Bai Shaoxing, Hong Jun, Li Ling, Su Su, Li Zhikang, Wang Wensheng, Zhang Fengli, Liang Wanqi, Zhang Dabing
Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
Rice (N Y). 2021 Sep 6;14(1):77. doi: 10.1186/s12284-021-00520-w.
Panicle architecture is one of the major factors influencing productivity of rice crops. The regulatory mechanisms underlying this complex trait are still unclear and genetic resources for rice breeders to improve panicle architecture are limited. Here, we have performed a genome-wide association study (GWAS) to analyze and identify genetic determinants underlying three panicle architecture traits. A population of 340 rice accessions from the 3000 Rice Genomes Project was phenotyped for panicle length, primary panicle number and secondary branch number over two years; GWAS was performed across the whole panel, and also across the japonica and indica sub-panels. A total of 153 quantitative trait loci (QTLs) were detected, of which 5 were associated with multiple traits, 8 were unique to either indica or japonica sub-panels, while 37 QTLs were stable across both years. Using haplotype and expression analysis, we reveal that genetic variations in the OsSPL18 promoter significantly affect gene expression and correlate with panicle length phenotypes. Three new candidate genes with putative roles in determining panicle length were also identified. Haplotype analysis of OsGRRP and LOC_Os03g03480 revealed high association with panicle length variation. Gene expression of DSM2, involved in abscisic acid biosynthesis, was up-regulated in long panicle accessions. Our results provide valuable information and resources for further unravelling the genetic basis determining rice panicle architecture. Identified candidate genes and molecular markers can be used in marker-assisted selection to improve rice panicle architecture through molecular breeding.
穗型结构是影响水稻产量的主要因素之一。这一复杂性状背后的调控机制仍不清楚，可供水稻育种者改良穗型结构的遗传资源也很有限。在此，我们开展了一项全基因组关联研究（GWAS），以分析和鉴定三种穗型结构性状背后的遗传决定因素。对来自“3000份水稻基因组计划”的340份水稻种质资源进行了为期两年的穗长、一次枝梗数和二次枝梗数表型分析；在整个群体以及粳稻和籼稻亚群体中分别进行了GWAS。共检测到153个数量性状位点（QTL），其中5个与多个性状相关，8个是粳稻或籼稻亚群体特有的，37个QTL在两年间都很稳定。通过单倍型和表达分析，我们发现OsSPL18启动子区的遗传变异显著影响基因表达，并与穗长表型相关。还鉴定出了三个在决定穗长方面可能起作用的新候选基因。对OsGRRP和LOC_Os03g03480的单倍型分析表明，它们与穗长变异高度相关。参与脱落酸生物合成的DSM2的基因表达在长穗种质中上调。我们的研究结果为进一步阐明决定水稻穗型结构的遗传基础提供了有价值的信息和资源。鉴定出的候选基因和分子标记可用于分子标记辅助选择，通过分子育种改良水稻穗型结构。
