Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce ( Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species

An Axiom SNP genotyping array for Douglas-fir

(2020) Glenn T. Howe et al.   BMC GENOMICS

Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies)

(2020) Xi Wang et al.   Genome Biology and Evolution

Development of a single nucleotide polymorphism array for population genomic studies in four European pine species

(2020) Annika Perry et al.   Molecular Ecology Resources

­­­­An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)

(2019) Carolina Bernhardsson et al.   G3-Genes Genomes Genetics

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

(2019) Sara Montanari et al.   BMC GENOMICS

Genome‐wide association study identified novel candidate loci affecting wood formation in Norway spruce

(2019) John Baison et al.   PLANT JOURNAL

Fourth cycle breeding and testing strategy for Pinus taeda in the NC State University Cooperative Tree Improvement Program

(2019) Fikret Isik et al.   Tree Genetics & Genomes

Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds

(2019) Malin Elfstrand et al.   MOLECULAR ECOLOGY

Adaptation in plant genomes: Bigger is different

(2018) Wenbin Mei et al.   AMERICAN JOURNAL OF BOTANY

A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies)

(2018) Aïda Azaiez et al.   BMC GENOMICS

Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce

(2018) Zhi-Qiang Chen et al.   BMC GENOMICS

A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array

(2018) Annarita Marrano et al.   PLANT BIOTECHNOLOGY JOURNAL

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding

(2018) Dario Grattapaglia et al.   Frontiers in Plant Science

Development and evaluation of high-density Axiom® CicerSNP  Array for high-resolution genetic mapping and breeding applications in chickpea

(2017) Manish Roorkiwal et al.   PLANT BIOTECHNOLOGY JOURNAL

Genotyping-by-Sequencing Derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

(2017) Waseem Hussain et al.   Scientific Reports

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

(2017) David B. Neale et al.   G3-Genes Genomes Genetics

Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut

(2017) Manish K. Pandey et al.   Scientific Reports

Performance of genomic prediction within and across generations in maritime pine

(2016) Jérôme Bartholomé et al.   BMC GENOMICS

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Intergenic GWAS SNPs are key components of the spatial and regulatory network for human growth

(2016) William Schierding et al.   HUMAN MOLECULAR GENETICS

The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?

(2016) Yoshiaki Tsuda et al.   MOLECULAR ECOLOGY

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations

(2016) Garrett J. McKinney et al.   Molecular Ecology Resources

Development and validation of the Axiom®Apple480K SNP genotyping array

(2016) Luca Bianco et al.   PLANT JOURNAL

Estimation of number and size of QTL effects in forest tree traits

(2016) David Hall et al.   Tree Genetics & Genomes

Development and application of a novel genome-wide SNP array reveals domestication history in soybean

(2016) Jiao Wang et al.   Scientific Reports

Sequence of the Sugar Pine Megagenome

(2016) Kristian A. Stevens et al.   GENETICS

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

(2016) Haiquan Li et al.   npj Genomic Medicine

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

(2015) Nahla V Bassil et al.   BMC GENOMICS

High-density SNP assay development for genetic analysis in maritime pine (Pinus pinaster)

(2015) C. Plomion et al.   Molecular Ecology Resources

Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

(2015) Nathalie Pavy et al.   Molecular Ecology Resources

A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240Eucalyptustree genomes across 12 species

(2015) Orzenil B. Silva-Junior et al.   NEW PHYTOLOGIST

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

(2015) René L. Warren et al.   PLANT JOURNAL

Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice

(2015) Nisha Singh et al.   Scientific Reports

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

(2014) J Beaulieu et al.   HEREDITY

Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers

(2014) Jin Pan et al.   Molecular Ecology Resources

Genomic selection in forest tree breeding: the concept and an outlook to the future

(2014) Fikret Isik   NEW FORESTS

Multiple Dimensions of Climate Change and Their Implications for Biodiversity

(2014) R. A. Garcia et al.   SCIENCE

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

(2013) Joseph Lachance et al.   BIOESSAYS

Development of high-density SNP genotyping arrays for white spruce (Picea glauca) and transferability to subtropical and nordic congeners

(2013) Nathalie Pavy et al.   Molecular Ecology Resources

A 34K SNP genotyping array forPopulus trichocarpa: Design, application to the study of natural populations and transferability to otherPopulusspecies

(2013) A. Geraldes et al.   Molecular Ecology Resources

A new phylogeny for the genus Picea from plastid, mitochondrial, and nuclear sequences

(2013) Jared D. Lockwood et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Dissection of complex traits in forest trees — opportunities for marker-assisted selection

(2013) Saravanan Thavamanikumar et al.   Tree Genetics & Genomes

Genomic Estimated Breeding Values Using Genomic Relationship Matrices in a Cloned Population of Loblolly Pine

(2013) Jaime Zapata-Valenzuela et al.   G3-Genes Genomes Genetics

Accuracy of Genomic Selection Methods in a Standard Data Set of Loblolly Pine (Pinus taeda L.)

(2012) M. F. R. Resende et al.   GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

(2011) Jean Beaulieu et al.   GENETICS

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

(2011) S. J. HELYAR et al.   Molecular Ecology Resources

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

Allelic Variation in Cell Wall Candidate Genes Affecting Solid Wood Properties in Natural Populations and Land Races of Pinus radiata

(2010) S. K. Dillon et al.   GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

Interpreting principal component analyses of spatial population genetic variation

(2008) John Novembre et al.   NATURE GENETICS