[HTML][HTML] AccuCalc: A python package for accuracy calculation in GWAS

J Biová, N Dietz, YO Chan, T Joshi, K Bilyeu… - Genes, 2023 - mdpi.com
The genome-wide association study (GWAS) is a popular genomic approach that identifies
genomic regions associated with a phenotype and, thus, aims to discover causative …

Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data

J Batley, G Barker, H O'Sullivan, KJ Edwards… - Plant …, 2003 - academic.oup.com
We have developed a computer based method to identify candidate single nucleotide
polymorphisms (SNPs) and small insertions/deletions from expressed sequence tag data …

[PDF][PDF] Single nucleotide polymorphism identification in polyploids: a review, example, and recommendations

J Clevenger, C Chavarro, SA Pearl, P Ozias-Akins… - Molecular plant, 2015 - cell.com
Understanding the relationship between genotype and phenotype is a major biological
question and being able to predict phenotypes based on molecular genotypes is integral to …

[HTML][HTML] Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids

HU Jan, M Guan, M Yao, W Liu, D Wei, A Abbadi… - Plant science, 2019 - Elsevier
Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have
attempted to provide reliable and quick methods to identify genome regions in parental lines …

[HTML][HTML] Watch out for a second SNP: focus on multi-nucleotide variants in coding regions and rescued stop-gained

F Degalez, F Jehl, K Muret, M Bernard, F Lecerf… - Frontiers in …, 2021 - frontiersin.org
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the
fraction usually studied is harbored in protein-coding regions because potential impacts on …

Pitfalls of predicting complex traits from SNPs

NR Wray, J Yang, BJ Hayes, AL Price… - Nature Reviews …, 2013 - nature.com
The success of genome-wide association studies (GWASs) has led to increasing interest in
making predictions of complex trait phenotypes, including disease, from genotype data …

[HTML][HTML] Prediction strategies for leveraging information of associated traits under single-and multi-trait approaches in soybeans

R Persa, A Bernardeli, D Jarquin - Agriculture, 2020 - mdpi.com
The availability of molecular markers has revolutionized conventional ways to improve
genotypes in plant and animal breeding through genome-based predictions. Several …

Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment

Y Li, P Ruperao, J Batley, D Edwards… - The Plant …, 2022 - Wiley Online Library
Achieving yield potential in chickpea (Cicer arietinum L.) is limited by many constraints that
include biotic and abiotic stresses. Combining next‐generation sequencing technology with …

[HTML][HTML] Comparing genomic prediction models by means of cross validation

MF Schrauf, G de Los Campos, S Munilla - Frontiers in Plant Science, 2021 - frontiersin.org
In the two decades of continuous development of genomic selection, a great variety of
models have been proposed to make predictions from the information available in dense …

[HTML][HTML] TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline

JC Glaubitz, TM Casstevens, F Lu, J Harriman… - PloS one, 2014 - journals.plos.org
Genotyping by sequencing (GBS) is a next generation sequencing based method that takes
advantage of reduced representation to enable high throughput genotyping of large …