- Professor, Plant Science
- Professor, BIO5 Institute
- Professor, Molecular and Cellular Biology
- Professor, Genetics - GIDP
- Ph.D. Molecular, Cell & Developmental Biology
- UCLA, Los Angeles, California
- Regional specification and cellular differentiation during early plant embryogenesis
- B.S. Biological Sciences
- UC Irvine, Irvine, California
- Shirley O'Brien Diversity Award
- CALS, Spring 2013
SCI 295B: Research Readiness: Arizona's Science, Engineering, and Math Scholars (ASEMS); PLS 560: Current Topics in Plant Biology
Transcriptional control of early seed development, Endosperm development in maize and Arabidopsis, Early reproductive development in angiosperms, Epigenetic regulation of plant gene expression
Plant Molecular BiologyPLS 358 (Spring 2021)
Directed ResearchPLS 592 (Fall 2020)
Directed RsrchMCB 492 (Fall 2020)
Mechanisms in Plant DevECOL 440 (Fall 2020)
Mechanisms in Plant DevMCB 440 (Fall 2020)
Mechanisms in Plant DevPLS 440 (Fall 2020)
Mechanisms: Plant DevelopmentPLS 540 (Fall 2020)
PreceptorshipSCI 491 (Fall 2020)
ResearchPLS 900 (Fall 2020)
Independent StudyPLS 399 (Spring 2020)
ResearchPLS 900 (Spring 2020)
Advanced Plant BiologyPLS 560 (Fall 2019)
Intro to ResearchPLP 695C (Fall 2019)
Intro to ResearchPLS 695C (Fall 2019)
PreceptorshipSCI 491 (Fall 2019)
ResearchPLS 900 (Fall 2019)
Master's ReportPLS 909 (Spring 2019)
ResearchPLS 900 (Spring 2019)
ThesisPLS 910 (Spring 2019)
Mechanisms in Plant DevMCB 440 (Fall 2018)
Mechanisms in Plant DevPLS 440 (Fall 2018)
Mechanisms: Plant DevelopmentPLS 540 (Fall 2018)
PreceptorshipSCI 491 (Fall 2018)
ResearchPLS 900 (Fall 2018)
DissertationPLS 920 (Spring 2018)
Independent StudyPLS 599 (Spring 2018)
ResearchPLS 900 (Spring 2018)
Advanced Plant BiologyPLS 560 (Fall 2017)
DissertationPLS 920 (Fall 2017)
Independent StudyPLS 599 (Fall 2017)
Independent StudyPLS 699 (Fall 2017)
ResearchPLS 900 (Fall 2017)
Directed ResearchPLS 492 (Spring 2017)
DissertationPLS 920 (Spring 2017)
Independent StudyPLS 599 (Spring 2017)
Directed RsrchMCB 492 (Fall 2016)
DissertationPLS 920 (Fall 2016)
Independent StudyPLS 599 (Fall 2016)
PreceptorshipSCI 391 (Fall 2016)
Research ReadinessSCI 295B (Fall 2016)
DissertationPLS 920 (Spring 2016)
ResearchPLS 900 (Spring 2016)
Research ReadinessSCI 295B (Spring 2016)
- Zhan, J., Dannenhoffer, J. M., & Yadegari, R. (2017). Endosperm Development and Cell Specialization. In Maize Kernel Development(pp 28-43). United Kingdom: CAB International.
- Zhan, J., Li, G., Ryu, C. H., Ma, C., Zhang, S., Lloyd, A., Hunter, B. G., Larkins, B. A., Drews, G. N., Wang, X., & Yadegari, R. (2018). Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm. The Plant cell, 30(10), 2425-2446.More infoDevelopment of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products, and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize () bZIP transcription factor Opaque-2 (O2). Here, we mapped in vivo binding sites of O2 in B73 endosperm and compared the results with genes differentially expressed in B73 and B73 We identified 186 putative direct O2 targets and 1677 indirect targets, encoding a broad set of gene functionalities. Examination of the temporal expression patterns of O2 targets revealed at least two distinct modes of O2-mediated gene activation. Two O2-activated genes, and (), encode transcription factors, which can in turn coactivate other O2 network genes with O2. NKD2 (with its paralog NKD1) was previously shown to be involved in regulation of aleurone development. Collectively, our results provide insights into the complexity of the O2-regulated network and its role in regulation of endosperm cell differentiation and function.
- Zhang, S., Thakare, D., & Yadegari, R. (2018). Laser-Capture Microdissection of Maize Kernel Compartments for RNA-Seq-Based Expression Analysis. Methods in molecular biology (Clifton, N.J.), 1676, 153-163. doi:https://doi.org/10.1007/978-1-4939-7315-6_9More infoLaser-capture microdissection (LCM) enables isolation of single cells or groups of cells for a variety of downstream applications including transcriptome profiling. Recently, this methodology has found a more widespread use particularly with the advent of next-generation sequencing techniques that enable deep profiling of the limited amounts of RNA obtained from fixed or frozen sections. When used with fixed tissues, a major experimental challenge is to balance the tissue integrity needed for microscopic visualization of the cell types of interest with that of the RNA quality necessary for deep profiling. Complex biological structures such as seeds or kernels pose an especially difficult case in this context as in many instances the key internal structures such as the embryo and the endosperm are relatively inaccessible. Here, we present an optimized LCM protocol for maize kernel that has been developed specifically to enable profiling of the early stages of endosperm development using RNA-Seq.
- Zhang, S., Wang, D., Zhang, H., Skaggs, M. I., Lloyd, A., Ran, D., An, L., Schumaker, K. S., Drews, G. N., & Yadegari, R. (2018). FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development. Plant physiology, 177(1), 285-299.More infoEarly endosperm development presents a unique system in which to uncover epigenetic regulatory mechanisms because the contributing maternal and paternal genomes possess differential epigenetic modifications. In Arabidopsis (), the initiation of endosperm coenocytic growth upon fertilization and the transition to endosperm cellularization are regulated by the FERTILIZATION-INDEPENDENT SEED (FIS)-Polycomb Repressive Complex 2 (PRC2), a putative H3K27 methyltransferase. Here, we address the possible role of the FIS-PRC2 complex in regulating the type I MADS-box gene family, which has been shown previously to regulate early endosperm development. We show that a subclass of type I MADS-box genes (C2 genes) was expressed in distinct domains of the coenocytic endosperm in wild-type seeds. Furthermore, the C2 genes were mostly up-regulated biallelically during the extended coenocytic phase of endosperm development in the FIS-PRC2 mutant background. Using allele-specific expression analysis, we also identified a small subset of C2 genes subjected to FIS-PRC2-dependent maternal or FIS-PRC2-independent paternal imprinting. Our data support a dual role for the FIS-PRC2 complex in the regulation of C2 type I MADS-box genes, as evidenced by a generalized role in the repression of gene expression at both alleles associated with endosperm cellularization and a specialized role in silencing the maternal allele of imprinted genes.
- Zhang, S., Zhan, J., & Yadegari, R. (2018). Maize opaque mutants are no longer so opaque. Plant reproduction, 31(3), 319-326.More infoThe endosperm of angiosperms is a zygotic seed organ that stores nutrient reserves to support embryogenesis and seed germination. Cereal endosperm is also a major source of human calories and an industrial feedstock. Maize opaque endosperm mutants commonly exhibit opaque, floury kernels, along with other abnormal seed and/or non-seed phenotypes. The opaque endosperm phenotype is sometimes accompanied by a soft kernel texture and increased nutritional quality, including a higher lysine content, which are valuable agronomic traits that have drawn attention of maize breeders. Recently, an increasing number of genes that underlie opaque mutants have been cloned, and their characterization has begun to shed light on the molecular basis of the opaque endosperm phenotype. These mutants are categorized by disruption of genes encoding zein or non-zein proteins localized to protein bodies, enzymes involved in endosperm metabolic processes, or transcriptional regulatory proteins associated with endosperm storage programs.
- Monihan, S. M., Magness, C. A., Yadegari, R., Smith, S. E., & Schumaker, K. S. (2016). Arabidopsis CALCINEURIN B-LIKE10 Functions Independently of the SOS Pathway during Reproductive Development in Saline Conditions. Plant physiology, 171(1), 369-79.More infoThe accumulation of sodium in soil (saline conditions) negatively affects plant growth and development. The Salt Overly Sensitive (SOS) pathway in Arabidopsis (Arabidopsis thaliana) functions to remove sodium from the cytosol during vegetative development preventing its accumulation to toxic levels. In this pathway, the SOS3 and CALCINEURIN B-LIKE10 (CBL10) calcium sensors interact with the SOS2 protein kinase to activate sodium/proton exchange at the plasma membrane (SOS1) or vacuolar membrane. To determine if the same pathway functions during reproductive development in response to salt, fertility was analyzed in wild type and the SOS pathway mutants grown in saline conditions. In response to salt, CBL10 functions early in reproductive development before fertilization, while SOS1 functions mostly after fertilization when seed development begins. Neither SOS2 nor SOS3 function in reproductive development in response to salt. Loss of CBL10 function resulted in reduced anther dehiscence, shortened stamen filaments, and aborted pollen development. In addition, cbl10 mutant pistils could not sustain the growth of wild-type pollen tubes. These results suggest that CBL10 is critical for reproductive development in the presence of salt and that it functions in different pathways during vegetative and reproductive development.
- Schumaker, K. S., Smith, S. E., Yadegari, R., Magness, C. A., & Monihan, S. M. (2016). Arabidopsis CALCINEURIN B-LIKE10 functions independently of the SOS pathway during reproductive development in saline conditions. Plant Physiology, 171, 369-379.
- Palanivelu, R., Yadegari, R., & Qin, Y. (2015). ACTIN-RELATED PROTEIN 6 regulates DISRUPTED MEIOTIC cDNA 1 gene expression in Arabidposis thaliana ovules. Molecular Reproduction and Development, 82, 499--499.
- Zhan, J., Thakare, D., Ma, C., Lloyd, A., Nixon, N. M., Arakaki, A. M., Burnett, W. J., Logan, K. O., Wang, D., Wang, X., Drews, G. N., & Yadegari, R. (2015). RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. The Plant cell, 27(3), 513-31.More infoEndosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the genetic networks that regulate endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the maize (Zea mays) kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene coexpression network analysis identified coexpression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a coexpression module highly correlated with the basal endosperm transfer layer (BETL) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types.
- Leroux, B. M., Goodyke, A. J., Schumacher, K. I., Abbott, C. P., Clore, A. M., Yadegari, R., Larkins, B. A., & Dannenhoffer, J. M. (2014). Maize early endosperm growth and development: from fertilization through cell type differentiation. American journal of botany, 101(8), 1259-74.
- Li, G., Wang, D., Yang, R., Logan, K., Chen, H., Zhang, S., Skaggs, M. I., Lloyd, A., Burnett, W. J., Laurie, J. D., Hunter, B. G., Dannenhoffer, J. M., Larkins, B. A., Drews, G. N., Wang, X., & Yadegari, R. (2014). Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. Proceedings of the National Academy of Sciences of the United States of America, 111(21), 7582-7.More infoCorresponding authors: XW and RY.
- Qin, Y., Zhao, L., Skaggs, M. I., Andreuzza, S., Tsukamoto, T., Panoli, A., Wallace, K. N., Smith, S., Siddiqi, I., Yang, Z., Yadegari, R., & Palanivelu, R. (2014). ACTIN-RELATED PROTEIN6 Regulates Female Meiosis by Modulating Meiotic Gene Expression in Arabidopsis. The Plant cell, 26(4), 1612-1628.More infoIn flowering plants, meiocytes develop from subepidermal cells in anthers and ovules. The mechanisms that integrate gene-regulatory processes with meiotic programs during reproductive development remain poorly characterized. Here, we show that Arabidopsis thaliana plants deficient in ACTIN-RELATED PROTEIN6 (ARP6), a subunit of the SWR1 ATP-dependent chromatin-remodeling complex, exhibit defects in prophase I of female meiosis. We found that this meiotic defect is likely due to dysregulated expression of meiotic genes, particularly those involved in meiotic recombination, including DMC1 (DISRUPTED MEIOTIC cDNA1). Analysis of DMC1 expression in arp6 mutant plants indicated that ARP6 inhibits expression of DMC1 in the megasporocyte and surrounding nonsporogeneous ovule cells before meiosis. After cells enter meiosis, however, ARP6 activates DMC1 expression specifically in the megasporocyte even as it continues to inhibit DMC1 expression in the nonsporogenous ovule cells. We further show that deposition of the histone variant H2A.Z, mediated by the SWR1 chromatin-remodeling complex at the DMC1 gene body, requires ARP6. Therefore, ARP6 regulates female meiosis by determining the spatial and temporal patterns of gene expression required for proper meiosis during ovule development.
- Thakare, D., Yang, R., Steffen, J. G., Zhan, J., Wang, D., Clark, R. M., Wang, X., & Yadegari, R. (2014). RNA-Seq analysis of laser-capture microdissected cells of the developing central starchy endosperm of maize. Genomics data, 2, 242-5.More infoEndosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected a high level of correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed developmental stage precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these storage programs. The mRNA-Seq data has been deposited in Gene Expression Omnibus (accession number GSE58504).
- Xin, M., Yang, R., Li, G., Chen, H., Laurie, J., Ma, C., Wang, D., Yao, Y., Larkins, B. A., Sun, Q., Yadegari, R., Wang, X., & Ni, Z. (2013). Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. The Plant Cell, 25(9), 3212-3227.
- Drews, G. N., Wang, D., Steffen, J. G., Schumaker, K. S., & Yadegari, R. (2011). Identification of genes expressed in the angiosperm female gametophyte. Journal of experimental botany, 62(5), 1593-9.More infoUntil recently, identification of gene regulatory networks controlling the development of the angiosperm female gametophyte has presented a significant challenge to the plant biology community. The angiosperm female gametophyte is fairly inaccessible because it is a highly reduced structure relative to the sporophyte and is embedded within multiple layers of the sporophytic tissue of the ovule. Moreover, although mutations affecting the female gametophyte can be readily isolated, their analysis can be difficult because most affect genes involved in basic cellular processes that are also required in the diploid sporophyte. In recent years, expression-based approaches in multiple species have begun to uncover gene sets expressed in specific female gametophyte cells as a means of identifying regulatory networks controlling cell differentiation in the female gametophyte. Here, recent efforts to identify and analyse gene expression programmes in the Arabidopsis female gametophyte are reviewed.
- Yadegari, R., Wang, D., Zhang, C., Hearn, D. J., Kang, I., Punwani, J. A., Skaggs, M. I., Drews, G. N., Schumaker, K. S., & Yadegari, R. -. (2010). Identification of transcription-factor genes expressed in the Arabidopsis female gametophyte. BMC plant biology, 10.More infoIn flowering plants, the female gametophyte is typically a seven-celled structure with four cell types: the egg cell, the central cell, the synergid cells, and the antipodal cells. These cells perform essential functions required for double fertilization and early seed development. Differentiation of these distinct cell types likely involves coordinated changes in gene expression regulated by transcription factors. Therefore, understanding female gametophyte cell differentiation and function will require dissection of the gene regulatory networks operating in each of the cell types. These efforts have been hampered because few transcription factor genes expressed in the female gametophyte have been identified. To identify such genes, we undertook a large-scale differential expression screen followed by promoter-fusion analysis to detect transcription-factor genes transcribed in the Arabidopsis female gametophyte.
- Chung, T., Wang, D., Kim, C. S., Yadegari, R., & Larkins, B. A. (2009). Plant SMU-1 and SMU-2 homologues regulate pre-mRNA splicing and multiple aspects of development. Plant physiology, 151(3), 1498-512.More infoIn eukaryotes, alternative splicing of pre-mRNAs contributes significantly to the proper expression of the genome. However, the functions of many auxiliary spliceosomal proteins are still unknown. Here, we functionally characterized plant homologues of nematode suppressors of mec-8 and unc-52 (smu). We compared transcript profiles of maize (Zea mays) smu2 endosperm with those of wild-type plants and identified pre-mRNA splicing events that depend on the maize SMU2 protein. Consistent with a conserved role of plant SMU-2 homologues, Arabidopsis (Arabidopsis thaliana) smu2 mutants also show altered splicing of similar target pre-mRNAs. The Atsmu2 mutants occasionally show developmental phenotypes, including abnormal cotyledon numbers and higher seed weights. We identified AtSMU1 as one of the SMU2-interacting proteins, and Atsmu1 mutations cause similar developmental phenotypes with higher penetrance than Atsmu2. The AtSMU2 and AtSMU1 proteins are localized to the nucleus and highly prevalent in actively dividing tissues. Taken together, our data indicated that the plant SMU-1 and SMU-2 homologues appear to be involved in splicing of specific pre-mRNAs that affect multiple aspects of development.
- Nodine, M. D., Yadegari, R., & Tax, F. E. (2007). RPK1 and TOAD2 are two receptor-like kinases redundantly required for arabidopsis embryonic pattern formation. Developmental cell, 12(6), 943-56.More infoAlthough the basic plant body plan is established during embryogenesis, the molecular basis of embryonic patterning remains to be fully understood. We have identified two receptor-like kinases, RECEPTOR-LIKE PROTEIN KINASE1 (RPK1) and TOADSTOOL2 (TOAD2), required for Arabidopsis embryonic pattern formation. Genetic analysis indicates that RPK1 and TOAD2 have overlapping embryonic functions. The zygotic gene dosage of TOAD2 in an rpk1 background is of critical importance, suggesting that signaling mediated by RPK1 and TOAD2 must be above a threshold level for proper embryo development. The localization of RPK1 and TOAD2 translational fusions to GFP coupled with the analysis of cell-type-specific markers indicate that RPK1 and TOAD2 are redundantly required for both pattern formation along the radial axis and differentiation of the basal pole during early embryogenesis. We propose that RPK1 and TOAD2 receive intercellular signals and mediate intracellular responses that are necessary for embryonic pattern formation.
- Yadegari, R., Wang, D., Tyson, M. D., Jackson, S. S., & Yadegari, R. -. (2006). Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 103(35).More infoIn Arabidopsis, a complex of Polycomb-group (PcG) proteins functions in the female gametophyte to control the initiation of seed development. Mutations in the PcG genes, including MEDEA (MEA) and FERTILIZATION-INDEPENDENT SEED 2 (FIS2), produce autonomous seeds where endosperm proliferation occurs in the absence of fertilization. By using a yeast two-hybrid screen, we identified MEA and a related protein, SWINGER (SWN), as SET-domain partners of FIS2. Localization data indicated that all three proteins are present in the female gametophyte. Although single-mutant swn plants did not show any defects, swn mutations enhanced the mea mutant phenotype in producing autonomous seeds. Thus, MEA and SWN perform partially redundant functions in controlling the initiation of endosperm development before fertilization in Arabidopsis.
- Dinneny, J. R., Yadegari, R., Fischer, R. L., Yanofsky, M. F., & Weigel, D. (2004). The role of JAGGED in shaping lateral organs. Development (Cambridge, England), 131(5), 1101-10.More infoPosition-dependent regulation of growth is important for shaping organs in multicellular organisms. We have characterized the role of JAGGED, a gene that encodes a protein with a single C(2)H(2) zinc-finger domain, in controlling the morphogenesis of lateral organs in Arabidopsis thaliana. Loss of JAGGED function causes organs to have serrated margins. In leaves, the blade region is most severely affected. In sepals, petals and stamens, the strongest defects are seen in the distal regions. By monitoring cell-cycle activity in developing petals with the expression of HISTONE 4, we show that JAGGED suppresses the premature differentiation of tissues, which is necessary for the formation of the distal region. The localization of defects overlaps with the expression domain of JAGGED, which is restricted to the growing regions of lateral organs. JAGGED expression is notably absent from the cryptic bract, the remnant of a leaf-like organ that subtends the flower in many species but does not normally develop in wild-type Arabidopsis. If misexpressed, JAGGED can induce the formation of bracts, suggesting that the exclusion of JAGGED from the cryptic bract is a cause of bractless flowers in Arabidopsis.
- Yadegari, R., & Drews, G. N. (2004). Female gametophyte development. The Plant cell, 16 Suppl, S133-41.
- Apuya, N. R., Yadegari, R., Fischer, R. L., Harada, J. J., Goldberg, R. B., & Harada, J. H. (2002). RASPBERRY3 gene encodes a novel protein important for embryo development. Plant physiology, 129(2), 691-705.More infoWe identified a new gene that is interrupted by T-DNA in an Arabidopsis embryo mutant called raspberry3. raspberry3 has "raspberry-like" cellular protuberances with an enlarged suspensor characteristic of other raspberry embryo mutants, and is arrested morphologically at the globular stage of embryo development. The predicted RASPBERRY3 protein has domains found in proteins present in prokaryotes and algae chloroplasts. Computer prediction analysis suggests that the RASPBERRY3protein may be localized in the chloroplast. Complementation analysis supports the possibility that the RASPBERRY3 protein may be involved in chloroplast development. Our experiments demonstrate the important role of the chloroplast, directly or indirectly, in embryo morphogenesis and development.
- Drews, G. N., & Yadegari, R. (2002). Development and function of the angiosperm female gametophyte. Annual review of genetics, 36, 99-124.More infoThe plant life cycle alternates between a diploid sporophyte generation and a haploid gametophyte generation. The angiosperm female gametophyte is critical to the reproductive process. It is the structure within which egg cell production and fertilization take place. In addition, the female gametophyte plays a role in pollen tube guidance, the induction of seed development, and the maternal control of seed development. Genetic analysis in Arabidopsis has uncovered mutations that affect female gametophyte development and function. Mutants defective in almost all stages of development have been identified, and analysis of these mutants is beginning to reveal features of the female gametophyte developmental program. Other mutations that affect female gametophyte function have uncovered regulatory genes required for the induction of endosperm development. From these studies, we are beginning to understand the regulatory networks involved in female gametophyte development and function. Further investigation of the female gametophyte will require complementary approaches including expression-based approaches to obtain a complete profile of the genes functioning within this critical structure.
- Apuya, N. R., Yadegari, R., Fischer, R. L., Harada, J. J., Zimmerman, J. L., & Goldberg, R. B. (2001). The Arabidopsis embryo mutant schlepperless has a defect in the chaperonin-60alpha gene. Plant physiology, 126(2), 717-30.More infoWe identified a T-DNA-generated mutation in the chaperonin-60alpha gene of Arabidopsis that produces a defect in embryo development. The mutation, termed schlepperless (slp), causes retardation of embryo development before the heart stage, even though embryo morphology remains normal. Beyond the heart stage, the slp mutation results in defective embryos with highly reduced cotyledons. slp embryos exhibit a normal apical-basal pattern and radial tissue organization, but they are morphologically retarded. Even though slp embryos are competent to transcribe two late-maturation gene markers, this competence is acquired more slowly as compared with wild-type embryos. slp embryos also exhibit a defect in plastid development-they remain white during maturation in planta and in culture. Hence, the overall developmental phenotype of the slp mutant reflects a lesion in the chloroplast that affects embryo development. The slp phenotype highlights the importance of the chaperonin-60alpha protein for chloroplast development and subsequently for the proper development of the plant embryo and seedling.
- Yadegari, R., Kinoshita, T., Lotan, O., Cohen, G., Katz, A., Choi, Y., Katz, A., Nakashima, K., Harada, J. J., Goldberg, R. B., Fischer, R. L., & Ohad, N. (2000). Mutations in the FIE and MEA genes that encode interacting polycomb proteins cause parent-of-origin effects on seed development by distinct mechanisms. The Plant cell, 12(12), 2367-2382.More infoIn flowering plants, two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus, which replicates to generate the endosperm, a tissue that supports embryo development. The FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) and MEDEA (MEA) genes encode WD and SET domain polycomb proteins, respectively. In the absence of fertilization, a female gametophyte with a loss-of-function fie or mea allele initiates endosperm development without fertilization. fie and mea mutations also cause parent-of-origin effects, in which the wild-type maternal allele is essential and the paternal allele is dispensable for seed viability. Here, we show that FIE and MEA polycomb proteins interact physically, suggesting that the molecular partnership of WD and SET domain polycomb proteins has been conserved during the evolution of flowering plants. The overlapping expression patterns of FIE and MEA are consistent with their suppression of gene transcription and endosperm development in the central cell as well as their control of seed development after fertilization. Although FIE and MEA interact, differences in maternal versus paternal patterns of expression, as well as the effect of a recessive mutation in the DECREASE IN DNA METHYLATION1 (DDM1) gene on mutant allele transmission, indicate that fie and mea mutations cause parent-of-origin effects on seed development by distinct mechanisms.
- Kinoshita, T., Yadegari, R., Harada, J. J., Goldberg, R. B., & Fischer, R. L. (1999). Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. The Plant cell, 11(10), 1945-52.More infoIn flowering plants, two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus that replicates to generate the endosperm, which is a tissue that supports embryo development. MEDEA (MEA) encodes an Arabidopsis SET domain Polycomb protein. Inheritance of a maternal loss-of-function mea allele results in embryo abortion and prolonged endosperm production, irrespective of the genotype of the paternal allele. Thus, only the maternal wild-type MEA allele is required for proper embryo and endosperm development. To understand the molecular mechanism responsible for the parent-of-origin effects of mea mutations on seed development, we compared the expression of maternal and paternal MEA alleles in the progeny of crosses between two Arabidopsis ecotypes. Only the maternal MEA mRNA was detected in the endosperm from seeds at the torpedo stage and later. By contrast, expression of both maternal and paternal MEA alleles was observed in the embryo from seeds at the torpedo stage and later, in seedling, leaf, stem, and root. Thus, MEA is an imprinted gene that displays parent-of-origin-dependent monoallelic expression specifically in the endosperm. These results suggest that the embryo abortion observed in mutant mea seeds is due, at least in part, to a defect in endosperm function. Silencing of the paternal MEA allele in the endosperm and the phenotype of mutant mea seeds supports the parental conflict theory for the evolution of imprinting in plants and mammals.
- Kiyosue, T., Ohad, N., Yadegari, R., Hannon, M., Dinneny, J., Wells, D., Katz, A., Margossian, L., Harada, J. J., Goldberg, R. B., & Fischer, R. L. (1999). Control of fertilization-independent endosperm development by the MEDEA polycomb gene in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 96(7), 4186-91.More infoHigher plant reproduction is unique because two cells are fertilized in the haploid female gametophyte. Egg and sperm nuclei fuse to form the embryo. A second sperm nucleus fuses with the central cell nucleus that replicates to generate the endosperm, a tissue that supports embryo development. To understand mechanisms that initiate reproduction, we isolated a mutation in Arabidopsis, f644, that allows for replication of the central cell and subsequent endosperm development without fertilization. When mutant f644 egg and central cells are fertilized by wild-type sperm, embryo development is inhibited, and endosperm is overproduced. By using a map-based strategy, we cloned and sequenced the F644 gene and showed that it encodes a SET-domain polycomb protein. Subsequently, we found that F644 is identical to MEDEA (MEA), a gene whose maternal-derived allele is required for embryogenesis [Grossniklaus, U., Vielle-Calzada, J.-P., Hoeppner, M. A. & Gagliano, W. B. (1998) Science 280, 446-450]. Together, these results reveal functions for plant polycomb proteins in the suppression of central cell proliferation and endosperm development. We discuss models to explain how polycomb proteins function to suppress endosperm and promote embryo development.
- Ohad, N., Yadegari, R., Margossian, L., Hannon, M., Michaeli, D., Harada, J. J., Goldberg, R. B., & Fischer, R. L. (1999). Mutations in FIE, a WD polycomb group gene, allow endosperm development without fertilization. The Plant cell, 11(3), 407-16.More infoA fundamental problem in biology is to understand how fertilization initiates reproductive development. Higher plant reproduction is unique because two fertilization events are required for sexual reproduction. First, a sperm must fuse with the egg to form an embryo. A second sperm must then fuse with the adjacent central cell nucleus that replicates to form an endosperm, which is the support tissue required for embryo and/or seedling development. Here, we report cloning of the Arabidopsis FERTILIZATION-INDEPENDENT ENDOSPERM (FIE) gene. The FIE protein is a homolog of the WD motif-containing Polycomb proteins from Drosophila and mammals. These proteins function as repressors of homeotic genes. A female gametophyte with a loss-of-function allele of fie undergoes replication of the central cell nucleus and initiates endosperm development without fertilization. These results suggest that the FIE Polycomb protein functions to suppress a critical aspect of early plant reproduction, namely, endosperm development, until fertilization occurs.
- Goldberg, R. B., de Paiva, G., & Yadegari, R. (1994). Plant embryogenesis: zygote to seed. Science (New York, N.Y.), 266(5185), 605-14.More infoMost differentiation events in higher plants occur continuously in the postembryonic adult phase of the life cycle. Embryogenesis in plants, therefore, is concerned primarily with establishing the basic shoot-root body pattern of the plant and accumulating food reserves that will be used by the germinating seedling after a period of embryonic dormancy within the seed. Recent genetics studies in Arabidopsis have identified genes that provide new insight into how embryos form during plant development. These studies, and others using molecular approaches, are beginning to reveal the underlying processes that control plant embryogenesis.
- Yadegari, R., Paiva, G., Laux, T., Koltunow, A. M., Apuya, N., Zimmerman, J. L., Fischer, R. L., Harada, J. J., & Goldberg, R. B. (1994). Cell Differentiation and Morphogenesis Are Uncoupled in Arabidopsis raspberry Embryos. The Plant cell, 6(12), 1713-1729.More infoWe identified two Arabidopsis embryo mutants, designated as raspberry1 and raspberry2, by screening T-DNA-mutagenized Arabidopsis lines. Embryogenesis in these mutants is indistinguishable from that of wild-type plants until the late-globular stage, after which raspberry1 and raspberry2 embryos fail to undergo the transition to heart stage, remain globular shaped, and proliferate an enlarged suspensor region. raspberry1 and raspberry2 embryo-proper regions enlarge during embryogenesis, become highly vacuolate, and display prominent convex, or "raspberry-like" protuberances on their outer cell layers. In situ hybridization studies with several embryo cell-specific mRNA probes indicated that the raspberry1 and raspberry2 embryo-proper regions differentiate tissue layers in their correct spatial contexts and that the regulation of cell-specific genes within these layers is normal. Surprisingly, a similar spatial and temporal pattern of mRNA accumulation occurs within the enlarged suspensor region of raspberry1 and raspberry2 embryos, suggesting that a defect in embryo-proper morphogenesis can cause the suspensor to take on an embryo-proper-like state and differentiate a radial tissue-type axis. We conclude that cell differentiation can occur in the absence of both organ formation and morphogenesis during plant embryogenesis and that interactions occur between the embryo-proper and suspensor regions.
- Yadegari, R. (2019, April). Gene networks of maize endosperm. UC Davis Plant Biology Group Seminar. Davis, CA: UC Davis Plant Biology.
- Yadegari, R. (2019, March). Gene regulatory networks of early maize endosperm. Society for Developmental Biology Southwest Regional Meeting. Anschutz, CO: Society for Developmental Biology.
- Yadegari, R. (2019, October). Early endosperm developmental programs in maize and their contribution to seed size (and quality?). Annual Meeting of the W4168 Multistate Research Project on Environmental and Genetic Determinants of Seed Quality and Performance. Lexington, KY: Univ KY Ag College.
- Yadegari, R. (2018, June). Gene regulatory networks of early maize endosperm.. 25th International Congress on Sexual Plant Reproduction (Plant Reproduction 2018). Gifu, Japan: International Association of Sexual Plant Reproduction.
- Yadegari, R. (2018, June). Gene regulatory networks of early maize endosperm. Annual Meeting of the Multistate Research Project: Environmental and Genetic Determinants of Seed Quality and Performance (W3168),. Corvallis, OR: W3168 Working Group, USDA.
- Yadegari, R. (2018, November). ASEMS: Arizona’s Science, Engineering, and Math Scholars Program.. Workshop “Broadening the Impact of Plant Science Through Community-Based Innovation, Evaluation and Sharing of Outreach Programs”. UC Davis: RCN: Arabidopsis Research and Training for the 21st century (ART-21).
- Yadegari, R. (2017, April). Gene regulatory networks of maize endosperm. Bob Fischer Symposium. Los Angeles, CA: UCLA.More infoA symposium to honor the career of Robert L. Fischer (UC Berkeley, my postdoc adviser) as he has decided to retire.
- Yadegari, R. (2017, November). Early Endosperm Gene Regulatory Networks. 24th Seed Institute Conference. Los Angeles, CA: Bob Goldberg/UCLA Luskin Center.More infoI gave an introduction to our research followed by three talks from my research group:(1) "Identification of gene networks regulating early endosperm development inmaize" by Shanshan Zhang; (2) "Understanding MRP-1 regulatory networks controlling BETL differentiation in maize endosperm" by Guosheng Li; and "Analysis of the Opaque-2 regulatory network in maize endosperm" by Junpeng Zhan.
- Yadegari, R. (2017, November). Gene regulatory networks of early maize endosperm – implications for drought response in young kernels. 2nd International Workshop on Plant Development and Drought Stress. Pacific Grove, CA: American Society for Plant Biology.
- Yadegari, R. (2017, September). The Future of Research in Seed Biology. 12th Triennial Conference of the International Society for Seed Science. Monterey, CA: International Society for Seed Science.More infoPresentation and panel discussion on the "Future of Research and Practice in Seed Biology, Seed Technology and Seed Ecology."
- Yadegari, R. (2016, December). Understanding Seed Development: Molecular Control Mechanisms of Early Endosperm Proliferation and Cell Differentiation. Seminar, CEAC. Tucson, Arizona: Controlled Environment Agriculture Center, CALS.
- Yadegari, R. (2016, December). Understanding gene regulatory networks driving early endosperm development in maize. Seminar, ALARC. Maricopa, Arizona: ALARC, USDA.
- Yadegari, R. (2016, February). An integrated analysis of gene networks regulating endosperm development in plants. Annual Meeting of the Multistate Research Project: Environmental and Genetic Determinants of Seed Quality and Performance. San Antonio, Texas: USDA, W3168 Multistate Research Project.
- Yadegari, R. (2016, October). Gene regulatory networks for endosperm development in maize. Seminar, South Dakota State Univ.. Brookings, South Dakota: Dept. Agronomy, Horticulture & Plant Science, South Dakota State University.
- Yadegari, R. (2015, October). An integrated analysis of gene networks regulating endosperm development in plants. Society for Developmental Biology Annual Southwest Regional Meeting. Dallas, TX: UT Southwestern Medical Center.
- Yadegari, R. (2014, April). Deciphering regulatory networks controlling endosperm development. Biotechnology / Life Sciences Seminar Series, University of Nebraska. Lincoln, Nebraska: University of Nebraska, Lincoln.
- Yadegari, R. (2014, September). Gene regulatory networks controlling maize endosperm development. SPLS Seminar Series, University of Arizona. Tucson, Arizona: University of Arizona.
- Yadegari, R. (2014, September). Understanding gene regulatory networks controlling endosperm development in maize. PBS Colloquium Seminar Series, University of Minnesota. Minneapolis, Minnesota: University of Minnesota.
- Yadegari, R. (2013, April). Gene Networks in Early Endosperm Development.. Seminar at Department of Genetics, Development, and Cell Biology, Iowa State Univ.. Ames, IA.
- Yadegari, R. (2013, April). Gene Networks in Early Endosperm Development.. Seminar at Section of Molecular, Cell and Developmental Biology, Univ. Texas. Austin, TX.
- Yadegari, R. (2013, January). Gene Networks in Early Endosperm Development in Maize & Arabidopsis. Talk at the School of Plant Sciences Research Retreat. Oracle, AZ.
- Yadegari, R. (2013, September). Spatiotemporal patterns of gene expression in early maize endosperm. Seminar at Arid-Land Agricultural Research Center (USDA-ARS). Maricopa, AZ.
- Yadegari, R. (2012, April). Gene Regulatory Networks in Early Endosperm of Arabidopsis and Maize. Invited Seminar, North Carolina State University. Raleigh, NC.
- Yadegari, R. (2012, May). Gene Networks in Early Endosperm Development in Arabidopsis and Maize. Invited Seminar, UC Riverside. Riverside, CA.
- Zhang, S., & Yadegari, R. (2012, July). Polycomb Repressive Complex 2 regulates type 1 MADS-box gene expression during endosperm development in Arabidopsis. Plant Biology 2012. Austin, Texas: American Society for Plant Biology.
- Yadegari, R. (2011, March 2011). Polycomb-group Proteins and Control of Early Endosperm Development in Arabidopsis. Invited Seminar, Danforth Plant Sciences Center. St. Louis, MO.
- Pan, X., Zhang, S., Zhan, J., Li, G., Ryu, C., Nixon, N., King, S., Spears, C., Adhikari, B., Wu, H., Becraft, P. W., Dannenhoffer, J. M., Drews, G. N., & Yadegari, R. (2019, September). Gene Regulatory Networks in the Maize Endosperm. NSF Plant Genome Research Program 22th Annual Awardee Meeting. Alexandria, VA: NSF.
- Gurley, W., Zhang, S., Zhan, J., Li, G., Ryu, C., Pan, X., Rabiger, D., Nixon, N., King, S., Spears, C., Danek, J., Waldron, V., Adhikari, B., Wu, H., Becraft, P. W., Dannenhoffer, J. M., Drews, G. N., & Yadegari, R. (2018, September). Gene Regulatory Networks in the Maize Endosperm. NSF Plant Genome Research Program 21th Annual Awardee Meeting. Alexandria, VA: NSF.
- Zhan, J., Li, G., Ryu, C., Zhang, S., Ma, C., Lloyd, A., Drews, G. N., Wang, X., & Yadegari, R. (2018, January). The Opaque-2 Regulatory Network in Maize Endosperm. PAG XXVI - Plant & Animal Genome Conference. San Diego, CA: Plant & Genome/Scherago International.
- Wu, H., Adhikari, B., Zhan, J., Li, G., Yadegari, R., & Becraft, P. W. (2017, March). Nkd1, Nkd2 and Opaque2 play essential roles in gene regulatory network of maize endosperm development. 59th Annual Maize Genetics Conference. St. Louis, MO: Maize genetics community.
- Zhan, J., Li, G., Ryu, C., Zhang, S., Ma, C., Wang, X., & Yadegari, R. (2017, November). Analysis of the Opaque-2 regulatory network uncovers the timing and complexity of storage-program gene regulation during maize endosperm development. Plant Genomes & Biotechnology: from genes to networks. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
- Zhang, S., Wang, D., Zhang, H., Skaggs, M. I., Lloyd, A., Ran, D., An, L., Schumaker, K. S., Drews, G. N., & Yadegari, R. (2017, June). Differential spatiotemporal and epigenetic regulation of type I MADS-box gene expression by Polycomb Repressive Complex 2 during early endosperm development in Arabidopsis. The 28th International Conference on Arabidopsis Research. St. Louis, MO: ICAR.
- Zhang, S., Zhan, J., Li, G., Ryu, C., Rabiger, D., Nixon, N., King, S., Lloyd, A., Schumacher, K. I., Danek, J., Waldron, V., Adhikari, B., Wu, H., Ramsey, T., Becraft, P. W., Dannenhoffer, J. M., Drews, G. N., & Yadegari, R. (2017, September). Gene Regulatory Networks in the Maize Endosperm. NSF Plant Genome Research Program 20th Annual Awardee Meeting. Arlington, VA: NSF.
- Zhan, J., Li, G., Ryu, C., Ma, C., Wang, X., & Yadegari, R. (2016, March). Analysis of the Opaque-2 gene regulatory network in maize endosperm. Plant Reproduction 2016. Tucson, AZ: International Association of Sexual Plant Reproduction Research (IASPRR).
- Zhang, S., Ran, D., Ryu, C., Drews, G. N., Wang, X., & Yadegari, R. (2016, March). Identification of temporal gene regulatory networks in early maize endosperm development. Plant Reproduction 2016. Tucson, AZ: International Association of Sexual Plant Reproduction Research (IASPRR).
- Blachon, S., Grenouilloux, A., Collura, V., Moncion, T., Subramanian, S., Li, G., Yadegari, R., Grimanelli, D., Tripathi, P., Rushton, P., & Formstecher, E. (2015, July). Development of New Tools for High-Quality Yeast Two-Hybrid Analysis of Crop Interactomes. Plant Biology 2015. Minneapolis, MN: American Society for Plant Biology.
- Zhan, J., Li, G., Ma, C., Wang, X., & Yadegari, R. (2015, July). Genome-wide analyses of genes regulated by the endosperm-specific maize transcription factor Opaque-2. Plant Biology 2015. Minneapolis, MN: American Society for Plant Biology.
- Zhan, J., Thakare, D., Ma, C., Lloyd, A., Nixon, N., Arakaki, A., Burnett, W., Logan, K., Li, G., Zhang, S., Wang, D., Wang, X., Drews, G., & Yadegari, R. (2015, July). Identification of cell differentiation networks in maize endosperm using laser-capture microdissection and RNA sequencing. Plant Biology 2015. Minneapolis, MN: American Society for Plant Biology.
- Zhan, J., Thakare, D., Ma, C., Lloyd, A., Nixon, N., Arakaki, A., Burnett, W., Logan, K., Li, G., Zhang, S., Wang, X., Drews, G., & Yadegari, R. (2015, March). Deciphering gene regulatory networks controlling cell differentiation in maize endosperm. Maize Genetics Conference. St. Charles, IL.
- Zhang, S., Ran, D., Li, G., Zhan, J., & Yadegari, R. (2015, March). Identification of temporal regulatory modules in early maize endosperm development. Maize Genetics Conference. St. Charles, IL.
- Tafelmeyer, P., Grenouilloux, A., Collura, V., Moncion, T., Subramanian, S., Li, G., Yadegari, R., Grimanelli, D., Tripathi, P., Rushton, P., & Formstecher, E. (2014, July). Development of new tools for high-quality yeast two-hybrid analysis of crop interactomes. Plant Biology 2014. Portland, Oregon: American Society of Plant Biologists.
- Guosheng, L., Thakare, D., Zhang, S., Wang, D., Logan, K., Skaggs, M. I., Hunter, B., Laurie, J., Larkins, B. A., Drews, G. N., & Yadegari, R. (2013, March). Expression of Transcription Factor Genes in Early Endosperm Development in Maize. 55th Annual Maize Genetics Conference. St. Charles, IL.
- Laurie, J., Minta, A., Hunter, B., Chen, H., Wang, X., Dannenhoffer, J., Yadegari, R., & Larkins, B. A. (2013, March). The maize nucellus contributes to early kernel development through cell cycle arrest accompanied by post-pollination expansion. 55th Annual Maize Genetics Conference. St. Charles, IL.
- Logan, K., Li, G., Thakare, D., Yadegari, R., & Drews, G. N. (2013, March). Spatial-Temporal RNA Profiling of Early Endosperm Development In Maize. 55th Annual Maize Genetics Conference. St. Charles, IL.
- Wang, D., & Yadegari, R. (2013, July). Analysis of fis2, an endosperm-defective mutant, revealed potential cross-talks between zygotic and maternal tissues.. Plant Biology 2013. Providence, RI.
- Yadegari, R. (2013, September). Regulation of early endosperm development in maize.. NSF-PGRP Awardee Meeting. Arlington, VA.
- Logan, K., Drews, G. N., & Yadegari, R. (2012, March). Early endosperm development in maize. 54th Annual Maize Genetics Conference. Portland, OR.
- Yadegari, R. -. (2012, September). Regulation of Early Endosperm Development in Maize. NSF's annual Plant Genome Awardee Meeting. Arlington, VA.More infoPoster describing the latest results of our NSF maize endosperm project
- Zhang, S., Wang, D., Zhang, H., Lloyd, A., Skaggs, M. I., An, L., Drews, G. N., Schumaker, K. S., & Yadegari, R. (2012, July). Polycomb repressive complex 2 regulates type I MADS-box gene expression during endosperm development in Arabidopsis. Plant Biology 2012. Austin, TX.More infoAlso an oral presentation by Shanshan Zhang in a minisymposium.
- Yadegari, R. -. (2011, September). Regulation of Early Endosperm Development in Maize. NSF's annual Plant Genome Awardee Meeting. Arlington, VA.More infoPoster describing the latest results of our NSF maize endosperm project.