Uncovering the Phylogenetic Relationships of Lentil (Lens culinaris Medik.) Accessions from Germany

Lentil ( Lens culinaris Medik.) is a valuable grain legume that contributes to sustainable agriculture. In Germany, for decades, lentil cultivation and breeding have disappeared, resulting in dependence on imports and the loss of locally adapted genetic resources. This study aimed to assess the genetic diversity and relationships among German lentil accessions to support conservation and future breeding efforts. A total of 29 lentil accessions, including German landraces, cultivars, and wild relatives, were obtained from IPK Genebank and analyzed using Genotyping-by-Sequencing. Seed traits were evaluated and used for principal component analysis (PCA). Seed phenotyping revealed clear differentiation among accessions. Although German accessions were clearly distinguishable from one another, they remained closely related. Notably, Thuringian accessions formed two closely related yet distinct groups, differing in seed size and color. Overall, morphological variation was observed, from very small-seeded wild relatives to large-seeded cultivated types. PCA of seed traits explained 94% of the total variation, with seed size–related traits accounting for most of the observed diversity. Phylogenetic network analysis revealed nine major clades with multiple subclades, reflecting strong divergence between wild and domesticated lentils as well as fine-scale genetic structure among German cultivars. Genetic clustering was largely consistent with geographic origin and seed phenotype, while network reticulations indicated historical gene flow and admixture, particularly among German materials. These findings demonstrate genetic structuring among German lentils shaped by regional diversification, breeding history, and admixture, underscoring the importance of conserving and characterizing lentil germplasm and wild relatives for crop improvement.