全球籼稻种质资源库中水稻粒形和垩白的全基因组关联研究
Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions.
作者信息
Wang Nansheng, Chen Huguang, Qian Yingzhi, Liang Zhaojie, Zheng Guiqiang, Xiang Jun, Feng Ting, Li Min, Zeng Wei, Bao Yaling, Liu Erbao, Zhang Chaopu, Xu Jianlong, Shi Yingyao
机构信息
College of Agronomy, Anhui Agricultural University, Hefei 230036, China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
出版信息
Plants (Basel). 2023 Jan 17;12(3):419. doi: 10.3390/plants12030419.
Rice ( L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (, , , , , , , , , , , , , , , and ) were identified for haplotype analysis. Among these QTLs, two ( and ), were overlapped with and , respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction.
水稻（L.）的外观品质主要由粒形和垩白度决定，是水稻育种的一个重要目标。在本研究中，我们首先对137份籼稻品种进行了重测序，然后利用每个性状的最佳线性无偏预测（BLUP）值，对2,998,034个衍生单核苷酸多态性（SNP）进行全基因组关联研究（GWAS），以研究六个农艺性状。结果显示，195个SNP与这六个农艺性状存在显著关联。基于全基因组连锁不平衡（LD）块，在相关SNP位点上下游100 kb范围内检测到目标性状的候选基因。结果表明，鉴定出了六个与六个性状（，，，，，，，，，，，，，，，和）显著相关的数量性状位点（QTL）用于单倍型分析。在这些QTL中，两个（和）分别与和重叠，其余四个是新的QTL。这些候选基因通过单倍型块构建得到了进一步验证。
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