1 September 2019 | Volume 10 | Article 872 ORIGINAL RESEARCH doi: 10.3389/fgene.2019.00872 published: 18 September 2019 Frontiers in Genetics | www.frontiersin.org Edited by: Michael David Martin, Norwegian University of Science and Technology, Norway Reviewed by: Hamid Khazaei, University of Saskatchewan, Canada Giorgio Bertorelle, University of Ferrara, Italy *Correspondence: Stefano Pavan stefano.pavan@uniba.it Specialty section: This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics Received: 30 April 2019 Accepted: 20 August 2019 Published: 18 September 2019 Citation: Pavan S, Bardaro N, Fanelli V, Marcotrigiano AR, Mangini G, Taranto F, Catalano D, Montemurro C, De Giovanni C, Lotti C and Ricciardi L (2019) Genotyping by Sequencing of Cultivated Lentil (Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables. Front. Genet. 10:872. doi: 10.3389/fgene.2019.00872 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 1,2 *, Nicoletta Bardaro 1 , Valentina Fanelli 1 , Angelo Raffaele Marcotrigiano 1 , Giacomo Mangini 1 , Francesca Taranto 1,3 , Domenico Catalano 2 , Cinzia Montemurro 1 , Claudio De Giovanni 1 , Concetta Lotti 4 and Luigi Ricciardi 1 1 Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy, 2 Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy, 3 CREA Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy, 4 Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy 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 F ST 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. Keywords: breeding, conservation genetics, genetic structure, genotyping-by-sequencing, lentil INTRODUCTION Lentil (Lens culinaris Medik., 2n = 2x = 14) is one of the crops signing the birth of agriculture in the Neolithic Near East. Starting from the Fertile Crescent, lentil cultivation spreads westward to the Mediterranean Basin, the Nile Area, and Central Europe and eastward to Asia. More recently, lentil was introduced to North America and Australia (Cubero, 1984; Matny, 2015).