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| DOI: | 10.1093/aob/mcw081 |
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| Web URL(s): | https://academic.oup.com/aob/article/118/1/71/2196286/An-ultra-high-density-genetic-linkage-map-of
Last checked: 03/02/2017
Access conditions: Item is within a limited-access website
Notes: Guide Page |
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| Publication Type:
| Refereed |
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| Author(s): | Velmurugan, Janaki;
Mollison, Ewan;
Barth, Susanne;
Marshall, David;
Milne, Linda;
Creevey, Christopher J.;
Lynch, Bridget;
Meally, Helena;
McCabe, Matthew;
Milbourne, Dan |
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| Author Affiliation: | Velmurugan, Mollison, Barth, Meally, and Milbourne: Crops, Environment and Land Use Programme, Oak Park Research Centre, Teagasc Carlow; Creevey and McCabe: Animal and Grassland Research and Innovation Centre, Teagasc Grange; Velmurugan and Lynch: School of Agriculture and Food Science, University College Dublin, Dublin, Ireland; Mollison, Marshall, and Milne: Information and Computational Sciences Group; Mollison: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, UK |
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| 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 |
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| Section: | Original articles
Other records with the "Original articles" Section
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| Source: | Annals of Botany. Vol. 118, No. 1, July 2016, p. 71-87. |
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| Publishing Information: | London, England, United Kingdom: Academic Press Inc. Limited |
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| # of Pages: | 17 |
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| Keywords: | TIC Keywords: Genetic analysis; Genetic linkage; Genetic markers; Genetics model; Genotyping; Lolium perenne; Single nucleotide polymorphism
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| Abstract/Contents: | "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. Methods: 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. Key Results: The assembly comprises 424750 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. Conclusions: The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community." |
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| Language: | English |
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| References: | 50 |
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| Note: | Figures
Tables
Graphs |
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| ASA/CSSA/SSSA Citation (Crop Science-Like - may be incomplete):
Velmurugan, J., E. Mollison, S. Barth, D. Marshall, L. Milne, C. J. Creevey, et al. 2016. An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. Ann. Bot. 118(1):p. 71-87. |
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| DOI: 10.1093/aob/mcw081 |
| Web URL(s):
https://academic.oup.com/aob/article/118/1/71/2196286/An-ultra-high-density-genetic-linkage-map-of
Last checked: 03/02/2017
Access conditions: Item is within a limited-access website
Notes: Guide Page |
| 
MSU catalog number: b2209341a |
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