背景:作为光周期敏感和自花授粉的物种,生育期性状对大豆的适应性和产量起着重要作用。为了研究大豆生长期的遗传结构,我们使用一组278个大豆种质和34,710个单核苷酸多态性(SNPs)进行了全基因组关联研究(GWAS),这些多态性的次要等位基因频率(MAF)高于0.04,通过特异性位点扩增片段测序(SLAF-seq)检测到,平均测序深度为6.14倍.GWAS是通过压缩混合线性模型(CMLM)进行的,该模型涉及相对亲属关系和种群结构。
结果:GWAS显示,37个显著的SNP峰与大豆开花时间或其他生育期相关性状相关,包括盛开,开始pod,满舱,开始的种子,在-log10(P)>3.75或-log10(P)>4.44的两个或两个以上环境中,全种子分布在14条染色体上,包括染色体1、2、3、5、6、9、11、12、13、14、15、17、18、19。14个SNP是新基因座,23个SNP位于已知的QTL或75kb附近。五个候选基因(Glyma.05G101800,Glyma.11G140100,Glyma.11G142900,Glyma.19G099700,Glyma.19G100900)位于四个重要SNP(Gm5_27111367,Gm11_10629613,Gm11_10950924)的每一侧的90kb基因组区域中。基于AT880.1的G这些基因编码FRI(FRIGIDA),PUB13(装置U型盒13),MYB59康斯坦斯,FUS3和FUS3蛋白分别可能在控制大豆生育期中起重要作用。
结论:本研究确定了与大豆生长期性状相关的推测SNP标记,可用于大豆生育期性状的标记辅助选择。此外,预测了大豆开花时间调控可能的候选基因。
BACKGROUND: As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association
study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure.
RESULTS: GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods.
CONCLUSIONS: This
study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.