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

doi:10.1007/978-1-0716-0235-5_8

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 paper › Chapter › peer-review

12 Citations (Scopus)

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 language	English
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Chapter	8
Pages	159-187
Number of pages	29
Volume	2107
DOIs	https://doi.org/10.1007/978-1-0716-0235-5_8
Publication status	Published - 1 Jan 2020

Publication series

Name	Methods in Molecular Biology
Volume	2107
ISSN (Print)	1064-3745
ISSN (Electronic)	1940-6029

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10.1007/978-1-0716-0235-5_8

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Severn-Ellis, A. A., Scheben, A., Neik, T. X., Saad, N. S. M., Pradhan, A., & Batley, J. (2020). Genotyping for species identification and diversity assessment using double-digest restriction site-associated DNA sequencing (ddRAD-Seq). In Methods in Molecular Biology (Vol. 2107, pp. 159-187). (Methods in Molecular Biology; Vol. 2107). Humana Press Inc.. https://doi.org/10.1007/978-1-0716-0235-5_8

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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.",

keywords = "ddRAD-seq, Double-digest restriction site-associated DNA sequencing, GBS, Genotyping-by-sequencing, Whole-genome sequencing, Restriction enzyme, Single nucleotide polymorphism",

author = "Severn-Ellis, {Anita A.} and Armin Scheben and Neik, {Ting Xiang} and Saad, {Nur Shuhadah Mohd} and Aneeta Pradhan and Jacqueline Batley",

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Severn-Ellis, AA, Scheben, A, Neik, TX, Saad, NSM, Pradhan, A & Batley, J 2020, Genotyping for species identification and diversity assessment using double-digest restriction site-associated DNA sequencing (ddRAD-Seq). in Methods in Molecular Biology. vol. 2107, Methods in Molecular Biology, vol. 2107, Humana Press Inc., pp. 159-187. https://doi.org/10.1007/978-1-0716-0235-5_8

Genotyping for species identification and diversity assessment using double-digest restriction site-associated DNA sequencing (ddRAD-Seq). / Severn-Ellis, Anita A.; Scheben, Armin; Neik, Ting Xiang et al.
Methods in Molecular Biology. Vol. 2107 Humana Press Inc., 2020. p. 159-187 (Methods in Molecular Biology; Vol. 2107).

Research output: Chapter in Book/Conference paper › Chapter › peer-review

TY - CHAP

T1 - Genotyping for species identification and diversity assessment using double-digest restriction site-associated DNA sequencing (ddRAD-Seq)

AU - Severn-Ellis, Anita A.

AU - Scheben, Armin

AU - Neik, Ting Xiang

AU - Saad, Nur Shuhadah Mohd

AU - Pradhan, Aneeta

AU - Batley, Jacqueline

PY - 2020/1/1

Y1 - 2020/1/1

N2 - 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.

AB - 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.

KW - ddRAD-seq

KW - Double-digest restriction site-associated DNA sequencing

KW - GBS

KW - Genotyping-by-sequencing

KW - Whole-genome sequencing, Restriction enzyme, Single nucleotide polymorphism

UR - http://www.scopus.com/inward/record.url?scp=85077447227&partnerID=8YFLogxK

UR - https://link.springer.com/book/10.1007/978-1-0716-0235-5#about

U2 - 10.1007/978-1-0716-0235-5_8

DO - 10.1007/978-1-0716-0235-5_8

M3 - Chapter

C2 - 31893447

AN - SCOPUS:85077447227

VL - 2107

T3 - Methods in Molecular Biology

SP - 159

EP - 187

BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

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

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