The loss of vernalization requirement in narrow‐leafed lupin is associated with a deletion in the promoter and de‐repressed expression of a Flowering Locus T (FT) homologue

Abstract

SummaryAdaptation of Lupinus angustifolius (narrow-leafed lupin) to cropping in southern Australian and northern Europe was transformed by a dominant mutation (Ku) that removed vernalization requirement for flowering. The Ku mutation is now widely used in lupin breeding to confer early flowering and maturity. We report here the identity of the Ku mutation.We used a range of genetic, genomic and gene expression approaches to determine whether Flowering Locus T (FT) homologues are associated with the Ku locus.One of four FT homologues present in the narrow-leafed lupin genome, LanFTc1, perfectly co-segregated with the Ku locus in a reference mapping population. Expression of LanFTc1 in the ku (late-flowering) parent was strongly induced by vernalization, in contrast to the Ku (early-flowering) parent, which showed constitutively high LanFTc1 expression. Cosegregation of this expression phenotype with the LanFTc1 genotype indicated that the Ku mutation impairs cis-regulation of LanFTc1. Sequencing of LanFTc1 revealed a 1.4-kb deletion in the promoter region, which was perfectly predictive of vernalization response in 216 wild and domesticated accessions. Linkage disequilibrium rapidly decayed around LanFTc1, suggesting that this deletion caused the loss of vernalization response. This is the first time a legume FTc subclade gene has been implicated in the vernalization response.

INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow‐leafed lupin (Lupinus angustifolius L.)

“…Both Tanjil and the P27255 wild‐type LanFTc1 sequence (GenBank ID KT862491) served as references to genotype the 1,423‐bp INDEL polymorphism previously identified by Nelson et al () in the 5' regulatory region and to survey for other alternative INDEL variations in this same region. After discovering additional INDELs in the 7‐Kb sequence upstream of LanFTc1 , PCR primers were designed in the immediately adjacent sequences to screen for presence/absence of these INDELs for those accessions (Krasnolistny, Kazan, Mirela, and Sur) for which no re‐sequencing data were obtained.…”

“…Relative to P27255, representing the wild‐type LanFTc1 sequence, three large, distinct INDELs were identified in the 5' regulatory region. Two of the INDELs, which were associated with modified gene expression and phenology, were assessed relative to the wild‐type for the presence/absence of transcription factor binding site motifs previously identified by Nelson et al (). Putative binding site motifs were identified in that study using two open‐access web‐interface platforms, including JASPAR 2014, which contains CORE Plantae matrix models (Mathelier et al, ), and PLACE, which contains cis ‐acting regulatory DNA elements in plants (Higo, Ugawa, Iwamoto, & Korenaga, ).…”

“…Recently, the genetic identify of Ku was revealed as a FLOWERING LOCUS T ( FT ) homologue, LanFTc1 (Nelson et al, ). In Arabidopsis , FT has a well‐defined role as a floral integrator gene, coordinating signals from the vernalization, photoperiod, and circadian clock pathways to promote flowering at an opportune time (Turck, Fornara, & Coupland, ).…”

“…In Arabidopsis , FT has a well‐defined role as a floral integrator gene, coordinating signals from the vernalization, photoperiod, and circadian clock pathways to promote flowering at an opportune time (Turck, Fornara, & Coupland, ). A 1,423‐bp deletion in the promoter region of LanFTc1 was implicated as the casual mutation for the Ku allele, as its presence was perfectly predictive of vernalization responsiveness in 216 wild and domesticated accessions and was associated with derepressed expression of LanFTc1 in the absence of vernalization (Nelson et al, ). Given the demonstrated capacity for mutations in the noncoding sequence of this gene to modify its expression and plant phenology, we endeavoured to find other polymorphisms that may affect cis ‐regulation of LanFTc1 and provide alternative sources of flowering time variation.…”

Quantitative Trait Loci for Cold Tolerance in Chickpea

“…We mapped the vernalization gene (MtVRN2), a repressor of the flowering locus T (FT) gene homolog from Medicago truncatula, to the CTCa-3.1 confidence interval using the CDC Frontier chickpea reference genome ( Jaudal et al, 2016). In a more distantly related legume, Lupinus angustifolius L., a gene (LanFTc1) also interacts with flowering locus T (FT), controlling its vernalization requirement in lupin (Nelson et al, 2017) Efl1, an ELF3 ortholog in chickpea, was mapped to the early flowering QTL on chickpea LG5, so it likely is not the vernalization gene in chickpea (Ridge et al, 2017). A draft genome was published for both CRIL2 parents, which should facilitate this endeavor ( Jain et al, 2013;Gupta et al, 2016).…”