Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine
2011
Chancerel, Emilie, E. | Lepoittevin, Camille | Le Provost, Grégoire, G. | Lin, Yao-Cheng | Jaramillo-Correa, Juan Pablo | Eckert, Andrew J. | Wegrzyn, Jill L. | Zelenika, Diana | Boland, Anne | Frigerio, Jean-Marc | Chaumeil, Philippe | Garnier‐géré, Pauline | Boury, Christophe, C. | Grivet, Delphine | González-Martínez, Santiago C. | Rouzé, Pierre | van de Peer, Yves | Neale, David B. | Cervera, Maria T. | Kremer, Antoine | Plomion, Christophe | Biodiversité, Gènes & Communautés (BioGeCo) ; Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB) | Center for Plant Systems Biology (PSB Center) ; Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB) | Instituto de Ecologia ; Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM) | University of California [Davis] (UC Davis) ; University of California (UC) | Commissariat à l'énergie atomique et aux énergies alternatives (CEA) | Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA) | Department of Forest Ecology and GeneticsForest Research Centre ; Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA)
Article n°368
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显示更多 [+] 显示较少 [-]英语. *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.
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