ArticleBMC genomics2011
Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 74 citations in OpenAlex.
- Needle and Branch Trait Variation Analysis and Associated SNP Loci Mining inInternational journal of molecular sciences · 2024Article
- Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing.BMC plant biology · 2023Article
- Identifying and testing marker-trait associations for growth and phenology in three pine species: Implications for genomic prediction.Evolutionary applications · 2022Article
- QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine.BMC plant biology · 2022Article
- An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony.G3 (Bethesda, Md.) · 2020Article
- Measuring viability selection from prospective cohort mortality studies: A case study in maritime pine.Evolutionary applications · 2019Article
- A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting.Ecology and evolution · 2018Article
- Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species,Frontiers in plant science · 2018Article
- Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.PloS one · 2016Article
- Evidence of intense chromosomal shuffling during conifer evolution.Genome biology and evolution · 2015Article
- Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae).Genetics · 2015Article
- Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease.Frontiers in plant science · 2015Article
- Insights into conifer giga-genomes.Plant physiology · 2014Review
- The genetics of water-use efficiency and its relation to growth in maritime pine.Journal of experimental botany · 2014Article
- Article
- Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine.BMC genomics · 2014Article
- A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection.PloS one · 2014Article
- Open access to tree genomes: the path to a better forest.Genome biology · 2013Article
- SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Article
Corrections and comments
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Authors and funding
21 authors at 10 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle 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.
resultsWe 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.
conclusionsOur 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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