Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25

Abstract

Background: Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC₁S₃ generation, derived from crosses of 25 wild barley accessions with cv. Barke.

Results: In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected.

Conclusions: To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.

Keywords: Greenhouse trials; HEB-25; Hordeum vulgare; Hordeum vulgare ssp. spontaneum; Nested association mapping (NAM); Rhynchosporium commune; Rrs; Scald resistance; Wild barley.

Fig. 1

Circos plot indicating QTLs involved in scald resistance. Barley chromosomes are indicated as coloured bars on the inner circle. Grey connector lines represent the link between the genetic position (in cM) of SNPs in the inner circle and the physical position on the outer circle (in Mbp). QTLs and resistance genes from literature are indicated inside the circle and their position is given as outlined boxes on the cM scale. The dots represent the detection rate of each SNP in 100 cross-validation runs with horizontal reference lines at 0, 50 and 100 detections. Red dots represent an average trait-increasing effect, while blue dots represent an average trait-decreasing effect across all HEB families. Black lines on the outer track indicate the range of SNPs on the physical map that have been cumulated for estimating the family-specific effect, which is presented above. Here, the lower box indicates the family with the minimal GWAS effect, while the upper box represents the family with the maximal GWAS effect. The colour code indicates the strength of the effects as a heat map, i.e. darker colour represents a stronger effect. Figure created by use of Circos [58]

Fig. 2

Heat map of family-specific effects at major scald QTLs. For each QTL (columns) GWAS effects of different HEB families (rows) are shown. The colours range from − 2.5 (dark blue) to 2.5 (dark red) scoring units difference as compared to the reference Barke allele. The minimum effect was obtained for F05 at QRs.2H (− 2.22), while the maximum effect was obtained for F23 at QRs.3H (+ 0.54)

Fig. 3

Cumulated donor effect of 8 major scald QTLs. Grey-shaded bars represent the estimated donor effect for each HEB family. Effect was obtained by summarizing family-specific QTL effects of the eight major QTLs, which are represented as coloured dots