An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly

Janaki Velmurugan, Ewan Mollison, Susanne Barth, David Marshall, Linda Milne, Christopher J. Creevey, Bridget Lynch, Helena Meally, Matthew McCabe, Dan Milbourne

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Background and Aims High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing.\r\n\r\nMethods The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3–40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4–9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach.\r\n\r\nKey Results The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly.\r\n\r\nConclusions The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.
Original languageEnglish
Pages (from-to)71-87
Number of pages17
JournalAnnals of Botany
Volume118
Issue number1
Early online date6 Jun 2016
DOIs
Publication statusPrint publication - 1 Jul 2016
Externally publishedYes

Fingerprint

genome assembly
Lolium perenne
genotyping
chromosome mapping
genome
grandparents
genes
DNA libraries
jumping
barcoding
bioinformatics
inbred lines
single nucleotide polymorphism
sequence analysis
nucleotides
organisms

Keywords

  • GBS
  • Lolium perenne
  • genome assembly
  • genotyping by sequencing
  • linkage mapping
  • perennial ryegrass
  • presence/absence variation
  • single nucleotide polymorphism

Cite this

Velmurugan, Janaki ; Mollison, Ewan ; Barth, Susanne ; Marshall, David ; Milne, Linda ; Creevey, Christopher J. ; Lynch, Bridget ; Meally, Helena ; McCabe, Matthew ; Milbourne, Dan. / An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. In: Annals of Botany. 2016 ; Vol. 118, No. 1. pp. 71-87.
@article{986a2c8f446b42f6bd4d7e86f571ab44,
title = "An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly",
abstract = "Background and Aims High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing.\r\n\r\nMethods The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3–40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4–9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach.\r\n\r\nKey Results The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly.\r\n\r\nConclusions The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.",
keywords = "GBS, Lolium perenne, genome assembly, genotyping by sequencing, linkage mapping, perennial ryegrass, presence/absence variation, single nucleotide polymorphism",
author = "Janaki Velmurugan and Ewan Mollison and Susanne Barth and David Marshall and Linda Milne and Creevey, {Christopher J.} and Bridget Lynch and Helena Meally and Matthew McCabe and Dan Milbourne",
year = "2016",
month = "7",
day = "1",
doi = "10.1093/aob/mcw081",
language = "English",
volume = "118",
pages = "71--87",
journal = "Annals of Botany",
issn = "0305-7364",
publisher = "Oxford University Press",
number = "1",

}

An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. / Velmurugan, Janaki; Mollison, Ewan; Barth, Susanne; Marshall, David; Milne, Linda; Creevey, Christopher J.; Lynch, Bridget; Meally, Helena; McCabe, Matthew; Milbourne, Dan.

In: Annals of Botany, Vol. 118, No. 1, 01.07.2016, p. 71-87.

Research output: Contribution to journalArticle

TY - JOUR

T1 - An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly

AU - Velmurugan, Janaki

AU - Mollison, Ewan

AU - Barth, Susanne

AU - Marshall, David

AU - Milne, Linda

AU - Creevey, Christopher J.

AU - Lynch, Bridget

AU - Meally, Helena

AU - McCabe, Matthew

AU - Milbourne, Dan

PY - 2016/7/1

Y1 - 2016/7/1

N2 - Background and Aims High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing.\r\n\r\nMethods The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3–40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4–9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach.\r\n\r\nKey Results The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly.\r\n\r\nConclusions The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.

AB - Background and Aims High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing.\r\n\r\nMethods The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3–40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4–9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach.\r\n\r\nKey Results The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly.\r\n\r\nConclusions The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.

KW - GBS

KW - Lolium perenne

KW - genome assembly

KW - genotyping by sequencing

KW - linkage mapping

KW - perennial ryegrass

KW - presence/absence variation

KW - single nucleotide polymorphism

UR - http://www.mendeley.com/research/ultrahigh-density-genetic-linkage-map-perennial-ryegrass-lolium-perenne-using-genotyping-sequencing

U2 - 10.1093/aob/mcw081

DO - 10.1093/aob/mcw081

M3 - Article

VL - 118

SP - 71

EP - 87

JO - Annals of Botany

JF - Annals of Botany

SN - 0305-7364

IS - 1

ER -