Identification and mapping of expressed genes associated with the 2DL QTL for fusarium head blight resistance in the wheat line Wuhan 1

Abstract

Background: Fusarium head blight (FHB) is a problem of great concern in small grain cereals, especially wheat. A quantitative trait locus (QTL) for FHB resistance (FHB_SFI) located on the long arm of chromosome 2D in the spring wheat genotype Wuhan 1 is a resistance locus which has potential to improve the FHB resistance of bread wheat since it confers effective resistance to wheat breeding lines. Recently, differentially expressed genes (DEG) have been identified by comparing near isogenic lines (NIL) carrying the susceptible and resistant alleles for the 2DL QTL, using RNA-Seq. In the present study, we aimed to identify candidate genes located within the genetic interval for the 2DL QTL for FHB resistance, as assessed by single floret inoculation (FHB_SFI), and possibly contributing to it.

Results: Combining previous and additional bioinformatics analyses, 26 DEG that were located on chromosome arm 2DL were selected for further characterization of their expression profile by RT-qPCR. Seven of those DEG showed a consistent differential expression profile between either three pairs of near isogenic lines or other genotypes carrying the R and S alleles for the 2DL QTL for FHB resistance. UN25696, which was identified in previous expression work using microarray was also confirmed to have a differential expression pattern. Those eight candidate genes were further characterized in 85 lines of a double haploid mapping population derived from the cross Wuhan 1/Nyubai, the population where the 2DL QTL was originally identified. The expression QTL for gene Traes_2DL_179570792 overlapped completely with the mapping interval for the 2DL QTL for FHB_SFI while the expression QTL for UN25696 mapped near the QTL, but did not overlap with it. None of the other genes had a significant eQTL on chromosome 2DL. Higher expression of Traes_2DL_179570792 and UN25696 was associated with the resistant allele at that locus.

Conclusions: Of the 26 DEG from the 2DL chromosome further characterized in this study, only two had an expression QTL located in or near the interval for the 2DL QTL. Traes_2DL_179570792 is the first expression marker identified as associated with the 2DL QTL.

Keywords: 2DL FHB resistance QTL; Expression QTL; Fusarium head blight; RNA-Seq; Wheat; Wuhan 1.

Fig. 1

Overall strategy used in this study for the identification of candidate genes associated with the 2DL QTL for FHB resistance. The identification of DEG between tissues of a wheat NIL containing the 2DL QTL (2–2618) and a NIL without the 2DL QTL (2–2890) were described in Biselli et al. [32]. The RNA-Seq data for Wuhan 1 and Nyubai is described in [37]. UN25696 was first identified as TA.25696 in [31]. sp., spikelet; rach, rachis; Fg, F. graminearum; DEG, differentially expressed genes; log₂ FC, log base 2 fold change

Fig. 2

Relative expression patterns for three DEG and UN25696 in three pairs of NIL segregating for the FHB resistance QTL on 2DL. RT-qPCR was carried out on three pairs of NIL using three biological replicates per treatment per NIL. UN25696 was from [31]. H, water (mock) inoculation; F, F. graminearum inoculation; sp., spikelet; rach, rachis; − and +, S and R allele for 2DL QTL; no visible bar in a panel means that there was no detectable expression or expression level was too low to show on the figure

Fig. 3

Relative expression patterns for seven DEG and UN25696 in four genotypes. Wuhan 1 and HC374 carry the + allele for the FHB resistance QTL on 2DL, while Nyubai and Shaw carry the - allele. RT-qPCR was carried out using three biological replicates per treatment; samples were collected at 2 and 4 dai after water (H₂O) or F. graminearum (Fg) inoculation

Fig. 4

Genetic positioning of the FHB_SFI QTL and expression QTL for candidate genes on 2D genetic linkage map. The genetic linkage map of chromosome 2D was constructed from a wheat DH population of 104 lines while expression data from 85 lines were used for the eQTL mapping.

Fig. 5

Relative expression patterns for TaWRKY70, TaACT and NPR1-like. Wuhan 1 and HC374 carry the + allele for the FHB resistance QTL on 2DL, while Nyubai and Shaw carry the - allele. RT-qPCR was carried out using three biological replicates per treatment; samples were collected at 2 and 4 dai after water (H₂O) or F. graminearum (Fg) inoculation. TaWRKY70, TaACT and NPR1-like were identified in [33, 48]