Genetic analysis of Vrn-B1 for vernalization requirement by using linked dCAPS markers in bread wheat ( Triticum aestivum L.).

To identify a molecular marker closely linked to Vrn-B1, the Vrn-1 ortholog on chromosome 5B, sequence polymorphism at four orthologous RFLP loci closely linked to the Vrn-1 gene family was analyzed by using near-isogenic lines of "Triple Dirk." At Xwg644, a RFLP locus, three types of nucleotide sequence differing by the number of (TG) repeats, two or three times, and base changes were detected. A (TG)(3)-type sequence proved to be specific to chromosome 5B by nulli-tetrasomic analysis, and substitution of single nucleotide (C/T) was detected between TD(B) carrying the former Vrn2 allele and TD(C) carrying the vrn2 allele. A mismatch primer was designed for dCAPS analysis of this single nucleotide polymorphism (SNP). Polymorphism was successfully detected between two NILs, through nested PCR by using a (TG)(3)-specific primer (1st) and a dCAPS primer (2nd) followed by a NsiI digest. The analysis of a BF(2) population [(TD(B)//TD(C)] revealed the close linkage (1.7 cM) between WG644-5B and Vrn2. It was therefore concluded that the former Vrn2 locus is located on chromosome 5B and equivalent to Vrn-B1.