大豆地方种质资源鲜籽粒可溶性糖含量的全基因组关联分析

Genome Wide Association Analysis of Soluble Sugar Content in Fresh Seeds of Soybean Landraces

【目的】可溶性糖含量是鲜食大豆重要的品质性状之一,研究大豆鲜籽粒可溶性糖含量的遗传变异,深入解析可溶性糖含量的遗传机制,为鲜食大豆种质创新及品质育种提供依据。【方法】利用来自东北大豆生态区、北方大豆生态区、黄淮海大豆生态区和南方大豆生态区的133份大豆地方种质,在2021年连江春季、福清春季和秋季3个环境下对鲜籽粒可溶性糖含量进行表型测定,结合82187个高质量SNP标记,基于混合线性模型MLM(Q+K)对可溶性糖含量进行全基因组关联分析,挖掘可溶性糖含量显著相关的SNP位点,并以显著SNP位点为中心,两端各扩展119.07 kb连锁不平衡衰减距离为候选区间,根据候选区间内基因的注释和组织表达信息预测候选基因。【结果】3个环境下,鲜籽粒可溶性糖含量的变异范围为3.37—33.84 mg·g^(-1),遗传变异系数为24.59%—32.69%,可溶性糖含量遗传率为68.14%。通过全基因组关联分析,连江春季、福清春季和秋季3个环境下分别检测到与鲜籽粒可溶性糖含量显著关联的SNP有6、8和22个,表型变异解释率为12.43%—29.27%,以表型变异解释率较高的9个显著SNP位点所在的候选区间进行搜索,共获得86个基因,结合基因注释和组织表达信息,进一步筛选到9个候选基因,主要涉及转录因子、糖蛋白家族和糖类合成转运等生物学过程。其中,Glyma.01g016500、Glyma.13g042100、Glyma.16g131800和Glyma.16g155300在大豆种子及荚中表达水平较高,可作为大豆鲜籽粒可溶性糖的最具潜力候选基因。【结论】通过全基因组关联分析,检测到36个与鲜籽粒可溶性糖含量显著关联的SNP,进一步筛选出9个候选基因可能参与大豆鲜籽粒可溶性糖含量的调控,其中,Glyma.01g016500、Glyma.13g042100、Glyma.16g131800和Glyma.16g155300可作为调控大豆鲜籽粒可溶性糖含量的关键目标基因。

【Objective】Soluble sugar content is one of the important quality traits of vegetable soybean.The genetic variation and genetic mechanism of soluble sugar content in fresh soybean seeds were studied to provide a basis for germplasm innovation and quality breeding of vegetable soybean.【Method】Using 133 soybean landraces from the Northeast region,the North region,the Huanghuaihai region and the South region,the soluble sugar content of fresh seeds was determined in the three environments of Lianjiang in spring,Fuqing in spring and autumn,in 2021.In combination with 82187 high-quality SNP markers,the whole genome association analysis of soluble sugar content was conducted based on the mixed linear model MLM(Q+K),and the SNP loci with significantly related to soluble sugar content were identified.The candidate intervals were selected by the significant SNP loci and the extension of 119.07 kb linkage disequilibrium decay distance at both ends.The candidate genes were predicted according to the annotation and tissue expression information of the genes in the candidate intervals.【Result】The variation range of soluble sugar content in fresh seeds under three environments was 3.37-33.84 mg·g^(-1),the genetic variation coefficient was 24.59%-32.69%,and the heritability of soluble sugar content was 68.14%.6,8 and 22 SNPs were significantly associated with the soluble sugar content of fresh seeds were detected in Lianjiang in spring,Fuqing in spring and autumn,respectively,and phenotypic variation was 12.43%-29.27%.A total of 86 genes were obtained in the candidate regions of 9 significant SNP loci with higher interpretation rate of phenotypic variation,and 9 candidate genes were further screened by gene annotation and tissue expression information.These candidate genes are mainly involved in biological processes such as transcription factors,glycoprotein families and carbohydrate synthesis and transport.Among them,Glyma.01g016500,Glyma.13g042100,Glyma.16g131800 and Glyma.16g155300 were more highly expressed in soybean seeds and pods,which can be used as the most potential candidate genes for soluble sugar in fresh soybean seeds.【Conclusion】Through genome-wide association analysis,36 SNPs significantly associated with soluble sugar content in fresh seeds were detected,and 9 candidate genes were further screened out,which may be involved in the regulation of soluble sugar content in fresh soybean seeds.Among them,Glyma.01g016500,Glyma.13g042100,Glyma.16g131800 and Glyma.16g155300 can be the key candidate genes for regulating soluble sugar content in fresh soybean seeds.