Application of CAPS markers for genomic studies in wild emmer wheat

Wild emmer wheat, Triticum dicoccoides, the tetraploid progenitor of domesticated wheat, is a promising source for crop improvement. Wild wheat populations harbor broad phenotypic diversity for numerous agronomic traits such as yield, grain quality, disease resistance, tolerance to abiotic stresses, and phenological characters. Wheat is of great societal and economic importance. However, it possesses a large and complex genome due to polyploidy and a high proportion of repetitive DNA, making genomic analysis and development of markers for wheat improvement a significant challenge. Singlenucleotide polymorphisms (SNPs) are considered among the most reliable and reproducible types of sequence-based genetic markers. SNP genotyping by cleaved amplified polymorphic sequences (CAPS) and derived CAPS (dCAPS) markers are commonly used to target specific chromosome regions in genetic and breeding projects. However, the application of CAPS markers for genetic mapping in polyploid wheat is complicated by the presence of both paralogous and homoeologous gene copies. Therefore, an essential part of any mapping strategy is the development of genome- specific markers. Previously, the development of CAPS markers was based on very limited resources such as wheat expressed sequence tags (EST) and syntenic information from rice, making the allocation of loci on homoeologous genomes a very laborious task. Nevertheless, CAPS markers served as a major tool for high-resolution genetic mapping and QTL cloning of the high grain protein transcription factor Gpc-B1 and the slowrusting resistance gene, Yr36, derived from wild emmer wheat. The recent efforts to develop whole-genome sequence and chromosome-specific bacterial artificial chromosome (BAC) libraries have permitted the establishment of large-scale wheat genomics resources. An increase in wheat sequence data and the sequencing of complete model grass genomes, used to infer wheat gene content and order based on comparative genomics, had a major impact on CAPS marker development. Gene isolation projects, including the powdery mildew resistance genes PmG16 and PmG3M, as well as the stripe rust resistance genes Yr15 and YrH52 derived from wild emmer wheat, are currently underway. In these projects, the development of genome-specific CAPS primers is based on comparisons of wheat genome survey sequence data of individually sorted chromosome arms. Although high throughput development and genotyping of markers has progressed significantly in wheat, CAPS markers remain the method of choice for fine genetic dissection and positional cloning of genes derived from T. dicoccoides and other species in the genus because they provide simple analysis of complex genomes.