ArticleG3 (Bethesda, Md.)2014
A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping.
Article in G3 (Bethesda, Md.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 84 citations in OpenAlex.
- Genomic models for accurate estimation of breeding values in Sitka spruce (Picea sitchensis Bong. Carr).Heredity · 2026Article
- Development of a 101.6K liquid-phased probe for GWAS and genomic selection in pine wilt disease-resistance breeding in Masson pine.The plant genome · 2025Article
- High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers.G3 (Bethesda, Md.) · 2024Article
- Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce.BMC genomics · 2024Article
- Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica).BMC plant biology · 2022Article
- Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch.Molecular ecology resources · 2022Article
- NLR diversity and candidate fusiform rust resistance genes in loblolly pine.G3 (Bethesda, Md.) · 2022Article
- QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine.BMC plant biology · 2022Article
- Quantitative Trait Loci Analysis Based on High-Density Mapping of Single-Nucleotide Polymorphisms by Genotyping-by-Sequencing Against Pine Wilt Disease in Japanese Black Pine (Frontiers in plant science · 2022Article
- Efficient construction of a linkage map and haplotypes for Mentha suaveolens using sequence capture.G3 (Bethesda, Md.) · 2021Article
- Regional Heritability Mapping of Quantitative Trait Loci Controlling Traits Related to Growth and Productivity in Popcorn (Plants (Basel, Switzerland) · 2021Article
- Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance.Communications biology · 2021Article
- Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq forG3 (Bethesda, Md.) · 2019Article
- Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii).BMC plant biology · 2019Article
- Genetic Mapping of Prince Rupprecht's Larch (Genes · 2019Article
- Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the Conifers Pinus taeda and Pinus elliottii.Genome biology and evolution · 2019Article
- The first genetic linkage map for Fraxinus pennsylvanica and syntenic relationships with four related species.Plant molecular biology · 2019Article
- Article
- A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata.PloS one · 2019Article
- High-density genetic map construction and quantitative trait loci identification for growth traits in (Taxodium distichum var. distichum × T. mucronatum) × T. mucronatum.BMC plant biology · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Loblolly pine (Pinus taeda L.) is an economically and ecologically important conifer for which a suite of genomic resources is being generated. Despite recent attempts to sequence the large genome of conifers, their assembly and the positioning of genes remains largely incomplete. The interspecific synteny in pines suggests that a gene-based map would be useful to support genome assemblies and analysis of conifers. To establish a reference gene-based genetic map, we performed exome sequencing of 14729 genes on a mapping population of 72 haploid samples, generating a resource of 7434 sequence variants segregating for 3787 genes. Most markers are single-nucleotide polymorphisms, although short insertions/deletions and multiple nucleotide polymorphisms also were used. Marker segregation in the population was used to generate a high-density, gene-based genetic map. A total of 2841 genes were mapped to pine's 12 linkage groups with an average of one marker every 0.58 cM. Capture data were used to detect gene presence/absence variations and position 65 genes on the map. We compared the marker order of genes previously mapped in loblolly pine and found high agreement. We estimated that 4123 genes had enough sequencing depth for reliable detection of markers, suggesting a high marker conversation rate of 92% (3787/4123). This is possible because a significant portion of the gene is captured and sequenced, increasing the chances of identifying a polymorphic site for characterization and mapping. This sub-centiMorgan genetic map provides a valuable resource for gene positioning on chromosomes and guide for the assembly of a reference pine genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.