QTL mapping of vernalization-insensitive and photoperiod-independent early flowering in yellow lupin (Lupinus luteus L.)

Recent decades have seen noticeable warming, causing in mid and high latitudes longer growing season, more summer droughts, and decreased spring vernalization, prompting plant breeders to focus on improving plant adaptation to these new conditions. One of the key traits is responsiveness to vernalization, a typical characteristic of temperate grain legumes, including yellow lupin ( Lupinus luteus L.), a potential European alternative to soybeans for sandy soils. Although beneficial for autumn sowing in warmer areas, vernalization responsiveness can be unfavorable for spring sowing due to delayed flowering. To facilitate studies on genetics of vernalization responsiveness in yellow lupin, a recombinant inbred line (RIL) population was developed from a cross between a thermoneutral, rapid flowering breeding line PRH444/14 and a vernalization-responsive, moderately late flowering cultivar, Parys. The RILs were phenotyped in a greenhouse under ambient long-day photoperiod across three spring seasons (2022-2024) and short-day photoperiod during the winter season (2023/4). The difference in flowering time between early and late RILs reached ~39 days in long days and ~68 days in short days. Following DArT-seq genotyping, a linkage map comprising 1,448 loci and anchoring all yellow lupin pseudochromosomes was constructed. Despite moderate fragmentation of the map (63 linkage groups versus 26 chromosomes), there was a high level of collinearity. Composite interval mapping of flowering-related traits identified a major quantitative trait locus (QTL), significant throughout all years and in both photoperiods, located on chromosome YL-16 and explaining up to 34% of the phenotypic variance. This QTL co-localized with a LlutFTc1 gene, one of the four Flowering locus T ( FT ) homologues from the yellow lupin genome. The marker developed for the 2,227 bp indel from the LlutFTc1 promoter exhibited the highest correlation with plant phenology among all markers on this linkage map. Additionally, several minor QTLs were identified on other chromosomes, including one on chromosome YL-04, significant under long-day photoperiod and explaining up to 5% of phenotypic variance, and another on chromosome YL-14, specific to the short-day photoperiod, accounting for up to 9%. Candidate genes for these QTLs include known flowering time regulators, such as EAF1B-like and CIB2-like genes for YL-04, and bHLH93-like for YL-14.