High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing
Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice qu...
| Main Authors: | , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-01-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1050882/full |
| _version_ | 1797955308987875328 |
|---|---|
| author | Su-Kui Jin Su-Kui Jin Su-Kui Jin Su-Kui Jin Su-Kui Jin Li-Na Xu Qing-Qing Yang Qing-Qing Yang Qing-Qing Yang Qing-Qing Yang Ming-Qiu Zhang Ming-Qiu Zhang Ming-Qiu Zhang Ming-Qiu Zhang Shui-Lian Wang Shui-Lian Wang Ruo-An Wang Tao Tao Tao Tao Tao Tao Tao Tao Lian-Min Hong Lian-Min Hong Lian-Min Hong Lian-Min Hong Qian-Qian Guo Qian-Qian Guo Qian-Qian Guo Qian-Qian Guo Shu-Wen Jia Tao Song Tao Song Yu-Jia Leng Yu-Jia Leng Yu-Jia Leng Yu-Jia Leng Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao |
| author_facet | Su-Kui Jin Su-Kui Jin Su-Kui Jin Su-Kui Jin Su-Kui Jin Li-Na Xu Qing-Qing Yang Qing-Qing Yang Qing-Qing Yang Qing-Qing Yang Ming-Qiu Zhang Ming-Qiu Zhang Ming-Qiu Zhang Ming-Qiu Zhang Shui-Lian Wang Shui-Lian Wang Ruo-An Wang Tao Tao Tao Tao Tao Tao Tao Tao Lian-Min Hong Lian-Min Hong Lian-Min Hong Lian-Min Hong Qian-Qian Guo Qian-Qian Guo Qian-Qian Guo Qian-Qian Guo Shu-Wen Jia Tao Song Tao Song Yu-Jia Leng Yu-Jia Leng Yu-Jia Leng Yu-Jia Leng Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao |
| author_sort | Su-Kui Jin |
| collection | DOAJ |
| description | Rice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits—the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness—of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%–61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality. |
| first_indexed | 2024-04-10T23:31:03Z |
| format | Article |
| id | doaj.art-c4d842b0dd5b4f97b9ef8950b722b420 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-10T23:31:03Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c4d842b0dd5b4f97b9ef8950b722b4202023-01-12T06:44:08ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-01-011310.3389/fpls.2022.10508821050882High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencingSu-Kui Jin0Su-Kui Jin1Su-Kui Jin2Su-Kui Jin3Su-Kui Jin4Li-Na Xu5Qing-Qing Yang6Qing-Qing Yang7Qing-Qing Yang8Qing-Qing Yang9Ming-Qiu Zhang10Ming-Qiu Zhang11Ming-Qiu Zhang12Ming-Qiu Zhang13Shui-Lian Wang14Shui-Lian Wang15Ruo-An Wang16Tao Tao17Tao Tao18Tao Tao19Tao Tao20Lian-Min Hong21Lian-Min Hong22Lian-Min Hong23Lian-Min Hong24Qian-Qian Guo25Qian-Qian Guo26Qian-Qian Guo27Qian-Qian Guo28Shu-Wen Jia29Tao Song30Tao Song31Yu-Jia Leng32Yu-Jia Leng33Yu-Jia Leng34Yu-Jia Leng35Xiu-Ling Cai36Xiu-Ling Cai37Xiu-Ling Cai38Xiu-Ling Cai39Xiu-Ling Cai40Ji-Ping Gao41Ji-Ping Gao42Ji-Ping Gao43Ji-Ping Gao44Ji-Ping Gao45Ji-Ping Gao46JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaShanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaShanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaJiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, ChinaJiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, ChinaNational Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences (CAS) Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, ChinaInnovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, ChinaRice is a major food crop that sustains approximately half of the world population. Recent worldwide improvements in the standard of living have increased the demand for high-quality rice. Accurate identification of quantitative trait loci (QTLs) for rice grain quality traits will facilitate rice quality breeding and improvement. In the present study, we performed high-resolution QTL mapping for rice grain quality traits using a genotyping-by-sequencing approach. An F2 population derived from a cross between an elite japonica variety, Koshihikari, and an indica variety, Nona Bokra, was used to construct a high-density genetic map. A total of 3,830 single nucleotide polymorphism markers were mapped to 12 linkage groups spanning a total length of 2,456.4 cM, with an average genetic distance of 0.82 cM. Seven grain quality traits—the percentage of whole grain, percentage of head rice, percentage of area of head rice, transparency, percentage of chalky rice, percentage of chalkiness area, and degree of chalkiness—of the F2 population were investigated. In total, 15 QTLs with logarithm of the odds (LOD) scores >4 were identified, which mapped to chromosomes 6, 7, and 9. These loci include four QTLs for transparency, four for percentage of chalky rice, four for percentage of chalkiness area, and three for degree of chalkiness, accounting for 0.01%–61.64% of the total phenotypic variation. Of these QTLs, only one overlapped with previously reported QTLs, and the others were novel. By comparing the major QTL regions in the rice genome, several key candidate genes reported to play crucial roles in grain quality traits were identified. These findings will expedite the fine mapping of these QTLs and QTL pyramiding, which will facilitate the genetic improvement of rice grain quality.https://www.frontiersin.org/articles/10.3389/fpls.2022.1050882/fullricegrain qualityquantitative trait locusgenotyping by sequencinghigh-density genetic map |
| spellingShingle | Su-Kui Jin Su-Kui Jin Su-Kui Jin Su-Kui Jin Su-Kui Jin Li-Na Xu Qing-Qing Yang Qing-Qing Yang Qing-Qing Yang Qing-Qing Yang Ming-Qiu Zhang Ming-Qiu Zhang Ming-Qiu Zhang Ming-Qiu Zhang Shui-Lian Wang Shui-Lian Wang Ruo-An Wang Tao Tao Tao Tao Tao Tao Tao Tao Lian-Min Hong Lian-Min Hong Lian-Min Hong Lian-Min Hong Qian-Qian Guo Qian-Qian Guo Qian-Qian Guo Qian-Qian Guo Shu-Wen Jia Tao Song Tao Song Yu-Jia Leng Yu-Jia Leng Yu-Jia Leng Yu-Jia Leng Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Xiu-Ling Cai Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao Ji-Ping Gao High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing Frontiers in Plant Science rice grain quality quantitative trait locus genotyping by sequencing high-density genetic map |
| title | High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing |
| title_full | High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing |
| title_fullStr | High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing |
| title_full_unstemmed | High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing |
| title_short | High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing |
| title_sort | high resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing |
| topic | rice grain quality quantitative trait locus genotyping by sequencing high-density genetic map |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1050882/full |
| work_keys_str_mv | AT sukuijin highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT sukuijin highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT sukuijin highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT sukuijin highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT sukuijin highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT linaxu highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qingqingyang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qingqingyang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qingqingyang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qingqingyang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT mingqiuzhang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT mingqiuzhang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT mingqiuzhang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT mingqiuzhang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT shuilianwang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT shuilianwang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT ruoanwang highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT taotao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT taotao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT taotao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT taotao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT lianminhong highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT lianminhong highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT lianminhong highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT lianminhong highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qianqianguo highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qianqianguo highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qianqianguo highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT qianqianguo highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT shuwenjia highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT taosong highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT taosong highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT yujialeng highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT yujialeng highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT yujialeng highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT yujialeng highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT xiulingcai highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT xiulingcai highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT xiulingcai highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT xiulingcai highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT xiulingcai highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT jipinggao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT jipinggao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT jipinggao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT jipinggao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT jipinggao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing AT jipinggao highresolutionquantitativetraitlocusmappingforricegrainqualitytraitsusinggenotypingbysequencing |