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Article|07 Mar 2022|OPEN
Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history 
Stefano Pavan1 , ,† , Chiara Delvento1 ,† , Nelson Nazzicari2 , Barbara Ferrari2 , Nunzio D’Agostino3 , Francesca Taranto4 , Concetta Lotti5 , Luigi Ricciardi1 and Paolo Annicchiarico,2 ,
1Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
2Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, viale Piacenza 29, 26900 Lodi, Italy
3Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, Italy
4Institute of Biosciences and Bioresources, National Research Council of Italy, Via Amendola 165/A, 70126 Bari, Italy
5Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71100 Foggia, Italy
*Corresponding author. E-mail: stefano.pavan@uniba.it,paolo.annicchiarico@crea.gov.it
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhab062 (2022)
doi: https://doi.org/10.1093/hr/uhab062
Views: 270

Received: 20 Apr 2021
Accepted: 14 Nov 2021
Published online: 07 Mar 2022

Abstract

Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections – a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.