1
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Deans NC, Talbot JERB, Li M, Sáez-González C, Hövel I, Heavens D, Stam M, Hollick JB. Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats. PLoS Genet 2024; 20:e1011296. [PMID: 38814980 PMCID: PMC11166354 DOI: 10.1371/journal.pgen.1011296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/11/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024] Open
Abstract
Exceptions to Mendelian inheritance often highlight novel chromosomal behaviors. The maize Pl1-Rhoades allele conferring plant pigmentation can display inheritance patterns deviating from Mendelian expectations in a behavior known as paramutation. However, the chromosome features mediating such exceptions remain unknown. Here we show that small RNA production reflecting RNA polymerase IV function within a distal downstream set of five tandem repeats is coincident with meiotically-heritable repression of the Pl1-Rhoades transcription unit. A related pl1 haplotype with three, but not one with two, repeat units also displays the trans-homolog silencing typifying paramutations. 4C interactions, CHD3a-dependent small RNA profiles, nuclease sensitivity, and polyadenylated RNA levels highlight a repeat subregion having regulatory potential. Our comparative and mutant analyses show that transcriptional repression of Pl1-Rhoades correlates with 24-nucleotide RNA production and cytosine methylation at this subregion indicating the action of a specific DNA-dependent RNA polymerase complex. These findings support a working model in which pl1 paramutation depends on trans-chromosomal RNA-directed DNA methylation operating at a discrete cis-linked and copy-number-dependent transcriptional regulatory element.
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Affiliation(s)
- Natalie C. Deans
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Joy-El R. B. Talbot
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Mowei Li
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Cristian Sáez-González
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | | | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Jay B. Hollick
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
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2
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Liu C, Mao B, Zhang Y, Tian L, Ma B, Chen Z, Wei Z, Li A, Shao Y, Cheng G, Li L, Li W, Zhang D, Ding X, Peng J, Peng Y, He J, Ye N, Yuan D, Chu C, Duan M. The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:709-730. [PMID: 38483018 DOI: 10.1111/jipb.13640] [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: 10/24/2023] [Accepted: 02/23/2024] [Indexed: 04/11/2024]
Abstract
Hybrid rice (Oryza sativa) generally outperforms its inbred parents in yield and stress tolerance, a phenomenon termed heterosis, but the underlying mechanism is not completely understood. Here, we combined transcriptome, proteome, physiological, and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000 (CY1000). In addition to surpassing the mean values for its two parents (mid-parent heterosis), CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents (over-parent heterosis or heterobeltiosis). Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance, acting in an overdominant fashion in CY1000. Furthermore, we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and OsAAT30. The salt-sensitive phenotypes were associated with the OsWRKY72paternal genotype or the OsAAT30maternal genotype in core rice germplasm varieties. OsWRKY72paternal specifically repressed the expression of OsGSTU26 under salt stress, leading to salinity sensitivity, while OsWRKY72maternal specifically repressed OsAAT30, resulting in salinity tolerance. These results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice, providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.
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Affiliation(s)
- Citao Liu
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Yanxia Zhang
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Lei Tian
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Biao Ma
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhuo Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongwei Wei
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Aifu Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Gongye Cheng
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Lingling Li
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Wenyu Li
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Di Zhang
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoping Ding
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | | | - Yulin Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Jiwai He
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Nenghui Ye
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Dingyang Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Chengcai Chu
- College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Meijuan Duan
- Hunan Provincial Key Laboratory of Stress Biology, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
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3
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Wang B, Hou M, Shi J, Ku L, Song W, Li C, Ning Q, Li X, Li C, Zhao B, Zhang R, Xu H, Bai Z, Xia Z, Wang H, Kong D, Wei H, Jing Y, Dai Z, Wang HH, Zhu X, Li C, Sun X, Wang S, Yao W, Hou G, Qi Z, Dai H, Li X, Zheng H, Zhang Z, Li Y, Wang T, Jiang T, Wan Z, Chen Y, Zhao J, Lai J, Wang H. De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis. Nat Genet 2023; 55:312-323. [PMID: 36646891 DOI: 10.1038/s41588-022-01283-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023]
Abstract
Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal production. However, the molecular mechanisms of heterosis remain obscure. Here we show that structural variants (SVs) between the parental lines have a predominant role underpinning maize heterosis. De novo assembly and analyses of 12 maize founder inbred lines (FILs) reveal abundant genetic variations among these FILs and, through expression quantitative trait loci and association analyses, we identify several SVs contributing to genomic and phenotypic differentiations of various heterotic groups. Using a set of 91 diallel-cross F1 hybrids, we found strong positive correlations between better-parent heterosis of the F1 hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of genetic complementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.
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Affiliation(s)
- Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Lixia Ku
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiang Ning
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Hua Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhijing Bai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dexin Kong
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Hongbin Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yifeng Jing
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Zhouyan Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Hu Hailing Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Xinyu Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Chunhui Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Xuan Sun
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Shuaishuai Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China
| | - Wen Yao
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Gege Hou
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Zhi Qi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, Inner Mongolia University, Hohhot, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing, China
| | | | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China.,Guangzhou Laboratory, Guangzhou, China
| | - Zhaoman Wan
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Yanhui Chen
- College of Agronomy and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China.
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences, Beijing, China.
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
| | - Haiyang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
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4
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Yu D, Gu X, Zhang S, Dong S, Miao H, Gebretsadik K, Bo K. Molecular basis of heterosis and related breeding strategies reveal its importance in vegetable breeding. HORTICULTURE RESEARCH 2021; 8:120. [PMID: 34059656 PMCID: PMC8166827 DOI: 10.1038/s41438-021-00552-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 05/02/2023]
Abstract
Heterosis has historically been exploited in plants; however, its underlying genetic mechanisms and molecular basis remain elusive. In recent years, due to advances in molecular biotechnology at the genome, transcriptome, proteome, and epigenome levels, the study of heterosis in vegetables has made significant progress. Here, we present an extensive literature review on the genetic and epigenetic regulation of heterosis in vegetables. We summarize six hypotheses to explain the mechanism by which genes regulate heterosis, improve upon a possible model of heterosis that is triggered by epigenetics, and analyze previous studies on quantitative trait locus effects and gene actions related to heterosis based on analyses of differential gene expression in vegetables. We also discuss the contributions of yield-related traits, including flower, fruit, and plant architecture traits, during heterosis development in vegetables (e.g., cabbage, cucumber, and tomato). More importantly, we propose a comprehensive breeding strategy based on heterosis studies in vegetables and crop plants. The description of the strategy details how to obtain F1 hybrids that exhibit heterosis based on heterosis prediction, how to obtain elite lines based on molecular biotechnology, and how to maintain heterosis by diploid seed breeding and the selection of hybrid simulation lines that are suitable for heterosis research and utilization in vegetables. Finally, we briefly provide suggestions and perspectives on the role of heterosis in the future of vegetable breeding.
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Affiliation(s)
- Daoliang Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kiros Gebretsadik
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Science, Aksum University, Shire Campus, Shire, Ethiopia
| | - Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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5
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Genetic control of non-genetic inheritance in mammals: state-of-the-art and perspectives. Mamm Genome 2020; 31:146-156. [PMID: 32529318 PMCID: PMC7369129 DOI: 10.1007/s00335-020-09841-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Thought to be directly and uniquely dependent from genotypes, the ontogeny of individual phenotypes is much more complicated. Individual genetics, environmental exposures, and their interaction are the three main determinants of individual's phenotype. This picture has been further complicated a decade ago when the Lamarckian theory of acquired inheritance has been rekindled with the discovery of epigenetic inheritance, according to which acquired phenotypes can be transmitted through fertilization and affect phenotypes across generations. The results of Genome-Wide Association Studies have also highlighted a big degree of missing heritability in genetics and have provided hints that not only acquired phenotypes, but also individual's genotypes affect phenotypes intergenerationally through indirect genetic effects. Here, we review available examples of indirect genetic effects in mammals, what is known of the underlying molecular mechanisms and their potential impact for our understanding of missing heritability, phenotypic variation. and individual disease risk.
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6
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Liu J, Li M, Zhang Q, Wei X, Huang X. Exploring the molecular basis of heterosis for plant breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:287-298. [PMID: 30916464 DOI: 10.1111/jipb.12804] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/13/2019] [Indexed: 05/18/2023]
Abstract
Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.
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Affiliation(s)
- Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Mengjie Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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7
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Liu H, Wang Q, Chen M, Ding Y, Yang X, Liu J, Li X, Zhou C, Tian Q, Lu Y, Fan D, Shi J, Zhang L, Kang C, Sun M, Li F, Wu Y, Zhang Y, Liu B, Zhao XY, Feng Q, Yang J, Han B, Lai J, Zhang XS, Huang X. Genome-wide identification and analysis of heterotic loci in three maize hybrids. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:185-194. [PMID: 31199059 PMCID: PMC6920156 DOI: 10.1111/pbi.13186] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 05/18/2023]
Abstract
Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large-scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield-related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete-incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow-up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants.
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Affiliation(s)
- Hongjun Liu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Yahui Ding
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Xuerong Yang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
| | - Xiaohan Li
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Congcong Zhou
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Qilin Tian
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Yiqi Lu
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Danlin Fan
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Lin Zhang
- College of AgricultureNortheast Agricultural UniversityHarbinChina
| | - Congbin Kang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Mingfei Sun
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Fangyuan Li
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Yujian Wu
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Yongzhong Zhang
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Baoshen Liu
- State Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai'anChina
| | - Xiang Yu Zhao
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Qi Feng
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Jinliang Yang
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Bin Han
- National Center for Gene ResearchCAS Center for Excellence of Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement CenterDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Xian Sheng Zhang
- State Key Laboratory of Crop BiologyCollege of Life SciencesShandong Agricultural UniversityTai'anChina
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular SciencesCollege of Life SciencesShanghai Normal UniversityShanghaiChina
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8
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Chen E, Huang X, Tian Z, Wing RA, Han B. The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:639-665. [PMID: 31035826 DOI: 10.1146/annurev-arplant-050718-100320] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.
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Affiliation(s)
- Erwang Chen
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;
| | - Bin Han
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
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9
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Wang H, Zhang X, Yang H, Liu X, Li H, Yuan L, Li W, Fu Z, Tang J, Kang D. Identification of heterotic loci associated with grain yield and its components using two CSSL test populations in maize. Sci Rep 2016; 6:38205. [PMID: 27917917 PMCID: PMC5137037 DOI: 10.1038/srep38205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 11/07/2016] [Indexed: 11/17/2022] Open
Abstract
Heterosis has widely been used to increase grain yield and quality. In this study, the genetic basis of heterosis on grain yield and its main components in maize were examined over 2 years in two locations in two test populations constructed from a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058). Of the 169 heterotic loci (HL) associated with grain yield and its five components identified in CSSL × Zheng58 and CSSL × Xun9058 test populations, only 25 HL were detected in both populations. The comparison of quantitative trait loci (QTLs) detected in the CSSL population with HL detected in the two test populations revealed that only 15.46% and 17.35% of the HL in the given populations respectively, shared the same chromosomal regions as that of the corresponding QTLs and showed dominant effects as well as pleiotropism with additive and dominant effects. In addition, most of the HL (74.23% and 74.49%) had overdominant effects. These results suggest that overdominance is the main contributor to the effects of heterosis on grain yield and its components in maize, and different HL are associated with heterosis for different traits in different hybrids.
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Affiliation(s)
- Hongqiu Wang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huili Yang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyang Liu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huimin Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liang Yuan
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434023, China
| | - Dingming Kang
- College of Agriculture and Biotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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11
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Huang X, Yang S, Gong J, Zhao Q, Feng Q, Zhan Q, Zhao Y, Li W, Cheng B, Xia J, Chen N, Huang T, Zhang L, Fan D, Chen J, Zhou C, Lu Y, Weng Q, Han B. Genomic architecture of heterosis for yield traits in rice. Nature 2016; 537:629-633. [PMID: 27602511 DOI: 10.1038/nature19760] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/22/2016] [Indexed: 12/18/2022]
Abstract
Increasing grain yield is a long-term goal in crop breeding to meet the demand for global food security. Heterosis, when a hybrid shows higher performance for a trait than both parents, offers an important strategy for crop breeding. To examine the genetic basis of heterosis for yield in rice, here we generate, sequence and record the phenotypes of 10,074 F2 lines from 17 representative hybrid rice crosses. We classify modern hybrid rice varieties into three groups, representing different hybrid breeding systems. Although we do not find any heterosis-associated loci shared across all lines, within each group, a small number of genomic loci from female parents explain a large proportion of the yield advantage of hybrids over their male parents. For some of these loci, we find support for partial dominance of heterozygous locus for yield-related traits and better-parent heterosis for overall performance when all of the grain-yield traits are considered together. These results inform on the genomic architecture of heterosis and rice hybrid breeding.
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Affiliation(s)
- Xuehui Huang
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qilin Zhan
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Zhao
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Wenjun Li
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Benyi Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junhui Xia
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Neng Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tao Huang
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lei Zhang
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danlin Fan
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiaying Chen
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Congcong Zhou
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yiqi Lu
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qijun Weng
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
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Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proc Natl Acad Sci U S A 2016; 113:E4248-56. [PMID: 27382183 DOI: 10.1073/pnas.1607851113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hybrids displayed nonadditive DNA methylation levels, termed methylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differentially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interactions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution.
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Fort A, Ryder P, McKeown PC, Wijnen C, Aarts MG, Sulpice R, Spillane C. Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2016; 209:590-9. [PMID: 26395035 DOI: 10.1111/nph.13650] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/05/2015] [Indexed: 05/10/2023]
Abstract
Heterosis is the phenomenon whereby hybrid offspring of genetically divergent parents display superior characteristics compared with their parents. Although hybridity and polyploidy can influence heterosis in hybrid plants, the differential contributions of hybridity vs polyploidy to heterosis effects remain unknown. To address this question, we investigated heterosis effects on rosette size and growth rate of 88 distinct F1 lines of Arabidopsis thaliana consisting of diploids, reciprocal triploids and tetraploids in isogenic and hybrid genetic contexts. 'Heterosis without hybridity' effects on plant size can be generated in genetically isogenic F1 triploid plants. Paternal genome excess F1 triploids display positive heterosis, whereas maternal genome excess F1 s display negative heterosis effects. Paternal genome dosage increases plant size in F1 hybrid triploid plants by, on average, 57% (in contrast with 35% increase displayed by F1 diploid hybrids). Such effects probably derive from differential seed size, as the growth rate of triploids was similar to diploids. Tetraploid plants display a lower growth rate compared with other ploidies, whereas hybrids display increased early stage growth rate. By disaggregating heterosis effects caused by hybridity vs genome dosage, we advance our understanding of heterosis in plants and facilitate novel paternal genome dosage-based strategies to enhance heterosis effects in crop plants.
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Affiliation(s)
- Antoine Fort
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Peter C McKeown
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Cris Wijnen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Building 107, 6708, PB Wageningen, the Netherlands
| | - Mark G Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Building 107, 6708, PB Wageningen, the Netherlands
| | - Ronan Sulpice
- Systems Biology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Áras de Brún, University Road, Galway, Ireland
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Giacopelli BJ, Hollick JB. Trans-Homolog Interactions Facilitating Paramutation in Maize. PLANT PHYSIOLOGY 2015; 168:1226-36. [PMID: 26149572 PMCID: PMC4528761 DOI: 10.1104/pp.15.00591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/03/2015] [Indexed: 05/13/2023]
Abstract
Paramutations represent locus-specific trans-homolog interactions affecting the heritable silencing properties of endogenous alleles. Although examples of paramutation are well studied in maize (Zea mays), the responsible mechanisms remain unclear. Genetic analyses indicate roles for plant-specific DNA-dependent RNA polymerases that generate small RNAs, and current working models hypothesize that these small RNAs direct heritable changes at sequences often acting as transcriptional enhancers. Several studies have defined specific sequences that mediate paramutation behaviors, and recent results identify a diversity of DNA-dependent RNA polymerase complexes operating in maize. Other reports ascribe broader roles for some of these complexes in normal genome function. This review highlights recent research to understand the molecular mechanisms of paramutation and examines evidence relevant to small RNA-based modes of transgenerational epigenetic inheritance.
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Affiliation(s)
- Brian John Giacopelli
- Department of Molecular Genetics, Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Jay Brian Hollick
- Department of Molecular Genetics, Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
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15
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Cis-acting determinants of paramutation. Semin Cell Dev Biol 2015; 44:22-32. [DOI: 10.1016/j.semcdb.2015.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022]
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16
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Huang X, Yang S, Gong J, Zhao Y, Feng Q, Gong H, Li W, Zhan Q, Cheng B, Xia J, Chen N, Hao Z, Liu K, Zhu C, Huang T, Zhao Q, Zhang L, Fan D, Zhou C, Lu Y, Weng Q, Wang ZX, Li J, Han B. Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis. Nat Commun 2015; 6:6258. [PMID: 25651972 PMCID: PMC4327311 DOI: 10.1038/ncomms7258] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/09/2015] [Indexed: 01/08/2023] Open
Abstract
Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena.
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Affiliation(s)
- Xuehui Huang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yan Zhao
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hao Gong
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Wenjun Li
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qilin Zhan
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Benyi Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junhui Xia
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Neng Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Zhongna Hao
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kunyan Liu
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Chuanrang Zhu
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Tao Huang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qiang Zhao
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Lei Zhang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Danlin Fan
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Congcong Zhou
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yiqi Lu
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qijun Weng
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Zi-Xuan Wang
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiayang Li
- National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
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Ding H, Qin C, Luo X, Li L, Chen Z, Liu H, Gao J, Lin H, Shen Y, Zhao M, Lübberstedt T, Zhang Z, Pan G. Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. Int J Mol Sci 2014; 15:13892-915. [PMID: 25116687 PMCID: PMC4159830 DOI: 10.3390/ijms150813892] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/01/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022] Open
Abstract
Heterosis, or hybrid vigor, contributes to superior agronomic performance of hybrids compared to their inbred parents. Despite its importance, little is known about the genetic and molecular basis of heterosis. Early maize ear inflorescences formation affects grain yield, and are thus an excellent model for molecular mechanisms involved in heterosis. To determine the parental contributions and their regulation during maize ear-development-genesis, we analyzed genome-wide digital gene expression profiles in two maize elite inbred lines (B73 and Mo17) and their F1 hybrid using deep sequencing technology. Our analysis revealed 17,128 genes expressed in these three genotypes and 22,789 genes expressed collectively in the present study. Approximately 38% of the genes were differentially expressed in early maize ear inflorescences from heterotic cross, including many transcription factor genes and some presence/absence variations (PAVs) genes, and exhibited multiple modes of gene action. These different genes showing differential expression patterns were mainly enriched in five cellular component categories (organelle, cell, cell part, organelle part and macromolecular complex), five molecular function categories (structural molecule activity, binding, transporter activity, nucleic acid binding transcription factor activity and catalytic activity), and eight biological process categories (cellular process, metabolic process, biological regulation, regulation of biological process, establishment of localization, cellular component organization or biogenesis, response to stimulus and localization). Additionally, a significant number of genes were expressed in only one inbred line or absent in both inbred lines. Comparison of the differences of modes of gene action between previous studies and the present study revealed only a small number of different genes had the same modes of gene action in both maize seedlings and ear inflorescences. This might be an indication that in different tissues or developmental stages, different global expression patterns prevail, which might nevertheless be related to heterosis. Our results support the hypotheses that multiple molecular mechanisms (dominance and overdominance modes) contribute to heterosis.
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Affiliation(s)
- Haiping Ding
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China; E-Mail:
| | - Xirong Luo
- Zunyi Academy of Agricultural Sciences, Zunyi 563102, China; E-Mail:
| | - Lujiang Li
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Zhe Chen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Jian Gao
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
| | - Maojun Zhao
- Life Science College, Sichuan Agricultural University, Ya’an 625014, China; E-Mail:
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA; E-Mail:
| | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Authors to whom correspondence should be addressed; E-Mails: (Z.Z.); (G.P.); Tel.: +86-28-8629-0917 (G.P.); Fax: +86-28-8629-0916 (G.P.)
| | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China; E-Mails: (H.D.); ; (C.Q.); (L.L.); (Z.C.); (H.L.); (J.G.); (H.L.); (Y.S.)
- Authors to whom correspondence should be addressed; E-Mails: (Z.Z.); (G.P.); Tel.: +86-28-8629-0917 (G.P.); Fax: +86-28-8629-0916 (G.P.)
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Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids. Proc Natl Acad Sci U S A 2014; 111:2017-22. [PMID: 24449910 DOI: 10.1073/pnas.1323656111] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hybridization in plants leads to transinteractions between the parental genomes and epigenomes that can result in changes to both 24 nt siRNA and cytosine methylation ((m)C) levels in the hybrid. In Arabidopsis the principle processes altering the hybrid methylome are Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM) in which the (m)C pattern of a genomic segment attains the same (m)C pattern of the corresponding segment on the other parental chromosome. We examined two loci that undergo TCM/TCdM in the Arabidopsis C24/Landsberg erecta (Ler) F1 hybrids, which show patterns of inheritance dependent on the properties of the particular donor and recipient chromosomal segments. At At1g64790 the TCM- and TCdM-derived (m)C patterns are maintained in the F2 generation but are transmitted in outcrosses or backcrosses only by the C24 genomic segment. At a region between and adjacent to At3g43340 and At3g43350, the originally unmethylated Ler genomic segment receives the C24 (m)C pattern in the F1, which is then maintained in backcross plants independent of the presence of the parental C24 segment. In backcrosses to an unmethylated Ler allele, the newly methylated F1 Ler segment may act as a TCM source in a process comparable to paramutation in maize. TCM-derived (m)C patterns are associated with reduced expression of both At3g43340 and At3g43350 in F1 and F2 plants, providing support for such events influencing the transcriptome. The inheritance of the F1 (m)C patterns and the segregation of other genetic and epigenetic determinants may contribute to the reduced hybrid vigor in the F2 and subsequent generations.
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Regulski M, Lu Z, Kendall J, Donoghue MTA, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen RA. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Res 2013; 23:1651-62. [PMID: 23739895 PMCID: PMC3787262 DOI: 10.1101/gr.153510.112] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.
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Affiliation(s)
- Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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20
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Schnable PS, Springer NM. Progress toward understanding heterosis in crop plants. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:71-88. [PMID: 23394499 DOI: 10.1146/annurev-arplant-042110-103827] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Although heterosis, or hybrid vigor, is widely exploited in agriculture, a complete description of its molecular underpinnings has remained elusive despite extensive investigation. It appears that there is not a single, simple explanation for heterosis. Instead, it is likely that heterosis arises in crosses between genetically distinct individuals as a result of a diversity of mechanisms. Heterosis generally results from the action of multiple loci, and different loci affect heterosis for different traits and in different hybrids. Hence, multigene models are likely to prove most informative for understanding heterosis. Complementation of allelic variation, as well as complementation of variation in gene content and gene expression patterns, is likely to be an important contributor to heterosis. Epigenetic variation has the potential to interact in hybrid genotypes via novel mechanisms. Several other intriguing hypotheses are also under investigation. In crops, heterosis must be considered within the context of the genomic impacts of prior selection for agronomic traits.
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Affiliation(s)
- Patrick S Schnable
- Center for Plant Genomics and Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA.
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21
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Hollick JB. Paramutation: a trans-homolog interaction affecting heritable gene regulation. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:536-543. [PMID: 23017240 DOI: 10.1016/j.pbi.2012.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Revised: 07/17/2012] [Accepted: 09/05/2012] [Indexed: 06/01/2023]
Abstract
Paramutation describes both the process and results of trans-sensing between chromosomes that causes specific heritable changes in gene regulation. RNA molecules are implicated in mediating similar events in maize, mouse, and Drosophila. Changes in both small RNA profiles and cytosine methylation patterns in Arabidopsis hybrids represent a potential molecular equivalent to the interactions responsible for paramutations. Despite a seemingly unifying feature of RNA-directed changes, both recent and historical works show that paramutations in maize require plant-specific proteins and lack expected hallmarks of a trans-effect mediated solely by RNAs. Recent examples of nearby transposons affecting RNA polymerase II functions lead to an opinion that paramutations represent an emergent property of the transcriptional dynamics ongoing in plant genomes between repetitious features and nearby genes.
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Affiliation(s)
- Jay B Hollick
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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22
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McEachern LA, Lloyd VK. The maize b1 paramutation control region causes epigenetic silencing in Drosophila melanogaster. Mol Genet Genomics 2012; 287:591-606. [DOI: 10.1007/s00438-012-0702-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
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23
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Barbour JER, Liao IT, Stonaker JL, Lim JP, Lee CC, Parkinson SE, Kermicle J, Simon SA, Meyers BC, Williams-Carrier R, Barkan A, Hollick JB. required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. THE PLANT CELL 2012; 24:1761-1775. [PMID: 22562610 PMCID: PMC3442568 DOI: 10.1105/tpc.112.097618] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 03/29/2012] [Accepted: 04/11/2012] [Indexed: 05/27/2023]
Abstract
Meiotically heritable epigenetic changes in gene regulation known as paramutations are facilitated by poorly understood trans-homolog interactions. Mutations affecting paramutations in maize (Zea mays) identify components required for the accumulation of 24-nucleotide RNAs. Some of these components have Arabidopsis thaliana orthologs that are part of an RNA-directed DNA methylation (RdDM) pathway. It remains unclear if small RNAs actually mediate paramutations and whether the maize-specific molecules identified to date define a mechanism distinct from RdDM. Here, we identify a novel protein required for paramutation at the maize purple plant1 locus. This required to maintain repression2 (RMR2) protein represents the founding member of a plant-specific clade of predicted proteins. We show that RMR2 is required for transcriptional repression at the Pl1-Rhoades haplotype, for accumulation of 24-nucleotide RNA species, and for maintenance of a 5-methylcytosine pattern distinct from that maintained by RNA polymerase IV. Genetic tests indicate that RMR2 is not required for paramutation occurring at the red1 locus. These results distinguish the paramutation-type mechanisms operating at specific haplotypes. The RMR2 clade of proteins provides a new entry point for understanding the diversity of epigenomic control operating in higher plants.
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Affiliation(s)
- Joy-El R. Barbour
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200
| | - Irene T. Liao
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jennifer L. Stonaker
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jana P. Lim
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Clarissa C. Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Susan E. Parkinson
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
| | - Jerry Kermicle
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Stacey A. Simon
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | - Blake C. Meyers
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102
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24
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Erhard KF, Hollick JB. Paramutation: a process for acquiring trans-generational regulatory states. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:210-216. [PMID: 21420347 DOI: 10.1016/j.pbi.2011.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/14/2011] [Accepted: 02/21/2011] [Indexed: 05/30/2023]
Abstract
Basic tenets of Mendelian inheritance are violated by paramutations in which trans-homolog interactions lead to heritable changes in gene regulation and phenotype. First described in plants, similar behaviors have now been noted in diverse eukaryotes. Genetic and molecular studies of paramutations occurring in maize indicate that components of a small interfering RNA (siRNA) biogenesis pathway are required for the maintenance of meiotically heritable regulatory states. Although these findings lead to a hypothesis that siRNAs themselves mediate paramutation interactions, an assessment of existing data supports the opinion that siRNAs alone are insufficient. Recent evidence implies that transcription of paramutation-associated repeats and siRNA-facilitated chromatin changes at affected loci are involved in directing and maintaining the heritable changes in gene regulation that typify paramutations.
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Affiliation(s)
- Karl F Erhard
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
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25
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Abstract
Paramutation describes a heritable change of gene expression that is brought about through interactions between homologous chromosomes. Genetic analyses in plants and, more recently, in mouse indicate that genomic sequences related to transcriptional control and molecules related to small RNA biology are necessary for specific examples of paramutation. Some of the molecules identified in maize are also required for normal plant development. These observations indicate a functional relationship between the nuclear mechanisms responsible for paramutation and modes of developmental gene control.
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Affiliation(s)
- Jay B Hollick
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA.
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26
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Stonaker JL, Lim JP, Erhard KF, Hollick JB. Diversity of Pol IV function is defined by mutations at the maize rmr7 locus. PLoS Genet 2009; 5:e1000706. [PMID: 19936246 PMCID: PMC2775721 DOI: 10.1371/journal.pgen.1000706] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 10/15/2009] [Indexed: 12/03/2022] Open
Abstract
Mutations affecting the heritable maintenance of epigenetic states in maize identify multiple small RNA biogenesis factors including NRPD1, the largest subunit of the presumed maize Pol IV holoenzyme. Here we show that mutations defining the required to maintain repression7 locus identify a second RNA polymerase subunit related to Arabidopsis NRPD2a, the sole second largest subunit shared between Arabidopsis Pol IV and Pol V. A phylogenetic analysis shows that, in contrast to representative eudicots, grasses have retained duplicate loci capable of producing functional NRPD2-like proteins, which is indicative of increased RNA polymerase diversity in grasses relative to eudicots. Together with comparisons of rmr7 mutant plant phenotypes and their effects on the maintenance of epigenetic states with parallel analyses of NRPD1 defects, our results imply that maize utilizes multiple functional NRPD2-like proteins. Despite the observation that RMR7/NRPD2, like NRPD1, is required for the accumulation of most siRNAs, our data indicate that different Pol IV isoforms play distinct roles in the maintenance of meiotically-heritable epigenetic information in the grasses. Multicellular plants possess a unique set of DNA–dependent RNA polymerase complexes (RNAPs) that prevent certain repetitious regions of the genome from being copied into stable RNAs. Two distinct RNAPs, termed Pol IV and Pol V, are required for this type of genome-silencing behavior in the eudicot Arabidopsis thaliana, but the mechanism by which these RNAPs accomplish this function is still relatively unknown. Using genetic and molecular methodologies, we identified a Pol IV–type subunit protein as being involved in a process of meiotically-heritable gene silencing in the maize plant known as paramutation. Our analyses of the available plant genome sequences indicate that monocots have a greater potential for RNAP diversity due to having duplicate variants of this particular subunit. Consistent with this inferred diversity, comparative analyses with plants defective in a different core Pol IV subunit indicate that the Pol IV–type RNAP in maize has distinct functional isoforms. The mechanistic and biological role(s) of these specific RNAPs in mediating genome regulation and heritable gene silencing in large genome cereals should now be tractable by biochemical approaches.
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Affiliation(s)
- Jennifer L. Stonaker
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jana P. Lim
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Karl F. Erhard
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jay B. Hollick
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
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27
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Stam M. Paramutation: a heritable change in gene expression by allelic interactions in trans. MOLECULAR PLANT 2009; 2:578-588. [PMID: 19825640 DOI: 10.1093/mp/ssp020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Epigenetic gene regulation involves the stable propagation of gene activity states through mitotic, and sometimes even meiotic, cell divisions without changes in DNA sequence. Paramutation is an epigenetic phenomenon involving changes in gene expression that are stably transmitted through mitosis as well as meiosis. These heritable changes are mediated by in trans interactions between homologous DNA sequences on different chromosomes. During these in trans interactions, epigenetic information is transferred from one allele of a gene to another allele of the same gene, resulting in a change in gene expression. Although paramutation was initially discovered in plants, it has recently been observed in mammals as well, suggesting that the mechanisms underlying paramutation might be evolutionarily conserved. Recent findings point to a crucial role for small RNAs in the paramutation process. In mice, small RNAs appear sufficient to induce paramutation, whereas in maize, it seems not to be the only player in the process. In this review, potential mechanisms are discussed in relation to the various paramutation phenomena.
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Affiliation(s)
- Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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28
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Differential Gene Expression Between Hybrids and Their Parents During the Four Crucial Stages of Cotton Growth and Development. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(09)60021-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Epigenetic Phenomena and Epigenomics in Maize. Epigenomics 2008. [DOI: 10.1007/978-1-4020-9187-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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30
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Han Z, Mtango NR, Patel BG, Sapienza C, Latham KE. Hybrid vigor and transgenerational epigenetic effects on early mouse embryo phenotype. Biol Reprod 2008; 79:638-48. [PMID: 18562704 DOI: 10.1095/biolreprod.108.069096] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Mouse embryos display a strain-dependent propensity for blastomere cytofragmentation at the two-cell stage. The maternal pronucleus exerts a predominant, transcription-dependent effect on this phenotype, with lesser effects of the ooplasm and the paternal pronucleus. A parental origin effect has been observed as an inequality in the cytofragmentation rate of embryos produced through genetic crosses of reciprocal F(1) hybrid females. To understand the basis for this, we conducted an extensive series of pronuclear transfer studies employing different combinations of inbred and F(1) hybrid maternal and paternal genotypes. We find that the parental origin effect is the result of a transgenerational epigenetic modification, whereby the inherited maternal grandpaternal contribution interacts with the fertilizing paternal genome and the ooplasm. This result indicates that some epigenetic information related to grandparental origins of chromosomes (i.e., imprinting of chromosomes in the mother) is retained through oogenesis and transmitted to progeny, where it affects gene expression from the maternal pronucleus and subsequent embryo phenotype. These results reveal for the first time that mammalian embryonic development can be affected by the epigenotype of at least three individuals. Additionally, we observe a significant suppression of fragmentation by F(1) hybrid ooplasm when it is separated from the F(1) hybrid maternal pronucleus. This latter effect is a striking example of heterosis in the early mammalian embryo, and it provides a new opportunity for examining the molecular mechanisms of heterosis. These results are relevant to our understanding of the mechanisms of epigenetic effects on development and the possible fertility effects of genetic and epigenetic interactions in reproductive medicine.
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Affiliation(s)
- Zhiming Han
- The Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140-5101, USA
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31
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Abstract
Maize (Zea mays) is an excellent model for basic research. Genetic screens have informed our understanding of developmental processes, meiosis, epigenetics and biochemical pathways--not only in maize but also in other cereal crops. We discuss the forward and reverse genetic screens that are possible in this organism, and emphasize the available tools. Screens exploit the well-studied behaviour of transposon systems, and the distinctive chromosomes allow an integration of cytogenetics into mutagenesis screens and analyses. The imminent completion of the maize genome sequence provides the essential resource to move seamlessly from gene to phenotype and back.
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32
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Gross SM, Hollick JB. Multiple trans-sensing interactions affect meiotically heritable epigenetic states at the maize pl1 locus. Genetics 2007; 176:829-39. [PMID: 17435245 PMCID: PMC1894611 DOI: 10.1534/genetics.107.072496] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Interactions between specific maize purple plant1 (pl1) alleles result in heritable changes of gene regulation that are manifested as differences in anthocyanin pigmentation. Transcriptionally repressed states of Pl1-Rhoades alleles (termed Pl') are remarkably stable and invariably facilitate heritable changes of highly expressed states (termed Pl-Rh) in Pl'/Pl-Rh plants. However, Pl' can revert to Pl-Rh when hemizygous, when heterozygous with pl1 alleles other than Pl1-Rhoades, or in the absence of trans-acting factors required to maintain repressed states. Cis-linked features of Pl1-Rhoades responsible for these trans-sensing behaviors remain unknown. Here, genetic tests of a pl1 allelic series identify two potentially separate cis-linked features: one facilitating repression of Pl-Rh and another stabilizing Pl' in trans. Neither function is affected in ethyl-methanesulfonate-induced Pl1-Rhoades derivatives that produce truncated PL1 peptides, indicating that PL1 is unlikely to mediate trans interactions. Both functions, however, are impaired in a spontaneous Pl1-Rhoades derivative that fails to produce detectable pl1 RNA. Pl'-like states can also repress expression of a pl1-W22 allele, but this repression is not meiotically heritable. As the Pl' state is not associated with unique small RNA species representing the pl1-coding region, the available data suggest that interactions between elements required for transcription underlie Pl1-Rhoades epigenetic behaviors.
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Affiliation(s)
| | - Jay B. Hollick
- Corresponding author: Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720-3102. E-mail:
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33
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Springer NM, Stupar RM. Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res 2007; 17:264-75. [PMID: 17255553 DOI: 10.1101/gr.5347007] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this review, we discuss the recent research on allelic variation in maize and possible implications of this work toward our understanding of heterosis. Heterosis, or hybrid vigor, is the increased performance of a hybrid relative to the parents, and is a result of the variation that is present within a species. Intraspecific comparisons of sequence and expression levels in maize have documented a surprisingly high level of allelic variation, which includes variation for the content of genic fragments, variation in repetitive elements surrounding genes, and variation in gene expression levels. There is evidence that transposons and repetitive DNA play a major role in the generation of this allelic diversity. The combination of allelic variants provides a more comprehensive suite of alleles in the hybrid that may be involved in novel allelic interactions. A major unresolved question is how the combined allelic variation and interactions in a hybrid give rise to heterotic phenotypes. An understanding of allelic variation present in maize provides an opportunity to speculate on mechanisms that might lead to heterosis. Variation for the presence of genes, the presence of novel beneficial alleles, and modified levels of gene expression in hybrids may all contribute to the heterotic phenotypes.
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Affiliation(s)
- Nathan M Springer
- Cargill Center for Microbial and Plant Genomics, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108, USA.
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34
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Sekhon RS, Peterson T, Chopra S. Epigenetic modifications of distinct sequences of the p1 regulatory gene specify tissue-specific expression patterns in maize. Genetics 2006; 175:1059-70. [PMID: 17179091 PMCID: PMC1840062 DOI: 10.1534/genetics.106.066134] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tandemly repeated endogenous genes are common in plants, but their transcriptional regulation is not well characterized. In maize, the P1-wr allele of pericarp color1 is composed of multiple copies arranged in a head-to-tail fashion. P1-wr confers a white kernel pericarp and red cob glume pigment phenotype that is stably inherited over generations. To understand the molecular mechanisms that regulate tissue-specific expression of P1-wr, we have characterized P1-wr*, a spontaneous loss-of-function epimutation that shows a white kernel pericarp and white cob glume phenotype. As compared to its progenitor P1-wr, the P1-wr* is hypermethylated in exon 1 and intron 2 regions. In the presence of the epigenetic modifier Ufo1 (Unstable factor for orange1), P1-wr* plants exhibit a range of cob glume pigmentation whereas pericarps remain colorless. In these plants, the level of cob pigmentation directly correlates with the degree of DNA demethylation in the intron 2 region of p1. Further, genomic bisulfite sequencing indicates that a 168-bp region of intron 2 is significantly hypomethylated in both CG and CNG context in P1-wr* Ufo1 plants. Interestingly, P1-wr* Ufo1 plants did not show any methylation change in a distal enhancer region that has previously been implicated in Ufo1-induced gain of pericarp pigmentation of the P1-wr allele. These results suggest that distinct regulatory sequences in the P1-wr promoter and intron 2 regions can undergo independent epigenetic modifications to generate tissue-specific expression patterns.
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Affiliation(s)
- Rajandeep S Sekhon
- Department of Crop and Soil Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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35
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Hollick JB, Kermicle JL, Parkinson SE. Rmr6 maintains meiotic inheritance of paramutant states in Zea mays. Genetics 2005; 171:725-40. [PMID: 16020780 PMCID: PMC1456783 DOI: 10.1534/genetics.105.045260] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 07/08/2005] [Indexed: 11/18/2022] Open
Abstract
Paramutation generates heritable changes affecting regulation of specific alleles found at several Zea mays (maize) loci that encode transcriptional regulators of anthocyanin biosynthetic genes. Although the direction and extent of paramutation is influenced by poorly understood allelic interactions occurring in diploid sporophytes, two required to maintain repression loci (rmr1 and rmr2), as well as mediator of paramutation1 (mop1), affect this process at the purple plant1 (pl1) locus. Here we show that the rmr6 locus is required for faithful transmission of weakly expressed paramutant states previously established at both pl1 and red1 (r1) loci. Transcriptional repression occurring at both pl1 and booster1 (b1) loci as a result of paramutation also requires Rmr6 action. Reversions to highly expressed, nonparamutant states at both r1 and pl1 occur in plants homozygous for rmr6 mutations. Pedigree analysis of reverted pl1 alleles reveals variable latent susceptibilities to spontaneous paramutation in future generations, suggesting a quantitative nature of Rmr6-based alterations. Genetic tests demonstrate that Rmr6 encodes a common component required for establishing paramutations at diverse maize loci. Our analyses at pl1 and r1 suggest that this establishment requires Rmr6-dependent somatic maintenance of meiotically heritable epigenetic marks.
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Affiliation(s)
- Jay B Hollick
- Laboratory of Genetics, University of Wisconsin, Madison, 53706, USA.
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36
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Stam M, Mittelsten Scheid O. Paramutation: an encounter leaving a lasting impression. TRENDS IN PLANT SCIENCE 2005; 10:283-90. [PMID: 15949762 DOI: 10.1016/j.tplants.2005.04.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/07/2005] [Accepted: 04/26/2005] [Indexed: 05/02/2023]
Abstract
Paramutation is the result of heritable changes in gene expression that occur upon interaction between alleles. Whereas Mendelian rules, together with the concept of genetic transmission via the DNA sequence, can account for most inheritance in sexually propagating organisms, paramutation-like phenomena challenge the exclusiveness of Mendelian inheritance. Most paramutation-like phenomena have been observed in plants but there is increasing evidence for its occurrence in other organisms, including mammals. Our knowledge of the underlying mechanisms, which might involve RNA silencing, physical pairing of homologous chromosomal regions or both, is still limited. Here, we discuss the characteristics of different paramutation-like interactions in the light of arguments supporting each of these alternative mechanisms.
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Affiliation(s)
- Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands.
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37
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Chandler VL, Stam M. Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 2004; 5:532-44. [PMID: 15211355 DOI: 10.1038/nrg1378] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vicki L Chandler
- Department of Plant Sciences, 303 Forbes Building, University of Arizona, Tucson, Arizona 85721, USA.
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38
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Auger DL, Ream TS, Birchler JA. A test for a metastable epigenetic component of heterosis using haploid induction in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1017-23. [PMID: 15067387 DOI: 10.1007/s00122-003-1521-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2003] [Accepted: 10/27/2003] [Indexed: 05/10/2023]
Abstract
We conducted a test to detect if there is a heritable epigenetic component to hybrid vigor and/or inbreeding depression. The impetus for this work was a classical study of the effect of homozygosis on the expression of the maize red color ( r1) locus. It had been shown that maintaining R1 mottling alleles in the homozygous state over several generations produces a progressive decrease of their paternally imprinted expression. This effect is reversed by R1/r1 allele heterozygosity. If this behavior were characteristic of many regulatory genes, then such a phenomenon could contribute to inbreeding depression and heterosis. To examine this question, inbreds of Mo17 and B73 and the two reciprocally produced hybrids were crossed by Stock 6 to generate four classes of maternal haploids. The mature haploid plants were measured for several quantitative traits. If inbreeding depression results from an accumulating heritable effect that is reversed by the hybrid state, one would expect the haploids derived from the hybrids to perform better than those derived from the inbred lines. The hybrid-derived haploids did not exhibit greater average performance than the inbred-derived haploids. These data fail to support the hypothesis that inbreeding depression and heterosis have a metastable epigenetic component.
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Affiliation(s)
- D L Auger
- Division of Biological Sciences, University of Missouri, 117 Tucker Hall, Columbia, MO 65211-7400, USA
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39
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Kim JJ, Farnir F, Savell J, Taylor JF. Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. J Anim Sci 2003; 81:1933-42. [PMID: 12926775 DOI: 10.2527/2003.8181933x] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study was conducted to detect quantitative trait loci (QTL) affecting growth and beef carcass fatness traits in an experimental population of Angus and Brahman crossbreds. The three-generation mapping population was generated with 602 progeny from 29 reciprocal backcross and three F2 full-sib families, and 417 genetic markers were used to produce a sex-averaged map of the 29 autosomes spanning 2,642.5 Kosambi cM. Alternative interval-mapping approaches were applied under line-cross (LC) and random infinite alleles (RA) models to detect QTL segregating between and within breeds. A total of 35 QTL (five with genomewide significant and 30 with suggestive evidence for linkage) were found on 19 chromosomes. One QTL affecting yearling weight was found with genomewide significant evidence for linkage in the interstitial region of bovine autosome (BTA) 1, and an additional 19 QTL were detected with suggestive evidence for linkage under the LC model. Many of these QTL had a dominant (complete or overdominant) mode of gene action, and only a few of the QTL were primarily additive, which reflects the fact that heterosis for growth is known to be appreciable in crosses among Brahman and British breeds. Four QTL affecting growth were detected with genomewide significant evidence for linkage under the RA model on BTA 2 and BTA 6 for birth weight, BTA 5 for yearling weight, and BTA 23 for hot carcass weight. An additional 11 QTL were detected with suggestive evidence for linkage under the RA model. None of the QTL (except for yearling weight on BTA 5) detected under the RA model were found by the LC analyses, suggesting the segregation of alternate alleles within one or both of the parental breeds. Our results reveal the utility of implementing both the LC and RA models to detect dominant QTL and also QTL with similar allele frequency distributions within parental breeds.
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Affiliation(s)
- J J Kim
- Department of Animal Science, Texas A&M University, College Station 77843, USA.
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Vermerris W, Thompson KJ, McIntyre LM. The maize Brown midrib1 locus affects cell wall composition and plant development in a dose-dependent manner. Heredity (Edinb) 2002; 88:450-7. [PMID: 12180087 DOI: 10.1038/sj.hdy.6800078] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The four brown midrib (bm) mutants of maize have a reduced content and altered subunit composition of the cell wall polymer lignin. The bm mutations have traditionally been considered completely recessive, because the brown midrib phenotype is only apparent in plants homozygous for the mutation. In addition to an effect on cell wall composition, some bm mutations have been shown to affect flowering time. We had preliminary evidence for a dosage effect of the Bm1 locus on flowering time, which prompted this detailed study on the Bm1 locus. In this study, near-isogenic lines (in an A619 background) with zero, one or two bm1 mutant alleles were compared. The bm1 heterozygotes flowered significantly earlier than both the wild-type plants and bm1 mutants. This difference can at least be partly attributed to an accelerated growth rate in the later stages of plant development. Furthermore, Fourier transform infrared spectroscopy revealed that the cell wall composition of the bm1 heterozygous plants is distinct from both the bm1 and wild-type homozygotes. The combination of the data on flowering time and the data on cell wall composition provide evidence for a dosage effect at the Bm1 locus.
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Affiliation(s)
- W Vermerris
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA.
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Sidorenko LV, Peterson T. Transgene-induced silencing identifies sequences involved in the establishment of paramutation of the maize p1 gene. THE PLANT CELL 2001; 13:319-35. [PMID: 11226188 PMCID: PMC102245 DOI: 10.1105/tpc.13.2.319] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2000] [Accepted: 12/04/2000] [Indexed: 05/18/2023]
Abstract
A transgene carrying a distal enhancer element of the maize P1-rr promoter caused silencing of an endogenous P1-rr allele in the progeny of transgenic maize plants. Expression of both the transgene and the endogenous P1-rr allele was reduced in the affected plants. The silenced phenotype was observed in the progeny of seven of eight crosses involving three independent transgenic events tested (average frequency of 19%). This phenotype was associated with an induced epigenetic state of the P1-rr allele, termed P1-rr', which is characterized by increased methylation of the P1-rr flanking regions and decreased levels of P1-rr transcript. The P1-rr' epiallele is highly heritable in the absence of the inducing P1.2b::GUS transgene, and it can impose an equivalent state on a naive P1-rr allele in subsequent crosses (paramutation). In contrast, parallel experiments with two other P::GUS transgenes that contained the same basal P1-rr promoter fragment but different upstream sequences revealed no detectable silencing effect. Thus, transgenes carrying a specific enhancer fragment of the P1-rr gene promoter can trigger a paramutant state (P1-rr') of the endogenous P1-rr gene that is maintained in the absence of the inducing transgene. We discuss the potential role of the P1-rr distal enhancer element in the establishment and propagation of a paramutation system in maize.
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Affiliation(s)
- L V Sidorenko
- Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011, USA
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Hollick JB, Chandler VL. Genetic factors required to maintain repression of a paramutagenic maize pl1 allele. Genetics 2001; 157:369-78. [PMID: 11139517 PMCID: PMC1461487 DOI: 10.1093/genetics/157.1.369] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A genetic screen identified two novel gene functions required to maintain mitotically and meiotically heritable gene silencing associated with paramutation of the maize purple plant 1 (pl1) locus. Paramutation at pl1 leads to heritable alterations of pl1 gene regulation; the Pl-Rhoades (Pl-Rh) allele, which typically confers strong pigmentation to juvenile and adult plant structures, changes to a lower expression state termed Pl'-mahogany (Pl'). Paramutation spontaneously occurs at low frequencies in Pl-Rh homozygotes but always occurs when Pl-Rh is heterozygous with Pl'. We identified four mutations that caused increased Pl' pigment levels. Allelism tests revealed that three mutations identified two new maize loci, required to maintain repression 1 (rmr1) and rmr2 and that the other mutation represents a new allele of the previously described mediator of paramutation 1 (mop1) locus. RNA levels from Pl' are elevated in rmr mutants and genetic tests demonstrate that Pl' can heritably change back to Pl-Rh in rmr mutant individuals at variable frequencies. Pigment levels controlled by two pl1 alleles that do not participate in paramutation are unaffected in rmr mutants. These results suggest that RMR functions are intimately involved in maintaining the repressed expression state of paramutant Pl' alleles. Despite strong effects on Pl' repression, rmr mutant plants have no gross developmental abnormalities even after several generations of inbreeding, implying that RMR1 and RMR2 functions are not generally required for developmental homeostasis.
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Affiliation(s)
- J B Hollick
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA.
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Dorweiler JE, Carey CC, Kubo KM, Hollick JB, Kermicle JL, Chandler VL. mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. THE PLANT CELL 2000; 12:2101-18. [PMID: 11090212 PMCID: PMC150161 DOI: 10.1105/tpc.12.11.2101] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2000] [Accepted: 08/31/2000] [Indexed: 05/18/2023]
Abstract
Paramutation is the directed, heritable alteration of the expression of one allele when heterozygous with another allele. Here, the isolation and characterization of a mutation affecting paramutation, mediator of paramutation1-1 (mop1-1), are described. Experiments demonstrate that the wild-type gene Mop1 is required for establishment and maintenance of the paramutant state. The mop1-1 mutation affects paramutation at the multiple loci tested but has no effect on alleles that do not participate in paramutation. The mutation does not alter the amounts of actin and ubiquitin transcripts, which suggests that the mop1 gene does not encode a global repressor. Maize plants homozygous for mop1-1 can have pleiotropic developmental defects, suggesting that mop1-1 may affect more genes than just the known paramutant ones. The mop1-1 mutation does not alter the extent of DNA methylation in rDNA and centromeric repeats. The observation that mop1 affects paramutation at multiple loci, despite major differences between these loci in their gene structure, correlations with DNA methylation, and stability of the paramutant state, suggests that a common mechanism underlies paramutation. A protein-based epigenetic model for paramutation is discussed.
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Affiliation(s)
- J E Dorweiler
- Plant Sciences Department, University of Arizona, Tucson, Arizona 85721, USA
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Abstract
Paramutation is a heritable change in gene expression induced by allele interactions. This review summarizes key experiments on three maize loci, which undergo paramutation. Similarities and differences between the phenomenology at the three loci are described. In spite of many differences with respect to the stability of the reduced expression states at each locus or whether paramutation correlates with DNA methylation and repeated sequences within the loci, recent experiments are consistent with a common mechanism underlying paramutation at all three loci. Most strikingly, trans-acting mutants have been isolated that prevent paramutation at all three loci and lead to the activation of silenced Mutator transposable elements. Models consistent with the hypothesis that paramutation involves heritable changes in chromatin structure are presented. Several potential roles for paramutation are discussed. These include localizing recombination to low-copy sequences within the genome, establishing and maintaining chromatin domain boundaries, and providing a mechanism for plants to transmit an environmentally influenced expression state to progeny.
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Affiliation(s)
- V L Chandler
- Department of Plant Sciences, University of Arizona, Tucson 85721, USA.
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Omholt SW, Plahte E, Oyehaug L, Xiang K. Gene regulatory networks generating the phenomena of additivity, dominance and epistasis. Genetics 2000; 155:969-80. [PMID: 10835414 PMCID: PMC1461103 DOI: 10.1093/genetics/155.2.969] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We show how the phenomena of genetic dominance, overdominance, additivity, and epistasis are generic features of simple diploid gene regulatory networks. These regulatory network models are together sufficiently complex to catch most of the suggested molecular mechanisms responsible for generating dominant mutations. These include reduced gene dosage, expression or protein activity (haploinsufficiency), increased gene dosage, ectopic or temporarily altered mRNA expression, increased or constitutive protein activity, and dominant negative effects. As classical genetics regards the phenomenon of dominance to be generated by intralocus interactions, we have studied two one-locus models, one with a negative autoregulatory feedback loop, and one with a positive autoregulatory feedback loop. To include the phenomena of epistasis and downstream regulatory effects, a model of a three-locus signal transduction network is also analyzed. It is found that genetic dominance as well as overdominance may be an intra- as well as interlocus interaction phenomenon. In the latter case the dominance phenomenon is intimately connected to either feedback-mediated epistasis or downstream-mediated epistasis. It appears that in the intra- as well as the interlocus case there is considerable room for additive gene action, which may explain to some degree the predictive power of quantitative genetic theory, with its emphasis on this type of gene action. Furthermore, the results illuminate and reconcile the prevailing explanations of heterosis, and they support the old conjecture that the phenomenon of dominance may have an evolutionary explanation related to life history strategy.
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Affiliation(s)
- S W Omholt
- Department of Animal Science, Agricultural University of Norway, Aas.
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Hollick JB, Patterson GI, Asmundsson IM, Chandler VL. Paramutation alters regulatory control of the maize pl locus. Genetics 2000; 154:1827-38. [PMID: 10747073 PMCID: PMC1461010 DOI: 10.1093/genetics/154.4.1827] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The maize purple plant (pl) locus encodes a transcription factor required for anthocyanin pigment synthesis in vegetative and floral tissues. The strongly expressed Pl-Rhoades (Pl-Rh) allele is unstable, spontaneously changing to weaker expression states (Pl') at low frequencies and exclusively changing to Pl' in Pl'/Pl-Rh heterozygotes. The weakly expressed Pl' state is mitotically and meiotically stable, yet reversible. This type of allele-dependent, heritable alteration of gene control is called paramutation. Expression studies herein demonstrate that visible differences in anthocyanin pigment levels mirror pl RNA abundance and that pl paramutation is associated with reduced transcription of the pl gene. This transcriptional alteration is accompanied by acquisition of light-dependent regulation. Restriction endonuclease mapping indicates that these changes in pl gene regulation are not associated with detectable DNA alterations or with extensive changes in cytosine methylation patterns. Genetic tests show that Pl-Blotched (Pl-Bh), a structurally similar pl allele encoding an identical pl RNA and PL protein, does not participate in pl paramutation. This result suggests that if cis-acting sequences are required for pl paramutation they are distinct from the protein coding and immediately adjacent regions. A model is discussed in which pl paramutation results in heritable changes of chromatin structure that fundamentally alter regulatory interactions occurring during plant development.
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Affiliation(s)
- J B Hollick
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229, USA
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Abstract
Epigenetic inheritance systems enable the environmentally induced phenotypes to be transmitted between generations. Jablonka and Lamb (1991, 1995) proposed that these systems have a substantial role during speciation. They argued that divergence of isolated populations may be first triggered by the accumulation of (heritable) phenotypic differences that are later followed and strengthened by genetic changes. The plausibility of this idea is examined in this paper. At first, we discuss the "exploratory" behaviour of an epigenetic inheritance system on a one peak adaptive landscape. If a quantitative trait is far from the optimum, then it is advantageous to induce heritable phenotypic variation. Conversely, if the genotypes get closer to the peak, it is more favorable to canalize the phenotypic expression of the character. This process would lead to genetic assimilation. Next we show that the divergence of heritable epigenetic marks acts to reduce or to eliminate the genetic barrier between two adaptive peaks. Therefore, an epigenetic inheritance system can increase the probability of transition from one adaptive state to another. Peak shift might be initiated by (i) slight changes in the inducing environment or by (ii) genetic drift of the genes controlling epigenetic variability. Remarkably, drift-induced transition is facilitated even if phenotypic variation is not heritable. A corollary of our thesis is that evolution can proceed through suboptimal phenotypic states, without passing through a deep adaptive valley of the genotype. We also consider the consequences of this finding on the dynamics and mode of reproductive isolation.
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Affiliation(s)
- C Pál
- Department of Plant Taxonomy and Ecology, Loránd Eötvös University, Budapest, Ludovika 2, H-1083, Hungary.
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Abstract
The presence of homologous nucleic acid sequences can exert profound effects on chromosomal and gene function in a wide range of organisms. These homology effects reveal remarkable forms of regulation as well as suggest possible avenues for the development of new technologies.
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Affiliation(s)
- C T Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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