Chen Hongwei, Zhang Xue, Tian Shujun, Gao Hong, Sun Jian, Pang Xiu, Li Xiaowan, Li Quanying, Xie Wenxiao, Wang Lili, Liang Chengwei, Sui Guomin, Zheng Wenjing, Ma Zuobin
Rice Research Institute of Liaoning Province, Liaoning Academy of Agricultural Sciences, Shenyang, China.
Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
PeerJ. 2024 Dec 18;12:e18746. doi: 10.7717/peerj.18746. eCollection 2024.
Rice, a staple food for over half of the global population, exhibits significant diversity in grain shape characteristics, which impact not only appearance and milling quality but also grain weight and yield. Identifying genes and loci underlying these traits is crucial for improving rice breeding programs. Previous studies have identified multiple quantitative trait loci (QTLs) and genes regulating grain length, width, and length-width ratio; however, further investigation is necessary to elucidate their regulatory pathways and their practical application in crop improvement.
This study employed a genome-wide association study (GWAS) on 280 rice varieties from northern China to decipher the genetic basis of grain shape traits. Phenotyping included measurements of 11 grain-related traits, such as grain length, width, and area, along with their brown and white rice counterparts. High-density single nucleotide polymorphism (SNP) markers (33,579) were utilized for genotyping, and GWAS was performed using a mixed linear model (MLM) incorporating principal component analysis (PCA) and kinship (K) matrix to account for population structure and relatedness.
Our analysis detected 15 QTLs associated with the 11 grain shape traits, of which five major QTL clusters emerged as crucial. Candidate genes, including (), (, influencing , , and ), (, controlling , , , , and ), (, associated with , , , , and ), and (, linked to ), were identified based on functional annotations and haplotype analysis. These findings offer valuable insights into the genetic mechanisms underlying rice grain shape and suggest promising targets for marker-assisted selection to enhance rice quality and yield.
水稻是全球一半以上人口的主食，其粒形特征具有显著多样性，这不仅影响外观和碾磨品质，还影响粒重和产量。鉴定这些性状背后的基因和位点对于改进水稻育种计划至关重要。先前的研究已经鉴定出多个调控粒长、粒宽和长宽比的数量性状位点（QTL）和基因；然而，有必要进一步研究以阐明它们的调控途径及其在作物改良中的实际应用。
本研究对来自中国北方的280个水稻品种进行全基因组关联研究（GWAS），以解析粒形性状的遗传基础。表型分析包括测量11个与籽粒相关的性状，如粒长、粒宽和粒面积，以及它们的糙米和精米对应性状。利用高密度单核苷酸多态性（SNP）标记（33,579个）进行基因分型，并使用结合主成分分析（PCA）和亲缘关系（K）矩阵的混合线性模型（MLM）进行GWAS，以考虑群体结构和相关性。
我们的分析检测到与11个粒形性状相关的15个QTL，其中5个主要QTL簇至关重要。基于功能注释和单倍型分析，鉴定出候选基因，包括（）、（，影响，，和）、（，控制，，，，和）、（，与，，，，和相关）以及（，与相关）。这些发现为水稻粒形的遗传机制提供了有价值的见解，并为标记辅助选择以提高水稻品质和产量提出了有前景的目标。
