whole exome sequencing bread wheat

Although wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) is an important staple crop, providing 20% of all calories consumed by the world population, functional genome studies are still a big challenge, mainly due to the lack of complete reference genome sequence and to its highly complex genome. Nowadays, with the great advances of next-generation sequencing technologies, the identification of causal variants associated with a target phenotype has become easier and more feasible. For these reasons, here, by combining targeted sequence capture with next-generation sequencing, we were able to scan at exome-wide level 48 bread wheat genotypes obtained from crossing two contrasting parents, Lankaeoudali and Rebelde, resulting in a reliable discovery of single nucleotide polymorphisms (SNPs). High genetic variation was observed among all the genotypes under study, allowing us to generate an extensive catalog of SNPs located in both genic and non-genic regions. SNPs were classified based on genomic location and putative biological effect, providing a list of variants that may have a high impact at the protein level. Random SNPs were selected from the targeted enrichment analysis and successfully converted in eight Kompetitive Allele-Specific PCR (KASP) markers for molecular validation. The reliable probe set used here to capture genetic diversity provides researchers and breeders a findable, accessible, interoperable, and reusable (FAIR) molecular toolkit for scientific data management in bread wheat. Finally, results from this study can be exploited for the promotion of novel studies on bread wheat as well as breeding programs related to the improvement of different phenotypic traits.