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Multi-Environmental Genetic Analysis of Grain Size Traits Based on Chromosome Segment Substitution Line in Rice (Oryza sativa L.)

Yujia Leng1,#, Shuilian Wang1,2,3,#, Ruoan Wang2,#, Tao Tao1, Shuwen Jia1,2, Tao Song2,3, Lina Xu1,2, Xiuling Cai1,2, Sukui Jin1,2,*, Jiping Gao1,2,4,*
1 Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
2 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
3 University of Chinese Academy of Sciences, Beijing, 100049, China
4 Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
* Corresponding Authors: Jiping Gao. Email: ; Sukui Jin. Email:
# These authors contributed equally to this work
(This article belongs to this Special Issue: High-Yield Rice Physiology & Genetics)

Phyton-International Journal of Experimental Botany 2022, 91(5), 943-958.

Received 30 September 2021; Accepted 10 November 2021; Issue published 24 January 2022


Grain size traits are critical agronomic traits which directly determine grain yield, but the genetic bases of these traits are still not well understood. In this study, a total of 154 chromosome segment substitution lines (CSSLs) population derived from a cross between a japonica variety Koshihikari and an indica variety Nona Bokra was used to investigate grain length (GL), grain width (GW), length-width ratio (LWR), grain perimeter (GP), grain area (GA), and thousand grain weight (TGW) under four environments. QTL mapping analysis of six grain size traits was performed by QTL IciMapping 4.2 with an inclusive composite interval mapping (ICIM) model. A total of 64 QTLs were identified for these traits, which mapped to chromosomes 1, 2, 3, 4, 6, 7, 8, 10, 11, and 12 and accounted for 1.6%–27.1% of the total phenotypic variations. Among these QTLs, thirty-six loci were novel and seven QTLs were identified under four environments. One locus containing the known grain size gene, qGL3/GL3.1/OsPPKL1, also have been found. Moreover, five pairs of digenic epistatic interactions were identified except for GL and GP. These findings will facilitate fine mapping of the candidate gene and QTL pyramiding to genetically improve grain yield in rice.


Rice; grain size; quantitative trait loci; epistatic; chromosome segment substitution lines

Cite This Article

Leng, Y., Wang, S., Wang, R., Tao, T., Jia, S. et al. (2022). Multi-Environmental Genetic Analysis of Grain Size Traits Based on Chromosome Segment Substitution Line in Rice (Oryza sativa L.). Phyton-International Journal of Experimental Botany, 91(5), 943–958.

This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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