Background

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.

Objectives

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.

Methods

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.

Results

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.

Conclusions

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.

中文翻译：

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使用全基因组关联研究鉴定水稻中抗性淀粉、缓慢消化淀粉和快速消化淀粉的基因。

背景

淀粉的消化率对主食的营养价值很重要。尽管有几个基因负责抗性淀粉 (RS) 和慢消化淀粉 (SDS)，但由于淀粉消化率的复杂遗传机制，关于 RS 和 SDS 形成的分子基础仍然存在差距。

目标

本研究的目的是鉴定水稻淀粉消化率的新基因，并通过 GWAS 解释 RS 和 SDS 的遗传机制。

方法

通过使用压缩混合线性模型将 104 个重新测序的水稻品系的 RS 和 SDS 表型与 2,288,867 个位点的 SNP 数据集相关联，进行全基因组关联研究。根据 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。

结果

检测到 7 个数量性状位点 (QTL) 与 RS 含量相关，其中 SNP 6 m1765761 位于Waxy 上。检测到接近QTL qRS-I4的淀粉分支酶IIa ( BEIIa )，并进一步鉴定为INDICA中RS的特异性候选基因。两个 QTL 与 SDS 相关，编码脂肪酶的LOC_Os09g09360被鉴定为 SDS 的致病基因。

结论

GWAS 是一种有效的策略，可以对水稻中淀粉消化特性的形成进行遗传剖析。谷物中 RS 的形成取决于水稻类型；脂质也可能有助于淀粉消化率，应该是提高大米淀粉消化率的替代因素。