Genotyping-by-Sequencing on the Ion Torrent Platform in Barley

Abstract

The characterization of genetic polymorphism is a crucial step in both genetic studies and breeding programs. Genotyping-by-sequencing (GBS) constitutes one of the most attractive approaches for this purpose, especially in a genome as large as that of barley. The genome sequencing project undertaken by the International Barley Sequencing Consortium (IBSC) has produced a structured reference genome for the cultivar Morex [1] that can serve as an excellent resource for the analysis of GBS data. The genome assembly for this species [2] is thought to adequately capture the gene-rich portion of the genome (~80% of the entire genome). In this chapter, we describe the entire GBS process, from library preparation to the analysis of read data to produce a high-quality catalog of single nucleotide polymorphism (SNP) markers using the barley reference genome.

Keywords: Barley; Genotyping; High-throughput sequencing; Next-generation sequencing; Polymorphism; Reference genome; SNP marker; Variant calling.