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Identifying genes for resistant starch, slowly digestible starch, and rapidly digestible starch in rice using genome-wide association studies

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Abstract

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.

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Abbreviations

AAC:

Apparent amylose content

GWAS:

Genome-wide association study

QTL:

Quantitative trait loci

RDS:

Rapidly digestible starch

RS:

Resistant starch

SDS:

Slowly digestible starch

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Acknowledgements

We appreciate the financial support from the Chinese Ministry of Agriculture (2016ZX08001006) and National Science Foundation of China (No. 31571628). We also appreciate the sharing of SNP data from Professor Chengcai Chu.

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Correspondence to Xiaoli Shu or Wenjian Song.

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Zhang, N., Wang, M., Fu, J. et al. Identifying genes for resistant starch, slowly digestible starch, and rapidly digestible starch in rice using genome-wide association studies. Genes Genom 42, 1227–1238 (2020). https://doi.org/10.1007/s13258-020-00981-1

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