An Overview of Genotyping by Sequencing in Crop Species and Its Application in Pepper

Abstract

The exploitation of genetic variation in crops is essential to establish innovative breeding programs in the frame of global population increase and the sustainable intensification of agriculture. The advent of next generation sequencing technologies and the availability of complete or draft genome sequences of many crops allowed the development of several methods for SNP discovery. Genotyping by sequencing (GBS) has recently emerged as a promising approach to simultaneously allow SNP identification and genotyping. GBS provides a rapid, highly informative, high-throughput and cost-effective tool for exploring plant genetic diversity on a genome-wide scale and does not require any a priori knowledge on the genome of the species of interest. The features of GBS make it an attractive technology for (1) the assessment of population structure of germplasm collections; (2) the development of high density linkage maps and (3) genetic mapping studies. Herein, we present an overview of the GBS method and describe the main protocols in use, the principal methods for genetic diversity analysis and potential applications of the results in crop breeding programs. Finally, we illustrate the strategy we adopted to investigate the genetic diversity in cultivated pepper (Capsicum annuum).