Genotyping for species identification and diversity assessment using double-digest restriction site-associated DNA sequencing (ddRAD-Seq)

Anita A. Severn-Ellis, Armin Scheben, Ting Xiang Neik, Nur Shuhadah Mohd Saad, Aneeta Pradhan, Jacqueline Batley

Research output: Chapter in Book/Conference paperChapter

Abstract

Genotyping-by-sequencing (GBS) is a powerful approach for studying the genetic diversity of legume species. By using restriction enzymes or other methods to generate a reduced representation of the genome for sequencing, GBS can provide genome-wide single nucleotide polymorphisms (SNP) for diversity analysis at high throughput and low cost. Here we describe a novel double-digest restriction site-associated DNA sequencing (ddRAD-seq) approach. We also describe the downstream bioinformatic analysis of the sequencing data, including alignment to a reference genome, de novo assembly, SNP calling, phylogenetic analysis, and structure analysis.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press
Chapter8
Pages159-187
Number of pages29
Volume2107
DOIs
Publication statusPublished - 1 Jan 2020

Publication series

NameMethods in Molecular Biology
Volume2107
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

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