A PCR marker for growth habit in common wheat based on allelic variation at the VRN-A1 gene

Li Yan
University of Victoria
Jacob Sherman
California Institute of Integral Studies
Growth habit varies among accessions of hexaploid wheat. The winter habit genotype requires a cold treatment to induce flowering and is generally planted in the fall. Spring habit genotypes flower in the absence of a vernalization treatment. Spring habit is conferred by a dominant allele at any of the three VRN-1 loci, but varieties carrying the VRN-A1 locus are the most frequent and usually flower earlier. To facilitate selection in populations segregating at the VRN-A1 locus and to assist in genotyping wheat accessions of unknown VRN-1 composition, a PCR-based marker for growth habit would be useful. The VRN-A1 gene was recently cloned allowing for the development of markers for growth habit. In this report, we designed primer sets specific for the VRN-A1 locus, and used them to amplify an 810-bp segment of the VRN-A1 gene between intron 4 and exon 8 from 40 spring wheat lines and 37 winter wheat lines. Three diagnostic nucleotide changes were identified that differentiated the dominant Vrn-A1 and recessive vrn-A1 alleles in 75 out of the 77 genotypes analyzed in this study. One of these differences resulted in the presence of an additional AciI restriction site in the allele for spring growth habit. This difference was exploited to develop a cleavage amplification polymorphic sequence that can be used to determine the allelic state at VRN-A1 in germplasm collections, and as a marker in backcross breeding projects. An additional pair of dominant markers was developed from a different polymorphism.
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