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Wang C, Yu X, Wang J, Zhao Z, Wan J. Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice. J Genet Genomics 2024; 51:583-593. [PMID: 38325701 DOI: 10.1016/j.jgg.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.
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Affiliation(s)
- Chaolong Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, Jiangsu 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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2
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Myint ZM, Koide Y, Takanishi W, Ikegaya T, Kwan C, Hikichi K, Tokuyama Y, Okada S, Onishi K, Ishikawa R, Fujita D, Yamagata Y, Matsumura H, Kishima Y, Kanazawa A. OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata. iScience 2024; 27:109761. [PMID: 38706863 PMCID: PMC11067373 DOI: 10.1016/j.isci.2024.109761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/26/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
The genetic mechanisms of reproductive isolation have been widely investigated within Asian cultivated rice (Oryza sativa); however, relevant genes between diverged species have been in sighted rather less. Herein, a gene showing selfish behavior was discovered in hybrids between the distantly related rice species Oryza longistaminata and O. sativa. The selfish allele S13l in the S13 locus impaired male fertility, discriminately eliminating pollens containing the allele S13s from O. sativa in heterozygotes (S13s/S13l). Genetic analysis revealed that a gene encoding a chromatin-remodeling factor (CHR) is involved in this phenomenon and a variety of O. sativa owns the truncated gene OsCHR745, whereas its homologue OlCHR has a complete structure in O. longistaminata. CRISPR-Cas9-mediated loss of function mutants restored fertility in hybrids. African cultivated rice, which naturally lacks the OlCHR homologue, is compatible with both S13s and S13l carriers. These results suggest that OlCHR is a Killer gene, which leads to reproductive isolation.
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Affiliation(s)
- Zin Mar Myint
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Wakana Takanishi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Tomohito Ikegaya
- National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Choi Kwan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kiwamu Hikichi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoshiki Tokuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Shuhei Okada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kazumitsu Onishi
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Ryo Ishikawa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | | | | | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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3
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Liao B, Xiang YH, Li Y, Yang KY, Shan JX, Ye WW, Dong NQ, Kan Y, Yang YB, Zhao HY, Yu HX, Lu ZQ, Zhao Y, Zhao Q, Guo D, Guo SQ, Lei JJ, Mu XR, Cao YJ, Han B, Lin HX. Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier. Nat Commun 2024; 15:996. [PMID: 38307858 PMCID: PMC10837208 DOI: 10.1038/s41467-024-45377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
Postzygotic reproductive isolation, which results in the irreversible divergence of species, is commonly accompanied by hybrid sterility, necrosis/weakness, or lethality in the F1 or other offspring generations. Here we show that the loss of function of HWS1 and HWS2, a couple of duplicated paralogs, together confer complete interspecific incompatibility between Asian and African rice. Both of these non-Mendelian determinants encode the putative Esa1-associated factor 6 (EAF6) protein, which functions as a characteristic subunit of the histone H4 acetyltransferase complex regulating transcriptional activation via genome-wide histone modification. The proliferating tapetum and inappropriate polar nuclei arrangement cause defective pollen and seeds in F2 hybrid offspring due to the recombinant HWS1/2-mediated misregulation of vitamin (biotin and thiamine) metabolism and lipid synthesis. Evolutionary analysis of HWS1/2 suggests that this gene pair has undergone incomplete lineage sorting (ILS) and multiple gene duplication events during speciation. Our findings have not only uncovered a pair of speciation genes that control hybrid breakdown but also illustrate a passive mechanism that could be scaled up and used in the guidance and optimization of hybrid breeding applications for distant hybridization.
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Affiliation(s)
- Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan Li
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Kai-Yang Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Zhao
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qiang Zhao
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dongling Guo
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Shuang-Qin Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie-Jie Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Rui Mu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Jie Cao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Han
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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4
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Li J, Zhou J, Xu P, Yang Y, Deng X, Deng W, Zhang Y, Lv Y, Pu Q, Tao D. Improving bridge effect to overcome interspecific hybrid sterility by pyramiding hybrid sterile loci from Oryza glaberrima. Sci Rep 2023; 13:23057. [PMID: 38155162 PMCID: PMC10754949 DOI: 10.1038/s41598-023-49914-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023] Open
Abstract
In order to evaluate the genetic effect caused by hybrid sterile loci, NILs with O. glaberrima fragment at six hybrid sterile loci under O. sativa genetic background (single-locus-NILs) were developed; two lines harboring two hybrid sterile loci, one line harboring three hybrid sterile loci were further developed. A total of nine NILs were used to test cross with O. sativa recurrent parent, and O. glaberrima accessions respectively. The results showed that the sterility of pollen grains in F1 hybrids deepened with the increase of the number of hybrid sterile loci, when the nine lines test crossed with O. sativa recurrent parent. The F1 hybrids were almost completely sterile when three hybrid sterile loci were heterozygeous. On the other hand, the single-locus-NILs had limited bridge effect on improving pollen grain fertility of interspecific hybrids. Compared single-locus-NILs, the multiple-loci-NILs showed increasing effect on pollen fertility when test crossing with O. glaberrima accessions. Further backcrossing can improve the fertility of pollen grain and spikelet of interspecific hybrids. The optimal solution to improve the fertility of interspecific hybrid can be utilization of pyramiding bridge parent plus backcrossing. This report has potential for understanding the nature of interspecific hybrid sterility, and overcoming the interspecific hybrid F1 pollen grain sterility between O. sativa and O. glaberrima.
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Affiliation(s)
- Jing Li
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Jiawu Zhou
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Peng Xu
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Ying Yang
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Xianneng Deng
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Wei Deng
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Yu Zhang
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Yonggang Lv
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Qiuhong Pu
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China
| | - Dayun Tao
- Yunnan Seed Laboratory / Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, People's Republic of China.
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5
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You S, Zhao Z, Yu X, Zhu S, Wang J, Lei D, Zhou J, Li J, Chen H, Xiao Y, Chen W, Wang Q, Lu J, Chen K, Zhou C, Zhang X, Cheng Z, Guo X, Ren Y, Zheng X, Liu S, Liu X, Tian Y, Jiang L, Tao D, Wu C, Wan J. A toxin-antidote system contributes to interspecific reproductive isolation in rice. Nat Commun 2023; 14:7528. [PMID: 37980335 PMCID: PMC10657391 DOI: 10.1038/s41467-023-43015-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/18/2023] [Indexed: 11/20/2023] Open
Abstract
Breakdown of reproductive isolation facilitates flow of useful trait genes into crop plants from their wild relatives. Hybrid sterility, a major form of reproductive isolation exists between cultivated rice (Oryza sativa) and wild rice (O. meridionalis, Mer). Here, we report the cloning of qHMS1, a quantitative trait locus controlling hybrid male sterility between these two species. Like qHMS7, another locus we cloned previously, qHMS1 encodes a toxin-antidote system, but differs in the encoded proteins, their evolutionary origin, and action time point during pollen development. In plants heterozygous at qHMS1, ~ 50% of pollens carrying qHMS1-D (an allele from cultivated rice) are selectively killed. In plants heterozygous at both qHMS1 and qHMS7, ~ 75% pollens without co-presence of qHMS1-Mer and qHMS7-D are selectively killed, indicating that the antidotes function in a toxin-dependent manner. Our results indicate that different toxin-antidote systems provide stacked reproductive isolation for maintaining species identity and shed light on breakdown of hybrid male sterility.
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Affiliation(s)
- Shimin You
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Zhigang Zhao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Xiaowen Yu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Shanshan Zhu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Dekun Lei
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Jiawu Zhou
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, P. R. China
| | - Jing Li
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, P. R. China
| | - Haiyuan Chen
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Yanjia Xiao
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Weiwei Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiming Wang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Jiayu Lu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Keyi Chen
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Xin Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhijun Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiuping Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaoming Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China
| | - Dayun Tao
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, 650200, P. R. China.
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, China.
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Zhao Z, Shen R, Liu YG. Hybrid sterility genes with driving force for speciation in rice. Sci Bull (Beijing) 2023; 68:1845-1848. [PMID: 37563029 DOI: 10.1016/j.scib.2023.07.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Affiliation(s)
- Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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7
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Li S, Feng T, Zhang C, Zhang F, Li H, Chen Y, Liang L, Zhang C, Zeng W, Liu E, Shi Y, Li M, Meng L. Genetic Dissection of Salt Tolerance and Yield Traits of Geng ( japonica) Rice by Selective Subspecific Introgression. Curr Issues Mol Biol 2023; 45:4796-4813. [PMID: 37367054 DOI: 10.3390/cimb45060305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Salinity is a major factor limiting rice productivity, and developing salt-tolerant (ST) varieties is the most efficient approach. Seventy-eight ST introgression lines (ILs), including nine promising lines with improved ST and yield potential (YP), were developed from four BC2F4 populations from inter-subspecific crosses between an elite Geng (japonica) recipient and four Xian (indica) donors at the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences. Genome-wide characterization of donor introgression identified 35 ST QTLs, 25 of which harbor 38 cloned ST genes as the most likely QTL candidates. Thirty-four are Xian-Geng differentiated ones with the donor (Xian) alleles associated with ST, suggesting differentiated responses to salt stress were one of the major phenotypic differences between the two subspecies. At least eight ST QTLs and many others affecting yield traits were identified under salt/non-stress conditions. Our results indicated that the Xian gene pool contains rich 'hidden' genetic variation for developing superior Geng varieties with improved ST and YP, which could be efficiently exploited by selective introgression. The developed ST ILs and their genetic information on the donor alleles for ST and yield traits would provide a useful platform for developing superior ST and high-yield Geng varieties through breeding by design in the future.
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Affiliation(s)
- Simin Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Ting Feng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chenyang Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Fanlin Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Hua Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yanjun Chen
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Lunping Liang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chaopu Zhang
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wei Zeng
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Lijun Meng
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, China
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8
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Feng Y, Tang J, Liu R, Liu YG, Chen L, Xie Y. Characterization and fine-mapping of a new Asian rice selfish genetic locus S58 in Asian-African rice hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:87. [PMID: 36971843 DOI: 10.1007/s00122-023-04348-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
We identified and fine-mapped S58, a selfish genetic locus from Asian rice that confers hybrid male sterility in crosses between Asian and African cultivated rice, and found a natural neutral allele in Asian rice lines that will be useful for overcoming S58-mediated hybrid sterility. Hybrids between Asian cultivated rice (Oryza sativa L.) and African cultivated rice (Oryza glaberrima Steud) display severe hybrid sterility (HS), hindering the utilization of strong heterosis in hybrids between these species. Several African rice selfish loci causing HS in Asian-African cultivated rice hybrids have been identified, but few such Asian rice selfish loci have been found. In this study, we identified an Asian rice selfish locus, S58, which causes hybrid male sterility (HMS) in hybrids between the Asian rice variety 02428 and the African rice line CG14. Genetic analysis confirmed that S58 causes a transmission advantage for the Asian rice S58 allele in the hybrid offspring. Genetic mapping with near-isogenic lines and DNA markers delimited S58 to 186 kb and 131 kb regions of chromosome 1 in 02428 and CG14, respectively, and revealed complex genomic structural variation over these mapped regions. Gene annotation analysis and expression profiling analyses identified eight anther-expressed candidate genes potentially responsible for S58-mediated HMS. Comparative genomic analysis determined that some Asian cultivated rice varieties harbor a 140 kb fragment deletion in this region. Hybrid compatibility analysis showed that this large deletion allele in some Asian cultivated rice varieties can serve as a natural neutral allele, S58-n, that can overcome S58-mediated interspecific HMS. Our study demonstrates that this selfish genetic element from Asian rice is important for HMS between Asian and African cultivated rice, broadening our understanding of interspecific HS. This study also provides an effective strategy for overcoming HS in future interspecific rice breeding.
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Affiliation(s)
- Yaoming Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jintao Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Ruiying Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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9
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Mmbando GS. Challenges and prospects in using biotechnological interventions in O. glaberrima, an African cultivated rice. GM CROPS & FOOD 2022; 13:372-387. [DOI: 10.1080/21645698.2022.2149212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma (Udom), Dodoma, Tanzania
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10
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Abdul Aziz M, Brini F, Rouached H, Masmoudi K. Genetically engineered crops for sustainably enhanced food production systems. FRONTIERS IN PLANT SCIENCE 2022; 13:1027828. [PMID: 36426158 PMCID: PMC9680014 DOI: 10.3389/fpls.2022.1027828] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.
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Affiliation(s)
- Mughair Abdul Aziz
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Hatem Rouached
- Michigan State University, Plant and Soil Science Building, East Lansing, MI, United States
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
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11
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De Carvalho M, Jia GS, Nidamangala Srinivasa A, Billmyre RB, Xu YH, Lange JJ, Sabbarini IM, Du LL, Zanders SE. The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years. eLife 2022; 11:e81149. [PMID: 36227631 PMCID: PMC9562144 DOI: 10.7554/elife.81149] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Meiotic drivers are selfish elements that bias their own transmission into more than half of the viable progeny produced by a driver+/driver- heterozygote. Meiotic drivers are thought to exist for relatively short evolutionary timespans because a driver gene or gene family is often found in a single species or in a group of very closely related species. Additionally, drivers are generally considered doomed to extinction when they spread to fixation or when suppressors arise. In this study, we examine the evolutionary history of the wtf meiotic drivers first discovered in the fission yeast Schizosaccharomyces pombe. We identify homologous genes in three other fission yeast species, S. octosporus, S. osmophilus, and S. cryophilus, which are estimated to have diverged over 100 million years ago from the S. pombe lineage. Synteny evidence supports that wtf genes were present in the common ancestor of these four species. Moreover, the ancestral genes were likely drivers as wtf genes in S. octosporus cause meiotic drive. Our findings indicate that meiotic drive systems can be maintained for long evolutionary timespans.
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Affiliation(s)
- Mickaël De Carvalho
- Stowers Institute for Medical ResearchKansas CityUnited States
- Open UniversityMilton KeynesUnited Kingdom
| | - Guo-Song Jia
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua UniversityBeijingChina
- National Institute of Biological Sciences, BeijingBeijingChina
| | - Ananya Nidamangala Srinivasa
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
| | | | - Yan-Hui Xu
- National Institute of Biological Sciences, BeijingBeijingChina
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | | | - Li-Lin Du
- National Institute of Biological Sciences, BeijingBeijingChina
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua UniversityBeijingChina
| | - Sarah E Zanders
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular and Integrative Physiology, University of Kansas Medical CenterKansas CityUnited States
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12
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Wang J, Jian A, Wan H, Lei D, Zhou J, Zhu S, Ren Y, Lin Q, Lei C, Wang J, Zhao Z, Guo X, Zhang X, Cheng Z, Tao D, Jiang L, Zhao Z, Wan J. Genetic characterization and fine mapping of qHMS4 responsible for pollen sterility in hybrids between Oryza sativa L. and Oryza glaberrima Steud. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:47. [PMID: 37313516 PMCID: PMC10248710 DOI: 10.1007/s11032-022-01306-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
African cultivated rice (Oryza glaberrima Steud) contains many favorable genes for tolerance to biotic and abiotic stresses and F1 hybrids between Asian cultivated rice (Oryza sativa L.) show strong heterosis. However, the hybrids of two species often exhibit hybrid sterility. Here, we identified a male sterility locus qHMS4 on chromosome 4 (Chr.4), which induces pollen semi-sterility in F1 hybrids of japonica rice variety Dianjingyou1 (DJY1) and a near-isogenic line (NIL) carrying a Chr.4 segment from Oryza glaberrima accession IRGC101854. Cytological observations indicated that non-functional pollen grains produced by the hybrids and lacking starch accumulation abort at the late bicellular stage. Molecular genetic analysis revealed distorted segregation in male gametogenesis carrying qHMS4 allele from DJY1. Fine-mapping of qHMS4 using an F2 population of 22,500 plants delimited qHMS4 to a region of 110-kb on the short arm of Chr.4. Sequence analysis showed that the corresponding sequence region in DJY1 and Oryza glaberrima were 114-kb and 323-kb, respectively, and that the sequence homology was very poor. Gene prediction analysis identified 16 and 46 open reading frames (ORFs) based on the sequences of DJY1 and O. glaberrima, respectively, among which 3 ORFs were shared by both. Future map-based cloning of qHMS4 will help to understand the underlying molecular mechanism of hybrid sterility between the two cultivated rice species. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01306-8.
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Affiliation(s)
- Jian Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Anqi Jian
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hua Wan
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dekun Lei
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jiawu Zhou
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Ling Jiang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zhigang Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095 China
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13
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Koide Y. Influence of Gender Bias on Distribution of Hybrid Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:898206. [PMID: 35903237 PMCID: PMC9319209 DOI: 10.3389/fpls.2022.898206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Hybrid sterility genes define species identities, setting reproductive barriers between distantly related Oryza relatives. They induce allelic-specific selective gametic abnormalities by killing pollens, embryo sacs, or both, and thus resulting in the male specific transmission ratio distortion (mTRD), female specific transmission ratio distortion (f TRD), and/or sex-independent transmission ratio distortion (siTRD) in hybrids. Although more than 50 hybrid sterility genes have been reported, comprehensive analysis on the distributional pattern of TRD systems in Oryza species is limited. In this review, we surveyed the TRD systems and the underlying possible mechanisms in these species. In rice, pollen killers which cause mTRD are often observed in higher frequency than egg killers and gamete eliminators, which are factors affecting f TRD and siTRD, respectively. Due to the rather massive population of pollen grains, their reduction in the number caused by hybrid sterility possesses a smaller selective disadvantage to the hybrid individuals, in contrast to female gamete abortion. The pattern of TRD distribution displays less abundancy in siTRD. It suggests that fixation of siTRD might require a certain time rather than single sex-specific factors. The presence of linked sterility factors worked for mTRD and f TRD, and strength of their linkage in chromosomal regions might determine the type of sterility and TRD. The study of TRD systems has a potential to reveal the relationships between selfish genes and their functions for reproductive isolation.
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14
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Zhou J, Yang Y, Lv Y, Pu Q, Li J, Zhang Y, Deng X, Wang M, Wang J, Tao D. Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L. FRONTIERS IN PLANT SCIENCE 2022; 13:932737. [PMID: 35845644 PMCID: PMC9280345 DOI: 10.3389/fpls.2022.932737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.
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Affiliation(s)
- Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, 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, Kunming, China
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15
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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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16
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Zhang C, Wang J, Xiao X, Wang D, Yuan Z, Zhang X, Sun W, Yu S. Fine Mapping of Two Interacting Loci for Transmission Ratio Distortion in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:866276. [PMID: 35422832 PMCID: PMC9002327 DOI: 10.3389/fpls.2022.866276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Transmission ratio distortion (TRD) denotes the observed allelic or genotypic frequency deviation from the expected Mendelian segregation ratios in the offspring of a heterozygote. TRD can severely hamper gene flow between and within rice species. Here, we report the fine mapping and characterization of two loci (TRD4.1 and TRD4.2) for TRD using large F2 segregating populations, which are derived from rice chromosome segment substitution lines, each containing a particular genomic segment introduced from the japonica cultivar Nipponbare (NIP) into the indica cultivar Zhenshan (ZS97). The two loci exhibited a preferential transmission of ZS97 alleles in the derived progeny. Reciprocal crossing experiments using near-isogenic lines harboring three different alleles at TRD4.1 suggest that the gene causes male gametic selection. Moreover, the transmission bias of TRD4.2 was diminished in heterozygotes when they carried homozygous TRD4.1 ZS97. This indicates an epistatic interaction between these two loci. TRD4.2 was mapped into a 35-kb region encompassing one candidate gene that is specifically expressed in the reproductive organs in rice. These findings broaden the understanding of the genetic mechanisms of TRD and offer an approach to overcome the barrier of gene flow between the subspecies in rice, thus facilitating rice improvement by introgression breeding.
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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
| | - 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
| | - Xiongfeng Xiao
- 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
| | - 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
| | - Xiaodan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqiang Sun
- 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
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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17
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Understanding the genetic and molecular constitutions of heterosis for developing hybrid rice. J Genet Genomics 2022; 49:385-393. [PMID: 35276387 DOI: 10.1016/j.jgg.2022.02.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/31/2022]
Abstract
The wide adoption of hybrid rice has greatly increased rice yield in the last several decades. The utilization of heterosis facilitated by male sterility has been a common strategy for hybrid rice development. Here, we summarize our efforts in the genetic and molecular understanding of heterosis and male sterility together with the related progress from other research groups. Analyses of F1 diallel crosses show that strong heterosis widely exists in hybrids of diverse germplasms, and inter-subspecific hybrids often display higher heterosis. Using the elite hybrid Shanyou 63 as a model, an immortalized F2 population design is conducted for systematic characterization of the biological mechanism of heterosis, with identification of loci controlling heterosis of yield and yield component traits. Dominance, overdominance, and epistasis all play important roles in the genetic basis of heterosis; quantitative assessment of these components well addressed the three classical genetic hypotheses for heterosis. Environment-sensitive genic male sterility (EGMS) enables the development of two-line hybrids, and long noncoding RNAs often function as regulators of EGMS. Inter-subspecific hybrids show greatly reduced fertility; the identification and molecular characterization of hybrid sterility genes offer strategies for overcoming inter-subspecific hybrid sterility. These developments have significant implications for future hybrid rice improvement using genomic breeding.
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18
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Lee CM, Suh JP, Park HS, Baek MK, Jeong OY, Yun SJ, Cho YC, Kim SM. Identification of QTL Combinations that Cause Spikelet Sterility in Rice Derived from Interspecific Crosses. RICE (NEW YORK, N.Y.) 2021; 14:99. [PMID: 34874500 PMCID: PMC8651928 DOI: 10.1186/s12284-021-00540-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The exploitation of useful genes through interspecific and intersubspecific crosses has been an important strategy for the genetic improvement of rice. Postzygotic reproductive isolation routinely occurs to hinder the growth of pollen or embryo sacs during the reproductive development of the wide crosses. RESULT In this study, we investigated the genetic relationship between the hybrid breakdown of the population and transferred resistance genes derived from wide crosses using a near-isogenic population composed of 225 lines. Five loci (qSS12, qSS8, qSS11, ePS6-1, and ePS6-2) associated with spikelet fertility (SF) were identified by QTL and epistatic analysis, and two out of five epistasis interactions were found between the three QTLs (qSS12, qSS8 and qSS11) and background marker loci (ePS6-1 and ePS6-2) on chromosome 6. The results of the QTL combinations suggested a genetic model that explains most of the interactions between spikelet fertility and the detected loci with positive or negative effects. Moreover, the major-effect QTLs, qSS12 and qSS8, which exhibited additive gene effects, were narrowed down to 82- and 200-kb regions on chromosomes 12 and 8, respectively. Of the 13 ORFs present in the target regions, Os12g0589400 and Os12g0589898 for qSS12 and OS8g0298700 for qSS8 induced significantly different expression levels of the candidate genes in rice at the young panicle stage. CONCLUSION The results will be useful for obtaining a further understanding of the mechanism causing the hybrid breakdown of a wide cross and will provide new information for developing rice cultivars with wide compatibility.
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Affiliation(s)
- Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jung-Pil Suh
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Hyun-Su Park
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Man-Kee Baek
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - O-Young Jeong
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Song-Joong Yun
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Young-Chan Cho
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Suk-Man Kim
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea.
- Department of Ecological and Environmental System, Kyungpook National University, Sangju, Republic of Korea.
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Rao MJ, Wang L. CRISPR/Cas9 technology for improving agronomic traits and future prospective in agriculture. PLANTA 2021; 254:68. [PMID: 34498163 DOI: 10.1007/s00425-021-03716-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
In this review, we have focused on the CRISPR/Cas9 technology for improving the agronomic traits in plants through point mutations, knockout, and single base editing, and we highlighted the recent progress in plant metabolic engineering. CRISPR/Cas9 technology has immense power to reproduce plants with desired characters and revolutionizing the field of genome engineering by erasing the barriers in targeted genome editing. Agriculture fields are using this advance genome editing tool to get the desired traits in the crops plants such as increase yield, improve product quality attributes, and enhance resistance against biotic and abiotic stresses by identifying and editing genes of interest. This review focuses on CRISPR/Cas-based gene knockout for trait improvement and single base editing to boost yield, quality, stress tolerance, and disease resistance traits in crops. Use of CRISPR/Cas9 system to facilitate crop domestication and hybrid breeding are also touched. We summarize recent developments and up-gradation of delivery mechanism (nanotechnology and virus particle-based delivery system) and progress in multiplex gene editing. We also shed lights in advances and challenges of engineering the important metabolic pathways that contain a variety of dietary metabolites and phytochemicals. In addition, we endorsed substantial technical hurdles and possible ways to overcome the unpredictability of CRISPR/Cas technology for broader application across various crop species. We speculated that by making a strong interconnection among all genomic fields will give a gigantic bunt of knowledge to develop crop expressing desired traits.
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Affiliation(s)
- Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, 530004, People's Republic of China
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, People's Republic of China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, 530004, People's Republic of China.
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, People's Republic of China.
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Ahmad S, Tang L, Shahzad R, Mawia AM, Rao GS, Jamil S, Wei C, Sheng Z, Shao G, Wei X, Hu P, Mahfouz MM, Hu S, Tang S. CRISPR-Based Crop Improvements: A Way Forward to Achieve Zero Hunger. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8307-8323. [PMID: 34288688 DOI: 10.1021/acs.jafc.1c02653] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Zero hunger is one of the sustainable development goals set by the United Nations in 2015 to achieve global food security by 2030. The current harvest of crops is insufficient; feeding the world's population and meeting the goal of zero hunger by 2030 will require larger and more consistent crop production. Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) technology is widely used for the plant genome editing. In this review, we consider this technology as a potential tool for achieving zero hunger. We provide a comprehensive overview of CRISPR-Cas technology and its most important applications for food crops' improvement. We also conferred current and potential technological breakthroughs that will help in breeding future crops to end global hunger. The regulatory aspects of deploying this technology in commercial sectors, bioethics, and the production of transgene-free plants are also discussed. We hope that the CRISPR-Cas system will accelerate the breeding of improved crop cultivars compared with conventional breeding and pave the way toward the zero hunger goal.
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Affiliation(s)
- Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
- Maize Research Station, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Amos Musyoki Mawia
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Chen Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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Rao J, Wang X, Cai Z, Fan Y, Yang J. Genetic Analysis of S5-Interacting Genes Regulating Hybrid Sterility in Rice. RICE (NEW YORK, N.Y.) 2021; 14:11. [PMID: 33423160 PMCID: PMC7797014 DOI: 10.1186/s12284-020-00452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/26/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Asian cultivated rice (Oryza sativa L.) comprises two subspecies, O. sativa subsp. indica and subsp. japonica, and the hybrids between them display strong heterosis. However, hybrid sterility (HS) limits practical use of the heterosis between these two subspecies. S5 is a major-effect locus controlling the HS of female gametes in rice, consisting of three closely-linked genes ORF3, ORF4 and ORF5 that act as a killer-protector system. The HS effects of S5 are inconsistent for different genetic backgrounds, indicating the existence of interacting genes within the genome. RESULTS In the present study, the S5-interacting genes (SIG) and their effects on HS were analyzed by studying the hybrid progeny between an indica rice, Dular (DL) and a japonica rice, BalillaORF5+ (BLORF5+), with a transgenic ORF5+ allele. Four interacting quantitative trait loci (QTL): qSIG3.1, qSIG3.2, qSIG6.1, and qSIG12.1, were genetically mapped. To analyze the effect of each interacting locus, four near-isogenic lines (NILs) were developed. The effect of each specific locus was investigated while the other three loci were kept DL homozygous (DL/DL). Of the four loci, qSIG3.1 was the SIG with the greatest effects in which the DL allele was completely dominant. Furthermore, the DL allele displayed incomplete dominance at qSIG3.2, qSIG6.1, and qSIG12.1. qSIG3.1 will be the first choice for further fine-mapping. CONCLUSIONS Four S5-interacting QTL were identified by genetic mapping and the effect of each locus was analyzed using advanced backcrossed NILs. The present study will facilitate elucidation of the molecular mechanism of rice HS caused by S5. Additionally, it would provide the basis to explore the origin and differentiation of cultivated rice, having practical significance for inter-subspecific hybrid rice breeding programs.
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Affiliation(s)
- Jianglei Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xing Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Zhongquan Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yourong Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
| | - Jiangyi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
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Pramanik D, Shelake RM, Kim MJ, Kim JY. CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement. MOLECULAR PLANT 2021; 14:127-150. [PMID: 33152519 DOI: 10.1016/j.molp.2020.11.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/14/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
The central dogma (CD) of molecular biology is the transfer of genetic information from DNA to RNA to protein. Major CD processes governing genetic flow include the cell cycle, DNA replication, chromosome packaging, epigenetic changes, transcription, posttranscriptional alterations, translation, and posttranslational modifications. The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation. Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population. CRISPR technology enables programmable editing of CD processes to alter DNA, RNA, or protein, which would have been impossible in the past. Here, an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided. Furthermore, CRISPR applications in major thriving areas of research, such as gene discovery (allele mining and cryptic gene activation), introgression (de novo domestication and haploid induction), and application of desired traits beneficial to farmers or consumers (biotic/abiotic stress-resilient crops, plant cell factories, and delayed senescence), are described. Finally, the global regulatory policies, challenges, and prospects for CRISPR-mediated crop improvement are discussed.
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Affiliation(s)
- Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Mi Jung Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
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Kuniyoshi D, Masuda I, Kanaoka Y, Shimazaki-Kishi Y, Okamoto Y, Yasui H, Yamamoto T, Nagaki K, Hoshino Y, Koide Y, Takamure I, Kishima Y. Diploid Male Gametes Circumvent Hybrid Sterility Between Asian and African Rice Species. FRONTIERS IN PLANT SCIENCE 2020; 11:579305. [PMID: 33224168 PMCID: PMC7674174 DOI: 10.3389/fpls.2020.579305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
In F1 hybrids of Oryza sativa (Asian rice) and Oryza glaberrima (African rice), heterozygosity leads to a complete gamete abortion because of allelic conflict at each of the 13 hybrid sterility (HS) loci. We systematically produced 19 plants from the F1 hybrids of both the rice species by the anther culture (AC) method. Five of the 19 interspecific hybrid plants were partially fertile and able to produce seeds. Unlike ordinal doubled haploid plants resulting from AC, these regenerated plants showed various ploidy levels (diploid to pentaploid) and different zygosities (completely homozygous, completely heterozygous, and a combination). These properties were attributable to meiotic anomalies in the interspecific hybrid F1 plants. Examination of the genetic structures of the regenerated plants suggested meiotic non-reduction took place in the interspecific hybrid F1 plants. The centromeric regions in the regenerated plants revealed that the abnormal first and/or second divisions of meiosis, namely the first division restitution (FDR) and/or second division restitution (SDR), had occurred in the interspecific hybrid. Immunohistochemical observations also verified these phenomena. FDR and SDR occurrences at meiosis might strongly lead to the formation of diploid microspores. The results demonstrated that meiotic anomalies functioned as a reproductive barrier occurred before the HS genes acted in gamete of the interspecific hybrid. Although such meiotic anomalies are detrimental to pollen development, the early rescue of microspores carrying the diploid gamete resulted in the fertile regenerated plants. The five partially fertile plants carrying tetraploid genomes with heterozygous alleles of the HS loci produced fertile diploid pollens, implying that the diploid gametes circumvented the allelic conflicts at the HS loci. We also proposed how diploid male gametes avoid HS with the killer-protector model.
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Affiliation(s)
- Daichi Kuniyoshi
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Itaru Masuda
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoshitaka Kanaoka
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yuki Shimazaki-Kishi
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Okamoto
- Laboratory of Plant Breeding, Rakuno Gakuen University, Ebetsu, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kiyotaka Nagaki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yoichiro Hoshino
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Yohei Koide
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Itsuro Takamure
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Xia F, Ouyang Y. Recurrent breakdown and rebalance of segregation distortion in the genomes: battle for the transmission advantage. ABIOTECH 2020; 1:246-254. [PMID: 36304131 PMCID: PMC9590546 DOI: 10.1007/s42994-020-00023-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/28/2020] [Indexed: 01/25/2023]
Abstract
Mendel's laws state that each of the two alleles would segregate during gamete formation and show the same transmission ratio in the next generation. However, an unexpected biased allele transmission was first detected in Drosophila a century ago, and was subsequently observed in other animals, plants, and microorganisms. Such segregation distortion (SD) shows substantial effects in population structure and fitness of the progenies, which would ultimately lead to reproductive isolation and speciation. Here, we trace the early investigations on the violation of Mendelian genetic principle, which appears as a wide-existence phenomenon rather than a case of exception. The occurence of SD in the whole genome was observed in a number of plant species at the single- and multi-locus level. Biased transmission ratio might occur at meiosis stage due to asymmetric movement of the chromosome; transmission ratio advantage is also caused by interaction and battle between the alleles from respective genomes at the genetic and molecular level. The origin of a SD system is likely to be determined by coevolution of the killer and protector via recurrent breakdown or rebalance loop. These updated understandings also promote genetic improvement of hybrid crops.
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Affiliation(s)
- Fan Xia
- 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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Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol 2020; 21:661-677. [PMID: 32973356 DOI: 10.1038/s41580-020-00288-9] [Citation(s) in RCA: 323] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/26/2022]
Abstract
The prokaryote-derived CRISPR-Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR-Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR-Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR-Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR-Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR-Cas-related plant biotechnologies, including CRISPR-Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology.
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Li J, Zhou J, Zhang Y, Yang Y, Pu Q, Tao D. New Insights Into the Nature of Interspecific Hybrid Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:555572. [PMID: 33072142 PMCID: PMC7538986 DOI: 10.3389/fpls.2020.555572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/01/2020] [Indexed: 06/01/2023]
Abstract
Interspecific and intraspecific hybrid sterility is a typical and common phenomenon of postzygotic reproductive barrier in rice. This is an indicator of speciation involved in the formation of new species or subspecies, and it significantly hampers the utilization of favorable genes from distant parents for rice improvement. The Oryza genus includes eight species with the same AA genome and is a model plant for studying the nature of hybrid sterility and its relationship with speciation. Hybrid sterility in rice is mostly controlled by nuclear genes, with more than 50 sterility loci genetically identified to date, of which 10 hybrid sterility loci or pairs were cloned and characterized at the molecular level. Comparing the mapping results for all sterility loci reported indicated that some of these loci from different species should be allelic to each other. Further research revealed that interactions between the multiple alleles at the hybrid sterility locus caused various genetic effect. One hypothesis for this important phenomenon is that the hybrid sterility loci are orthologous loci, which existed in ancient ancestors of rice. When one or more ancestors drifted to different continents, genetic divergence occurred because of adaptation, selection, and isolation among them such that various alleles from orthologous loci emerged over evolutionary time; hence, interspecific hybrid sterility would be mainly controlled by a few orthologous loci with different alleles. This hypothesis was tested and supported by the molecular characterization of hybrid sterility loci from S1, S5, Sa, qHMS7, and S27. From this, we may further deduce that both allelic and non-allelic interactions among different loci are the major genetic basis for the interspecific hybrid sterility between O. sativa and its AA genome relatives, and the same is true for intraspecific hybrid sterility in O. sativa. Therefore, it is necessary to raise the near-isogenic lines with various alleles/haplotypes and pyramided different alleles/haplotypes from sterile loci in the same genetic background aiming to study allelic and non-allelic interaction among different hybrid sterility loci in the AA genome species. Furthermore, the pyramiding lines ought to be used as bridge parents to overcome hybrid sterility for rice breeding purposes.
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28
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Evaluation of Drosophila chromosomal segments proposed by means of simulations of possessing hybrid sterility genes from reproductive isolation. J Genet 2020. [DOI: 10.1007/s12041-020-01215-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Long W, Dan D, Yuan Z, Chen Y, Jin J, Yang W, Zhang Z, Li N, Li S. Deciphering the Genetic Basis of Lodging Resistance in Wild Rice Oryza longistaminata. FRONTIERS IN PLANT SCIENCE 2020; 11:628. [PMID: 32547576 PMCID: PMC7274161 DOI: 10.3389/fpls.2020.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/23/2020] [Indexed: 05/27/2023]
Abstract
The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the quantitative trait loci (QTLs)/genes for lodging resistance breeding. Oryza longistaminata exhibits a strong stem and high biomass productivity, which could be a candidate gene pool for cultivars lodging resistance improvement. Here, a set of 152 BC2F20 lines derived from a cross between a cultivated line 93-11 and O. longistaminata was evaluated for lodging resistance. QTL mapping analysis combined with single-nucleotide polymorphism (SNP) marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL), and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were first identified from O. longistaminata. A major QTL, qLR1, which was delimited to a region ∼80 kb on chromosome 1, increased stem diameter, stem length, and breaking strength. Another major QTL, qLR8, that was delimited in an interval ∼120 kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that O. longistaminata can be exploited to develop lodging-resistant rice lines.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
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30
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Mi J, Li G, Xu C, Yang J, Yu H, Wang G, Li X, Xiao J, Song H, Zhang Q, Ouyang Y. Artificial Selection in Domestication and Breeding Prevents Speciation in Rice. MOLECULAR PLANT 2020; 13:650-657. [PMID: 31962168 DOI: 10.1016/j.molp.2020.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 12/13/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Speciation has long been regarded as an irreversible process once the reproductive barriers had been established. However, unlike in natural populations, artificial selection might either accelerate or prevent speciation processes in domesticated species. Asian cultivated rice is a target crop for both domestication and artificial breeding; it contains two subspecies of indica and japonica, which usually produce sterile inter-subspecific hybrids due to reproductive barriers. In this study, we constructed the evolutionary trajectory of a reproductive isolation system S5, which regulates fertility in indica-japonica hybrids via three adjacent genes, based on the data of 606 accessions including two cultivated and 11 wild rice species. Although hybrid sterility haplotypes at S5 lead to establishment of a killer-protector reproductive barrier, origin of wide-compatibility haplotypes by complex hybridization and recombination provides an opposing force to reproductive isolation and thus prevents speciation during domestication. Analysis in a diallel set of 209 crosses involving 21 parents showed that the wide-compatibility genotypes largely rescued fertility of indica-japonica hybrids, indicating that the wide-compatibility gene would enable gene flow to maintain species coherence. This counteracting system indicates that combined effects of natural evolution and artificial selection may result in reversible processes of speciation in rice, which may also have implications for genetic improvement of rice.
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Affiliation(s)
- Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guangwei Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Conghao Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jiangyi Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Huihui Yu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Gongwei Wang
- 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
| | - Huazhi Song
- 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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Sakata M, Takano-Kai N, Miyazaki Y, Kanamori H, Wu J, Matsumoto T, Doi K, Yasui H, Yoshimura A, Yamagata Y. Domain Unknown Function DUF1668-Containing Genes in Multiple Lineages Are Responsible for F 1 Pollen Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:632420. [PMID: 33574828 PMCID: PMC7870705 DOI: 10.3389/fpls.2020.632420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/29/2020] [Indexed: 05/03/2023]
Abstract
Postzygotic reproductive isolation maintains species integrity and uniformity and contributes to speciation by restricting the free gene flow between divergent species. In this study we identify causal genes of two Mendelian factors S22A and S22B on rice chromosome 2 inducing F1 pollen sterility in hybrids between Oryza sativa japonica-type cultivar Taichung 65 (T65) and a wild relative of rice species Oryza glumaepatula. The causal gene of S22B in T65 encodes a protein containing DUF1668 and gametophytically expressed in the anthers, designated S22B_j. The O. glumaepatula allele S22B-g, allelic to S22B_j, possesses three non-synonymous substitutions and a 2-bp deletion, leading to a frameshifted translation at the S22B C-terminal region. Transcription level of S22B-j and/or S22B_g did not solely determine the fertility of pollen grains by genotypes at S22B. Western blotting of S22B found that one major band with approximately 46 kDa appeared only at the mature stage and was reduced on semi-sterile heterozygotes at S22B, implying that the 46 kDa band may associated in hybrid sterility. In addition, causal genes of S22A in T65 were found to be S22A_j1 and S22A_j3 encoding DUF1668-containing protein. The allele of a wild rice species Oryza meridionalis Ng at S22B, designated S22B_m, is a loss-of-function allele probably due to large deletion of the gene lacking DUF1668 domain and evolved from the different lineage of O. glumaepatula. Phylogenetic analysis of DUF1668 suggested that many gene duplications occurred before the divergence of current crops in Poaceae, and loss-of-function mutations of DUF1668-containing genes represent the candidate causal genetic events contributing to hybrid incompatibilities. The duplicated DUF1668-domain gene may provide genetic potential to induce hybrid incompatibility by consequent mutations after divergence.
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Affiliation(s)
- Mitsukazu Sakata
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
| | - Noriko Takano-Kai
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yuta Miyazaki
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takashi Matsumoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
- Laboratory of Plant Molecular Breeding, Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Kazuyuki Doi
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Atsushi Yoshimura
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Yoshiyuki Yamagata
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- *Correspondence: Yoshiyuki Yamagata,
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Advances in Molecular Genetics and Genomics of African Rice ( Oryza glaberrima Steud). PLANTS 2019; 8:plants8100376. [PMID: 31561516 PMCID: PMC6843444 DOI: 10.3390/plants8100376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023]
Abstract
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
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Ouyang Y. Understanding and breaking down the reproductive barrier between Asian and African cultivated rice: a new start for hybrid rice breeding. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1114-1116. [PMID: 31297692 DOI: 10.1007/s11427-019-9592-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/10/2019] [Indexed: 11/30/2022]
Affiliation(s)
- 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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An asymmetric allelic interaction drives allele transmission bias in interspecific rice hybrids. Nat Commun 2019; 10:2501. [PMID: 31175302 PMCID: PMC6555797 DOI: 10.1038/s41467-019-10488-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/15/2019] [Indexed: 12/30/2022] Open
Abstract
Hybrid sterility (HS) between Oryza sativa (Asian rice) and O. glaberrima (African rice) is mainly controlled by the S1 locus. However, our limited understanding of the HS mechanism hampers utilization of the strong interspecific heterosis. Here, we show that three closely linked genes (S1A4, S1TPR, and S1A6) in the African S1 allele (S1-g) constitute a killer-protector system that eliminates gametes carrying the Asian allele (S1-s). In Asian–African rice hybrids (S1-gS1-s), the S1TPR-S1A4-S1A6 interaction in sporophytic tissues generates an abortion signal to male and female gametes. However, S1TPR can rescue S1-g gametes, while the S1-s gametes selectively abort for lacking S1TPR. Knockout of any of the S1-g genes eliminates the HS. Evolutionary analysis suggests that S1 may have arisen from newly evolved genes, multi-step recombination, and nucleotide variations. Our findings will help to overcome the interspecific reproductive barrier and use Asian–African hybrids for increasing rice production. Our limited understanding of the hybrid sterility (HS) mechanism in Asian–African rice hybrids hampers utilization of the interspecific heterosis for rice production. Here, the authors identify S1-mediated HS-related tripartite gamete killer-protector system, and explore their evolutionary relationship.
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Abstract
In sexual reproduction, opportunities are limited and the stakes are high. This inevitably leads to conflict. One pervasive conflict occurs within genomes between alternative alleles at heterozygous loci. Each gamete and thus each offspring will inherit only one of the two alleles from a heterozygous parent. Most alleles 'play fair' and have a 50% chance of being included in any given gamete. However, alleles can gain an enormous advantage if they act selfishly to force their own transmission into more than half, sometimes even all, of the functional gametes. These selfish alleles are known as 'meiotic drivers', and their cheating often incurs a high cost on the fertility of eukaryotes ranging from plants to mammals. Here, we review how several types of meiotic drivers directly and indirectly contribute to infertility, and argue that a complete picture of the genetics of infertility will require focusing on both the standard alleles - those that play fair - as well as selfish alleles involved in genetic conflict.
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Affiliation(s)
- Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
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Abstract
Natural selection works best when the two alleles in a diploid organism are transmitted to offspring at equal frequencies. Despite this, selfish loci known as meiotic drivers that bias their own transmission into gametes are found throughout eukaryotes. Drive is thought to be a powerful evolutionary force, but empirical evolutionary analyses of drive systems are limited by low numbers of identified meiotic drive genes. Here, we analyze the evolution of the wtf gene family of Schizosaccharomyces pombe that contains both killer meiotic drive genes and suppressors of drive. We completed assemblies of all wtf genes for two S. pombe isolates, as well as a subset of wtf genes from over 50 isolates. We find that wtf copy number can vary greatly between isolates and that amino acid substitutions, expansions and contractions of DNA sequence repeats, and nonallelic gene conversion between family members all contribute to dynamic wtf gene evolution. This work demonstrates the power of meiotic drive to foster rapid evolution and identifies a recombination mechanism through which transposons can indirectly mobilize meiotic drivers.
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Affiliation(s)
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sarah E Zanders
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
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Profile of Dr. Yao-Guang Liu. SCIENCE CHINA. LIFE SCIENCES 2019; 62:734-736. [PMID: 31119559 DOI: 10.1007/s11427-019-9555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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Xie Y, Shen R, Chen L, Liu YG. Molecular mechanisms of hybrid sterility in rice. SCIENCE CHINA-LIFE SCIENCES 2019; 62:737-743. [PMID: 31119561 DOI: 10.1007/s11427-019-9531-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/02/2019] [Indexed: 01/09/2023]
Abstract
Hybrid sterility presents a major bottleneck in hybrid crop breeding and causes postzygotic reproductive isolation in speciation. Here, we summarize the current understanding of the genetics of rice hybrid sterility and highlight new advances in deciphering the molecular basis of the major genetic loci for hybrid sterility in rice. We also discuss practical strategies for overcoming reproductive barriers to utilize hybrid vigor in inter-specific and inter-subspecific hybrid rice breeding.
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Affiliation(s)
- Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China.,Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China.,College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.,Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China.,College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China. .,Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China. .,College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China. .,Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, 510642, China. .,College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 631] [Impact Index Per Article: 126.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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40
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Sweigart AL, Brandvain Y, Fishman L. Making a Murderer: The Evolutionary Framing of Hybrid Gamete-Killers. Trends Genet 2019; 35:245-252. [DOI: 10.1016/j.tig.2019.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/21/2018] [Accepted: 01/23/2019] [Indexed: 11/15/2022]
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41
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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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42
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Fang C, Li L, He R, Wang D, Wang M, Hu Q, Ma Q, Qin K, Feng X, Zhang G, Fu X, Liu Z. Identification of S23 causing both interspecific hybrid male sterility and environment-conditioned male sterility in rice. RICE (NEW YORK, N.Y.) 2019; 12:10. [PMID: 30820693 PMCID: PMC6395467 DOI: 10.1186/s12284-019-0271-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/18/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Oryza glumaepatula represents an important resource of genetic diversity that can be used to improve rice production. However, hybrid sterility severely restricts gene flow between Oryza species, and hinders the utilization of distant heterosis in hybrid rice breeding. RESULTS In order to fully exploit the beneficial genes of O. glumaepatula and facilitate the conservation of these gene resources, a set of chromosome single-segment substitution lines (SSSLs) was developed using an indica variety HJX74 as the recurrent parent and an accession of O. glumaepatula as the donor parent. During the process of SSSLs development, S23, a locus conferring hybrid male sterility between O. sativa and O. glumaepatula, was identified and fine mapped to 11.54 kb and 7.08 kb genomic region in O. sativa and O. glumaepatula, respectively, encoding three and two candidate ORFs, respectively. qRT-PCR and sequence analysis excluded one common ORF as the candidate gene. In addition, hybrid male sterility caused by S23 was environment-sensitive, and could be observed only in natural short-day (NSD). CONCLUSION Identification and candidate genes analysis of S23 in this study provides a valuable example to study the crosstalk between interspecific F1 hybrid male sterility and environment-conditioned male sterility in rice, facilitates reserving and utilizing favorable genes or alleles of wild Oryza species, and allows for a more efficient exploitation of distant heterosis in hybrid rice breeding.
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Affiliation(s)
- Chaowei Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Le Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
- Present address: Huazhi Rice Bio-Tech Co., Ltd., Changsha, 410124, China
| | - Runming He
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
- Present address: Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510642, China
| | - Daiqi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Qianru Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Kaiyi Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xueye Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Guiquan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Xuelin Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ziqiang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Li J, Zhou J, Xu P, Deng X, Deng W, Zhang Y, Yang Y, Tao D. Mapping five novel interspecific hybrid sterility loci between Oryza sativa and Oryza meridionalis. BREEDING SCIENCE 2018; 68:516-523. [PMID: 30697112 PMCID: PMC6345236 DOI: 10.1270/jsbbs.18001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/22/2018] [Indexed: 05/27/2023]
Abstract
Oryza meridionalis is a potential source for improving Asian cultivated rice O. sativa via direct hybridization and backcrossing. However, hybrid sterility between O. sativa and O. meridionalis is the main barrier of reproduction hindering the transfer of favorable genes from O. meridionalis to O. sativa. To investigate the nature of hybrid sterility between O. sativa and O. meridionalis, three accessions of O. meridionalis were used as male parents to cross Dianjingyou 1, an O. sativa subsp. japonica cultivar following the backcross with the recurrent parent of Dianjingyou 1. Twenty pollen sterility NILs (BC6F1) were obtained and genotyped by using simple sequence repeat (SSR) markers distributed across the 12 rice chromosomes. The heterozygous markers were employed to genotype the corresponding segregation populations for mapping sterility genes. As a result, five novel loci for pollen sterility between O. sativa and O. meridionalis were identified and designated as S51(t), S52(t), S53(t), S54(t) and S55(t), respectively. The genetic behavior of five novel loci followed one-locus allelic interaction model. The disharmonious interaction between Asian cultivated rice allele and wild relative allele led to the partial or full abortion of male gametes for one parent allele in the heterozygotes. These results will be useful for elucidating the mechanism of interspecific hybrid sterility and further utilizing favorable genes from O. meridionalis for enhancement of rice breeding.
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44
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Birchler JA. An overview of rice genetics research in China. J Genet Genomics 2018; 45:563-564. [PMID: 30482272 DOI: 10.1016/j.jgg.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
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45
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Kanaoka Y, Kuniyoshi D, Inada E, Koide Y, Okamoto Y, Yasui H, Kishima Y. Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility. PLANT METHODS 2018; 14:102. [PMID: 30473723 PMCID: PMC6240274 DOI: 10.1186/s13007-018-0370-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND To investigate plant hybrid sterility, we studied interspecific hybrids of two cultivated rice species, Asian rice (Oryza sativa) and African rice (O. glaberrima). Male gametes of these hybrids display complete sterility owing to a dozen of hybrid sterility loci, termed HS loci, but this complicated genetic system remains poorly understood. RESULTS Microspores from these interspecific hybrids form sterile pollen but are viable at the immature stage. Application of the anther culture (AC) method caused these immature microspores to induce callus. The segregation distortion of 11 among 13 known HS loci was assessed in the callus population. Using many individual calli, fine mapping of the HS loci was attempted based on heterozygotes produced from chromosome segment substitution lines (CSSLs). Transmission ratio distortion (TRD) from microspores was detected at 6 of 11 HS loci in the callus population. The fine mapping of S 1 and S 19 loci using CSSLs revealed precise distances of markers from the positions of HS loci exhibiting excessive TRD. CONCLUSIONS We demonstrated that AC to generate callus populations derived from immature microspores is a useful methodology for genetic study. The callus population facilitated detection of TRD at multiple HS loci and dramatically shortened the process for mapping hybrid sterility genes.
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Affiliation(s)
- Yoshitaka Kanaoka
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Daichi Kuniyoshi
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Eri Inada
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Yohei Koide
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Yoshihiro Okamoto
- Laboratory of Plant Breeding, Rakuno Gakuen University, Bunkyodai-Midorimachi, Ebetsu, 069-8501 Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
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Ouyang Y, Zhang Q. The molecular and evolutionary basis of reproductive isolation in plants. J Genet Genomics 2018; 45:613-620. [PMID: 30459118 DOI: 10.1016/j.jgg.2018.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/19/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022]
Abstract
Reproductive isolation is defined as processes that prevent individuals of different populations from mating, survival or producing fertile offspring. Reproductive isolation is critical for driving speciation and maintaining species identity, which has been a fundamental concern in evolutionary biology. In plants, reproductive isolation can be divided into prezygotic and postzygotic reproductive barriers, according to its occurrence at different developmental stages. Postzygotic reproductive isolation caused by reduced fitness in hybrids is frequently observed in plants, which hinders gene flow between divergent populations and has substantial effects on genetic differentiation and speciation, and thus is a major obstacle for utilization of heterosis in hybrid crops. During the past decade, China has made tremendous progress in molecular and evolutionary basis of prezygotic and postzygotic reproductive barriers in plants. Present understandings in reproductive isolation especially with new data in the last several years well support three evolutionary genetic models, which represent a general mechanism underlying genomic differentiation and speciation. The updated understanding will offer new approaches for the development of wide-compatibility or neutral varieties, which facilitate breeding of hybrid rice as well as other hybrid crops.
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Affiliation(s)
- Yidan Ouyang
- 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
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Birchler JA. WITHDRAWN: An overview of rice genetics research in China. J Genet Genomics 2018. [DOI: 10.1016/j.jgg.2018.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Li J, Zhou J, Xu P, Deng X, Deng W, He M, Yang Y, Zhang Y, Tao D. Neutral alleles at hybrid sterility loci of Oryza glaberrima from AA genome relatives in Genus Oryza. BREEDING SCIENCE 2018; 68:343-351. [PMID: 30100801 PMCID: PMC6081293 DOI: 10.1270/jsbbs.18006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/11/2018] [Indexed: 05/10/2023]
Abstract
Hybrid sterility between Oryza sativa and O. glaberrima is a main reproduction barrier when transferring the favorable alleles from O. glaberrima to O. sativa and it happens due to allelic interaction at sterility loci. Neutral alleles at each locus have the potential to overcome the sterility between the two cultivated rice species. In this study, an O. sativa cultivar Dianjingyou 1 (DJY1) and its near-isogenic lines (NILs) harboring the single sterility allele S1-glab, S19-glab, S20-glab, S37-glab, S38-glab and S39-glab as the tested lines were crossed with O. glaberrima, O. rufipogon, O. nivara, O. glumaepatula, O. barthii, O. meridionalis and O. sativa so as to detect the neutral alleles of these loci. Pollen fertility was investigated in the paired F1s based on two seasons' result and genotypic segregation was also analyzed in some F2 populations to confirm the results of pollen fertility investigation. The neutral alleles of S38-n and S39-n were identified based upon the pollen fertility and genotypic segregation analysis for the first time. The neutral alleles of sterility loci detected from present report have the potential to know of the nature of interspecific hybrid sterility, and to overcome the interspecific hybrid sterility between O. sativa and O. glaberrima.
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Affiliation(s)
- Jing Li
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Jiawu Zhou
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Peng Xu
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Xianneng Deng
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Wei Deng
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Mingzhu He
- East China Normal University,
Shanghai 200241,
P. R. China
| | - Ying Yang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Yu Zhang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
- Corresponding author (e-mail: )
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Fishman L, Sweigart AL. When Two Rights Make a Wrong: The Evolutionary Genetics of Plant Hybrid Incompatibilities. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:707-731. [PMID: 29505737 DOI: 10.1146/annurev-arplant-042817-040113] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hybrids between flowering plant species often exhibit reduced fitness, including sterility and inviability. Such hybrid incompatibilities create barriers to genetic exchange that can promote reproductive isolation between diverging populations and, ultimately, speciation. Additionally, hybrid breakdown opens a window into hidden molecular and evolutionary processes occurring within species. Here, we review recent work on the mechanisms and origins of hybrid incompatibility in flowering plants, including both diverse genic interactions and chromosomal incompatibilities. Conflict and coevolution among and within plant genomes contributes to the evolution of some well-characterized genic incompatibilities, but duplication and drift also play important roles. Inversions, while contributing to speciation by suppressing recombination, rarely cause underdominant sterility. Translocations cause severe F1 sterility by disrupting meiosis in heterozygotes, making their fixation in outcrossing sister species a paradox. Evolutionary genomic analyses of both genic and chromosomal incompatibilities, in the context of population genetic theory, can explicitly test alternative scenarios for their origins.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA;
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
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Zhang Y, Zhou J, Li J, Yang Y, Xu P, Tao D. Mapping of S56(t) responsible for interspecific hybrid sterility between Oryza sativa and Oryza glumaepatula. BREEDING SCIENCE 2018; 68:242-247. [PMID: 29875608 PMCID: PMC5982189 DOI: 10.1270/jsbbs.17116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/13/2017] [Indexed: 05/25/2023]
Abstract
Oryza glumaepatula originates from South America continent and contains many valuable traits, such as tolerance to abiotic stress, high yield and good cooking qualities. However, hybrid sterility severely hindered the utilization of favorable genes of O. glumaepatula by interspecific hybridization. In order to further understand the nature of hybrid sterility between O. sativa and O. glumaepatula, a near isogenic line (NIL) was developed using a japonica variety Dianjingyou 1 as the recurrent parent and an accession of O. glumaepatula as the donor parent. A novel gene S56(t) for pollen sterility was mapped into the region between RM20797 and RM1093 on the short arm of chromosome 7, the physical distance between the two markers was about 469 kb. The genetic behavior of S56(t) followed one-locus allelic interaction model, the male gametes carrying the alleles of O. sativa in the heterozygotes were aborted completely. These results would help us clone S56(t) gene and understand the role of S56(t) in interspecific sterility.
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