Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.)

Abstract

Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT(®)) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1-4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar(®) markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar(®) assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM-ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.

Independent mis‐splicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication

“…The KASP assay is a quick and cost-effective genotyping assay for single SNP analysis (Terracciano et al, 2013;Semagn et al, 2014) that has been applied successfully in polyploids such as wheat (Allen et al, 2011) and cotton (Byers et al, 2012); thus, it is a useful SNP genotyping platform for marker-assisted breeding. In this study, the two causal mutations that result in the nonfunctional transcript of TaPHS1 were successfully converted into KASP markers, SNP.646 and SNP.666.…”

Validation of simple sequence repeats associated with quality traits in durum wheat

“…In fact, the effectiveness of molecular markers needs to be validated by determining the target phenotype in independent populations and different genetic backgrounds; this is referred to as marker validation (Sharp et al 2001). New approaches have recently been proposed to avoid spurious associations due to population structure in quantitative trait loci, such as investigating molecular marker association using germplasm collections of randomly sampled unrelated individuals (FlintGarcia et al 2005;Roy et al 2006;Terracciano et al 2013). Compared to quantitative trait locus analyses, association studies have the potential to directly mine the allelic diversity of genetic resources and identify alleles that are beneficial for the trait of interest (Haussmann et al 2004;Maccaferri et al 2006Maccaferri et al , 2010Maccaferri et al , 2011.…”

Rapid and convenient gel‐free screening of SCAR markers in wheat using SYBR green‐based melt‐profiling

“…, Terracciano et al. ), the inability to perform it on regular real‐time PCR instruments due to requirement of specific dyes, instrumentation and analytical software is limiting its widespread use.…”

“…), conserved orthologs set‐SNP (COS‐SNP) markers (Terracciano et al. ), single nucleotide polymorphism (SNP) arrays (Wang et al. ) and KASPar assay (Smith and Maughan ).…”