基于BSA-seq发掘水稻抽穗期相关QTLs及候选基因

Discovering of QTLs and Candidate Genes Related to Rice Heading Period Traits Based on BSA-seq

抽穗期作为水稻重要的性状之一,不仅与水稻生育时期密切相关,还与水稻产量、品质和抗逆性密切相关,决定了水稻品种的种植地区和季节适应性,因此,定位水稻抽穗期相关基因在水稻生产中有着重要的作用。利用HQ20和金23B及其杂交构建的F4群体为试验材料,根据群体中水稻抽穗期划分3个等级:抽穗期早、抽穗期适中、大青棵(不抽穗),并构建早、中、青3个混池,采用BSA-seq(bulked-segregant analysis sequencing)方法挖掘水稻抽穗期基因。结果表明,BSA-seq结果与参考基因组比对率在94%以上,4×基因组覆盖率在80%以上;基于此,在置信度为0.95时,经SNP-index算法获得位于4条染色体(6、7、8和9号)的17个SNPs与Indels一致的关联区间,进一步分析区域内的候选基因,发现61个基因存在非同义突变。GO与KEGG富集分析表明,与水稻抽穗期密切相关的途径有UDP-糖基转移酶活性、细胞周期G2/M期转变的正向调控和植物激素信号转导等。结合3K水稻数据库中的单倍型分析与已公布的表达量数据,挖掘出3个抽穗期关键候选基因:LOC_Os07g22720、LOC_Os07g23740、LOC_Os08g07200。以上结果为开展水稻抽穗期性状遗传改良以及遗传基础解析奠定了基础。

As one of the important traits of rice,rice heading date is closely related not only to the rice growth period but also to rice yield,quality and stress resistance,which determines the planting area and seasonal adaptability of rice varieties.Therefore,the location of rice heading date related genes plays an important role in rice production.In this study,HQ20,Jin 23B and their F4 population constructed were used as the materials.According to the heading stage of the rice in the population,it was divided into 3 levels including early,middle and green plant(not heading),and 3 mixed pools of early,middle and green were constructed.The bulked-segregant analysis sequencing(BSA-seq)method was used to discover rice heading period genes.The results showed that the comparison rate between BSA-seq results and the reference genome was over 94%,and the 4×genome coverage rate was over 80%.Based on this,when the confidence level was 0.95,by SNP-index algorithm 17 SNPs located on 4 chromosomes(6,7,8 and 9)were obtained which had consistent association intervals with indel.Further analysis of candidate genes in the region found that 61 genes had non-synonymous mutations.GO and KEGG enrichment analysis showed that pathways closely related to rice heading stage included UDP-glycosyltransferase activity,positive regulation of cell cycle G2/M phase transition,and phytohormone signal transduction.Finally,combining haplotype analysis in the 3K rice database and published expression data,3 key candidate genes for heading stage were discovered including LOC_Os07g22720,LOC_Os07g23740 and LOC_Os08g07200.The above results laid the foundation for genetic improvement of rice heading period traits and analysis of genetic basis.