Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design

(2021) Yuhua Chen et al.   G3-Genes Genomes Genetics

Haplotype- and SNP-Based GWAS for Growth and Wood Quality Traits in Eucalyptus cladocalyx Trees under Arid Conditions

(2021) Camilo E. Valenzuela et al.   Plants-Basel

Genome‐wide association study of cyanogenic glycosides, proline, sugars, and pigments in Eucalyptus cladocalyx after 18 consecutive dry summers

(2021) Freddy Mora‐Poblete et al.   PHYSIOLOGIA PLANTARUM

Evaluating the accuracy of genomic prediction for the management and conservation of relictual natural tree populations

(2021) Sebastián Arenas et al.   Tree Genetics & Genomes

Mutations introduced in susceptibility genes through CRISPR/Cas9 genome editing confer increased late blight resistance in potatoes

(2021) Nam Phuong Kieu et al.   Scientific Reports

Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods

(2021) Bartosz Ulaszewski et al.   Forests

Genetic containment in vegetatively propagated forest trees: CRISPR disruption of LEAFY function in Eucalyptus gives sterile indeterminate inflorescences and normal juvenile development

(2021) Estefania Elorriaga et al.   PLANT BIOTECHNOLOGY JOURNAL

The genetic basis of adaptation in phenology in an introduced population of Black Cottonwood (Populus trichocarpa, Torr. & Gray)

(2021) Rami-Petteri Apuli et al.   BMC PLANT BIOLOGY

Erratum to: Genome-wide association studies reveal the coordinated regulatory networks underlying photosynthesis and wood formation in Populus

(2021) Mingyang Quan et al.   JOURNAL OF EXPERIMENTAL BOTANY

An Axiom SNP genotyping array for Douglas-fir

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

Impact of sorghum racial structure and diversity on genomic prediction of grain yield components

(2020) Sirjan Sapkota et al.   CROP SCIENCE

Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce

(2020) Patrick R. N. Lenz et al.   HEREDITY

Genomic Prediction Accuracy of Seven Breeding Selection Traits Improved by QTL Identification in Flax

(2020) Samuel Lan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat

(2020) Congwei Sun et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic parameters of growth and adaptive traits in aspen (Populus tremuloides): Implications for tree breeding in a warming world

(2020) Chen Ding et al.   PLoS One

Exploring Deep Learning for Complex Trait Genomic Prediction in Polyploid Outcrossing Species

(2020) Laura M. Zingaretti et al.   Frontiers in Plant Science

Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx

(2020) Paulina Ballesta et al.   Plants-Basel

Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of Norway spruce

(2020) Linghua Zhou et al.   BMC GENOMICS

Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook

(2020) Sunny Ahmar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5 , linked to Heterobasidion parviporum resistance

(2020) Malin Elfstrand et al.   PLANT CELL AND ENVIRONMENT

Genomic selection for resistance to spruce budworm in white spruce and relationships with growth and wood quality traits

(2020) Jean Beaulieu et al.   Evolutionary Applications

Tree breeding and silviculture: Douglas-fir volume gains with minimal wood quality loss under variable planting densities

(2020) Miriam Isaac-Renton et al.   FOREST ECOLOGY AND MANAGEMENT

Selecting for water use efficiency, wood chemical traits and biomass with genomic selection in a Eucalyptus breeding program

(2020) Jean-Marc Bouvet et al.   FOREST ECOLOGY AND MANAGEMENT

A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement

(2020) Sunny Ahmar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genome-wide prediction for complex traits under the presence of dominance effects in simulated populations using GBLUP and machine learning methods

(2020) Anderson Antonio Carvalho Alves et al.   JOURNAL OF ANIMAL SCIENCE

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

(2020) Annika Perry et al.   Molecular Ecology Resources

Effective reduction in chimeric mutants of poplar trees produced by CRISPR/Cas9 through a second round of shoot regeneration

(2020) Liping Ding et al.   Plant Biotechnology Reports

Linkage disequilibrium vs. pedigree: Genomic selection prediction accuracy in conifer species

(2020) Frances R. Thistlethwaite et al.   PLoS One

Expected benefits of genomic selection for growth and wood quality traits in Eucalyptus grandis

(2020) Makobatjatji M. Mphahlele et al.   Tree Genetics & Genomes

Genomic Studies Reveal Substantial Dominant Effects and Improved Genomic Predictions in an Open-Pollinated Breeding Population of Eucalyptus pellita

(2020) Saravanan Thavamanikumar et al.   G3-Genes Genomes Genetics

CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology

(2020) Erika N. Dort et al.   Frontiers in Plant Science

A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants

(2020) Juan M. Debernardi et al.   NATURE BIOTECHNOLOGY

A 3K Axiom SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer tree Araucaria angustifolia (Bert.) Kuntze

(2020) Pedro Italo T. Silva et al.   PLoS One

Overexpression of the Transcription Factor GROWTH-REGULATING FACTOR5 Improves Transformation of Dicot and Monocot Species

(2020) Jixiang Kong et al.   Frontiers in Plant Science

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

(2020) Hari B. Chhetri et al.   Frontiers in Plant Science

Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

(2020) Andrés J. Cortés et al.   Frontiers in Plant Science

Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine

(2020) Ainhoa Calleja-Rodriguez et al.   BMC GENOMICS

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

(2020) Carolina Bernhardsson et al.   Molecular Ecology Resources

Efficient multiplex genome editing by CRISPR/Cas9 in common wheat

(2020) Jihu Li et al.   PLANT BIOTECHNOLOGY JOURNAL

GRF-GIF Chimeras Boost Plant Regeneration

(2020) Guangbin Luo et al.   TRENDS IN PLANT SCIENCE

Efficient Genome Editing in Populus Using CRISPR/Cas12a

(2020) Yi An et al.   Frontiers in Plant Science

Genome-Wide Prediction of Complex Traits in Two Outcrossing Plant Species Through Deep Learning and Bayesian Regularized Neural Network

(2020) Carlos Maldonado et al.   Frontiers in Plant Science

Gene Editing in Plants– Progress and Challenges

(2019) Yanfei Mao et al.   National Science Review

Efficient Targeted Mutagenesis in Apple and First Time Edition of Pear Using the CRISPR-Cas9 System

(2019) Aurélie Charrier et al.   Frontiers in Plant Science

Bayesian Mapping Reveals Large-Effect Pleiotropic QTLs for Wood Density and Slenderness Index in 17-Year-Old Trees of Eucalyptus cladocalyx

(2019) Camilo Valenzuela et al.   Forests

Improving genomic prediction of growth and wood traits in Eucalyptus using phenotypes from non-genotyped trees by single-step GBLUP

(2019) Eduardo P. Cappa et al.   PLANT SCIENCE

Multi‐trait genomic selection for weevil resistance, growth, and wood quality in Norway spruce

(2019) Patrick R.N. Lenz et al.   Evolutionary Applications

Efficient TALEN mediated gene editing in wheat

(2019) Ming Luo et al.   PLANT BIOTECHNOLOGY JOURNAL

Combining pedigree and genomic information to improve prediction quality: an example in sorghum

(2019) Julio G. Velazco et al.   THEORETICAL AND APPLIED GENETICS

Mapping quantitative trait loci for growth and wood property traits in Cryptomeria japonica across multiple environments

(2019) Hideki Mori et al.   Tree Genetics & Genomes

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype

(2019) Bojian Yin et al.   BIOINFORMATICS

Evaluating the Efficiency of gRNAs in CRISPR/Cas9 Mediated Genome Editing in Poplars

(2019) Tobias Bruegmann et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Breeding crops to feed 10 billion

(2019) Lee T. Hickey et al.   NATURE BIOTECHNOLOGY

Genomic Prediction of Additive and Non-additive Effects Using Genetic Markers and Pedigrees

(2019) Janeo Eustáquio de Almeida Filho et al.   G3-Genes Genomes Genetics

Time trends of genetic parameters and genetic gains and optimum selection age for growth traits in sugi (Cryptomeria japonica) based on progeny tests conducted throughout Japan

(2019) Yuichiro Hiraoka et al.   Journal of Forest Research

CRISPR / dC as9 platforms in plants: strategies and applications beyond genome editing

(2019) Mahdi Moradpour et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR-based tools for targeted transcriptional and epigenetic regulation in plants

(2019) Joanne E. Lee et al.   PLoS One

A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata

(2019) Emily Telfer et al.   PLoS One

Extension of a haplotype-based genomic prediction model to manage multi-environment wheat data using environmental covariates

(2019) Sang He et al.   THEORETICAL AND APPLIED GENETICS

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

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

(2019) Paulina Ballesta et al.   Plants-Basel

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa

(2019) Fernando P. Guerra et al.   BMC GENOMICS

Within-family genomic selection in rubber tree (Hevea brasiliensis) increases genetic gain for rubber production

(2019) David Cros et al.   INDUSTRIAL CROPS AND PRODUCTS

Core set construction and association analysis of Pinus massoniana from Guangdong province in southern China using SLAF-seq

(2019) Qingsong Bai et al.   Scientific Reports

Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping

(2019) Fang Liu et al.   G3-Genes Genomes Genetics

Genomic Selection in Rubber Tree Breeding: A Comparison of Models and Methods for Managing G×E Interactions

(2019) Livia M. Souza et al.   Frontiers in Plant Science

Genomic selection for non-key traits in radiata pine when the documented pedigree is corrected using DNA marker information

(2019) Yongjun Li et al.   BMC GENOMICS

Assessing the sensitivities of genomic selection for growth and wood quality traits in lodgepole pine using Bayesian models

(2019) Nicholas K. Ukrainetz et al.   Tree Genetics & Genomes

Thirteen years under arid conditions: exploring marker-trait associations in Eucalyptus cladocalyx for complex traits related to flowering, stem form and growth

(2018) Osvin Arriagada et al.   BREEDING SCIENCE

Genomic selection using principal component regression

(2018) Caroline Du et al.   HEREDITY

Efficiency of genomic prediction across two Eucalyptus nitens seed orchards with different selection histories

(2018) Mari Suontama et al.   HEREDITY

Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa

(2018) Athena D. McKown et al.   NEW PHYTOLOGIST

Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum ) using a DNA repair template

(2018) Yidong Ran et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomic-based multiple-trait evaluation in Eucalyptus grandis using dominant DArT markers

(2018) Eduardo P. Cappa et al.   PLANT SCIENCE

Benefits and risks of using clones in forestry – a review

(2018) Harry X. Wu   SCANDINAVIAN JOURNAL OF FOREST RESEARCH

Molecular cloning and characterization of a brassinosteriod biosynthesis-related gene PtoDWF4 from Populus tomentosa

(2018) Yun Shen et al.   TREE PHYSIOLOGY

Selection on Expected Maximum Haploid Breeding Values Can Increase Genetic Gain in Recurrent Genomic Selection

(2018) Dominik Müller et al.   G3-Genes Genomes Genetics

Haplotype-Based Genome-Wide Prediction Models Exploit Local Epistatic Interactions Among Markers

(2018) Yong Jiang et al.   G3-Genes Genomes Genetics

Optimising Genomic Selection in Wheat: Effect of Marker Density, Population Size and Population Structure on Prediction Accuracy

(2018) Adam Norman et al.   G3-Genes Genomes Genetics

Landscape genomic prediction for restoration of a Eucalyptus foundation species under climate change

(2018) Megan Ann Supple et al.   eLife

CRISPR/Cas9-Mediated Mutagenesis of Four Putative Symbiosis Genes of the Tropical Tree Parasponia andersonii Reveals Novel Phenotypes

(2018) Arjan van Zeijl et al.   Frontiers in Plant Science

Dissection of Insertion–Deletion Variants within Differentially Expressed Genes Involved in Wood Formation in Populus

(2018) Chenrui Gong et al.   Frontiers in Plant Science

Variation in Mutation Spectra Among CRISPR/Cas9 Mutagenized Poplars

(2018) Estefania Elorriaga et al.   Frontiers in Plant Science

Genome Size Diversity and Its Impact on the Evolution of Land Plants

(2018) et al.   Genes

The draft genome sequence of cork oak

(2018) António Marcos Ramos et al.   Scientific Data

Are tree breeders properly predicting genetic gain? A case study involving Corymbia species

(2018) Evandro Vagner Tambarussi et al.   EUPHYTICA

OUP accepted manuscript

(2018)   JOURNAL OF HEREDITY

Independent and Joint-GWAS for growth traits in Eucalyptus by assembling genome-wide data for 3373 individuals across four breeding populations

(2018) Bárbara S. F. Müller et al.   NEW PHYTOLOGIST

Performance of multi-trait genomic selection for Eucalyptus robusta breeding program

(2018) Tahina Rambolarimanana et al.   Tree Genetics & Genomes

Effect of genomic prediction on response to selection in forest tree breeding

(2018) J. Stejskal et al.   Tree Genetics & Genomes

Multiple-trait BLUP: a suitable strategy for genetic selection of Eucalyptus

(2018) Rodrigo Silva Alves et al.   Tree Genetics & Genomes

Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar)

(2018) Yuichiro Hiraoka et al.   Frontiers in Plant Science

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

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

(2018) Sreya Ghosh et al.   Nature Protocols

Genomic architecture of complex traits in loblolly pine

(2018) Amanda R. De La Torre et al.   NEW PHYTOLOGIST

Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree

(2018) Wellington Muchero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speed breeding orphan crops

(2018) Tinashe Chiurugwi et al.   THEORETICAL AND APPLIED GENETICS

Back to the future: revisiting MAS as a tool for modern plant breeding

(2018) Joshua N. Cobb et al.   THEORETICAL AND APPLIED GENETICS

Genomic Prediction of Growth and Stem Quality Traits in Eucalyptus globulus Labill. at Its Southernmost Distribution Limit in Chile

(2018) Paulina Ballesta et al.   Forests

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar

(2018) Renaud Rincent et al.   G3-Genes Genomes Genetics

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding

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

Genome Editing in Trees: From Multiple Repair Pathways to Long-Term Stability

(2018) William Patrick Bewg et al.   Frontiers in Plant Science

Genome-Wide Association Studies to Improve Wood Properties: Challenges and Prospects

(2018) Qingzhang Du et al.   Frontiers in Plant Science

A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction

(2017) Boby Mathew et al.   HEREDITY

CRISPR/Cas9: An RNA-guided highly precise synthetic tool for plant genome editing

(2017) Yeliz Demirci et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Short communication: The combined use of linkage disequilibrium–based haploblocks and allele frequency–based haplotype selection methods enhances genomic evaluation accuracy in dairy cattle

(2017) Dávid Jónás et al.   JOURNAL OF DAIRY SCIENCE

SNP discovery from next-generation transcriptome sequencing data and their validation using KASP assay in wheat (Triticum aestivum L.)

(2017) Saket Chandra et al.   MOLECULAR BREEDING

Reproductive modification in forest plantations: impacts on biodiversity and society

(2017) Steven H. Strauss et al.   NEW PHYTOLOGIST

Saturated genic SNP mapping identified functional candidates and selection tools for the Pinus monticola Cr2 locus controlling resistance to white pine blister rust

(2017) Jun-Jun Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

New variants of CRISPR RNA-guided genome editing enzymes

(2017) Jana Murovec et al.   PLANT BIOTECHNOLOGY JOURNAL

PtrMYB57 contributes to the negative regulation of anthocyanin and proanthocyanidin biosynthesis in poplar

(2017) Shuzhen Wan et al.   PLANT CELL REPORTS

Trends in plant research using molecular markers

(2017) Jose Antonio Garrido-Cardenas et al.   PLANTA

Genomic prediction ability for yield-related traits in German winter barley elite material

(2017) Patrick Thorwarth et al.   THEORETICAL AND APPLIED GENETICS

Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing

(2017) Elsa Sverrisdóttir et al.   THEORETICAL AND APPLIED GENETICS

Mitigation of inbreeding while preserving genetic gain in genomic breeding programs for outbred plants

(2017) Zibei Lin et al.   THEORETICAL AND APPLIED GENETICS

Genomic predictions of breeding values in a cloned Eucalyptus globulus population in Chile

(2017) Ricardo Durán et al.   Tree Genetics & Genomes

PtoMYB170 positively regulates lignin deposition during wood formation in poplar and confers drought tolerance in transgenic Arabidopsis

(2017) Changzheng Xu et al.   TREE PHYSIOLOGY

Genomic Quantitative Genetics to Study Evolution in the Wild

(2017) Phillip Gienapp et al.   TRENDS IN ECOLOGY & EVOLUTION

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca

(2017) Blaise Ratcliffe et al.   G3-Genes Genomes Genetics

Which Individuals To Choose To Update the Reference Population? Minimizing the Loss of Genetic Diversity in Animal Genomic Selection Programs

(2017) Sonia E. Eynard et al.   G3-Genes Genomes Genetics

Genomics-assisted breeding – A revolutionary strategy for crop improvement

(2017) Peng-fei LENG et al.   Journal of Integrative Agriculture

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing

(2017) Aleksey V. Zimin et al.   GigaScience

Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set

(2017) Nicholas P Howard et al.   Horticulture Research

Exploration of genetic architecture through sib-ship reconstruction in advanced breeding population of Eucalyptus nitens

(2017) Jaroslav Klápště et al.   PLoS One

Estimation of genomic prediction accuracy from reference populations with varying degrees of relationship

(2017) S. Hong Lee et al.   PLoS One

Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.)

(2016) Mengmeng Lu et al.   BMC GENOMICS

Developing management strategies for tree improvement programs under climate change: Insights gained from long-term field trials with lodgepole pine

(2016) Laura K. Gray et al.   FOREST ECOLOGY AND MANAGEMENT

Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium

(2016) Pascal Schopp et al.   GENETICS

Genome engineering of woody plants: past, present and future

(2016) Yuriko Osakabe et al.   JOURNAL OF WOOD SCIENCE

Accessing marker effects and heritability estimates from genome prediction by Bayesian regularized neural networks

(2016) Leonardo Siqueira Glória et al.   Livestock Science

PediHaplotyper: software for consistent assignment of marker haplotypes in pedigrees

(2016) Roeland E. Voorrips et al.   MOLECULAR BREEDING

New resources for genetic studies inPopulus nigra: genome-wide SNP discovery and development of a 12k Infinium array

(2016) P. Faivre-Rampant et al.   Molecular Ecology Resources

Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

(2016) Annette M. Fahrenkrog et al.   NEW PHYTOLOGIST

Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus

(2016) Rafael Tassinari Resende et al.   NEW PHYTOLOGIST

Genomic selection in maritime pine

(2016) Fikret Isik et al.   PLANT SCIENCE

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness

(2016) Jérôme Bartholomé et al.   PLoS One

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

(2016) Michael K. K. Leung et al.   PROCEEDINGS OF THE IEEE

CRISPR/Cas9: an advanced tool for editing plant genomes

(2016) Milan Kumar Samanta et al.   TRANSGENIC RESEARCH

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

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

Dissection of additive, dominant, epistatic roles of allelic variation within heat shock factor genes in Chinese indigenous poplar (Populus simonii)

(2016) Qingzhang Du et al.   Tree Genetics & Genomes

Canopy Temperature and Vegetation Indices from High-Throughput Phenotyping Improve Accuracy of Pedigree and Genomic Selection for Grain Yield in Wheat

(2016) Jessica Rutkoski et al.   G3-Genes Genomes Genetics

Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass

(2016) Zibei Lin et al.   Plant Genome

Using Genetic Distance to Infer the Accuracy of Genomic Prediction

(2016) Marco Scutari et al.   PLoS Genetics

Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium

(2016) Pascal Schopp et al.   GENETICS

Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

(2016) Guozheng Liu et al.   PLoS One

CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.)

(2016) Chong Ren et al.   Scientific Reports

Estimating solid wood properties using Pilodyn and acoustic velocity on standing trees of Norway spruce

(2015) Zhi-Qiang Chen et al.   ANNALS OF FOREST SCIENCE

LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants: Fig. 1.

(2015) Mitchell J. Machiela et al.   BIOINFORMATICS

ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

(2015) Mario Di Guardo et al.   BIOINFORMATICS

Two molecular measures of relatedness based on haplotype sharing

(2015) David Edwards   BMC BIOINFORMATICS

Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

(2015) Omnia Gamal El-Dien et al.   BMC GENOMICS

Interferon gamma polymorphisms and hepatitis B virus-related liver cirrhosis risk in a Chinese population

(2015) Yifan Sun et al.   Cancer Cell International

Adding Genetically Distant Individuals to Training Populations Reduces Genomic Prediction Accuracy in Barley

(2015) Aaron J. Lorenz et al.   CROP SCIENCE

Making a chocolate chip: development and evaluation of a 6K SNP array forTheobroma cacao

(2015) Donald Livingstone et al.   DNA RESEARCH

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

(2015) Hans D. Daetwyler et al.   GENETICS

Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

(2015) Wirulda Pootakham et al.   GENOMICS

Impact of relationships between test and training animals and among training animals on reliability of genomic prediction

(2015) X. Wu et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Single-nucleotide polymorphism discovery and validation in high-density SNP array for genetic analysis in European white oaks

(2015) C. Lepoittevin 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

Genetic architecture of growth traits inPopulusrevealed by integrated quantitative trait locus (QTL) analysis and association studies

(2015) Qingzhang Du et al.   NEW PHYTOLOGIST

Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce

(2015) Mebarek Lamara et al.   NEW PHYTOLOGIST

Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennialPopulusreveals 4-coumarate:CoA ligase specificity and redundancy

(2015) Xiaohong Zhou et al.   NEW PHYTOLOGIST

Genetically engineered trees: Paralysis from good intentions

(2015) S. H. Strauss et al.   SCIENCE

Genome-wide association study, genomic prediction and marker-assisted selection for seed weight in soybean (Glycine max)

(2015) Jiaoping Zhang et al.   THEORETICAL AND APPLIED GENETICS

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

(2015) Hans D. Daetwyler et al.   GENETICS

CRISPRing into the woods

(2015) Chung-Jui Tsai et al.   GM Crops & Food-Biotechnology in Agriculture and the Food Chain

Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population

(2015) Beatriz CD Cuyabano et al.   BMC GENOMICS

Efficient CRISPR/Cas9-mediated Targeted Mutagenesis in Populus in the First Generation

(2015) Di Fan et al.   Scientific Reports

Evaluation of Genomic Selection Training Population Designs and Genotyping Strategies in Plant Breeding Programs Using Simulation

(2014) John M. Hickey et al.   CROP SCIENCE

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

(2014) A. Zimin et al.   GENETICS

Genome-Wide Regression and Prediction with the BGLR Statistical Package

(2014) P. Perez et al.   GENETICS

Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease

(2014) André M. Comeau et al.   Genome Biology and Evolution

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

(2014) J Beaulieu et al.   HEREDITY

Imputation of genotypes from low density (50,000 markers) to high density (700,000 markers) of cows from research herds in Europe, North America, and Australasia using 2 reference populations

(2014) J.E. Pryce et al.   JOURNAL OF DAIRY SCIENCE

The genome of Eucalyptus grandis

(2014) Alexander A. Myburg et al.   NATURE

Genetic parameter estimates informed by a marker-based pedigree: a case study with Eucalyptus cladocalyx in southern Australia

(2014) David Bush et al.   Tree Genetics & Genomes

Bayesian estimation of genetic parameters for growth, stem straightness, and survival in Eucalyptus globulus on an Andean Foothill site

(2014) Freddy Mora et al.   Tree Genetics & Genomes

Association mapping for wood quality and growth traits in Eucalyptus globulus ssp. globulus Labill identifies nine stable marker-trait associations for seven traits

(2014) Saravanan Thavamanikumar et al.   Tree Genetics & Genomes

Genomic prediction in an admixed population of Atlantic salmon (Salmo salar)

(2014) Jørgen ØdegÃ¥rd et al.   Frontiers in Genetics

The significance of single nucleotide polymorphisms (SNPs) in Eucalyptus globulus breeding programs

(2013) Saravanan Thavamanikumar et al.   AUSTRALIAN FORESTRY

Relatedness and Genotype × Environment Interaction Affect Prediction Accuracies in Genomic Selection: A Study in Cassava

(2013) Delphine Ly et al.   CROP SCIENCE

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

(2013) D. Gianola   GENETICS

Model comparison on genomic predictions using high-density markers for different groups of bulls in the Nordic Holstein population

(2013) H. Gao et al.   JOURNAL OF DAIRY SCIENCE

Valuation of pollinator forage services provided by Eucalyptus cladocalyx

(2013) Willem J. de Lange et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

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

Application of the CRISPR–Cas System for Efficient Genome Engineering in Plants

(2013) Yanfei Mao et al.   Molecular Plant

RNA guides genome engineering

(2013) Claudio Mussolino et al.   NATURE BIOTECHNOLOGY

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

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

‘Schmidt's Antonovka’ is identical to ‘Common Antonovka’, an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses

(2013) Anna Pikunova et al.   Tree Genetics & Genomes

Distribution of Long-Range Linkage Disequilibrium and Tajima’s D Values in Scandinavian Populations of Norway Spruce ( Picea abies )

(2013) Hanna Larsson et al.   G3-Genes Genomes Genetics

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

Potential and Optimization of Genomic Selection for Fusarium Head Blight Resistance in Six-Row Barley

(2012) A. J. Lorenz et al.   CROP SCIENCE

The Effect of Linkage Disequilibrium and Family Relationships on the Reliability of Genomic Prediction

(2012) Y. C. J. Wientjes et al.   GENETICS

Inferring Coancestry in Population Samples in the Presence of Linkage Disequilibrium

(2012) M. D. Brown et al.   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

Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding

(2012) G. de los Campos et al.   GENETICS

Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking

(2012) H. D. Daetwyler et al.   GENETICS

Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes1,2

(2012) K. L. Weber et al.   JOURNAL OF ANIMAL SCIENCE

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest treePopulus trichocarpa

(2012) Gancho T. Slavov et al.   NEW PHYTOLOGIST

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

Association genetics of chemical wood properties in black poplar (Populus nigra)

(2012) Fernando P. Guerra et al.   NEW PHYTOLOGIST

Three Members of the Arabidopsis Glycosyltransferase Family 8 Are Xylan Glucuronosyltransferases

(2012) E. A. Rennie et al.   PLANT PHYSIOLOGY

Development and Evaluation of a Genome-Wide 6K SNP Array for Diploid Sweet Cherry and Tetraploid Sour Cherry

(2012) Cameron Peace et al.   PLoS One

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Use of resampling to assess optimal subgroup composition for estimating genetic parameters from progeny trials

(2012) Martin Perron et al.   Tree Genetics & Genomes

SNP discovery, gene diversity, and linkage disequilibrium in wild populations of Populus tremuloides

(2012) Colin T. Kelleher et al.   Tree Genetics & Genomes

Genomic selection in French dairy cattle

(2012) D. Boichard et al.   Animal Production Science

Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat

(2012) Paulino Pérez-Rodríguez et al.   G3-Genes Genomes Genetics

Extension of the bayesian alphabet for genomic selection

(2011) David Habier et al.   BMC BIOINFORMATICS

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

Using the genomic relationship matrix to predict the accuracy of genomic selection

(2011) M.E. Goddard et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Genomic breeding value estimation using genetic markers, inferred ancestral haplotypes, and the genomic relationship matrix

(2011) A.P.W. de Roos et al.   JOURNAL OF DAIRY SCIENCE

Forest tree genomics: growing resources and applications

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

Discovery of polymorphisms in starch-related genes in rice germplasm by amplification of pooled DNA and deeply parallel sequencing†

(2011) Ardashir Kharabian-Masouleh et al.   PLANT BIOTECHNOLOGY JOURNAL

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

(2010) Allen Kovach et al.   BMC GENOMICS

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers

(2010) J. Crossa et al.   GENETICS

Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera)

(2010) Matthew S. Olson et al.   NEW PHYTOLOGIST

Multi-trait BLUP in half-sib selection of annual crops

(2010) J. M. S. Viana et al.   PLANT BREEDING

Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in Eucalyptus nitens full-sib families

(2010) Bala R. Thumma et al.   Tree Genetics & Genomes

Genomic selection in forest tree breeding

(2010) Dario Grattapaglia et al.   Tree Genetics & Genomes

Quantitative trait locus (QTL) analysis of wood quality traits in Eucalyptus nitens

(2009) Bala R. Thumma et al.   Tree Genetics & Genomes

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Accuracy of Genomic Selection Using Different Methods to Define Haplotypes

(2008) M. P. L. Calus et al.   GENETICS

The importance of haplotype length and heritability using genomic selection in dairy cattle

(2008) T.M. Villumsen et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE