Full TGIF Record # 274829
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DOI:10.1007/978-3-319-08714-6_9
Web URL(s):https://link.springer.com/chapter/10.1007/978-3-319-08714-6_9/fulltext.html
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https://link.springer.com/content/pdf/10.1007%2F978-3-319-08714-6_9.pdf
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Publication Type:
i
Report
Author(s):Ruttink, T.; Haegeman, A.; van Parijs, F.; Van Glabeke, S.; Muylle, H.; Byrne, S.; Asp, T.; Rold√°n-Ruiz, I.
Author Affiliation:Ruttink, Haegeman, van Parijs, Van Glabeke, Muylle, and Rold√°n-Ruiz: Plant Sciences Unit - Growth and Development, Institute for Agricultural and Fisheries Research, Melle, Belgium; Byrne and Asp: Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
Title:Genetic diversity in candidate genes for developmental traits and cell wall characteristics in perennial ryegrass (Lolium perenne)
Meeting Info.:Istanbul, Turkey: September 2014
Source:Molecular Breeding of Forage and Turf: The Proceedings of the 8th International Symposium on the Molecular Breeding of Forage and Turf. 2015, p. 93-109.
# of Pages:17
Publishing Information:s.l.: Springer International Publishing
Related Web URL:https://link.springer.com/chapter/10.1007/978-3-319-08714-6_9
    Last checked: 10/06/2017
    Notes: Abstract only
Keywords:TIC Keywords: Association mapping; Genetic diversity; Genotyping; Lolium perenne; Single nucleotide polymorphism
Abstract/Contents:"We investigated whether probe capture enrichment followed by next generation sequencing (NGS) can be used as genotyping tool in Lolium perenne, a species for which high SNP densities in genic regions have previously been reported. We annotated 177 known protein families from Brachypodium, rice, maize, sorghum, and Arabidopsis, in combination with predicted genes on our draft L. perenne genome sequence and selected 539 putative L. perenne orthologs for targeted resequencing. Using an in-house developed probe design strategy, we tiled the 539 target regions at about 3x tiling density, eliminated probes targeting repetitive sequences, and/or with high sequence similarity to non-target sequences, and designed a probe set that covers > 90 % of the intended 2.7 Mbp target length. As a proof of concept, we constructed indexed shotgun gDNA libraries of 95 genotypes originating from natural accessions from France and the inbred line used for genome sequencing. After pooling and probe capture enrichment, the library was split into two halves that were used for independent post-hybridization PCR-amplification, and sequenced on two HiSeq2000 lanes. Coverage and genotype calling saturation curves in function of sequencing depth per sample were constructed that can be used as guideline for the design of future probe capture experiments in L. perenne. A large fraction of the intended sequence length (> 95 %) was effectively covered by sequence reads, despite small gaps in the probe coverage. Furthermore, we identified a total of 96,593 SNPs, with a median polymorphism density across the 539 target regions of about 3.56 SNPs/100 bp. This comprehensive inventory of the sequence diversity in > 500 L. perenne genes can be used for association mapping (AM) or for de novo discovery of naturally occurring sequence variants that potentially disturb gene function."
Language:English
References:25
Note:"ISBN: 978-3-319-08713-9"
"ISBN: 978-3-319-08714-6"
"Chapter 9"
Includes map, "[Geographical origins in France]", p. 103
Figures
Tables
Graphs
ASA/CSSA/SSSA Citation (Crop Science-Like - may be incomplete):
Ruttink, T., A. Haegeman, F. van Parijs, S. Van Glabeke, H. Muylle, S. Byrne, et al. 2015. Genetic diversity in candidate genes for developmental traits and cell wall characteristics in perennial ryegrass (Lolium perenne). Molecular Breeding of Forage and Turf: The Proceedings of the 8th International Symposium on the Molecular Breeding of Forage and Turf. p. 93-109.
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DOI: 10.1007/978-3-319-08714-6_9
Web URL(s):
https://link.springer.com/chapter/10.1007/978-3-319-08714-6_9/fulltext.html
    Last checked: 10/06/2017
    Access conditions: Item is within a limited-access website
https://link.springer.com/content/pdf/10.1007%2F978-3-319-08714-6_9.pdf
    Last checked: 10/06/2017
    Requires: PDF Reader
    Access conditions: Item is within a limited-access website
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