Genotyping by Sequencing of Cultivated Lentil (Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables.

Stefano Pavan,Claudio De Giovanni,Giacomo Mangini,Concetta Lotti,Valentina Fanelli,Angelo Raffaele Marcotrigiano,Nicoletta Bardaro,Cinzia Montemurro,Luigi Ricciardi,Francesca Taranto,Domenico Catalano

doi:10.3389/fgene.2019.00872

Abstract

Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index FST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.

Highlights

IntroductionStarting from the Fertile Crescent, lentil cultivation spreads westward to the Mediterranean Basin, the Nile Area, and Central Europe and eastward to Asia
Lentil (Lens culinaris Medik., 2n = 2x = 14) is one of the crops signing the birth of agriculture in the Neolithic Near East
Sequencing of a multiplexed Genotyping by sequencing (GBS) library prepared from 188 lentil genotypes (Supplementary Table S1) generated about 467 million read pairs, corresponding to an average of about 2.4 million read pairs per sample

Summary

Introduction

Starting from the Fertile Crescent, lentil cultivation spreads westward to the Mediterranean Basin, the Nile Area, and Central Europe and eastward to Asia. Lentil was introduced to North America and Australia (Cubero, 1984; Matny, 2015). Elucidation of Patterns of Diversity in the Mediterranean Lentil. Lentil is the third most widespread cool-season grain legume in the world, after chickpea (Cicer arietinum L.) and pea (Pisum sativum L.) (FAOSTAT data, 2017). Lentil global area and production significantly increased during the last decade, reaching 6.6 million ha and 7.6 million tons, respectively, with Canada, India, and Turkey being the main lentil producers (FAOSTAT data, 2017). Similar to other legume species, lentil increases soil fertility through nitrogen fixation and has a positive impact on soil properties and conservation (Sultani et al, 2007). Lentils are of utmost importance for food security, as they represent an affordable source of dietary proteins, vitamins, and other nutrients (Pal et al, 2016)

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