Quantitative Trait Loci Analysis of Seed Quality Characteristics in Lentil using Single Nucleotide Polymorphism Markers

Seed shape, color, and pattern of lentil (Lens culinaris Medik. subsp. culinaris) are important quality traits as they determine market class and possible end uses. A recombinant inbred line population was phenotyped for seed dimensions over multiple site–years and classified according to cotyledon and seed coat color and pattern. The objectives were to determine the heritability of seed dimensions, identify genomic regions controlling these dimensions, and map seed coat and cotyledon color genes. A genetic linkage map consisting of 563 single nucleotide polymorphisms, 10 simple sequence repeats, and four seed color loci was developed for quantitative trait loci (QTL) analysis. Loci for seed coat color and pattern mapped to linkage groups 2 (Ggc), 3 (Tgc), and 6 (Scp) while the cotyledon color locus (Yc) mapped to linkage group 1. The broad sense heritability estimates were high for seed diameter (broad-sense heritability [H2] = 0.92) and seed plumpness (H2 = 0.94) while seed thickness (H2 = 0.60) and days to flowering (H2 = 0.45) were more moderate. There were significant seed dimension QTL on six of the seven linkage groups. The most significant QTL for diameter and plumpness was found at the cotyledon color locus (Yc). The markers identified in this study can be used to help enrich breeding populations for desired seed quality characteristics, thereby increasing efficiency in the lentil breeding program.