Genetic analysis of early phenology in lentil identifies distinct loci controlling component traits

Abstract

Reproductive phenology is well known to be a key feature of crop adaptation to diverse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with diverse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.