A GWAS study highlights significant associations between a series of indels in a FLOWERING LOCUS T gene promoter and flowering time in white lupin (Lupinus albus L.)

Background
White lupin (Lupinus albus L.) is a high-protein Old World grain legume with remarkable food and feed production interest. It is sown in autumn or early spring, depending on the local agroclimatic conditions. This study aimed to identify allelic variants associated with vernalization responsiveness, in order to improve our knowledge of legume flowering regulatory pathways and develop molecular selection tools for the desired phenology as required for current breeding and adaptation to the changing climate.
Results
Some 120 white lupin accessions originating from a wide range of environments of Europe, Africa, and Asia were phenotyped under field conditions in three environments with different intensities of vernalization, namely, a Mediterranean and a subcontinental climate sites of Italy under autumn sowing, and a suboceanic climate site of France under spring sowing. Two hundred sixty-two individual genotypes extracted from them were phenotyped in a greenhouse under long-day photoperiod without vernalization. Phenology data, and marker data generated by Diversity Arrays Technology sequencing (DArT-seq) and by PCR-based screening targeting published quantitative trait loci (QTLs) from linkage map and newly identified insertion/deletion polymorphisms in the promoter region of the FLOWERING LOCUS T homolog, LalbFTc1 gene (Lalb_Chr14g0364281), were subjected to a genome-wide association study (GWAS). Population structure followed differences in phenology and isolation by distance pattern. The GWAS highlighted numerous loci significantly associated with flowering time, including four LalbFTc1 gene promoter deletions: 2388 bp and 2126 bp deletions at the 5’ end, a 264 bp deletion in the middle and a 28 bp deletion at the 3’ end of the promoter. Besides LalbFTc1 deletions, this set contained DArT-seq markers that matched previously published major QTLs in chromosomes Lalb_Chr02, Lalb_Chr13 and Lalb_Chr16, and newly discovered QTLs in other chromosomes.
Conclusions
This study highlighted novel QTLs for flowering time and validated those already published, thereby providing novel evidence on the convergence of FTc1 gene functional evolution into the vernalization pathway in Old World lupin species. Moreover, this research provided the set of loci specific for extreme phenotypes (the earliest or the latest) awaiting further implementation in marker-assisted selection for spring- or winter sowing.