Impact of genotype‐calling methodologies on genome‐wide association and genomic prediction in polyploids

Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia, North America, and Europe

(2023) Joyce N. Njuguna et al.   Global Change Biology Bioenergy

How Population Structure Impacts Genomic Selection Accuracy in Cross-Validation: Implications for Practical Breeding

(2021) Christian R. Werner et al.   Frontiers in Plant Science

Impact of accounting for allele dosage on genomic prediction in a simulated autopolyploid sturgeon population

(2021) Hailiang Song et al.   AQUACULTURE

Benchmarking small-variant genotyping in polyploids

(2021) Daniel P. Cooke et al.   GENOME RESEARCH

Training Population Optimization for Genomic Selection in Miscanthus

(2020) Marcus O. Olatoye et al.   G3-Genes Genomes Genetics

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

(2019) Lindsay V. Clark et al.   G3-Genes Genomes Genetics

Genetic Mapping With Allele Dosage Information in Tetraploid Urochloa decumbens (Stapf) R. D. Webster Reveals Insights Into Spittlebug (Notozulia entreriana Berg) Resistance

(2019) Rebecca Caroline Ulbricht Ferreira et al.   Frontiers in Plant Science

Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction

(2019) Ivone de Bem Oliveira et al.   G3-Genes Genomes Genetics

Genome‐wide association and genomic prediction for biomass yield in a genetically diverse Miscanthus sinensis germplasm panel phenotyped at five locations in Asia and North America

(2019) Lindsay V. Clark et al.   Global Change Biology Bioenergy

Genomic Selection with Allele Dosage in Panicum maximum Jacq.

(2019) Letícia A. de C. Lara et al.   G3-Genes Genomes Genetics

How can a high-quality genome assembly help plant breeders?

(2019) Juliana Benevenuto et al.   GigaScience

Priors for Genotyping Polyploids

(2019) David Gerard et al.   BIOINFORMATICS

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato

(2018) Jeffrey B. Endelman et al.   GENETICS

Tools for Genetic Studies in Experimental Populations of Polyploids

(2018) Peter M. Bourke et al.   Frontiers in Plant Science

Genetic Variance Partitioning and Genome-Wide Prediction with Allele Dosage Information in Autotetraploid Potato

(2018) Jeffrey B. Endelman et al.   GENETICS

Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea

(2018) Lindsay V Clark et al.   ANNALS OF BOTANY

Molecular and Genetic Bases of Fruit Firmness Variation in Blueberry—A Review

(2018) Francesco Cappai et al.   Agronomy-Basel

Genetic mapping of biomass yield in three interconnected Miscanthus populations

(2017) Hongxu Dong et al.   Global Change Biology Bioenergy

Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application

(2017) Armin Scheben et al.   PLANT BIOTECHNOLOGY JOURNAL

Genotype Calling from Population-Genomic Sequencing Data

(2017) Takahiro Maruki et al.   G3-Genes Genomes Genetics

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

(2017) Kenta Shirasawa et al.   Scientific Reports

Impact of genotyping errors on statistical power of association tests in genomic analyses: A case study

(2016) Lin Hou et al.   GENETIC EPIDEMIOLOGY

Least-Squares Means: TheRPackagelsmeans

(2016) Russell V. Lenth   Journal of Statistical Software

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Application of genotyping by sequencing technology to a variety of crop breeding programs

(2016) Changsoo Kim et al.   PLANT SCIENCE

Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

(2016) M. E. Goddard et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Improving Genetic Gain with Genomic Selection in Autotetraploid Potato

(2016) Anthony T. Slater et al.   Plant Genome

AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example

(2016) Rodrigo R. Amadeu et al.   Plant Genome

The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

(2016) Wen Huang et al.   PLoS Genetics

Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies

(2016) Xiaolei Liu et al.   PLoS Genetics

The impact of genotype calling errors on family-based studies

(2016) Qi Yan et al.   Scientific Reports

Assessment of Genetic Heterogeneity in Structured Plant Populations Using Multivariate Whole-Genome Regression Models

(2015) C. Lehermeier et al.   GENETICS

Correction: Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

(2015) Jennifer Spindel et al.   PLoS Genetics

A footprint of past climate change on the diversity and population structure of Miscanthus sinensis

(2014) Lindsay V. Clark et al.   ANNALS OF BOTANY

Mapping the genome ofMiscanthus sinensisfor QTL associated with biomass productivity

(2014) Justin M. Gifford et al.   Global Change Biology Bioenergy

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

(2014) Jiangfeng He et al.   Frontiers in Plant Science

Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools

(2013) France Dufresne et al.   MOLECULAR ECOLOGY

From QTL to QTN: Candidate Gene Set Approach and a Case Study in Porcine IGF1-FoxO Pathway

(2013) Minghui Wang et al.   PLoS One

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids

(2013) Antonio A. F. Garcia et al.   Scientific Reports

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments

(2012) Vanessa S. Windhausen et al.   G3-Genes Genomes Genetics

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

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

(2011) Jeffrey B. Endelman   Plant Genome

Progress and Promise of Genome-Wide Association Studies for Human Complex Trait Genetics

(2010) B. E. Stranger et al.   GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Variability in GWAS analysis: the impact of genotype calling algorithm inconsistencies

(2010) K Miclaus et al.   PHARMACOGENOMICS JOURNAL

Practical Issues in Imputation-Based Association Mapping

(2008) Yongtao Guan et al.   PLoS Genetics