Identifying genes for resistant starch, slowly digestible starch, and rapidly digestible starch in rice using genome-wid
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Genes & Genomics https://doi.org/10.1007/s13258-020-00981-1
RESEARCH ARTICLE
Identifying genes for resistant starch, slowly digestible starch, and rapidly digestible starch in rice using genome-wide association studies Ning Zhang1 · Maike Wang1 · Ji Fu1 · Yi Shen1 · Yi Ding1 · Dianxing Wu1 · Xiaoli Shu1 · Wenjian Song1,2 Received: 21 April 2020 / Accepted: 29 July 2020 © The Genetics Society of Korea 2020
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. Keywords Rice · Resistant starch · Slowly digestible starch · GWAS 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
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13258-020-00981-1) contains supplementary material, which is available to authorized users. * Xiaoli Shu [email protected] * Wenjian Song [email protected] 1
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
2
With the rising economic development and crop yield, human lifestyle and dietary preferences have been changing, accompanied by high carbohydrate consumption, which is thought to be a major cause for the rising prevalence of obesity, type-2 diabetes and colon diseases (Chen et al. 2011; Zhan
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