a late stage of megagametogenesis. During later stages of ovule development, cells of the outer integument of a Bel1 ovule sometimes develop into a carpel-like structure with stigmatic papillae and second-order ovules. The frequency of carpel-like structures was highest when plants were grown under conditions that normally induced flowering and was correlated with ectopic expression in the ovule of AGAMOUS (AG), an organ-identity gene required for carpel formation. Together, these results suggested that BEL1 negatively regulates AG late in ovule development. Likewise, mutants homozygous for the strong AP2 allele ap2-6 sometimes displayed structures with carpel-like features in place of ovules. However, such abnormal Ap2 ovules are much less ovulelike in morphology and form earlier than the Bel1 carpel-like structures. Because one role of the AP2 gene is to negatively regulate AG expression early in flower development, it is possible that AP2 works in a similar manner in the ovule. A novel ovule phenotype observed in Bel1/Ap2-6 double mutants suggested that BEL1 and AP2 genes function independently during ovule development.
• Okuley, J., Lightner, J., Feldmann, K., Yadav, N., Lark, E., & Browse, J. (1994). Arabidopsis FAD2 gene encodes the enzyme that is essential for polyunsaturated lipid synthesis. Plant Cell, 6(1), 147-158.
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  PMID: 7907506;PMCID: PMC160423;Abstract: The polyunsaturated fatty acids linoleate and α-linolenate are important membrane components and are the essential fatty acids of human nutrition. The major enzyme responsible for the synthesis of these compounds is the plant oleate desaturase of the endoplasmic reticulum, and its activity is controlled in Arabidopsis by the fatty acid desaturation 2 (fad2) locus. A fad2 allele was identified in a population of Arabidopsis in which mutations had been created by T-DNA insertions. Genomic DNA flanking the T-DNA was cloned by plasmid rescue and used to isolate cDNA and genomic clones of FAD2. A cDNA containing the entire FAD2 coding sequence was expressed in fad2 mutant plants and shown to complement the mutant fatty acid phenotype. The deduced amino acid sequence from the cDNA showed homology to other plant desaturases, and this confirmed that FAD2 is the structural gene for the desaturase. Gel blot analyses of FAD2 mRNA levels showed that the gene is expressed throughout the plant and suggest that transcript levels are in excess of the amount needed to account for oleate desaturation. Sequence analysis identified histidine-rich motifs that could contribute to an iron binding site in the cytoplasmic domain of the protein. Such a position would facilitate interaction between the desaturase and cytochrome b5, which is the direct source of electrons for the desaturation reaction, but would limit interaction of the active site with the fatty acyl substrate.
• Rerie, W. G., Feldmann, K. A., & Marks, M. D. (1994). The GLABRA2 gene encodes a homeo domain protein required for normal trichome development in Arabidopsis. Genes and Development, 8(12), 1388-1399.
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  PMID: 7926739;Abstract: The GLABRA2 gene (GL2) is one of several genes known to have a role in trichome development in Arabidopsis. Mutations at this locus result in abnormal trichome expansion. We have identified several gl2 mutants from a T- DNA-mutagenized population of plants. The T-DNA insert in one of the mutant lines cosegregated with the recessive gl2 phenotype and thus served as a molecular tag to isolate genomic DNA at the putative GL2 locus. RFLP analysis of the segregating population and subsequent molecular complementation experiments established that the GL2 gene had been cloned. The predicted polypeptide from one of the ORFs contained on this fragment showed significant identity to the homeo domain sequence. The construction of a full-length cDNA by RT-PCR confirmed the presence of a homeo box in the GL2 gene and showed that it is substantially different from other recently cloned homeo box genes in plants. The expression pattern of GL2, as demonstrated by in situ hybridization, indicated that the gene is expressed in trichome progenitor cells and at stages associated with trichome development. This suggests that GL2 may regulate events required for the directional cell expansion observed during trichome formation.
• Shevell, D. E., Leu, W., Gilimor, C. S., Xia, G., Feldmann, K. A., & Chua, N. (1994). EMB30 is essential for normal cell division, cell expansion, and cell adhesion in Arabidopsis and encodes a protein that has similarity to Sec7. Cell, 77(7), 1051-1062.
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  PMID: 8020095;Abstract: The EMB30 gene is involved in apical-basal pattern formation in the Arabidopsis embryo. Mutations in this locus produce mutants with a wide range of seedling phenotypes, but all of the mutants lack a root and a true hypocotyl. We have cloned the EMB30 gene, and it encodes a protein that has similarity to the yeast Sec7 protein and to two other open reading frames identified in clones from humans and C. elegans. We refer to the region of similarity among these four sequences as the Sec7 domain. The emb30·1 allele has a mutation in the Sec7 domain that alters a residue conserved in all four of these sequences, suggesting that this domain may be important for EMB30 function. Molecular data and microscopy studies of emb30 seedlings presented here indicate that EMB30 affects cell division, elongation, and adhesion and functions in seedling and adult plants as well as during embryogenic pattern formation.
• Kleber, J. J., Rothenberg, M., Roman, G., Feldmann, K. A., & Ecker, J. R. (1993). CTR1, a negative regulator of the ethylene response pathway in arabidopsis, encodes a member of the raf family of protein kinases. Cell, 72(3), 427-441.
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  PMID: 8431946;Abstract: We isolated a recessive Arabidopsis mutant, ctr1, that constitutively exhibits seedling and adult phenotypes observed in plants treated with the plant hormone ethylene. The ctr1 adult morphology can be phenocopied by treatment of wild-type plants with exogenous ethylene and is due, at least in part, to inhibition of cell elongation. Seedlings and adult ctr1 plants show constitutive expression of ethylene-regulated genes. The epistasis of ctr1 and other ethylene response mutants has defined the position of CTR1 in the ethylene signal transduction pathway. The CTR1 gene has been cloned, and the DNA sequences of four mutant alleles were determined. The gene encodes a putative serine/threonine protein kinase that is most closely related to the Raf protein kinase family. Copyright © 1993 by Cell Press.
• McNevin, J. P., Woodward, W., Hannoufa, A., Feldmann, K. A., & Lemieux, B. (1993). Isolation and characterization of eceriferum (cer) mutants induced by T-DNA insertions in Arabidopsis thaliana. Genome, 36(3), 610-618.
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  Abstract: Thirteen Arabidopsis thaliana mutants with deviating epicuticular wax layers (i.e., cer mutants) were isolated by screening 13000 transformed lines produced by the seed transformation method. After crossing the 13 mutants to some of the previously known cer mutant lines, 12 of our mutants mapped to 6 of the 21 known complementation groups (cer1 through cer4 as well as cer6 and cer10), while the other mutant corresponded to a previously unknown locus, cer21. Mutant phenotypes of 6 of the 13 mutant lines were caused by T-DNA insertions within cer genes. We also analyzed the chemical composition of the epicuticular wax layers of the cer mutants isolated in this study relative to that of Arabidopsis wild-type plants. Our results suggest that the five genes we tagged regulate different steps in wax biosynthesis, i.e., the decarbonylation of fatty aldehydes to alkanes, the elongation of hexacosanoic acid to octacosanoic acid, the reduction of fatty aldehydes to primary alcohols and the production of free aldehydes, while an insertion in the fifth gene causes an alteration in the chain length distribution of the different classes of wax compounds.
• Roe, J. L., Rivin, C. J., Sessions, R. A., Feldmann, K. A., & Zambryski, P. C. (1993). The Tousled gene in A. Thaliana encodes a protein kinase homolog that is required for leaf and flower development. Cell, 75(5), 939-950.
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  PMID: 8252629;Abstract: Mutation at the TOUSLED locus of A. thaliana results in a complex phenotype, the most dramatic aspect of which being the abnormal flowers produced in mutant plants. tsl flowers show a random loss of floral organs, and organ development is impaired. The TSL gene appears to be required in the floral meristem for correct initiation of floral organ primordia and for proper development of organ primordia. Loss of TSL function also affects flowering time and leaf morphology. Using a mutation derived by T-DNA insertion mutagenesis, we have cloned the TSL gene and found that it encodes a protein kinase homolog with a novel N-terminal domain. This protein kinase gene identifies a novel signaling/regulatory pathway used during development in Arabidopsis.
• Tsay, Y., Schroeder, J. I., Feldmann, K. A., & Crawford, N. M. (1993). The herbicide sensitivity gene CHL1 of arabidopsis encodes a nitrate-inducible nitrate transporter. Cell, 72(5), 705-713.
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  PMID: 8453665;Abstract: This paper reports the identification and functional expression of a gene that is involved in nitrate uptake in plants, a process essential for the assimilation of nitrate and the biological removal of nitrate from the soil solution. The CHL1 gene of Arabidopsis, which when mutated confers resistance to the herbicide chlorate and a decrease In nitrate uptake, was isolated and found to encode a protein with 12 putative membrane-spanning segments. Injection of CHL1 mRNA into Xenopus oocytes produces a nitrate- and pH-dependent membrane depolarization, inward current, and nitrate uptake. These data show that the CHL1 gene encodes an electrogenic nitrate transporter. CHL1 mRNA is found predominantly in roots and displays nitrate- and pH-dependent regulation. Copyright © 1993 by Cell Press.
• Yadav, N. S., Wierzbicki, A., Aegerter, M., Caster, C. S., Pérez-Grau, L., Kinney, A. J., Hitz, W. D., Booth Jr., J. R., Schweiger, B., Stecca, K. L., Allen, S. M., Blackwell, M., Reiter, R. S., Carlson, T. J., Russell, S. H., Feldmann, K. A., Pierce, J., & Browse, J. (1993). Cloning of higher plant ω-3 fatty acid desaturases. Plant Physiology, 103(2), 467-476.
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  PMID: 8029334;PMCID: PMC159005;Abstract: Arabidopsis thaliana T-DNA transformants were screened for mutations affecting seed fatty acid composition. A mutant line was found with reduced levels of linolenic acid (18:3) due to a T-DNA insertion. Genomic DNA flanking the T-DNA insertion was used to obtain an Arabidopsis cDNA that encodes a polypeptide identified as a microsomal ω-3 fatty acid desaturase by its complementation of the mutation. Analysis of lipid content in transgenic tissues demonstrated that this enzyme is limiting for 18:3 production in Arabidopsis seeds and carrot hairy roots. This cDNA was used to isolate a related Arabidopsis cDNA, whose mRNA is accumulated to a much higher level in leaf tissue relative to root tissue. This related cDNA encodes a protein that is a homolog of the microsomal desaturase but has an N-terminal extension deduced to be a transit peptide, and its gene maps to a position consistent with that of the Arabidopsis fad D locus, which controls plastid ω-3 desaturation. These Arabidopsis cDN As were used as hybridization probes to isolate cDNAs encoding homologous proteins from developing seeds of soybean and rapeseed. The high degree of sequence similarity between these sequences suggests that the ω-3 desaturases use a common enzyme mechanism.
• Deng, X., Matsui, M., Wei, N., Wagner, D., Chu, A. M., Feldmann, K. A., & Quail, P. H. (1992). COP1, an arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a G_β homologous domain. Cell, 71(5), 791-801.
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  PMID: 1423630;Abstract: Plant seedling development is capable of following 1 of 2 distinct morphogenic pathways: skotomorphogenesis in darkness and photomorphogenesis in light. Dark-grown Arabidopsis seedlings with recessive mutations at the constitutively photomorphogenic (COP1) locus indicate that the wild-type COP1 protein represses photomorphogenesis in darkness and that light reverses this repressive activity. Using a T-DNA-tagged mutant, we have cloned the COP1 locus. The amino-terminal half of the encoded protein contains a conserved zinc-binding motif, whereas the carboxyl-terminal half contains a domain homologous to the WD-40 repeat motif of Gβ proteins. The presence of both a putative DNA-binding motif and a G protein-related domain in a single polypeptide suggests that COP1 may be the first of a new class of regulatory molecules. This novel structure could endow COP1 with the capacity to function as a negative transcriptional regulator capable of direct interaction with components of the G protein signaling pathway. Copyright © 1992 by Cell Press.
• LaBrie, S. T., Wilkinson, J. Q., Tsay, Y., Feldmann, K. A., & Crawford, N. M. (1992). Identification of two tungstate-sensitive molybdenum cofactor mutants, chl2 and chl7, of Arabidopsis thaliana. MGG Molecular & General Genetics, 233(1-2), 169-176.
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  PMID: 1534867;Abstract: The characterization of mutants that are resistant to the herbicide chlorate has greatly increased our understanding of the structure and function of the genes required for the assimilation of nitrate. Hundreds of chlorate-resistant mutants have been identified in plants, and almost all have been found to be defective in nitrate reduction due to mutations in either nitrate reductase (NR) structural genes or genes required for the synthesis of the NR cofactor molybdenum-pterin (MoCo). The chlorate-resistant mutant of Arabidopsis thaliana, ch12, is also impaired in nitrate reduction, but the defect responsible for this phenotype has yet to be explained. chl2 plants have low levels of NR activity, yet the map position of the chl2 mutation is clearly distinct from that of the two NR structural genes that have been identified in Arabidopsis. In addition, chl2 plants are not thought to be defective in MoCo, as they have near wild-type levels of xanthine dehydrogenase activity, which has been used as a measure of MoCo in other organisms. These results suggest that chl2 may be a NR regulatory mutant. We have examined chl2 plants and have found that they have as much NR (NIA2) mRNA as wild type a variable but often reduced level of NR protein, and one-eighth the NR activity of wild-type plants. It is difficult to explain these results by a simple regulatory model; therefore, we reexamined the MoCo levels in chl2 plants using a sensitive, specific assay for MoCo: complementation of Neurospora MoCo mutant extracts. We found that chl2 has low levels of MoCo - about one-eighth the wild-type level and less than the level in another Arabidopsis MoCo mutant chl6 (B73). To confirm this result we developed a new diagnostic assay for MoCo mutants, growth inhibition by tungstate. Both chl2 and chl6 are sensitive to tungstate at concentrations that have no effect on wildtype plants. The tungstate sensitivity as well as the chlorate resistance, low NR activity and low MoCo levels all cosegregate, indicating that all are due to a single mutation that maps to the chl2 locus, 10 centimorgans from erecta on chromosome 2. We also report on the isolation of a new chlorate-resistant mutant of Arabidopsis, ch17, which is a MoCo mutant with the same phenotypes as chl2 and chl6. © 1992 Springer-Verlag.
• Medford, J. I., Behringer, F. J., Callos, J. D., & Feldmann, K. A. (1992). Normal and abnormal development in the arabidopsis vegetative shoot apex. Plant Cell, 4(6), 631-643.
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  Abstract: Vegetative development in the Arabidopsis shoot apex follows both sequential and repetitive steps. Early in development, the young vegetative meristem is flat and has a rectangular shape with bilateral symmetry. The first pair of leaf primordia is radially symmetrical and is initiated on opposite sides of the meristem. As development proceeds, the meristem changes first to a bilaterally symmetrical trapezoid and then to a radially symmetrical dome. Vegetative development from the domed meristem continues as leaves are initiated in a repetitive manner. Abnormal development of the vegetative shoot apex is described for a number of mutants. The mutants we describe fall into at least three classes: (1) lesions in the shoot apex that do not show an apparent alteration in the shoot apical meristem, (2) lesions in the apical meristem that also (directly or indirectly) alter leaf primordia, and (3) lesions in the apical meristem that alter meristem size and leaf number but not leaf morphology. These mutations provide tools both to genetically analyze vegetative development of the shoot apex and to learn how vegetative development influences floral development.
• Reiter, R. S., G., J., Feldmann, K. A., Rafalski, J. A., Tingey, S. V., & Scolnik, P. A. (1992). Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proceedings of the National Academy of Sciences of the United States of America, 89(4), 1477-1481.
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  PMID: 1346933;PMCID: PMC48474;Abstract: A population of Arabidopsis thaliana recombinant inbred lines was constructed and used to develop a high-density genetic linkage map containing 252 random amplified polymorphic DNA markers and 60 previously mapped restriction fragment length polymorphisms. Linkage groups were correlated to the classical genetic map by inclusion of nine phenotypic markers in the mapping cross. We also applied a technique for local mapping that allows targeting of markers to a selected genome region by pooling DNA from recombinant inbred lines based on their genotype. We conclude that random amplified polymorphic DNAs, used in conjunction with a recombinant inbred population, can facilitate the genetic and physical characterization of the Arabidopsis genome and that this method is generally applicable to other organisms for which appropriate populations either are available or can be developed.
• Errampalli, D., Patton, D., Castle, L., Mickelson, L., Hansen, K., Schnall, J., Feldmann, K., & Meinke, D. (1991). Embryonic lethals and T-DNA insertional mutagenesis in Arabidopsis. Plant Cell, 3(2), 149-157.
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  Abstract: T-DNA insertional mutagenesis represents a promising approach to the molecular isolation of genes with essential functions during plant embryo development. We describe in this report the isolation and characterization of 18 mutants of Arabidopsis thaliana defective in embryo development following seed transformation with Agrobacterium tumefaciens. Random T-DNA insertion was expected to result in a high frequency of recessive embryonic lethals because many target genes are required for embryogenesis. The cointegrate Ti plasmid used in these experiments contained the nopaline synthase and neomycin phosphotransferase gene markers. Nopaline assays and resistance to kanamycin were used to estimate the number of functional inserts present in segregating families. Nine families appeared to contain a T-DNA insert either within or adjacent to the mutant gene. Eight families were clearly not tagged with a functional insert and appeared instead to contain mutations induced during the transformation process. DNA gel blot hybridization with internal and right border probes revealed a variety of rearrangements associated with T-DNA insertion. A general strategy is presented to simplify the identification of tagged embryonic mutants and facilitate the molecular isolation of genes required for plant embryogenesis.
• Feldmann, K. A. (1991). T-DNA insertion mutagenesis in Arabidopsis: Mutational spectrum. Plant Journal, 1(1), 71-82.
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  Abstract: More than 8000 transformants of Arabidopsis have been generated by treating germinating seeds with cultures of Agrobacterium tumefaciens. Genetic characterization of a subset of the transformants indicates that they contain an average of 1.4 inserts each, as assayed by kanamycin resistance. Molecular analysis shows that the inserts are predominantly concatamers of T-DNAs arranged as direct and inverted repeats. More recently these 8000 lines have been screened under a variety of growth conditions for visible alterations in phenotype. More than 1000 putative mutants were observed during the application of these screening procedures. These mutants fall into several general classes: seedling-lethals, size variants, pigment, embryo-defective, reduced-fertility, dramatic (morphological), and physiological. The majority of the mutants (88%) segregate in a Mendelian manner for the mutant phenotype. An analysis of approximately 50 mutants in this group shows that >80% are tagged with a functional insert. The wide spectrum of mutants observed suggests that it may be feasible to develop a comprehensive collection of mutant lines in which each gene is tagged by a T-DNA insertion.
• Yanofsky, M. F., Hong, M. a., Bowman, J. L., Drews, G. N., Feldmann, K. A., & Meyerowitz, E. M. (1990). The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature, 346(6279), 35-39.
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  PMID: 1973265;Abstract: Mutations in the homeotic gene agamous of the plant Arabidopsis cause the transformation of the floral sex organs. Cloning and sequence analysis of agamous suggest that it encodes a protein with a high degree of sequence similarity to the DNA-binding region of transcription factors from yeast and humans and to the product of a homeotic gene from Antirrhinum. The agamous gene therefore probably encodes a transcription factor that regulates genes determining stamen and carpel development in wild-type flowers.
• Feldmann, K. A., Marks, M. D., Christianson, M. L., & Quatrano, R. S. (1989). A dwarf mutant of Arabidopsis generated by T-DNA insertion mutagenesis. Science, 243(4896), 1351-1354.
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  Abstract: Most plant genes that control complex traits of tissues, organs, and whole plants are uncharacterized. Plant height, structure of reproductive organs, seed development and germination, for example, are traits of great agronomic importance. However, in the absence of knowledge of the gene products, current molecular approaches to isolate these important genes are limited. Infection of germinating seeds of Arabidopsis thaliana with Agrobacterium results in transformed lines in which the integrated T-DNA from Agrobacterium and its associated kanamycin-resistance trait cosegregate with stable, phenotypic alterations. A survey of 136 transformed lines produced plants segregating in a manner consistent with Mendelian predictions for phenotypes altered in height, flower structure, trichomes, gametogenesis, embryogenesis, and seedling development. This report is the characterization of a dwarf mutant in which the phenotype is inherited as a single recessive nuclear mutation that cosegregates with both the kanamycin-resistance trait and the T-DNA insert.
• Feldmann, K. A., & Marks, M. D. (1987). Agrobacterium-mediated transformation of germinating seeds of Arabidopsis thaliana: A non-tissue culture approach. MGG Molecular & General Genetics, 208(1-2), 1-9.
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  Abstract: Germinating seeds of Arabidopsis thaliana were cocultivated with an Agrobacterium tumefaciens strain (C58Clrif) carrying the pGV3850:pAK1003 Ti plasmid. This Ti plasmid contains the neomycin phosphotransferase II gene (NPT II) which confers resistance to kanamycin and G418. Seeds (T1 generation) imbibed for 12 h before a 24 h exposure to Agrobacterium gave rise to the highest number of transformed progeny (T2 generation). Over 200 kanamycin-resistant T2 seedlings were isolated. Some of the T2 seedlings and T3 families were characterized for genetic segregation of functional NPT II gene(s), NPT II activity, and the presence of T-DNA inserts (Southern analysis). Ninety percent of the T2 individuals transmitted the resistance factor to the T3 families in a Mendelian fashion. Of the T3 families segregating in a Mendelian fashion (n=111), 62% segregated for one functional insert, 29% for two unlinked or linked functional inserts, 5% for three unlinked inserts, 1% for four unlinked inserts, whereas 3% appeared to be homozygous for the insert(s). The 13 families that did not exhibit Mendelian segregation ratios fell into 2 classes, both of which had a deficiency of kanamycin-resistant seedlings. In the Group I T3 families (n=6) only 0%-2% of the seedlings were resistant to kanamycin (100 mg/l), whereas in the Group II families (n=7) 8%-63% of the seedlings were resistant. All of the kanamycin-resistant plants that were tested were found to possess NPT II activity. Southern analysis revealed that all of the resistant plants contained at least one copy of the T-DNA and that the majority of the plants had multiple inserts. Explants from kanamycin-resistant plants survived and formed callus when cultured on callus-inducing medium containg G418. © 1987 Springer-Verlag.
• Feldmann, K. A., & Marks, M. D. (1986). Rapid and efficient regeneration of plants from explants of Arabidopsis thaliana. Plant Science, 47(1), 63-69.
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  Abstract: A procedure is given for the regeneration in vitro of a previously difficult to regenerate plant, Arabidopsis thaliana (L.) Heynh. Leaf explants of Arabidopsis that are given a short exposure to a callus-inducing medium prior to incubation on a shoot-inducing medium exhibit high survivability and rapidly produce shoots. Some media combinations allow shoots to form on 100% of the explants and the majority of these explants form multiple shoots. The shoots are normal in appearance and most of them can be induced to form functional roots and retain fertility. This regeneration scheme should be of use in the development of an Arabidopsis transformation procedure and may also be applicable to other recalcitrant plant species. © 1986.
• Wang, X. -., Scholl, R. L., & Feldmann, K. A. (1986). Characterization of a chlorate-hypersensitive, high nitrate reductase Arabidopsis thaliana mutant. Theoretical and Applied Genetics, 72(3), 328-336.
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  PMID: 24247939;Abstract: A population of A. thaliana, produced by self-fertilization of ethylmethane sulfonate treated plants, was exposed to chlorate in the watering solution, and plants showing early susceptibility symptoms were rescued. Among the progeny lines of these plants five were shown to be repeatably chlorate-hypersusceptible. One of these lines (designated C-4) possessed elevated activity of nitrate reductase (NR). The NR activity of mutant C-4 was higher than that of normal plants throughout the life cycle. Nitrite reductase and glutamine synthetase activities of C-4 were normal, as were chlorate uptake rate and tissue nitrate content. The elevated NR activity apparently was responsible for the chlorate hypersusceptibility of C-4. Inheritance studies of NR indicated that the elevated activity of C-4 was probably controlled by a single recessive allele. © 1986 Springer-Verlag.