Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM)

Abstract

The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.

Development of barley introgression lines carrying the leaf rust resistance genes Rph1 to Rph15

“…Additionally, it also carries introgressions in chromosomes 3H and 7H. The introgression in 3HS overlaps with the Rph5 locus, and the one in chromosome 7H coincides with three other previously reported seedling resistance QTL, Rphq1 , Rphq8 , and QPh.7H‐2 (Marcel, Aghnoum, Durand, Varshney, & Niks, ; Schnaithmann et al., ; Vatter et al., ). It is unlikely that BW731 carries an allele of Rph5 based on the differential reactions it exhibits to specific P. hordei isolates.…”

“…It has introgressions in every chromosome except for 1H, some of which colocate to previously reported QTL for leaf rust resistance at the seedling stage. Although the presence of any of these QTL has not been confirmed in BW691, it should be noted that introgressions coincident with seedling resistance QTL exist, such as one unnamed QTL in chromosome 3HL reported by Jafary, Szabo, and Niks (), Rphq10 in 4HS, Rphq20 in 4HL, Rphq4 or QPh.5H‐1 in 5HS, Rphq7 or Rphq16 in 5HL, and QPh.6H‐3 in 6HL (Marcel et al., , ; Schnaithmann et al., , Vatter et al., ). BW709, derived from PI 405399, also exhibited resistance to isolates 90–3 and Neth 28 (Supplemental Tables S4).…”

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

“…The detected variation in resistance in the lines of the HEB-25 infected with Rhynchosporium commune reflected a great genetic diversity in the NAM population as shown before for resistance to net blotch ( Pyrenophora teres F. teres ) [ 52 ], stripe rust ( Puccinia striiformis f. sp. hordei ) and leaf rust ( Puccinia hordei ) [ 53 ].…”

“…This way potentially useful exotic alleles can be investigated in an adapted background, which is of special importance for allele mining of exotic resistance genes. In this regard NAM has been successfully applied to identify exotic sources of pathogen resistance in maize [48][49][50], barley [51][52][53] and wheat [54,55]. Vatter et al [52,53] could show that the wild barley NAM population HEB-25 contains numerous novel QTLs for net blotch, leaf rust and stripe rust.…”

“…In this regard NAM has been successfully applied to identify exotic sources of pathogen resistance in maize [ 48 – 50 ], barley [ 51 – 53 ] and wheat [ 54 , 55 ]. Vatter et al [ 52 , 53 ] could show that the wild barley NAM population HEB-25 contains numerous novel QTLs for net blotch, leaf rust and stripe rust. However, resistances were mostly conferred by the combination of multiple small-effect QTLs rather than single major QTLs.…”