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

Abstract

Flowering time in plants is a tightly regulated process. In barley (Hordeum vulgare L.), HvFT1, ortholog of FLOWERING LOCUS T, is the main integrator of the photoperiod and vernalization signals leading to the transition from vegetative to reproductive state of the plant. This gene presents sequence polymorphisms affecting flowering time in the first intron and in the promoter. Recently, copy number variation (CNV) has been described for this gene. An allele with more than one copy was linked to higher gene expression, earlier flowering, and an overriding effect of the vernalization mechanism. This study aims at (1) surveying the distribution of HvFT1 polymorphisms across barley germplasm and (2) assessing gene expression and phenotypic effects of HvFT1 alleles. We analyzed HvFT1 CNV in 109 winter, spring, and facultative barley lines. There was more than one copy of the gene (2–5) only in spring or facultative barleys without a functional vernalization VrnH2 allele. CNV was investigated in several regions inside and around HvFT1. Two models of the gene were found: one with the same number of promoters and transcribed regions, and another with one promoter and variable number of transcribed regions. This last model was found in Nordic barleys only. Analysis of HvFT1 expression showed that association between known polymorphisms at the HvFT1 locus and the expression of the gene was highly dependent on the genetic background. Under long day conditions the earliest flowering lines carried a sensitive PpdH1 allele. Among spring cultivars with different number of copies, no clear relation was found between CNV, gene expression and flowering time. This was confirmed in a set of doubled haploid lines of a population segregating for HvFT1 CNV. Earlier flowering in the presence of several copies of HvFT1 was only seen in cultivar Tammi, which carries one promoter, suggesting a relation of gene structure with its regulation. HvCEN also affected to a large extent flowering time.

The completely additive effects of two barley phenology‐related genes (eps2S and sdw1) are explained by specific effects at different periods within the crop growth cycle

“…() found some QTLs controlled only one phase in the ‘Henni’/‘Meltan’ population, some others the leaf and spikelet initiation phase and the stem elongation phase, and one both phases with contrasting effects for each one. The only major phenology gene segregating in the ‘Henni’/‘Meltan’ population is a promoter of VrnH3 (Loscos, Igartua, Contreras‐Moreira, Gracia, & Casas, ), and the major genes detected in ‘Baronesse’ × ‘Full Pint’ could have masked some other minor effects.…”

Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues

“…As mentioned before, the expression level of Vrn-H1 increases with exposure to cold temperatures, resulting in flower induction through repression of Vrn-H2 and activation of Vrn-H3 29,77 . Vrn-H3 corresponds to the HvFT1 gene, which is an orthologue of the Arabidopsis FT gene, the so called 'florigen' 33,78,79 . Vrn-H3 has a central role in flower induction integrating photoperiod and vernalization signals 79 Figure S4; Supplementary Table S8a).…”

“…Vrn-H3 corresponds to the HvFT1 gene, which is an orthologue of the Arabidopsis FT gene, the so called 'florigen' 33,78,79 . Vrn-H3 has a central role in flower induction integrating photoperiod and vernalization signals 79 Figure S4; Supplementary Table S8a). The wild barley allele of Vrn-H3 slowed down plant development between 2.2 and 6.6 days.…”

Selection footprints in barley breeding lines detected by combining genotyping-by-sequencing with reference genome information

“…In a second step, 130 plants from the 96V738 F2 population were analyzed with 11 microsatellite markers and a marker for the VrnH1 gene. Previous genotyping had established that Orria and Plaisant both carried the same winter allele at VrnH2 (Loscos et al 2014), and thus, full winter habit in this population was governed by segregation of the parental alleles at just VrnH1 (details on the control of the vernalization process by these genes are given in Distelfeld et al 2009). The F8 lines were genotyped using different sets of markers: SSRs, SNPs and flowering genes (Table S1).…”