1
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Dong X, Luo H, Yao J, Guo Q, Yu S, Ruan Y, Li F, Jin W, Meng D. The conservation of allelic DNA methylation and its relationship with imprinting in maize. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1376-1389. [PMID: 37935439 PMCID: PMC10901201 DOI: 10.1093/jxb/erad440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
Genomic imprinting refers to allele-specific expression of genes depending on parental origin, and it is regulated by epigenetic modifications. Intraspecific allelic variation for imprinting has been detected; however, the intraspecific genome-wide allelic epigenetic variation in maize and its correlation with imprinting variants remain unclear. Here, three reciprocal hybrids were generated by crossing Zea mays inbred lines CAU5, B73, and Mo17 in order to examine the intraspecific conservation of the imprinted genes in the kernel. The majority of imprinted genes exhibited intraspecific conservation, and these genes also exhibited interspecific conservation (rice, sorghum, and Arabidopsis) and were enriched in some specific pathways. By comparing intraspecific allelic DNA methylation in the endosperm, we found that nearly 15% of DNA methylation existed as allelic variants. The intraspecific whole-genome correlation between DNA methylation and imprinted genes indicated that DNA methylation variants play an important role in imprinting variants. Disruption of two conserved imprinted genes using CRISPR/Cas9 editing resulted in a smaller kernel phenotype. Our results shed light on the intraspecific correlation of DNA methylation variants and variation for imprinting in maize, and show that imprinted genes play an important role in kernel development.
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Affiliation(s)
- Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, Liaoning, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Jiabin Yao
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Qingfeng Guo
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, Liaoning, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, Liaoning, China
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Department of Agronomy, College of Agriculture & Resources and Environmental Sciences, Tianjin Agricultural University, Tianjin 300392, China
| | - Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
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2
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Jia Z, Gao P, Yin F, Quilichini TD, Sheng H, Song J, Yang H, Gao J, Chen T, Yang B, Kochian LV, Zou J, Patterson N, Yang Q, Gillmor CS, Datla R, Li Q, Xiang D. Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats. Commun Biol 2022; 5:1412. [PMID: 36564439 PMCID: PMC9789062 DOI: 10.1038/s42003-022-04374-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.
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Affiliation(s)
- Zhen Jia
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Peng Gao
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Feifan Yin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Teagen D. Quilichini
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Huajin Sheng
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jingpu Song
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Hui Yang
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Jie Gao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ting Chen
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Bo Yang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Leon V. Kochian
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jitao Zou
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Nii Patterson
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Qingyong Yang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - C. Stewart Gillmor
- grid.512574.0Langebio, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821 México
| | - Raju Datla
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Qiang Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Daoquan Xiang
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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3
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Conservation Study of Imprinted Genes in Maize Triparental Heterozygotic Kernels. Int J Mol Sci 2022; 23:ijms232315424. [PMID: 36499766 PMCID: PMC9735609 DOI: 10.3390/ijms232315424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting is a classic epigenetic phenomenon related to the uniparental expression of genes. Imprinting variability exists in seeds and can contribute to observed parent-of-origin effects on seed development. Here, we conducted allelic expression of the embryo and endosperm from four crosses at 11 days after pollination (DAP). First, the F1 progeny of B73(♀) × Mo17(♂) and the inducer line CAU5 were used as parents to obtain reciprocal crosses of BM-C/C-BM. Additionally, the F1 progeny of Mo17(♀) × B73(♂) and CAU5 were used as parents to obtain reciprocal crosses of MB-C/C-MB. In total, 192 and 181 imprinted genes were identified in the BM-C/C-BM and MB-C/C-MB crosses, respectively. Then, by comparing the allelic expression of these imprinted genes in the reciprocal crosses of B73 and CAU5 (BC/CB), fifty-one Mo17-added non-conserved genes were identified as exhibiting imprinting variability. Fifty-one B73-added non-conserved genes were also identified by comparing the allelic expression of imprinted genes identified in BM-C/C-BM, MB-C/C-MB and MC/CM crosses. Specific Gene Ontology (GO) terms were not enriched in B73-added/Mo17-added non-conserved genes. Interestingly, the imprinting status of these genes was less conserved across other species. The cis-element distribution, tissue expression and subcellular location were similar between the B73-added/Mo17-added conserved and B73-added/Mo17-added non-conserved imprinted genes. Finally, genotypic and phenotypic analysis of one non-conserved gene showed that the mutation and overexpression of this gene may affect embryo and kernel size, which indicates that these non-conserved genes may also play an important role in kernel development. The findings of this study will be helpful for elucidating the imprinting mechanism of genes involved in maize kernel development.
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Matilla AJ. Exploring Breakthroughs in Three Traits Belonging to Seed Life. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040490. [PMID: 35214823 PMCID: PMC8875957 DOI: 10.3390/plants11040490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 05/06/2023]
Abstract
Based on prior knowledge and with the support of new methodology, solid progress in the understanding of seed life has taken place over the few last years. This update reflects recent advances in three key traits of seed life (i.e., preharvest sprouting, genomic imprinting, and stored-mRNA). The first breakthrough refers to cloning of the mitogen-activated protein kinase-kinase 3 (MKK3) gene in barley and wheat. MKK3, in cooperation with ABA signaling, controls seed dormancy. This advance has been determinant in producing improved varieties that are resistant to preharvest sprouting. The second advance concerns to uniparental gene expression (i.e., imprinting). Genomic imprinting primarily occurs in the endosperm. Although great advances have taken place in the last decade, there is still a long way to go to complete the puzzle regarding the role of genomic imprinting in seed development. This trait is probably one of the most important epigenetic facets of developing endosperm. An example of imprinting regulation is polycomb repressive complex 2 (PRC2). The mechanism of PRC2 recruitment to target endosperm with specific genes is, at present, robustly studied. Further progress in the knowledge of recruitment of PRC2 epigenetic machinery is considered in this review. The third breakthrough referred to in this update involves stored mRNA. The role of the population of this mRNA in germination is far from known. Its relations to seed aging, processing bodies (P bodies), and RNA binding proteins (RBPs), and how the stored mRNA is targeted to monosomes, are aspects considered here. Perhaps this third trait is the one that will require greater experimental dedication in the future. In order to make progress, herein are included some questions that are needed to be answered.
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Affiliation(s)
- Angel J Matilla
- Departamento de Biología Funcional (Área Fisiología Vegetal), Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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5
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Wang W, Xiong H, Sun K, Zhang B, Sun MX. New insights into cell-cell communications during seed development in flowering plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:215-229. [PMID: 34473416 DOI: 10.1111/jipb.13170] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The evolution of seeds is a major reason why flowering plants are a dominant life form on Earth. The developing seed is composed of two fertilization products, the embryo and endosperm, which are surrounded by a maternally derived seed coat. Accumulating evidence indicates that efficient communication among all three seed components is required to ensure coordinated seed development. Cell communication within plant seeds has drawn much attention in recent years. In this study, we review current knowledge of cross-talk among the endosperm, embryo, and seed coat during seed development, and highlight recent advances in this field.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hanxian Xiong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kaiting Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Bo Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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Jiang H, Guo D, Ye J, Gao Y, Liu H, Wang Y, Xue M, Yan Q, Chen J, Duan L, Li G, Li X, Xie L. Genome-wide analysis of genomic imprinting in the endosperm and allelic variation in flax. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1697-1710. [PMID: 34228847 DOI: 10.1111/tpj.15411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes biased expression of maternally and paternally inherited alleles. In flowering plants, genomic imprinting predominantly occurs in the triploid endosperm and plays a vital role in seed development. In this study, we identified 248 candidate imprinted genes including 114 maternally expressed imprinted genes (MEGs) and 134 paternally expressed imprinted genes (PEGs) in flax (Linum usitatissimum L.) endosperm using deep RNA sequencing. These imprinted genes were neither clustered in specific chromosomal regions nor well conserved among flax and other plant species. MEGs tended to be expressed specifically in the endosperm, whereas the expression of PEGs was not tissue-specific. Imprinted single nucleotide polymorphisms differentiated 200 flax cultivars into the oil flax, oil-fiber dual purpose flax and fiber flax subgroups, suggesting that genomic imprinting contributed to intraspecific variation in flax. The nucleotide diversity of imprinted genes in the oil flax subgroup was significantly higher than that in the fiber flax subgroup, indicating that some imprinted genes underwent positive selection during flax domestication from oil flax to fiber flax. Moreover, imprinted genes that underwent positive selection were related to flax functions. Thirteen imprinted genes related to flax seed size and weight were identified using a candidate gene-based association study. Therefore, our study provides information for further exploration of the function and genomic variation of imprinted genes in the flax population.
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Affiliation(s)
- Haixia Jiang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Dongliang Guo
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiali Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanfang Gao
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Huiqing Liu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Yue Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Min Xue
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Qingcheng Yan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Jiaxun Chen
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Lepeng Duan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Gongze Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Xiao Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
| | - Liqiong Xie
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang, China
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7
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Khanday I, Sundaresan V. Plant zygote development: recent insights and applications to clonal seeds. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101993. [PMID: 33422964 DOI: 10.1016/j.pbi.2020.101993] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 05/22/2023]
Abstract
In flowering plants, haploid gametes - an egg cell and a sperm cell fuse to form the first diploid cell - the zygote. The zygote is the progenitor stem cell that gives rise to all the embryonic and post embryonic tissues and organs. Unlike animals, both maternal and paternal gene products participate in the initial development of zygotes in plants. Here, we discuss recent advances in understanding of the zygotic transition and embryo initiation in angiosperms, including the role of parental contributions to gene expression in the zygote. We further discuss utilization of this knowledge in agricultural biotechnology through synthetic apomixis. Parthenogenesis obtained by manipulation of embryogenic factors, combined with mutations that bypass meiosis, enables clonal propagation of hybrid crops through seeds.
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Affiliation(s)
- Imtiyaz Khanday
- Department of Plant Biology, University of California, Davis, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Plant Sciences, University of California, Davis, CA, USA.
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8
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Li Q, Wu Y. The encyclopedia of maize kernel gene expression. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:879-881. [PMID: 31456310 DOI: 10.1111/jipb.12869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/24/2019] [Indexed: 05/26/2023]
Abstract
This commentary highlights the recent two studies which uncovered dynamic maize kernel RNA-seq transcriptomes from early seed development, storage filling to maturation, day by day, hour by hour. These two studies provide a 'maize kernel gene expression dictionary' that will be powerful for the future studies in seed biology.
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Affiliation(s)
- Qi Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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9
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Suzuki M, Wu S, Mimura M, Alseekh S, Fernie AR, Hanson AD, McCarty DR. Construction and applications of a B vitamin genetic resource for investigation of vitamin-dependent metabolism in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:442-454. [PMID: 31520508 DOI: 10.1111/tpj.14535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 05/06/2023]
Abstract
The B vitamins provide essential co-factors for central metabolism in all organisms. In plants, B vitamins have surprising emerging roles in development, stress tolerance and pathogen resistance. Hence, there is a paramount interest in understanding the regulation of vitamin biosynthesis as well as the consequences of vitamin deficiency in crop species. To facilitate genetic analysis of B vitamin biosynthesis and functions in maize, we have mined the UniformMu transposon resource to identify insertional mutations in vitamin pathway genes. A screen of 190 insertion lines for seed and seedling phenotypes identified mutations in biotin, pyridoxine and niacin biosynthetic pathways. Importantly, isolation of independent insertion alleles enabled genetic confirmation of genotype-to-phenotype associations. Because B vitamins are essential for survival, null mutations often have embryo lethal phenotypes that prevent elucidation of subtle, but physiologically important, metabolic consequences of sub-optimal (functional) vitamin status. To circumvent this barrier, we demonstrate a strategy for refined genetic manipulation of vitamin status based on construction of heterozygotes that combine strong and hypomorphic mutant alleles. Dosage analysis of pdx2 alleles in endosperm revealed that endosperm supplies pyridoxine to the developing embryo. Similarly, a hypomorphic bio1 allele enabled analysis of transcriptome and metabolome responses to incipient biotin deficiency in seedling leaves. We show that systemic pipecolic acid accumulation is an early metabolic response to sub-optimal biotin status highlighting an intriguing connection between biotin, lysine metabolism and systemic disease resistance signaling. Seed-stocks carrying insertions for vitamin pathway genes are available for free, public distribution via the Maize Genetics Cooperation Stock Center.
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Affiliation(s)
- Masaharu Suzuki
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Manaki Mimura
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center for Plant Systems Biology, 4000, Plovdiv, Bulgaria
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida, 32611, USA
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10
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An L, Tao Y, Chen H, He M, Xiao F, Li G, Ding Y, Liu Z. Embryo-Endosperm Interaction and Its Agronomic Relevance to Rice Quality. FRONTIERS IN PLANT SCIENCE 2020; 11:587641. [PMID: 33424883 PMCID: PMC7793959 DOI: 10.3389/fpls.2020.587641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/09/2020] [Indexed: 05/07/2023]
Abstract
Embryo-endosperm interaction is the dominant process controlling grain filling, thus being crucial for yield and quality formation of the three most important cereals worldwide, rice, wheat, and maize. Fundamental science of functional genomics has uncovered several key genetic programs for embryo and endosperm development, but the interaction or communication between the two tissues is largely elusive. Further, the significance of this interaction for grain filling remains open. This review starts with the morphological and developmental aspects of rice grain, providing a spatial and temporal context. Then, it offers a comprehensive and integrative view of this intercompartmental interaction, focusing on (i) apoplastic nutrient flow from endosperm to the developing embryo, (ii) dependence of embryo development on endosperm, (iii) regulation of endosperm development by embryo, and (iv) bidirectional dialogues between embryo and endosperm. From perspective of embryo-endosperm interaction, the mechanisms underlying the complex quality traits are explored, with grain chalkiness as an example. The review ends with three open questions with scientific and agronomic importance that should be addressed in the future. Notably, current knowledge and future prospects of this hot research topic are reviewed from a viewpoint of crop physiology, which should be helpful for bridging the knowledge gap between the fundamental plant sciences and the practical technologies.
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Affiliation(s)
- Lu An
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yang Tao
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hao Chen
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Mingjie He
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Feng Xiao
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ganghua Li
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yanfeng Ding
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Zhenghui Liu
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Zhenghui Liu,
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11
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Armenta-Medina A, Gillmor CS. Genetic, molecular and parent-of-origin regulation of early embryogenesis in flowering plants. Curr Top Dev Biol 2019; 131:497-543. [DOI: 10.1016/bs.ctdb.2018.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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12
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Yang G, Liu Z, Gao L, Yu K, Feng M, Yao Y, Peng H, Hu Z, Sun Q, Ni Z, Xin M. Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization. THE PLANT CELL 2018; 30:37-47. [PMID: 29298834 PMCID: PMC5810578 DOI: 10.1105/tpc.17.00837] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/11/2017] [Accepted: 01/02/2018] [Indexed: 05/06/2023]
Abstract
Genomic imprinting is an epigenetic phenomenon that causes genes to be differentially expressed depending on their parent of origin. To evaluate the evolutionary conservation of genomic imprinting and the effects of ploidy on this process, we investigated parent-of-origin-specific gene expression patterns in the endosperm of diploid (Aegilops spp), tetraploid, and hexaploid wheat (Triticum spp) at various stages of development via high-throughput transcriptome sequencing. We identified 91, 135, and 146 maternally or paternally expressed genes (MEGs or PEGs, respectively) in diploid, tetraploid, and hexaploid wheat, respectively, 52.7% of which exhibited dynamic expression patterns at different developmental stages. Gene Ontology enrichment analysis suggested that MEGs and PEGs were involved in metabolic processes and DNA-dependent transcription, respectively. Nearly half of the imprinted genes exhibited conserved expression patterns during wheat hexaploidization. In addition, 40% of the homoeolog pairs originating from whole-genome duplication were consistently maternally or paternally biased in the different subgenomes of hexaploid wheat. Furthermore, imprinted expression was found for 41.2% and 50.0% of homolog pairs that evolved by tandem duplication after genome duplication in tetraploid and hexaploid wheat, respectively. These results suggest that genomic imprinting was evolutionarily conserved between closely related Triticum and Aegilops species and in the face of polyploid hybridization between species in these genera.
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Affiliation(s)
- Guanghui Yang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhenshan Liu
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lulu Gao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Man Feng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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