GSE123548
Characterization of QTL and eQTL linked with early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan -1 x Nyubai doubled-haploid wheat population at two days post inoculation
In this study, early infection by F. graminearum was characterized in a doubled-haploid population derived from the cross of the moderately FHB resistant wheat genotypes Wuhan 1 and Nyubai. Three significant QTL were identified: 1AL was associated with reduced deoxynivalenol levels, and 4BS and 5A were associated with reduced F. graminearum levels at 2 days after infection. The early resistance alleles for 1AL and 4BS were inherited from Wuhan 1, and those for the 5A QTL were inherited from Nyubai. The LOD support interval for the 5A QTL was in the same region as FHB5, a QTL previously associated with field resistance to FHB. Cis and trans eQTL were identified using RNA sequencing data from infected head samples. In total, 240 cis eQTL and 17,401 trans eQTL were identified within LOD support intervals for the three QTL. Hotspots for trans eQTL were identified within LOD support intervals for the 1AL and 4BS QTL. Differential gene expression analysis revealed twenty genes with cis eQTL within one of the 3 QTL support intervals, that had higher expression associated with FHB early resistance, and 17 genes with higher expression associated with FHB early susceptibility. Among those, genes with a cis eQTL peak coinciding with QTL peaks were enriched in functions related to signaling and protein-protein interaction, including NBS-LRR, BAH, LRR/F-box and TPR domain-containing proteins. Several genes located within one of the three QTL support intervals also had a trans eQTL with a peak at the same position as QTL peaks on other chromosomes, suggesting interactions between the QTL. Overall design: In this study, we have analyzed RNA-seq and genotype (SRR, SNP) data in two parent genotypes with moderate resistance to F. graminearum and 81 DH lines obtained by crossing the two parents at 2 dpi