High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers
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J. Woolliams | J. Cottrell | J. MacKay | B. Boyle | J. Laroche | J. Bousquet | Steve J. Lee | G. Gorjanc | G. Lopez | S. A'Hara | Hayley R. Tumas | M. Janes | P. Mclean | Joana J. Ilska | Sebastien Girardi
[1] D. Grattapaglia. Twelve Years into Genomic Selection in Forest Trees: Climbing the Slope of Enlightenment of Marker Assisted Tree Breeding , 2022, Forests.
[2] Richard A. Moore,et al. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. , 2022, The Plant journal : for cell and molecular biology.
[3] H. Dungey,et al. Genomics-Enabled Management of Genetic Resources in Radiata Pine , 2022, Forests.
[4] S. Salzberg,et al. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin , 2021, G3.
[5] X. Chen,et al. The Chinese pine genome and methylome unveil key features of conifer evolution , 2021, Cell.
[6] D. Ro,et al. The Taxus genome provides insights into paclitaxel biosynthesis , 2021, Nature Plants.
[7] J. Woolliams,et al. Stranger in a strange land: genetic variation of native insect resistance biomarkers in UK Sitka spruce (Picea sitchensis [Bong.] Carr.) , 2021, Forestry: An International Journal of Forest Research.
[8] Thomas M. Keane,et al. Twelve years of SAMtools and BCFtools , 2020, GigaScience.
[9] S. Abrahamsson,et al. Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine , 2020, BMC Genomics.
[10] J. Bohlmann,et al. Hydroxyacetophenone defenses in white spruce against spruce budworm , 2019, Evolutionary applications.
[11] A. Deslauriers,et al. The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs , 2019, Scientific Reports.
[12] Amanda R. De La Torre,et al. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families , 2019, Evolutionary applications.
[13] J. Beaulieu,et al. Multi‐trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce , 2019, Evolutionary applications.
[14] A. Schoettle,et al. Limber pine (Pinus flexilis James) genetic map constructed by exome-seq provides insight into the evolution of disease resistance and a genomic resource for genomics-based breeding. , 2019, The Plant journal : for cell and molecular biology.
[15] F. Gagnon,et al. A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies) , 2018, BMC Genomics.
[16] Douglas G. Scofield,et al. An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies) , 2018, G3: Genes, Genomes, Genetics.
[17] P. Rigault,et al. Expansion of the dehydrin gene family in the Pinaceae is associated with considerable structural diversity and drought-responsive expression , 2018, Tree physiology.
[18] Pasi Rastas,et al. Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data , 2017, Bioinform..
[19] J. MacKay,et al. Development of a Traceability System Based on a SNP Array for Large-Scale Production of High-Value White Spruce (Picea glauca) , 2017, Front. Plant Sci..
[20] J. Woolliams,et al. QTL analysis and genomic selection using RADseq derived markers in Sitka spruce: the potential utility of within family data , 2017, Tree Genetics & Genomes.
[21] L. Milne,et al. An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. , 2016, Annals of botany.
[22] F. Gagnon,et al. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana) , 2016, Molecular ecology resources.
[23] M. Cervera,et al. High‐density SNP assay development for genetic analysis in maritime pine (Pinus pinaster) , 2016, Molecular ecology resources.
[24] J. Schmutz,et al. Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01 , 2016, BMC Genomics.
[25] Michael S. Barker,et al. Early genome duplications in conifers and other seed plants , 2015, Science Advances.
[26] Florent Murat,et al. Evidence of Intense Chromosomal Shuffling during Conifer Evolution , 2015, Genome biology and evolution.
[27] K. Yelick,et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome , 2015, Genome Biology.
[28] Jean Bousquet,et al. Genomic selection accuracies within and between environments and small breeding groups in white spruce , 2014, BMC Genomics.
[29] J. Bohlmann,et al. Expression of the β-glucosidase gene Pgβglu-1 underpins natural resistance of white spruce against spruce budworm , 2014, The Plant journal : for cell and molecular biology.
[30] G. McVean,et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications , 2014, Nature Genetics.
[31] I. Birol,et al. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size , 2014, BMC Plant Biology.
[32] Steven J. M. Jones,et al. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size , 2014, BMC Plant Biology.
[33] S. Salzberg,et al. Sequencing and Assembly of the 22-Gb Loblolly Pine Genome , 2014, Genetics.
[34] Bing Ren,et al. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing , 2013, Nature Biotechnology.
[35] M. Kirst,et al. A High-Density Gene Map of Loblolly Pine (Pinus taeda L.) Based on Exome Sequence Capture Genotyping , 2013, G3: Genes, Genomes, Genetics.
[36] J. Chapman,et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) , 2013, The Plant journal : for cell and molecular biology.
[37] Inanç Birol,et al. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data , 2013, Bioinform..
[38] J. Gion,et al. High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination , 2013, BMC Biology.
[39] J. Gion,et al. High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination , 2013, BMC Biology.
[40] P. Rigault,et al. Development of high‐density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners , 2013, Molecular ecology resources.
[41] S. Aitken,et al. Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis × P. glauca) , 2013, Molecular ecology.
[42] P. Rigault,et al. A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers , 2012, BMC Biology.
[43] A. Leitch,et al. Ecological and genetic factors linked to contrasting genome dynamics in seed plants. , 2012, The New phytologist.
[44] J. Salse. In silico archeogenomics unveils modern plant genome organisation, regulation and evolution. , 2012, Current opinion in plant biology.
[45] Heng Li,et al. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..
[46] David M. A. Martin,et al. Genome sequence and analysis of the tuber crop potato , 2011, Nature.
[47] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[48] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[49] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[50] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[51] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .
[52] M. Gribskov,et al. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.
[53] M. Devey,et al. An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree , 1994, Theoretical and Applied Genetics.
[54] Cécile Fizames,et al. The 1993–94 Généthon human genetic linkage map , 1994, Nature Genetics.
[55] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[56] A. Sturtevant. A THIRD GROUP OF LINKED GENES IN DROSOPHILA AMPELOPHILA. , 1913, Science.
[57] F. Isik. Genomic Prediction of Complex Traits in Perennial Plants: A Case for Forest Trees. , 2022, Methods in molecular biology.
[58] OF REVISION , 2022 .
[59] I. Birol,et al. A high‐resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance , 2017, The Plant journal : for cell and molecular biology.
[60] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[61] P. Rigault,et al. Title: A white spruce gene catalogue for conifer genome analyses. , 2011 .
[62] D. Neale,et al. A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees. , 1999, Genetics.
[63] B. Weir,et al. Allozyme diversity in plant species. , 1990 .
[64] A. Harris. Sitka Spruce (Picea sitchensis (Bong.) Carr.) , 1984 .