Department of Plant Science, University of Manitoba, 222 Agriculture Building, Winnipeg, MB, R3T 2N2, Canada.
Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, R3C 3G8, Canada.
Theor Appl Genet. 2023 Aug 29;136(9):202. doi: 10.1007/s00122-023-04449-0.
Genome-wide association study of diverse barley genotypes identified loci, single nucleotide polymorphisms and candidate genes that control seed dormancy and therefore enhance resistance to preharvest sprouting. Preharvest sprouting (PHS) causes significant yield and quality loss in barley and it is strongly associated with the level of seed dormancy. This study performed genome-wide association study using a collection of 255 diverse barley genotypes grown over four environments to identify loci controlling dormancy/PHS. Our phenotypic analysis revealed substantial variation in germination index/dormancy levels among the barley genotypes. Marker-trait association and linkage disequilibrium (LD) decay analyses identified 16 single nucleotide polymorphisms (SNPs) and two QTLs associated with dormancy/PHS, respectively, on chromosome 3H and 5H explaining 6.9% to 11.1% of the phenotypic variation. QTL.5H consist of 14 SNPs of which 12 SNPs satisfy the FDR threshold of α = 0.05, and it may represent the SD2 locus. The QTL on 3H consists of one SNP that doesn't satisfy FDR (α = 0.05). Genes harbouring the significant SNPs were analyzed for their expression pattern in the seeds of selected dormant and non-dormant genotypes. Of these genes, HvRCD1, HvPSRP1 and HvF3H exhibited differential expression between the dormant and non-dormant seed samples, suggesting their role in controlling seed dormancy/PHS. Three SNPs located within the differentially expressed genes residing in QTL.5H explained considerable phenotypic variation (≥ 8.6%), suggesting their importance in regulating PHS resistance. Analysis of the SNP marker data in QTL.5H identified a haplotype for PHS resistance. Overall, the study identified loci, SNPs and candidate genes that control dormancy and therefore play important roles in enhancing PHS resistance in barley through marker-assisted breeding.
全基因组关联研究鉴定了控制种子休眠和抗穗发芽的位点、单核苷酸多态性和候选基因
穗发芽（PHS）会导致大麦严重减产和品质下降，与种子休眠水平密切相关。本研究利用 255 个不同大麦基因型在四个环境下种植的群体进行全基因组关联研究，以鉴定控制休眠/PHS 的基因座。我们的表型分析揭示了大麦基因型之间发芽指数/休眠水平的显著差异。标记-性状关联和连锁不平衡（LD）衰减分析分别在第 3H 和 5H 染色体上鉴定到与休眠/PHS 相关的 16 个单核苷酸多态性（SNP）和 2 个 QTL，分别解释了 6.9%至 11.1%的表型变异。QTL.5H 包含 14 个 SNP，其中 12 个 SNP 满足 FDR 阈值 α=0.05，可能代表 SD2 基因座。第 3H 染色体上的 QTL 包含一个不满足 FDR（α=0.05）的 SNP。对携带显著 SNP 的基因进行分析，以研究其在休眠和非休眠基因型种子中的表达模式。其中，HvRCD1、HvPSRP1 和 HvF3H 在休眠和非休眠种子样本之间表现出差异表达，表明它们在控制种子休眠/PHS 中的作用。位于 QTL.5H 中差异表达基因内的三个 SNP 解释了相当大的表型变异（≥8.6%），表明它们在调节 PHS 抗性中的重要性。在 QTL.5H 中对 SNP 标记数据的分析确定了一个与 PHS 抗性相关的单倍型。总的来说，该研究鉴定了控制休眠的基因座、SNP 和候选基因，它们通过标记辅助选择在提高大麦的 PHS 抗性方面发挥着重要作用。
