Matapax: an online high-throughput genome-wide association study pipeline.

Plant Physiology
Liam H ChildsDirk Walther

Abstract

High-throughput sequencing and genotyping methods are dramatically increasing the number of observable genetic intraspecies differences that can be exploited as genetic markers. In addition, automated phenotyping platforms and "omics" profiling technologies further enlarge the set of quantifiable macroscopic and molecular traits at an ever-increasing pace. Combined, both lines of technological advances create unparalleled opportunities to identify candidate gene regions and, ideally, even single genes responsible for observed variations in a particular trait via association studies. However, as of yet, this new potential is not sufficiently matched by enabling software solutions to easily exploit this wealth of genotype/phenotype information. We have developed Matapax, a Web-based platform to address this need. Initially, we built the infrastructure to support association studies in Arabidopsis (Arabidopsis thaliana) based on several genotyping efforts covering up to 1,375 Arabidopsis accessions. Based on the user-supplied trait information, associated single-nucleotide polymorphism markers and single-nucleotide polymorphism-harboring or -neighboring genes are identified using both the GAPIT and EMMA libraries developed for R. ...Continue Reading

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Citations

Jan 2, 2013·The Plant Cell·Ümit SerenMagnus Nordborg
Dec 27, 2015·Plant Science : an International Journal of Experimental Plant Biology·Stanislav KoprivaAnna Koprivova
Oct 5, 2016·Nucleic Acids Research·Daniel E CookErik C Andersen
Sep 21, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Masahiko KumagaiTakeshi Itoh
Apr 14, 2021·Plant Physiology·Alisdair R FernieJianbing Yan

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