HvFT1 (VrnH3) drives latitudinal adaptation in Spanish barleys

Abstract

In barley, three genes are responsible for the vernalization requirement: VrnH1, VrnH2 and VrnH3. The winter growth habit of barley requires the presence of a recessive VrnH1 allele, together with an active VrnH2 allele. The candidate for VrnH3 (HvFT1) has been recently identified, with evidences pointing at a central role in the integration of the vernalization and photoperiod pathways. Functional polymorphisms have been proposed, but experimental evidence of their role on agronomic performance and adaptation is needed. We examined allelic variation at the promoter and intron 1 of the HvFT1 gene in a landrace collection of barley, finding a high diversity level, with its geographic distribution correlated with latitude. Focusing on genotypes with winter alleles in VrnH1 and VrnH2, an association analysis of the four main HvFT1 haplotypes found in the landrace collection detected differences in time to flowering. Landraces with the intron 1 TC allele, prevalent in the south, flowered 6-7 days earlier than those with the AG allele, under natural conditions. These results were validated in an independent F(2) population. In both data sets, the effect found was similar, but in opposite direction to that described in literature. The polymorphism reported at intron 1 contributes to variation in flowering time under field conditions. We have found that polymorphisms at the promoter also contribute to the effect of the gene on flowering time under field and controlled conditions. The variety of HvFT1 alleles described constitutes an allelic series that may have been a factor in agro-ecological adaptation of barley.

HvFT1 polymorphism and effect—survey of barley germplasm and expression analysis

“…Yan et al (2006) found an association between growth habit and mutations in the first intron, but the sequencing of the HvFT1 alleles from populations previously used to map QTL for flowering time (Hemming et al, 2008) failed to reveal any significant association between the two linked SNPs in intron 1 and flowering time. Further results reported in other surveys of HvFT1 allelic variation (Cuesta-Marcos et al, 2010; Casas et al, 2011) were also in disagreement with Yan et al (2006) regarding the direction of the effect assigned to the functional polymorphism in the first intron. Yan et al (2006) also identified two promoter haplotypes, characterized by seven linked SNPs and two indels in the first 550 bp upstream of the start codon.…”

“…This variation has been linked to differences in flowering phenotypes in a number of studies (Yan et al, 2006; Hemming et al, 2008; Casas et al, 2011). It seems clear now that, in Arabidopsis , the FT promoter and first intron contain cis-regulatory sites that are important for its transcriptional regulation (Tiwari et al, 2010).…”

“…Yan et al (2006) also identified two promoter haplotypes, characterized by seven linked SNPs and two indels in the first 550 bp upstream of the start codon. Using primers specific to differentiate those indels, Casas et al (2011) analyzed natural variation for the promoter haplotypes (135–146 vs. 139–142 bp) and the intron 1 haplotypes (AG/TC) in a collection of barley landraces. In that study the intron AG haplotype was clearly associated with later flowering than the TC haplotype.…”

“…The results for the promoter haplotypes hinted at a role of these polymorphisms on flowering time, but of lesser magnitude than intron polymorphism. The combination of the 135–146 promoter with the TC intron was associated with earliest flowering (Casas et al, 2011; Ponce-Molina et al, 2012). Further evidence from other populations (Nitcher et al, 2013) confirmed the description of promoter haplotypes as “early” (135–146) and “late” (139–142).…”

“…Further evidence from other populations (Nitcher et al, 2013) confirmed the description of promoter haplotypes as “early” (135–146) and “late” (139–142). Another SNP in the promoter of the HvFT1 gene, upstream of the studied region was also suggested to have an additional role on flowering time (Cuesta-Marcos et al, 2010; Casas et al, 2011). …”