Genetic and transcriptomic analysis for pre-harvest sprouting resistance in red spring wheat

Abstract

Pre-harvest sprouting (PHS) affects wheat production globally as it reduces grain yield and end-use quality. Given PHS resistance is a quantitative trait and strongly influenced by genetic and environment factors. This thesis project is therefore aimed to identify molecular mechanisms regulating dormancy, quantitative trait loci (QTL) and candidate genes for PHS resistance. To this end, this PhD thesis project comprised of a genetic study involving a mapping population and a transcriptomic analysis. The genetic study investigated the dormancy phenotype of a doubled haploid (DH) mapping population derived from dormant/non-dormant parents and evaluated over five environments, and these data along with the genotypic data obtained using a 90 K SNP Chip array was used for detection PHS resistance QTL. A total of four PHS resistance QTLs were detected on chromosome 1D, 4A, 6B and 6D across the five environments; 4A QTL was identified as a major QTL as it explained 40-50% of phenotypic variation while 1D QTL is novel as it was not reported previously. The transcriptomic study investigated selected DH lines showing contrasting dormancy phenotype using RNA-Seq. Our analysis revealed a large number of differentially expressed genes (DEGs) between dormant and non-dormant seeds. The DEGs were found to be enriched in cell, cell part, intracellular and integral component of membrane gene ontology classes. Genes upregulated in dormant seeds are found to be enriched in the carotenoid biosynthesis including ABA metabolism, diterpenoid biosynthesis including gibberellin catabolism and flavonoid biosynthesis as well as ABA signaling pathways while those downregulated are enriched in auxin signaling and GA biosynthesis pathways. Mapping of the DEGs on previously detected QTLs (1D, 4A, 6B and 6D) identified potential candidate genes for seed dormancy. Of these DEGs, TaCYP71B11 and TaDOG1L-2 on 1D, TaPM19-A1 and A2 on 4A, an uncharacterized gene (Gene ID: TraesCS6B02G325000) on 6B and TaLEA4 on 6D showed upregulation in dormant seed while two uncharacterized genes (Gene IDs: TraesCS1D02G410700 and TraesCS4A02G317200) on 1D and 4A, TaRH8 on 6B and TaHIS4 on 6D QTLs showed downregulation. Furthermore, 2 to 25 SNPs were detected in seed dormancy candidate genes located within the four QTLs. Taken together, the results of this study foster a deeper understanding of the molecular and genetic mechanisms of seed dormancy and therefore facilitate PHS resistance breeding program in wheat.