A new genetic and deletion map of wheat chromosome 5A to detect candidate genes for quantitative traits

In the present study, a detailed deletion map for wheat chromosomes 5A and 5B is reported, as well as an integrated genetic linkage map of chromosome 5A enriched with single nucleotide polymorphism (SNP) markers, useful both for comparison studies with other existing maps and for mapping major genes and quantitative trait loci (QTLs). Physical mapping of 5,011 SNP markers was obtained using Chinese Spring bin deletion lines for the homoeologous chromosomes of group 5; 509 SNPs were also genetically mapped in a recombinant inbred line population segregating for chromosome 5A only, obtained by crossing the cultivar Chinese Spring and the disomic substitution line Chinese Spring-5A dicoccoides. The whole 5A genetic map, containing 572 markers, covered a total length of 248.7 cM distributed among three linkage groups of 83.5, 117.8 and 47.4, respectively. The majority of SNP markers physically mapped on 5A were mapped to a unique bin, while a small percentage was assigned a double location, suggesting the presence of a segment of 5A short arm which may have undergone a duplication followed by an insertion into the long arm of the same chromosome. A QTL analysis for yield components was performed, identifying a major QTL in the subtelomeric region of chromosome 5A, corresponding to the 5AL15-0.67-0.78 bin; the chromosome segment was 23.5 cM long and included 111 markers. Candidate genes for yield components on chromosome 5A were identified through a syntenic genomic approach by comparison with genomes of model species. Putative function analysis revealed genes involved in basic metabolism and in stress condition responses, including heat shock proteins, chaperones, serine/ threonine protein kinases and membrane transporters, located in the region of the QTL. This information represents an important step for map-based and candidate gene-based cloning of yield QTLs.