Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice |
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| Institution: | 1. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China;2. University of Chinese Academy of Sciences, Beijing 100049, China;3. Rice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;1. Department of Pediatrics, Guangzhou Women and Children''s Medical Center, Guangzhou Medical University, Guangzhou, China;2. Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 101300, China;3. University of Chinese Academy of Sciences, Beijing, 100049, China;4. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China;1. Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;2. Department of Genetics, SOKENDAI (the Graduate University for Advanced Science), Mishima, Shizuoka 411-8540, Japan;3. STAY GREEN Co., Ltd., Kisarazu, Chiba 292-0818, Japan;4. Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan;5. Plant Breeding Laboratory, Division of Genetics and Plant Breeding, Department of Applied Genetics and Pest Management, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan;1. National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China;2. College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China;3. National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;4. National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China |
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| Abstract: | The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice (Oryza sativa L.). In this study, we focus on two types of genomic footprints, introgression and differentiation, in a population of more than 1200 Chinese rice accessions. We found that a Xian/indica and a temperate Geng/japonica accession respectively contained an average of 19.3-Mb and 6.8-Mb alien introgressed chromosomal segments, of which many contained functional sequence variants, quantitative trait loci, or genes controlling flowering, grain, and resistance traits. Notably, we found most introgressions, including the known heterotic loci Hd3a and TAC1, were distributed differentially between the female and male parents of three-line indica hybrid rice, indicating their potential contribution to heterosis. We also found many differentiated regions between subgroups within a subpopulation contained agronomically important loci, such as DTH7, Hd1 for heading date, and qCT7 for cold tolerance, providing new candidates for studying local adaptation or heterosis. Tracing these footprints allows us to better understand the genetic exchange or differentiation underlying agronomic traits in modern Chinese rice cultivars. These findings also provide potential targets for rice genetic research and breeding. |
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| Keywords: | Rice Introgression Differentiation Genome-wide association study Adaptation Heterosis |
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