Genome-Wide Characterization of Genes Controlling Wheat Seed Dormancy and Pre-Harvest Sprouting Using RNA-Seq

Pre-harvest sprouting (PHS) in wheat causes significant reduction in grain yield and quality, and results in substantial economic losses. Inadequate seed dormancy is the key factor for PHS when long period of wet weather is available during harvesting seasons. Multiple genetic components and environmental factors are involved in the controlling PHS. To investigate genes controlling PHS, a genome-wide transcriptome analysis to profile the global gene expression was conducted using RNA-seq and near-isogenic lines (NILs) with contrasting alleles at TaPHS1, a PHS resistance gene cloned from chromosome arm 3AS. A total of 777 genes were differentially expressed (DE) in the PHS-resistant NIL compared to the PHS-susceptible NIL at 20 and 25 days after anthesis (DAA), which includes 517 up-regulated and 260 down-regulated genes. Gene Ontology (GO) enrichment analysis indicated that the key biological processes associated with multiple DE genes are involved in the maintenance of seed dormancy. Real-time RT-PCR validated the expression of several DE genes related to seed dormancy. The protein interactions between TaPHS1 and these DE genes were identified using yeast two-hybrid system and bimolecular fluorescence complementation (BiFC) assays. This work identified multiple genes that are associated with wheat PHS resistance, and provides in-depth genome-wide genetic information for further understanding genetic mechanisms of PHS resistance in wheat.