Unlocking genetic diversity for low input systems in a changing climate: participatory characterization and genome-wide association study of lentil landraces.

Abstract

Abstract Lentil is a crucial staple crop in a world seeking for sustainable and secure food, but its cultivation is threatened by yield instability: among the main causes of such instability is the lack of genetic diversity in pulses breeding programmes. In this study, we assembled and characterized the genetic and phenotypic diversity of a collection of 111 lentil genotypes representative of Italian landraces, with the aim to evaluate their breeding and cropping potential. Lentil landraces from Italy and beyond, either abandoned or still cultivated, were collected from genebanks, seed savers associations, universities and farmers. We characterized their phenotypic diversity with an augmented block design without replications, using a control plot (consisting in the commercial cv. Robin ) enabling a spatial analysis. We phenotyped the collection during two cropping seasons for its agronomic performance, involving local farmers and practitioners in a participatory variety evaluation. At the same time, we genotyped the landrace collection with a DNA sequencing approach, obtaining 179278 single nucleotide polymorphisms (SNPs). We used SNPs to describe the phylogenetic relation among landraces, unveiling their uniqueness, and then combined SNP data with measured traits to conduct a genome-wide associate study (GWAS) that led to the identification of 40 marker-trait associations (MTAs) pinpointing lentil genomic loci related with adaptation and performance. The results of this study offer new tools to unlock agrobiodiversity for lentil breeding in central Italy, identifying genetic factors responsible for traits of agronomic interest and providing possible sources of parental material for future breeding programs or for composing heterogeneous material.