Frontiers in Plant Science (Jan 2023)
High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing
- 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
Affiliations
- Su-Kui Jin
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Su-Kui Jin
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Su-Kui Jin
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Su-Kui Jin
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Su-Kui Jin
- National 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, China
- Li-Na Xu
- National 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, China
- Qing-Qing Yang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Qing-Qing Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Qing-Qing Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Qing-Qing Yang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Ming-Qiu Zhang
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Ming-Qiu Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Ming-Qiu Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Ming-Qiu Zhang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Shui-Lian Wang
- National 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, China
- Shui-Lian Wang
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
- Ruo-An Wang
- National 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, China
- Tao Tao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Tao Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Tao Tao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Tao Tao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Lian-Min Hong
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Lian-Min Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Lian-Min Hong
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Lian-Min Hong
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Qian-Qian Guo
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Qian-Qian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Qian-Qian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Qian-Qian Guo
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Shu-Wen Jia
- National 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, China
- Tao Song
- National 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, China
- Tao Song
- Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
- Yu-Jia Leng
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Yu-Jia Leng
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Yu-Jia Leng
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Yu-Jia Leng
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Xiu-Ling Cai
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Xiu-Ling Cai
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Xiu-Ling Cai
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Xiu-Ling Cai
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Xiu-Ling Cai
- National 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, China
- Ji-Ping Gao
- JiangsuKey Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Ji-Ping Gao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Ji-Ping Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou, China
- Ji-Ping Gao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Ji-Ping Gao
- National 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, China
- Ji-Ping Gao
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- DOI
- https://doi.org/10.3389/fpls.2022.1050882
- Journal volume & issue
-
Vol. 13
Abstract
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.
Keywords
