UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
BMC Plant Biol. 2021 Jan 21;21(1):53. doi: 10.1186/s12870-021-02824-x.
Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated.
Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines.
The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.
小麦收获前发芽（PHS）会严重损害籽粒产量和质量。对 PHS 的抗性是由位于 21 条小麦染色体上的许多基因控制的数量性状。本研究利用先前开发的几套近等基因系（NILs）针对一个控制 PHS 抗性的大效应数量性状位点（QTL）QPhs.ccsu-3A.1 进行了研究。通过 RNA 测序，对具有高度表型差异的两对 NILs在授粉后 15、25 和 35 天（DAP）发育种子的转录组谱进行了研究，以鉴定该 QTL 下的候选基因，并阐明基因对 PHS 抗性的影响。在每个 DAP，研究了等位系之间差异表达的基因（DEGs）。
等位系之间关键 DEGs 的基因本体论和 KEGG 途径富集分析表明，有六个候选基因位于 QPhs.ccsu-3A.1 下，负责小麦的 PHS 抗性。通过定量 RT-PCR 进一步验证了候选基因的表达。在目标 QTL 区间内，包括五个单核苷酸多态性（SNP）和 11 个插入缺失在内的 16 个遗传变异在抗性和敏感等位系之间表现出一致的多态性。
该目标 QTL 被确认为含有与激素信号通路相关的核心基因，可作为小麦 PHS 抗性的关键基因组区域，用于辅助选择。本研究中检测到的候选基因和 SNP/indel 标记是了解 PHS 抗性机制和辅助该性状标记选择的宝贵资源。
