Understanding the genomic relationship between wild and cultivated genomes would facilitate access to the untapped variability found in crop wild relatives. We developed genome assemblies of a cultivated lentil (Lens culinaris) as well as a wild relative (L. ervoides). Comparative analyses revealed large-scale structural rearrangements and additional repetitive DNA in the cultivated genome, resulting in regions of reduced recombination, segregation distortion and permanent heterozygosity in the offspring of a cross between the two species. These novel findings provide plant breeders with better insight into how best to approach accessing the novel variability available in wild relatives.

The zero-tannin trait in lentil is controlled by a single recessive gene (tan) that results in a phenotype characterized by green stems, white flowers, and thin, transparent, or translucent seed coats. Genes that result in zero-tannin characteristics are useful for studies of seed coat pigmentation and biochemical characters because they have altered pigmentation. In this study, one of the major groups of plant pigments, phenolic compounds, was compared among zero-tannin and normal phenotypes and genotypes of lentil. Biochemical data were obtained by liquid chromatography-mass spectrometry (LC-MS). Genomic sequencing was used to identify a candidate gene for the tan locus. Phenolic compound profiling revealed that myricetin, dihydromyricetin, flavan-3-ols, and proanthocyanidins are only detected in normal lentil phenotypes and not in zero-tannin types. The molecular analysis showed that the tan gene encodes a bHLH transcription factor, homologous to the A gene in pea. The results of this study suggest that tan as a bHLH transcription factor interacts with the regulatory genes in the biochemical pathway of phenolic compounds starting from flavonoid-3’,5’-hydroxylase (F3’5’H) and dihydroflavonol reductase (DFR).

Phytate, the storage form of P in seeds, is not well digested by monogastrics, thereby contributing to micronutrient deficiency, decreased feed efficiency, and environmental pollution. This research was aimed at developing a single nucleotide polymorphism (SNP) based genetic linkage map and mapping genomic regions associated with phytic acid‐phosphorus (PA‐P) concentration using a recombinant inbred line (RIL) population (PR‐15) derived from a cross between a low phytate (low phytic acid [lpa]) mutant pea (Pisum sativum L.) genotype, 1‐2347‐144, and a normal phytate cultivar CDC Meadow. A total of 163 RILs were genotyped using a 1536‐SNP Illumina GoldenGate array. Three hundred and sixty‐seven polymorphic SNP markers ordered into seven linkage groups (LGs) were used to generate a linkage map with a total length of 437.2 cM. PR‐15 lines were grown in replicated field trails in Saskatoon and Rosthern, SK, in 2012 and 2013. Chi‐square statistics confirmed the single gene inheritance of PA‐P concentration in these RILs. Phytic acid‐phosphorus (PA‐P) phenotype was mapped to LG5. Iron bioavailability (FEBIO) of PR‐15 lines estimated using the Caco‐2 cell culture bioassay was negatively correlated with PA‐P concentration. A quantitative trait locus (QTL) for FEBIO was mapped on to the same location on LG5 as phytic acid concentration. The QTL with a maximum LOD score of 15.1 explained 60.5% of the phenotypic variation in FEBIO. The markers flanking this QTL region can be employed in marker‐assisted selection to select pea lines with low phytate and greater Fe bioavailability.