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

Abstract

Modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond to the major global production environments. Reproductive phenology plays a key role in lentil adaptation to this diverse ecogeographic variation. Here, we dissect the characteristic earliness of the pilosae ecotype, suited to the typically short cropping season of South Asian environments. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering, and we show that DTF6a alone is sufficient to confer early flowering under extremely short photoperiods. Genomic synteny confirmed the presence of a conserved cluster of three florigen (FT) gene orthologs among potential candidate genes, and expression analysis in near-isogenic material showed that the early allele is associated with a strong derepression of the FTa1 gene in particular. Sequence analysis revealed a 7.4 kb deletion in the FTa1-FTa2 intergenic region in the pilosae parent, and a wide survey of over 350 accessions with diverse origin showed that the dtf6a allele is predominant in South Asian 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.

Mechanisms of Vernalization-Induced Flowering in Legumes

“…Extensive research revealed that the flowering-related genes are largely conserved between Arabidopsis and legumes [ 42 , 44 , 45 , 49 , 53 , 54 , 55 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 ]. However, the legumes generally lack any FLC orthologs, except for soybean, a vernalization-independent species, which retained one FLC copy in its paleopolyploid genome [ 42 , 98 , 99 ].…”

“…Legumes have three subclades of FT genes ( FTa, FTb and FTc ) with five Arabidopsis FT orthologs detected in pea Pisum sativum , and six orthologs in Medicago trancatula and Lens culinaris ( Table 1 ) [ 44 , 45 , 53 , 55 , 56 , 100 ]. Unlike pea and Medicago , chickpea Cicer arietinum has a single FTb gene, resulting in a family of five genes ( Table 1 ) [ 54 ].…”

“…A recent QTL analysis revealed that the DTF6a locus on lentil ( Lens culinaris ) chromosome 6 strongly contributes to early flowering of the Indian landrace ILL 2601 [ 55 ].…”

“…There were no differences in the coding regions of either gene, but the comparison of non-coding regions identified 136 nucleotide polymorphisms (SNPs) and 25 indels distinguishing two accessions. The most substantial difference was the 7441 bp deletion, comprising most of the FTa1–FTa2 intergenic region in the early ILL 2601 accession [ 55 ].…”

“…The results suggested that FTa1 ( LcFTa1 ) is the most prominent candidate for the early flowering and vernalization insensitivity of the early ILL 2601 accession [ 55 ]. As described above, FTa1 is responsible for early flowering in Medicago and pea [ 44 , 53 ].…”