Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat

Abstract

Winter wheats require a long exposure to cold temperatures (vernalization) to accelerate flowering. However, varieties differ in the length of the period of cold required to saturate the vernalization response. Here we show that single nucleotide polymorphisms (SNP) at the binding site of the GRP2 protein in the VRN-A1 first intron (henceforth, RIP3) are associated with significant differences in heading time after a partial vernalization treatment. The ancestral winter VRN-A1 allele in ‘Triple Dirk C’ has one SNP in the RIP3 region (1_SNP) relative to the canonical RIP3 sequence, whereas the derived ‘Jagger’ allele has three SNPs (3_SNPs). Both varieties have a single VRN-A1 copy encoding identical proteins. In an F2 population generated from a cross between these two varieties, plants with the 3_SNPs haplotype headed significantly earlier (P < 0.001) than those with the 1_SNP haplotype, both in the absence of vernalization (17 days difference) and after 3-weeks of vernalization (11 days difference). Plants with the 3_SNPs haplotype showed higher VRN-A1 transcript levels than those with the 1_SNP haplotype. The 3_SNPs haplotype was also associated with early heading in a panel of 127 winter wheat varieties grown in three separate controlled-environment experiments under partial vernalization (36 to 54 days, P < 0.001) and one experiment under field conditions (21 d, P < 0.0001). The RIP3 polymorphisms can be used by wheat breeders to develop winter wheat varieties adapted to regions with different duration or intensity of the cold season.Electronic supplementary materialThe online version of this article (10.1007/s00438-018-1455-0) contains supplementary material, which is available to authorized users.

Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat

“…A 424-bp insertion in the first intron of VRN-A1f-del/ins leaded to spring habit in T. timopheevii 54 . A SNP change at GRP2 protein binding site in the first intron of VRN-A1 gene was intimately related to the requirement of winter wheat vernalization 55 . Retrotransposon SORE-1 insertion in the first intron resulted in attenuation of FT2a gene expression 56 .…”

Experiencing winter for spring flowering: A molecular epigenetic perspective on vernalization

“…Ta_VRN1 plays a critical role in the acceleration of flowering by vernalization in wheat (Shimada et al 2009; Trevaskis 2010). Prior to cold exposure, the RNA‐binding protein GRP2 (GLYCINE‐RICH RNA‐BINDING PROTEIN 2) binds to a region in the first intron of the Ta_VRN1 pre‐mRNA, leading to a reduction in the levels of mature Ta_VRN1 mRNA (Kippes et al 2018). Prolonged cold exposure induces the expression of VERNALIZATION RELATED 2 ( VER2 ), encoding a jacalin‐like protein that can bind N‐acetylglucosamine (GlcNAc) (Yong et al 2003; Xiao et al 2014).…”

Identification of the vernalization gene VRN-B1 responsible for heading date variation by QTL mapping using a RIL population in wheat

“…Allelic variation at the VRN1 locus is one of the main resources of genetic variation in vernalization requirements in wheat. A single dominant allele of one of the three homeoloci is sufficient to confer a spring growth habit [ 15 – 17 ]. A previous study showed that the dominant Vrn1 with spring growth habit contained large deletions in the first intron, and a 2.8-kb conserved segment within the deletion region of recessive vrn1 was important for vernalization requirement in wheat [ 16 ].…”

“…A previous study showed that the dominant Vrn1 with spring growth habit contained large deletions in the first intron, and a 2.8-kb conserved segment within the deletion region of recessive vrn1 was important for vernalization requirement in wheat [ 16 ]. Additionally, the investigation of polymorphisms in the RNA immune precipitation fragment 3 (RIP3) of VRN-A1 first intron suggested that single nucleotide polymorphisms in RIP3 affected VRN-A1 transcript level, and are associated with differences in heading time of winter wheat cultivars from various geographic regions [ 17 ]. The differences between dominant and recessive alleles associated with the VRN-B1 locus lie near the first intron and mainly include a large deletion, SNPs, small deletions, and large insertion in the 5′-UTR region [ 16 , 18 – 22 ].…”