A Novel Haplotype of vrn-A1 at the Protein Level

The vrn-A1 sequences were used to search GenBank expressed sequence tags (EST) databases. Diploid wheat T. urartu (DQ291016) and tetraploid wheat T. turgidum ssp. durum (AY747598) have the same sequences at SNPs at both exon 4 and exon 7 as Jagger (Fig. 13.2), suggesting that the vrn-A1a allele in Jagger is the wild type. This result was confirmed using a PCR marker for another two accessions of diploid wheat T. urartu and 11 accessions of tetraploid wheat T. turgidum ssp. durum, ssp. dicocoides, and ssp. dicoccum (Table 13.1).

There are five hexaploid wheat cultivars, which VRN-A1 sequences are deposited in GenBank (Fig. 13.2). Chinese Spring was found to carry the vrn-A1a allele. Two winter wheat cultivars, Norstar and Recital, were found to carry the vrn-A1b allele. Norstar carrying the vrn-A1b allele was one of the most cold-hardy wheat cultivars. Interestingly, another two cultivars, IL369 and Nongda 3338, were found to have a novel haplotype at the protein level. The two cultivars have the mutation at Ala180/ Val180 but not at Leu117/Phe117. Therefore, the third haplotype differing from the

Fig. 13.2 Multiple sequence alignment of the VRN-A1 genes in different wheat species. The sequences of Jagger and 2174 were obtained in this study, and other sequences were from GenBank.

T. urartu: DQ291016; T. durum: Langdon, AY747598; CS: Chinese Spring, AM502869; Norstar, DY761363; Recital: CD872434, CD936812; IL369: AY747599; Nongda 3338: DQ512342. The two SNPs in exons 4 and 7 resulting in alternation of amino acids are highlighted. N indicates sequences between exon 4 and exon 7

Table 13.1 The vrn-A1 alleles in wheat cultivars

CAP coordinated agriculture project, SGP southern great plains, NGRP national genetic resources program (NGRP), U.S.

Jagger vrn-A1a allele and the 2174 vrn-A1b allele was referred to the vrn-A1c allele. These observations suggested that mutations from the wild type vrn-A1a allele to the vrn-A1b allele occurred twice, and the vrn-A1c allele is an intermediate type between them. The mutation in exon 7 should occur preceded to the mutation in exon 7 of vrn-A1.

The disassociation between Leu117/Phe117 and Ala180/Val180 suggested that the previously reported marker for Leu117/Phe117 (Fig. 13.1b) (Chen et al. 2009) cannot be used for the Ala180/Val180 mutation found in this study. A new marker has been developed for Ala180/Val180 PCR markers for vrn-A1 were developed to distinguish the SNP in exon 7 (Fig. 13.1c) between the Jagger and 2174 alleles.