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Wang C, Wang J, Lu J, Xiong Y, Zhao Z, Yu X, Zheng X, Li J, Lin Q, Ren Y, Hu Y, He X, Li C, Zeng Y, Miao R, Guo M, Zhang B, Zhu Y, Zhang Y, Tang W, Wang Y, Hao B, Wang Q, Cheng S, He X, Yao B, Gao J, Zhu X, Yu H, Wang Y, Sun Y, Zhou C, Dong H, Ma X, Guo X, Liu X, Tian Y, Liu S, Wang C, Cheng Z, Jiang L, Zhou J, Guo H, Jiang L, Tao D, Chai J, Zhang W, Wang H, Wu C, Wan J. A natural gene drive system confers reproductive isolation in rice. Cell 2023; 186:3577-3592.e18. [PMID: 37499659 DOI: 10.1016/j.cell.2023.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/02/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Hybrid sterility restricts the utilization of superior heterosis of indica-japonica inter-subspecific hybrids. In this study, we report the identification of RHS12, a major locus controlling male gamete sterility in indica-japonica hybrid rice. We show that RHS12 consists of two genes (iORF3/DUYAO and iORF4/JIEYAO) that confer preferential transmission of the RHS12-i type male gamete into the progeny, thereby forming a natural gene drive. DUYAO encodes a mitochondrion-targeted protein that interacts with OsCOX11 to trigger cytotoxicity and cell death, whereas JIEYAO encodes a protein that reroutes DUYAO to the autophagosome for degradation via direct physical interaction, thereby detoxifying DUYAO. Evolutionary trajectory analysis reveals that this system likely formed de novo in the AA genome Oryza clade and contributed to reproductive isolation (RI) between different lineages of rice. Our combined results provide mechanistic insights into the genetic basis of RI as well as insights for strategic designs of hybrid rice breeding.
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Affiliation(s)
- Chaolong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiayu Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yehui Xiong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhigang Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Li
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodong He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yonglun Zeng
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Rong Miao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Mali Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bosen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Zhu
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yunhui Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Weijie Tang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Benyuan Hao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Siqi Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaojuan He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Bowen Yao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Junwen Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xufei Zhu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunlei Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xi Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shijia Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunming Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiawu Zhou
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Huishan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liwen Jiang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Jijie Chai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wang D, Wang H, Xu X, Wang M, Wang Y, Chen H, Ping F, Zhong H, Mu Z, Xie W, Li X, Feng J, Zhang M, Fan Z, Yang T, Zhao J, Liu B, Ruan Y, Zhang G, Liu C, Liu Z. Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice. Nat Commun 2023; 14:4531. [PMID: 37507369 PMCID: PMC10382596 DOI: 10.1038/s41467-023-40189-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Understanding the evolutionary forces in speciation is a central goal in evolutionary biology. Asian cultivated rice has two subspecies, indica and japonica, but the underlying mechanism of the partial reproductive isolation between them remains obscure. Here we show a presence-absence variation (PAV) at the Se locus functions as an indica-japonica reproductive barrier by causing hybrid sterility (HS) in indica-japonica crosses. The locus comprises two adjacent genes: ORF3 encodes a sporophytic pollen killer, whereas ORF4 protects pollen in a gametophytic manner. In F1 of indica-japonica crosses, pollen with the japonica haplotype, which lacks the sequence containing the protective ORF4, is aborted due to the pollen-killing effect of ORF3 from indica. Evolutionary analysis suggests ORF3 is a gene associated with the Asian cultivated rice species complex, and the PAV has contributed to the reproductive isolation between the two subspecies of Asian cultivated rice. Our analyses provide perspectives on rice inter-subspecies post-zygotic isolation, and will promote efforts to overcome reproductive barriers in indica-japonica hybrid rice breeding.
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Affiliation(s)
- Daiqi Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomic Insitute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Xiaomei Xu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Man Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Yahuan Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Hong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Fei Ping
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Huanhuan Zhong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhengkun Mu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Wantong Xie
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Xiangyu Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Jingbin Feng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Milan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Zhilan Fan
- National Field Genebank for Wild Rice (Guangzhou), Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Tifeng Yang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Junliang Zhao
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Bin Liu
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Ying Ruan
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China
| | - Chunlin Liu
- Key Laboratory of Hunan Provincial on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha, Hunan, 410128, China
- College of Agronomy, Hunan Agricultural University, Changsha, Hunan, 410128, China
| | - Ziqiang Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510642, China.
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3
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Zhou P, Wang Z, Zhu X, Tang Y, Ye L, Yu H, Li Y, Zhang N, Liu T, Wang T, Wu Y, Cao D, Chen Y, Li X, Zhang Q, Xiao J, Yu S, Zhang Q, Mi J, Ouyang Y. A minimal genome design to maximally guarantee fertile inter-subspecific hybrid rice. MOLECULAR PLANT 2023; 16:726-738. [PMID: 36843324 DOI: 10.1016/j.molp.2023.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/02/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Hybrid rice has made considerable contributions to achieve the ambitious goal of food security for the world's population. Hybrid rice from indica/xian and japonica/geng subspecies shows much higher heterosis and is thereby an important innovation in promoting rice production in the next decade. However, such inter-subspecific hybrid rice has long suffered from serious hybrid sterility, which is a major challenge that needs to be addressed. In this study, we performed a genome design strategy to produce fertile inter-subspecific hybrid by creation of wide compatibility varieties that are able to overcome hybrid sterility. Based on combined genetic analyses in two indica-japonica crosses, we determined that four hybrid sterility loci, S5, f5, pf12 and Sc, are the major QTLs controlling inter-subspecific hybrid sterility and thus the minimal targets that can be manipulated for breeding sub-specific hybrid rice. We then cloned the pf12 locus, one of the most effective loci for hybrid male sterility, by map-based cloning, and showed that artificial disruption of pf12A gene at this locus could successfully rescue hybrid fertility. We further dissected the genetic basis of wide compatibility using three pairwise crosses from a wide-compatibility variety Dular and representative indica and japonica varieties. On this basis, we constructed and assembled different combinations of naturally compatible alleles of four loci, S5, Sc, pf12, and f5, and found that the improved lines could fully recover pollen and embryo sac fertility in test-crossed F1s, thereby completely fulfilling the demands of inter-subspecific hybrid spikelet fertility in agricultural production. This breeding scheme would facilitate redesign of future inter-subspecific hybrid rice with a higher yield potential.
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Affiliation(s)
- Penghui Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingchen Zhu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yao Tang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Ye
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Huihui Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yating Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ningke Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ting Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuying Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengyun Cao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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Zhang Y, Wang J, Pu Q, Yang Y, Lv Y, Zhou J, Li J, Deng X, Wang M, Tao D. Understanding the Nature of Hybrid Sterility and Divergence of Asian Cultivated Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:908342. [PMID: 35832226 PMCID: PMC9272003 DOI: 10.3389/fpls.2022.908342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Intraspecific hybrid sterility is a common form of postzygotic reproductive isolation in Asian cultivated rice, which is also the major obstacle to utilize the strong heterosis in the rice breeding program. Here, we review recent progress in classification and hybrid sterility in Asian cultivated rice. A genome-wide analysis of numerous wild relatives of rice and Asian cultivated rice has provided insights into the origin and differentiation of Asian cultivated rice, and divided Asian cultivated rice into five subgroups. More than 40 conserved and specific loci were identified to be responsible for the hybrid sterility between subgroup crosses by genetic mapping, which also contributed to the divergence of Asian cultivated rice. Most of the studies are focused on the sterile barriers between indica and japonica crosses, ignoring hybrid sterility among other subgroups, leading to neither a systematical understanding of the nature of hybrid sterility and subgroup divergence, nor effectively utilizing strong heterosis between the subgroups in Asian cultivated rice. Future studies will aim at identifying and characterizing genes for hybrid sterility and segregation distortion, comparing and understanding the molecular mechanism of hybrid sterility, and drawing a blueprint for intraspecific hybrid sterility loci derived from cross combinations among the five subgroups. These studies would provide scientific and accurate guidelines to overcome the intraspecific hybrid sterility according to the parent subgroup type identification, allowing the utilization of heterosis among subgroups, also helping us unlock the mysterious relationship between hybrid sterility and Asian cultivated rice divergence.
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Affiliation(s)
- Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
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5
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Wang P, Qi F, Yao H, Xu X, Li W, Meng J, Zhang Q, Xie W, Xing Y. Fixation of hybrid sterility genes and favorable alleles of key yield-related genes with dominance contribute to the high yield of the Yongyou series of intersubspecific hybrid rice. J Genet Genomics 2022; 49:448-457. [PMID: 35304326 DOI: 10.1016/j.jgg.2022.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/16/2022]
Abstract
In rice, the Yongyou series of Xian-Geng intersubspecific hybrids have excellent production performance, as shown by their extremely high yield. However, the mechanisms underlying the success of these rice hybrids are unclear. In this study, three F2 populations are generated from three Yongyou hybrids to determine the genetic basis of the extremely high yield of intersubspecific hybrids. Genome constitution analysis reveals that the female and male parental lines belong to the Geng and Xian subspecies, respectively, although introgression of 20% of the Xian ancestry and 14% of the Geng ancestry are observed. Twenty-five percent of the hybrid genomes carries homozygous Xian or Geng fragments, which harbors hybrid sterility genes such as Sd, Sc, f5 and qS12 and favorable alleles of key yield-related genes, including NAL1, Ghd7 and Ghd8. None of the parents carries the S5+ killer of the S5 killer-protector system. Compatible allele combinations of hybrid sterility genes ensure the fertility of these intersubspecific hybrids and overcome the bottleneck in applying intersubspecific hybrids. Additive effects of favorable alleles of yield-related genes fixed in both parents enhances midparent values. Many QTLs for yield and its key component spikelets per panicle shows dominance and the net positive dominant effects lead to heterosis. These factors result in an extremely high yield of the hybrids. These findings will aid in the development of new intersubspecific rice hybrids with diverse genetic backgrounds.
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Affiliation(s)
- Pengfei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Feixiang Qi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Honglin Yao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingbing Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianghu Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Wei C, Wang Z, Wang J, Teng J, Shen S, Xiao Q, Bao S, Feng Y, Zhang Y, Li Y, Sun S, Yue Y, Wu C, Wang Y, Zhou T, Xu W, Yu J, Wang L, Wang J. Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence. BMC Genomics 2021; 22:460. [PMID: 34147070 PMCID: PMC8214281 DOI: 10.1186/s12864-021-07776-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution. RESULTS Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19-5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77-9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangements after polyploidization are associated with ongoing gene conversion events, and they directly restrict recombination and inhibit duplicated gene conversion between homeologous regions. Furthermore, we found that the converted genes tended to have more similar expression patterns than nonconverted duplicates. Gene conversion affects biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, contributing to the occurrence of the gene conversion. CONCLUSION Duplicated genes in rice subspecies generated by grass polyploidization ~ 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.
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Affiliation(s)
- Chendan Wei
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Zhenyi Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jianyu Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jia Teng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shaoqi Shen
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Qimeng Xiao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Shoutong Bao
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yishan Feng
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yan Zhang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yuxian Li
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Sangrong Sun
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yuanshuai Yue
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Chunyang Wu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Yanli Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Tianning Zhou
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Wenbo Xu
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China
| | - Jigao Yu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Li Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China.
| | - Jinpeng Wang
- School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, Hebei, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China.
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Chen Z, Li X, Lu H, Gao Q, Du H, Peng H, Qin P, Liang C. Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice. J Genet Genomics 2020; 47:637-649. [DOI: 10.1016/j.jgg.2020.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/17/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023]
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Liu C, Wang J, Sun P, Yu J, Meng F, Zhang Z, Guo H, Wei C, Li X, Shen S, Wang X. Illegitimate Recombination Between Homeologous Genes in Wheat Genome. FRONTIERS IN PLANT SCIENCE 2020; 11:1076. [PMID: 32849677 PMCID: PMC7396543 DOI: 10.3389/fpls.2020.01076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/30/2020] [Indexed: 05/30/2023]
Abstract
Polyploidies produce a large number of duplicated regions and genes in genomes, which have a long-term impact and stimulate genetic innovation. The high similarity between homeologous chromosomes, forming different subgenomes, or homologous regions after genome repatterning, may permit illegitimate DNA recombination. Here, based on gene colinearity, we aligned the (sub)genomes of common wheat (Triticum aestivum, AABBDD genotype) and its relatives, including Triticum urartu (AA), Aegilops tauschii (DD), and T. turgidum ssp. dicoccoides (AABB) to detect the homeologous (paralogous or orthologous) colinear genes within and between (sub)genomes. Besides, we inferred more ancient paralogous regions produced by a much ancient grass-common tetraploidization. By comparing the sequence similarity between paralogous and orthologous genes, we assumed abnormality in the topology of constructed gene trees, which could be explained by gene conversion as a result of illegitimate recombination. We found large numbers of inferred converted genes (>2,000 gene pairs) suggested long-lasting genome instability of the hexaploid plant, and preferential donor roles by DD genes. Though illegitimate recombination was much restricted, duplicated genes produced by an ancient whole-genome duplication, which occurred millions of years ago, also showed evidence of likely gene conversion. As to biological function, we found that ~40% catalytic genes in colinearity, including those involved in starch biosynthesis, were likely affected by gene conversion. The present study will contribute to understanding the functional and structural innovation of the common wheat genome.
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Affiliation(s)
- Chao Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- National Key Laboratory for North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhikang Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
- National Key Laboratory for North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding, China
- Institute for Genomics and Bio-Big-Data, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Zhang C, Wang D, Wang J, Sun Q, Tian L, Tang X, Yuan Z, He H, Yu S. Genetic Dissection and Validation of Chromosomal Regions for Transmission Ratio Distortion in Intersubspecific Crosses of Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:563548. [PMID: 33193492 PMCID: PMC7655136 DOI: 10.3389/fpls.2020.563548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/17/2020] [Indexed: 05/17/2023]
Abstract
Transmission ratio distortion (TRD) refers to a widespread phenomenon in which one allele is transmitted by heterozygotes more frequently to the progeny than the opposite allele. TRD is considered as a mark suggesting the presence of a reproductive barrier. However, the genetic and molecular mechanisms underlying TRD in rice remain largely unknown. In the present study, a population of backcross inbred lines (BILs) derived from the cross of a japonica cultivar Nipponbare (NIP) and an indica variety 9311 was utilized to study the genetic base of TRD. A total of 18 genomic regions were identified for TRD in the BILs. Among them, 12 and 6 regions showed indica (9311) and japonica (NIP) alleles with preferential transmission, respectively. A series of F2 populations were used to confirm the TRD effects, including six genomic regions that were confirmed by chromosome segment substitution line (CSSL)-derived F2 populations from intersubspecific allelic combinations. However, none of the regions was confirmed by the CSSL-derived populations from intrasubspecific allelic combination. Furthermore, significant epistatic interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could positively contribute to breaking intersubspecific reproductive barriers. Our results have laid the foundation for identifying the TRD genes and provide an effective strategy to breakdown TRD for breeding wide-compatible lines, which will be further utilized in the intersubspecific hybrid breeding programs.
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Affiliation(s)
- Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jilin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Tian
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinxin Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hanzi He
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Hanzi He,
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Sibin Yu,
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Zhang H, Zhou L, Xu H, Wang L, Liu H, Zhang C, Li Q, Gu M, Wang C, Liu Q, Zhu Y. The qSAC3 locus from indica rice effectively increases amylose content under a variety of conditions. BMC PLANT BIOLOGY 2019; 19:275. [PMID: 31234778 PMCID: PMC6591921 DOI: 10.1186/s12870-019-1860-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 05/31/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Amylose content (AC) is a critical factor for the quality of rice. It is determined by the biosynthesis gene Waxy (Wx) and a variety of quantitative trait loci (QTLs). Although many QTLs have been reported to affect rice AC, few of them have been investigated under varying growth conditions, especially various temperatures, which are known to greatly influence the AC. RESULTS We analyzed the AC at different temperatures and planting seasons in a set of chromosome segment substitution lines (CSSLs) which were derived from a cross between the indica variety 9311 and the japonica variety Nipponbare carrying the same Wxb allele. A joint analysis detected a single locus, qSAC3, with a high logarithm of odds (LOD) score in four different conditions. The qSAC3 from indica 9311 (qSAC3ind) substantially increased the AC in japonica Nipponbare under all tested growth conditions. Furthermore, introducing the qSAC3ind into the soft rice variety Nangeng9108 with Wxmq, a mutant allele of Wxb, also moderately increased its AC and improved its appearance quality significantly by reducing the chalkiness of the polished rice. CONCLUSIONS Our results indicate that the qSAC3ind could increase the AC of japonica rice in different environments as well as in the background of different Wx alleles and that qSAC3 is a valuable locus for fine-tuning the rice AC and ameliorating the dull endosperm in rice varieties with the Wxmq allele.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Lihui Zhou
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Heng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Liangchao Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Huijie Liu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
| | - Changquan Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Qianfeng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Minghong Gu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Cailin Wang
- Jiangsu High Quality Rice Research and Development Center, Nanjing Branch of China National Center for Rice Improvement, Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Qiaoquan Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Ying Zhu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Key Laboratory of Creative Agriculture, Ministry of Agriculture, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Zhejiang, 310021 Hangzhou China
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11
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Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice. SCIENCE CHINA-LIFE SCIENCES 2019; 62:507-516. [DOI: 10.1007/s11427-018-9452-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/28/2018] [Indexed: 11/27/2022]
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12
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Kubo T, Yoshimura A, Kurata N. Genetic characterization and fine mapping of S25, a hybrid male sterility gene, on rice chromosome 12. Genes Genet Syst 2018; 92:205-212. [PMID: 28674278 DOI: 10.1266/ggs.17-00012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hybrid male sterility genes are important factors in creating postzygotic reproductive isolation barriers in plants. One such gene, S25, is known to cause severe transmission ratio distortion in inter-subspecific progeny of cultivated rice Oryza sativa ssp. indica and japonica. To further characterize the S25 gene, we fine-mapped and genetically characterized the S25 gene using near-isogenic lines with reciprocal genetic backgrounds. We mapped the S25 locus within the 0.67-1.02 Mb region on rice chromosome 12. Further genetic analyses revealed that S25 substantially reduced male fertility in the japonica background, but not in the indica background. In first-generation hybrid progeny, S25 had a milder effect than it had in the japonica background. These results suggest that the expression of S25 is epistatically regulated by at least one partially dominant gene present in the indica genome. This finding supports our previous studies showing that hybrid male sterility due to pollen killer genes results from epistatic interaction with other genes that are hidden in the genetic background.
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Affiliation(s)
- Takahiko Kubo
- Plant Genetics Laboratory, National Institute of Genetics
| | | | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics
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13
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Li G, Li X, Wang Y, Mi J, Xing F, Zhang D, Dong Q, Li X, Xiao J, Zhang Q, Ouyang Y. Three representative inter and intra-subspecific crosses reveal the genetic architecture of reproductive isolation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:349-362. [PMID: 28805257 DOI: 10.1111/tpj.13661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/25/2017] [Accepted: 08/07/2017] [Indexed: 05/28/2023]
Abstract
Systematic characterization of genetic and molecular mechanisms in the formation of hybrid sterility is of fundamental importance in understanding reproductive isolation and speciation. Using ultra-high-density genetic maps, 43 single-locus quantitative trait loci (QTLs) and 223 digenic interactions for embryo-sac, pollen, and spikelet fertility are depicted from three crosses between representative varieties of japonica and two varietal groups of indica, which provide an extensive archive for investigating the genetic basis of reproductive isolation in rice. Ten newly detected single-locus QTLs for inter- and intra-subspecific fertility are identified. Three loci for embryo-sac fertility are detected in both Nip × ZS97 and Nip × MH63 crosses, whereas QTLs for pollen fertility are not in common between the two crosses thus leading to fertility variation. Five loci responsible for fertility and segregation distortion are observed in the ZS97 × MH63 cross. The importance of two-locus interactions on fertility are quantified in the whole genome, which identify that three types of interaction contribute to fertility reduction in the hybrid. These results construct the genetic architecture with respect to various forms of reproductive barriers in rice, which have significant implications in utilization of inter-subspecific heterosis along with improvement in the fertility of indica-indica hybrids at single- and multi-locus level.
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Affiliation(s)
- Guangwei Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoting Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Dahan Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiyan Dong
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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14
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Sun Z, Yin X, Ding J, Yu D, Hu M, Sun X, Tan Y, Sheng X, Liu L, Mo Y, Ouyang N, Jiang B, Yuan G, Duan M, Yuan D, Fang J. QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'. PLoS One 2017; 12:e0175692. [PMID: 28422981 PMCID: PMC5396889 DOI: 10.1371/journal.pone.0175692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/29/2017] [Indexed: 02/04/2023] Open
Abstract
Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar ‘Nipponbare’ as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.
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Affiliation(s)
- Zhizhong Sun
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Xiaoling Yin
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Jia Ding
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Dong Yu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Miao Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
| | - Xuewu Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Xiabing Sheng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Ling Liu
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Yi Mo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Ning Ouyang
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Beibei Jiang
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Guilong Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Meijuan Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| | - Dingyang Yuan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
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Glick L, Sabath N, Ashman TL, Goldberg E, Mayrose I. Polyploidy and sexual system in angiosperms: Is there an association? AMERICAN JOURNAL OF BOTANY 2016; 103:1223-1235. [PMID: 27352832 DOI: 10.3732/ajb.1500424] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/19/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Flowering plants display a variety of sexual systems, ranging from complete cosexuality (hermaphroditism) to separate-sexed individuals (dioecy). While dioecy is relatively rare, it has evolved many times and is present in many plant families. Transitions in sexual systems are hypothesized to be affected by large genomic events such as whole-genome duplication, or polyploidy, and several models have been proposed to explain the observed patterns of association. METHODS In this study, we assessed the association between ploidy and sexual system (separate or combined sexes). To this end, we assembled a database of ploidy levels and sexual systems for ∼1000 species, spanning 18 genera and 15 families. We applied several phylogenetic comparative approaches, including Pagel's coevolutionary framework and sister clade analyses, for detecting correlations between ploidy level and sexual system. KEY RESULTS Our results indicate a broad association between polyploidy and sexual system dimorphism, with low evolutionary stability of the diploid-dioecious condition observed in several clades. A detailed examination of the clades exhibiting this correlation reveals that it is underlain by various patterns of transition rate asymmetry. CONCLUSIONS We conclude that the long-hypothesized connection between ploidy and sexual system holds in some clades, although it may well be affected by factors that differ from clade to clade. Our results further demonstrate that to better understand the evolutionary processes involved, more sophisticated methods and extensive and detailed data sets are required for both broad and focused inquiry.
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Affiliation(s)
- Lior Glick
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Niv Sabath
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Tia-Lynn Ashman
- Department of Biological Sciences University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
| | - Emma Goldberg
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota 55108-6097 USA
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
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Zhang H, Duan L, Dai JS, Zhang CQ, Li J, Gu MH, Liu QQ, Zhu Y. Major QTLs reduce the deleterious effects of high temperature on rice amylose content by increasing splicing efficiency of Wx pre-mRNA. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:273-82. [PMID: 24162153 DOI: 10.1007/s00122-013-2216-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/14/2013] [Indexed: 05/12/2023]
Abstract
We discovered four QTLs that maintain proper rice amylose content at high temperature by increasing the splicing efficiency of Wx gene. Amylose content mainly controlled by Wx gene is a key physicochemical property for eating and cooking quality in rice. During the grain filling stage, high temperature can harm rice grain quality by significantly reducing the amylose content in many rice varieties. Here, we provide genetic evidences between Wx gene expression and rice amylose content at high temperature, and identified several quantitative trait loci (QTLs) in this pathway. We performed a genome-wide survey on a set of chromosome segment substitution lines (CSSLs) which carried chromosomal segments from the heat resistant indica 9311 in the heat-sensitive japonica Nipponbare background. Four QTLs, qHAC4, qHAC8a, qHAC8b and qHAC10, which can reduce the deleterious effects of amylose content at high temperature, were identified and mapped to chromosome 4, 8, 8 and 10, respectively. The major QTL qHAC8a, with the highest LOD score of 6.196, was physically mapped to a small chromosome segment (~300 kb). The CSSLs carrying the qHAC8a, qHAC8b and/or qHAC4 from 9311 have the high pre-mRNA splicing efficiency of Wx gene and likely lead to stable amylose content at high temperature. Thus, increasing pre-mRNA processing efficiency of Wx gene could be an important regulation mechanism for maintaining stable amylose content in rice seeds at high temperature. In addition, our results provide a theoretical basis for breeding heat-stable grain in rice.
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Affiliation(s)
- Hua Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Ashman TL, Kwok A, Husband BC. Revisiting the dioecy-polyploidy association: alternate pathways and research opportunities. Cytogenet Genome Res 2013; 140:241-55. [PMID: 23838528 DOI: 10.1159/000353306] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The evolutionary transition from hermaphroditism (combined sexes) to dioecy (separate sexes) is associated with whole genome duplication (polyploidy) in several flowering plant genera. Moreover, there is evidence for transitions in the opposite direction, i.e. a loss of dioecy with an increase in ploidy. Here, we review evidence for these associations, synthesize previous ideas on the mechanism underlying the patterns and explore alternative pathways. Specifically, we examine potential ecological and genetic mechanisms, differentiated by whether ploidy or gender (functional sex expression of the plant) changes are the primary cause and whether the effect is direct or indirect. An analysis of 22 genera variable for both ploidy and gender indicates that gender monomorphism (hermaphroditism, monoecy) is more common among diploid than polyploid species, whereas gender dimorphism (dioecy, gynodioecy, subdioecy) is more frequent among polyploid species. The transition from diploid hermaphroditic to polyploid gender-dimorphic taxa may arise directly through changes in gender as a result of genome duplication through genomic rearrangements or homeologous recombination, or changes in gender may result in increased unreduced gamete production leading to polyploid formation. Alternatively, the transition may occur through the indirect effects of genome duplication on mating system and inbreeding depression, which favor selection for unisexuality, or habitat shifts associated with unisexuality may simultaneously cause increased unreduced gamete production. Novel mechanisms for transitions in the opposite direction (from dioecy to hermaphroditism with increase in ploidy) include disruption of genetic sex determination and the benefits of reproductive assurance. We highlight key questions requiring further attention and promising approaches for answering them and better clarifying the genesis of sexual system polyploidy associations. See also the sister article focusing on animals by Wertheim et al. in this themed issue.
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Affiliation(s)
- T-L Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260-3929, USA. tia1 @ pitt.edu
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Zhang H, Zhao Q, Sun ZZ, Zhang CQ, Feng Q, Tang SZ, Liang GH, Gu MH, Han B, Liu QQ. Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare. J Genet Genomics 2011; 38:603-11. [PMID: 22196403 DOI: 10.1016/j.jgg.2011.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 11/06/2011] [Accepted: 11/15/2011] [Indexed: 11/29/2022]
Abstract
Chromosome segment substitution lines (CSSLs) are useful for the precise mapping of quantitative trait loci (QTLs) and dissection of the genetic basis of complex traits. In this study, two whole-genome sequenced rice cultivars, the japonica Nipponbare and indica 9311 were used as recipient and donor, respectively. A population with 57 CSSLs was developed after crossing and back-crossing assisted by molecular markers, and genotypes were identified using a high-throughput resequencing strategy. Detailed graphical genotypes of 38 lines were constructed based on resequencing data. These CSSLs had a total of 95 substituted segments derived from indica 9311, with an average of about 2.5 segments per CSSL and eight segments per chromosome, and covered about 87.4% of the rice whole genome. A multiple linear regression QTL analysis mapped four QTLs for 1000-grain weight. The largest-effect QTL was located in a region on chromosome 5 that contained a cloned major QTL GW5/qSW5 for grain size in rice. These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice, and offer ideal materials and foundations for japonica breeding.
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Affiliation(s)
- Hua Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou 225009, China
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