Single nucleotide polymorphisms (SNPs) associated with the vernalization response In wheat

摘要

In the era of genomics, the availability of sequence information has allowed the development of single nucleotide polymorphisms (SNPs) as molecular markers. SNPs have been employed extensively in humans in a quest to identify markers associated with diseases. In plants, very little information is available on the extent of linkage disequilibrium. In our research, we have used SNP analysis in a large sample of wheat varieties to investigate whether a gene tightly linked to the vernalization response is indeed Vrn-Al. We surveyed the status of seven SNPs, located within a 3 kb region of our target gene, in 80 wheat varieties. Most winter and European spring varieties fell into two distinct haplotype groups. This demonstrated that the SNPs could be used as diagnostic markers for Vrn-Al in European germplasm. However, the association between growth habit and haplotype was imperfect. Five spring varieties displayed the winter haplotype, and one winter variety was classified as spring based on the genotypic data. Interpretation of the data as to the identity of the target gene was complicated by the hexaploid nature of wheat. Indeed, a spring phenotype can be caused by spring alleles at any of the homoeologous Vrn-A J, Vrn-Bl or Vrn-Dl loci. At least one of the five varieties was known to contain the Vrn-Bl gene. Our data demonstrate that, in many cases, association studies alone will not be sufficient to confirm the identity of candidate genes.