Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing.

F Taranto,T Cardi,P Tripodi,B Greco,N D’Agostino

doi:10.1186/s12864-016-3297-7

Abstract

BackgroundKnowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes.ResultsGBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features.ConclusionsGBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3297-7) contains supplementary material, which is available to authorized users.

Highlights

Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection
The availability of large germplasm collections facilitates the evaluation of population diversity and genetic structure, providing vital information for genome-wide association mapping and allele mining studies that can be exploited by plant breeders for the development of novel varieties and seed conservation programs [8,9,10]
For genetic diversity and the associated population structure analysis we considered only a collection of 222 C. annuum accessions with different biological status: 110 landraces, 72 varieties, 15 hybrids, 13 ornamentals, 8 breeding lines and 4 wild lines (Additional file 1: Table S1)

Summary

Introduction

Knowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. We used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes. Among the domesticated Capsicum spp., C. annuum is the most widely grown species in the world as sweet and hot pepper [2] and it is the most used in breeding programs. The availability of large germplasm collections facilitates the evaluation of population diversity and genetic structure, providing vital information for genome-wide association mapping and allele mining studies that can be exploited by plant breeders for the development of novel varieties and seed conservation programs [8,9,10]

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Discussion

Conclusion