DNA sequence polymorphisms and their application to bread wheat quality

Abstract

Single-nucleotide polymorphisms (SNPs) constitute an abundant source of DNA polymorphisms, which have been successfully used to identify loci that are associated with a particular phenotype. Additionally, such markers could be efficiently used in combination with doubled haploid technology to improve the efficiency of breeding programmes. Information on such markers in plants is still scarce. For bread wheat, SNP data are restricted to a few genes. This can be explained by the hexaploidy of Triticum aestivum which makes SNP discovery difficult. We developed a novel method for SNP discovery in bread wheat. The strategy is based on the development of highly specific PCR-primers, which were used to sequence 27 lines. SNPs were discovered from sequence alignment data. Some SNPs were identified by mass spectrometry in a collection of 113 lines, which were both evaluated for agronomic traits and genotyped at 42 neutral microsatellite loci. Traits investigated include: protein content, the quantity of high-molecular-weight glutenins and that of the GluBx subunit. The 42 markers were used to infer population structure, which was included in linear models for association studies. The results of this preliminary study showed 89 SNPs in approximately 20 kbp, i.e., one SNP every 223 bp on average. Six SNPs were genotyped: three were located along the sequence of Glu-B1-1, while three non-synonymous SNPs were located along the sequence of the B homoeologous gene coding for SPA (Storage Protein Activator). The SNPs from Glu-B1-1 had a significant effect on the studied variables, whereas those of SPA had no effect. Such results might indicate that some haplotypes for Glu-B1-1 are linked to higher protein content, through an increased amount of high-molecular-weight glutenins, especially the GluBx subunit.