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Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

Emilie Chancerel, Camille Lepoittevin, Gregoire Le Provost, Yao-Cheng Lin UGent, Juan Pablo Jaramillo-Correa, Andrew J Eckert, Jill L Wegrzyn, Diana Zelenika, Anne Boland and Jean-Marc Frigerio, et al. (2011) BMC GENOMICS. 12.
abstract
Background: Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe. Results: We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. Conclusions: Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SINGLE NUCLEOTIDE POLYMORPHISMS, PROTEIN MARKERS, ALGORITHM, RAPD, CONSTRUCTION, PINASTER AIT, VITIS-VINIFERA L., LINKAGE MAP, TAEDA L., GENOME LENGTH
journal title
BMC GENOMICS
BMC Genomics
volume
12
article_number
368
pages
14 pages
Web of Science type
Article
Web of Science id
000293281600001
JCR category
BIOTECHNOLOGY & APPLIED MICROBIOLOGY
JCR impact factor
4.073 (2011)
JCR rank
26/157 (2011)
JCR quartile
1 (2011)
ISSN
1471-2164
DOI
10.1186/1471-2164-12-368
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
1888550
handle
http://hdl.handle.net/1854/LU-1888550
date created
2011-08-12 18:57:53
date last changed
2013-02-27 09:11:08
@article{1888550,
  abstract     = {Background: Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe.
Results: We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6\% and 74.8\% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4\% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species.
Conclusions: Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.},
  articleno    = {368},
  author       = {Chancerel, Emilie and Lepoittevin, Camille and Le Provost, Gregoire and Lin, Yao-Cheng and Jaramillo-Correa, Juan Pablo and Eckert, Andrew J and Wegrzyn, Jill L and Zelenika, Diana and Boland, Anne and Frigerio, Jean-Marc and Chaumeil, Philippe and Garnier-Gere, Pauline and Boury, Christophe and Grivet, Delphine and Gonzalez-Martinez, Santiago C and Rouz{\'e}, Pierre and Van de Peer, Yves and Neale, David B and Cervera, Maria T and Kremer, Antoine and Plomion, Christophe},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keyword      = {SINGLE NUCLEOTIDE POLYMORPHISMS,PROTEIN MARKERS,ALGORITHM,RAPD,CONSTRUCTION,PINASTER AIT,VITIS-VINIFERA L.,LINKAGE MAP,TAEDA L.,GENOME LENGTH},
  language     = {eng},
  pages        = {14},
  title        = {Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine},
  url          = {http://dx.doi.org/10.1186/1471-2164-12-368},
  volume       = {12},
  year         = {2011},
}

Chicago
Chancerel, Emilie, Camille Lepoittevin, Gregoire Le Provost, Yao-Cheng Lin, Juan Pablo Jaramillo-Correa, Andrew J Eckert, Jill L Wegrzyn, et al. 2011. “Development and Implementation of a Highly-multiplexed SNP Array for Genetic Mapping in Maritime Pine and Comparative Mapping with Loblolly Pine.” Bmc Genomics 12.
APA
Chancerel, E., Lepoittevin, C., Le Provost, G., Lin, Y.-C., Jaramillo-Correa, J. P., Eckert, A. J., Wegrzyn, J. L., et al. (2011). Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC GENOMICS, 12.
Vancouver
1.
Chancerel E, Lepoittevin C, Le Provost G, Lin Y-C, Jaramillo-Correa JP, Eckert AJ, et al. Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC GENOMICS. 2011;12.
MLA
Chancerel, Emilie, Camille Lepoittevin, Gregoire Le Provost, et al. “Development and Implementation of a Highly-multiplexed SNP Array for Genetic Mapping in Maritime Pine and Comparative Mapping with Loblolly Pine.” BMC GENOMICS 12 (2011): n. pag. Print.