State Key Laboratory of Rice Biology and Key Lab of the Ministry of Agriculture for Nuclear Agricultural Sciences, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, P.R. China.
Agricultural Technology Extension Center, Zhejiang University, Hangzhou, 310029, P.R. China.
Genes Genomics. 2020 Nov;42(11):1227-1238. doi: 10.1007/s13258-020-00981-1. Epub 2020 Sep 8.
The digestibility of starch is important for the nutritive value of staple food. Although several genes are responsible for resistant starch (RS) and slowly digestible starch (SDS), gaps persist concerning the molecular basis of RS and SDS formation due to the complex genetic mechanisms of starch digestibility.
The objective of this study was to identify new genes for starch digestibility in rice and interprete the genetic mechanisms of RS and SDS by GWAS.
Genome-wide association studies were conducted by associating the RS and SDS phenotypes of 104 re-sequenced rice lines to an SNP dataset of 2,288,867 sites using a compressed mixed linear model. Candidate genes were identified according to the position of the SNPs based on data from the MSU Rice Genome Annotation Project.
Seven quantitative trait loci (QTLs) were detected to be associated with the RS content, among which the SNP 6 m1765761 was located on Waxy. Starch branching enzymes IIa (BEIIa) close to QTL qRS-I4 was detected and further identified as a specific candidate gene for RS in INDICA. Two QTLs were associated with SDS, and the LOC_Os09g09360 encoding lipase was identified as a causal gene for SDS.
GWAS is a valid strategy to genetically dissect the formation of starch digestion properties in rice. RS formation in grains is dependent on the rice type; lipid might also contribute to starch digestibility and should be an alternative factor to improve rice starch digestibility.
淀粉的消化率对于主食的营养价值很重要。尽管有几个基因负责抗性淀粉（RS）和缓慢消化淀粉（SDS），但由于淀粉消化率的复杂遗传机制，RS 和 SDS 形成的分子基础仍存在差距。
本研究旨在鉴定水稻中淀粉消化率的新基因，并通过 GWAS 解释 RS 和 SDS 的遗传机制。
通过将 104 个重测序水稻系的 RS 和 SDS 表型与 2,288,867 个位点的 SNP 数据集相关联，使用压缩混合线性模型对全基因组关联研究进行了分析。根据 SNP 基于 MSU 水稻基因组注释项目的数据，根据 SNP 的位置确定候选基因。
检测到 7 个与 RS 含量相关的数量性状位点（QTL），其中 SNP 6 m1765761 位于蜡质基因上。在 QTL qRS-I4 附近检测到淀粉分支酶 IIa（BEIIa），并进一步鉴定为 INDICA 中 RS 的特定候选基因。与 SDS 相关的 2 个 QTL，编码脂肪酶的 LOC_Os09g09360 被鉴定为 SDS 的候选基因。
GWAS 是遗传剖析水稻淀粉消化特性形成的有效策略。谷物中 RS 的形成依赖于水稻类型；脂质也可能有助于淀粉消化率，应该是提高水稻淀粉消化率的替代因素。
