利用全基因组关联分析挖掘粳稻直链淀粉含量调控基因

Identification of regulation genes influencing amylose content in japonica rice using genome-wide association analysis

直链淀粉含量是评价稻米蒸煮食味品质关键指标,挖掘控制该性状QTLs/基因对于改良稻米品质具有重要意义。研究利用295份粳稻种质组成的自然群体为试验材料,测定2019年和2020年稻米直链淀粉含量,结合重测序得到788 396个高质量SNP,利用Tassel 5.0软件混合线性模型(MLM,Q+K)作全基因组关联分析。结果表明,两年共检测到12个与稻米直链淀粉含量相关QTL,分布在水稻第3、4、11和12染色体上,贡献率范围为8.78%~11.62%,其中qAAC4-2和qAAC12-2在两年中重复检测到。进一步针对这两个QTL区间内所有基因作单倍型分析,结合基因注释和前人研究结果,推测LOC_Os04g33640为影响稻米直链淀粉含量新候选基因。

Amylose content is a key index to evaluate the cooking and eating quality in rice,and it is important to explore the QTLs/genes controlling this trait for improving rice quality.In this study,295 japonica rice germplasms were used as experimental materials to determine the amylose content in2019 and 2020.Combining with 788396 high-quality SNPs obtained by resequencing,genome-wide association analysis(GWAS)was performed by mixed linear model(MLM)of TASSEL 5.0 software.The results showed that a total of 12 QTLs associated with amylose content were detected on chromosome 3,4,11 and 12 in two consecutive years,and the R^(2) ranged from 8.78%to 11.62%,among which,qAAC4-2 and qAAC12-2 were detected repeatedly in two years.Haplotype analysis of all the genes in the two QTL intervals was further performed.Combining with genes annotation and previous studies,LOC_Os04g33640 was speculated to be a new candidate gene affecting amylose content in rice.