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

Allele

Species

Cultivar/line

Source

vrn-A1a

L117/A180

2X

DQ291016

GenBank

PI428180, PI428183, PI428323

NGRP

4X

AY747598

GenBank

Rugby and Maier (ND)

CAP

PI14082, PI113393, PI191654, PI265004, PI286061, PI347135, PI352541, PI366990, PI384392

NGRP

Chinese Spring (AM502869)

GenBank

Jagger (OK, NE), UC1110 (CA), ID0556 and Zak

(ID), McNeal and Thatcher (MT), Louise and Panawawa (WA), GRN*5/ND614-A (MN), Heyne and KS01HW163-4 (KS), Jupeteco (TX)

CAP

6X

Jagalene, Overley, Santa Fe, Shocker, Protection

SGT

vrn-A1b

F117/V180

6X

Norstar (DY761363), Recital (CD872434, CD936812)

GenBank

2174 (OK), CIMMYT-2 (PI610750) (CA), Platte and CO940610 (CO), SS550 and PIONEER

26R46 (GA), Rio Blanco and IDO444 (ID), Harry and Wesley (KS), Stephens and OR9900553 (OR), TAM105 (NE), P91193 and P92201 (IN), NY18/

Clark's Cream 40–1 (MN), Pio 25R26 and Foster (OH), Cayuga and Caledonia (NY), Weebill (TX), USG3209 (VA), Finch and Eltan (WA)

CAP

Above, Centerfield, Custer, Cutter, Danby, Deliver, Doans, Duster, Endurance, Fannin, Fuller, Guymon, Hatcher, Intrada, JEI 110, Lakin, Neosho, Okfield, Ok102, Ripper, TAM 110, TAM 111, TAM 112, Trego

SGT

vrn-A1c

F117/A180

6X

IL369 (AY747599), Nongda 3338 (DQ512342)

GenBank

Jaypee (VA), Pio 26R61 (NY)

CAP

OK Bullet

SGT

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.

 
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