abstract
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Drought tolerance is one of the main components of yield and its stability, and its improvement is a major challenge to breeders. Genes codifying for transcription factors are particularly interesting, since they are components of the signal transduction pathways that coordinate the expression of several downstream genes. In particular, the dehydration responsive element binding factors (DREB proteins) are trans-acting elements endowed with a highly conserved AP2/EREBP domain, through which they bind specifically to DRE (dehydration responsive element), inducing the expression of functional downstream genes. A DREB2-related gene, namely TdDRF1 (Triticum durum dehydration responsive factor1), was isolated in durum wheat and its expression was related to the water deficit response. The gene was isolated, cloned and sequenced from different varieties and by the analysis of polymorphisms and the comparison with homologous sequences of Triticum urartuand Aegilops speltoides, different features, distinctive for A or B genome copies, were identified, allowing to recognize between homeologous (intravarietal) and homologous (intervarietal) SNPs,at the base of designing new markers.Thus, the intervarietal SNPs were used to design 26 specific KASP markers to be used in KASP assays for testing 288 lines of durum wheat. These lines represent a subset of the final Durum Wheat Reference Collection (DWRC) panel, organized and managed by Durum Wheat Genomics and Breeding Expert Working Group, in the frame of the activities of the Wheat Initiative. In particular, this subset included all elite lines and some landraces. The KASP (Kompetitive Allele Specific PCR) genotyping technology (patented by LGC Ltd) represents a new high-throughput and low cost genotyping platform, lacking limitations of low throughput, labour intensiveness and high costs characterizing common SNP genotyping, as allele-specific PCR (ASPCR), cleaved amplified polymorphic sequences (CAPS) and temperature-switch PCR (TSPCR). Our results showed that most designed KASP assays was not able to distinguish the genotypes, due to the presence of just one allele in all analysed DNAs. It is worth of noting that two KASP assays were able to cluster the 288 genotypes into two groups, meaning that both alleles were present. The possible association of one of the two alleles with a trait of agronomic/industrial interest will allow to transform the polymorphism into a new marker for breeding programs.