Development of a SNP marker assay for the Lr67 gene of wheat using a genotyping by sequencing approach

Abstract

The recently characterised and mapped adult plant resistance gene Lr67 contributes to the breeding of durable resistance against multiple fungal pathogens of wheat. Lack of tightly linked markers has so far prevented widespread use of Lr67 in breeding programmes. Exhaustive screening of available SSR markers and 9,000 gene-associated SNPs using bulk segregant analysis yielded several linked markers but none close enough to the gene for routine breeding applications. In contrast, genotyping by sequencing identified several better-linked SNP-based markers that were converted into single-marker KASPar assays. Marker csSNP856 co-segregated with Lr67 in two mapping populations and was significantly associated with stripe rust resistance in an association mapping population of 972 wheat lines. High frequency (43 %, 29/66) of the Lr67-associated SNP allele in landraces from the Indian subcontinent suggests the origin of Lr67 from this region. While marker csSNP856 is not diagnostic for the presence of Lr67, it represents a significant step towards assisting the transfer of this adult plant resistance gene into elite germplasm via marker-assisted breeding.

Mapping QTL for Resistance to New Virulent Races of Wheat Stripe Rust from Two Argentinean Wheat Cultivars

“…QYr.caas-4DL, identified in the cultivar 'Bainong 64' (Ren et al, 2012), was associated with leaf rust and powdery mildew resistance, suggesting that it may be Lr67/Yr46 (Ren et al, 2015). By contrast, QYr.caas-4DL.2, identified in 'Lumai 21', is likely not Lr67/Yr46, as its tightly linked marker csSNP856 was not polymorphic in this population (Forrest et al, 2014;Ren et al, 2015). This QTL is also unlikely to be the same as QYr.ucw-4DL because their peaks are located ?190 Mb apart.…”

“…QYr.wgp-4D, identified in PI 182103, was mapped on the centromeric region of chromosome 4D, and its long arm border (IWA4044; Feng et al, 2018) was mapped >150 Mb proximal to QYr.ucw-4DL, indicating that they do not correspond to the same resistance gene. By contrast, QYr.caas-4DL.2, identified in 'Lumai 21', is likely not Lr67/Yr46, as its tightly linked marker csSNP856 was not polymorphic in this population (Forrest et al, 2014;Ren et al, 2015). By contrast, QYr.caas-4DL.2, identified in 'Lumai 21', is likely not Lr67/Yr46, as its tightly linked marker csSNP856 was not polymorphic in this population (Forrest et al, 2014;Ren et al, 2015).…”

Bulked sample analysis in genetics, genomics and crop improvement

“…To identify metabolite QTL (mQTL), the genetic and metabolic basis of glucosinolate accumulation was dissected in oilseed rape/canola ( Brassica napus ) through analysis of total glucosinolate concentration and its individual components in both leaves and seeds of a DH mapping population (Feng et al ., ). QTL that had effect on glucosinolate concentration in either or both of the organs were integrated, resulting in 105 mQTL.…”

“…The examples of BSA based on DNA/RNA/ chip are summarized in Table 2. The method has been used to study a dozen of recessive mutants in maize (Liu et al, 2010), leaf rust in wheat (Forrest et al, 2014), sulphur and selenium contents in Arabidopsis thaliana (Becker et al, 2011), salt resistance in cotton (Rodriguez-Uribe et al, 2011), bean common mosaic virus in common bean (Bello et al, 2014), Phytophthora root rot in pepper and photosynthetic traits in poplar (Wang et al, 2014a).…”

Progress in breeding for resistance to Ug99 and other races of the stem rust fungus in CIMMYT wheat germplasm

“…Three pleiotropic APR genes in addition to Sr2 (= Yr30) locus, viz. Sr55 (= Lr67/Yr46/Pm46), Sr57 (= Lr34/Yr18/Pm38/Sb1/Bdv1) and Sr58 (= Lr46/ Yr29/Pm39), conferring multi-pathogen resistance [73][74][75][76] were identified in CIMMYT wheat germplasm and used in marker assisted selection (Table 3) [77][78][79][80] . These genes in combination with other APR genes confer enhanced APR to the three rusts [81] .…”