Unlocking genetic diversity for low-input systems in a changing climate through participatory characterization and GWAS of lentil landraces

Lentils are a vital staple crop in a world seeking sustainable and secure food, but their cultivation face a threat due to yield instability, mainly arising from a lack of genetic diversity in breeding programmes. In this study, we assembled and characterized the genetic and phenotypic diversities of a collection of 106 lentil genotypes, to evaluate their breeding and cropping potential. Lentil landraces from Italy and beyond, either abandoned or still cultivated, were collected from genebanks, seed savers, universities and farmers. We characterized their phenotypic diversity with an augmented block design, using a control plot enabling a spatial analysis. We phenotyped the collection during two cropping seasons for its agronomic performance, involving local practitioners in a participatory variety evaluation. Meanwhile, we genotyped the landrace collection with a DNA sequencing approach, obtaining 91,136 high quality single nucleotide polymorphisms (SNPs). We used SNPs to describe the phylogenetic relation among landraces, unveiling their uniqueness, and combined SNP data with measured traits to conduct a genome-wide association study (GWAS) that led to the identification of 32 unique marker-trait associations highlighting lentil genomic loci related with adaptation and performance. The results of this study offer new tools to unlock agrobiodiversity for lentil breeding in the Mediterranean, towards the identification of genetic factors responsible for traits of agronomic interest and providing possible sources of parental material.