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Methods ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01192

LD-Annot: a bioinformatics tool to automatically provide candidate SNPs with annotations for genetically linked genes

 Julien Prunier1, 2, 3*,  Audrey Lemaçon1, 3, Alexandre Bastien4, Mohsen Jafarikia5,  Ilga M. Porth2, 6, Claude Robert4 and Arnaud Droit1, 3*
  • 1Research Center of the CHU de Québec, Canada
  • 2Centre for Forest Research, Laval University, Canada
  • 3Laval University, Canada
  • 4Faculty of Agricultural Sciences and Food, Laval University, Canada
  • 5Other, Canada
  • 6Department of Wood Science and Forestry, Faculty of Forestry, Geography and Geomatics, Laval University, Canada

A multitude of model and non-model species studies have now taken full advantage of powerful high-throughput genotyping advances such as SNP arrays and genotyping-by-sequencing (GBS) technology to investigate the genetic basis of trait variation. However, due to incomplete genome coverage by these technologies, the identified SNPs are likely in linkage disequilibrium (LD) with the causal polymorphisms, rather than be causal themselves. In addition, researchers could benefit from annotations for the identified candidate SNPs and, simultaneously, for all neighbouring genes in genetic linkage. In such case, LD extent estimation surrounding the candidate SNPs is required to determine the regions encompassing genes of interest. We describe here an automated pipeline, “LD-Annot”, designed to delineate specific regions of interest for a given experiment and candidate polymorphisms on the basis of LD extent, and furthermore, provide annotations for all genes within such regions.
LD-Annot uses standard file formats, bioinformatics tools and languages to provide identifiers, coordinates and annotations for genes in genetic linkage with each candidate polymorphism. Although the focus lies upon SNP arrays and GBS data as they are being routinely deployed, this pipeline can be applied to a variety of datasets as long as genotypic data are available for a high number of polymorphisms and formatted into a vcf file. A checkpoint procedure in the pipeline allows to test several threshold values for linkage without having to rerun the entire pipeline, thus saving the user computational time and resources.
We applied this new pipeline to four different sample sets: two breeding populations GBS datasets, one within-pedigree SNP set coming from whole genome sequencing (WGS), and a very large multi-varieties SNP dataset obtained from WGS, representing variable sample sizes, and numbers of polymorphisms. LD-annot performed within minutes, even when very high numbers of polymorphisms are investigated and thus, will efficiently assist research efforts aimed at identifying biologically meaningful genetic polymorphisms underlying phenotypic variation. LD-Annot tool is available under a GPL license from https://github.com/ArnaudDroitLab/LD-annot .

Keywords: Linkage disequiblibrium, candidate SNP, SNP annotation, Bioinformatics tool, Variant Call Format (VCF), SNP chip analyses

Received: 02 Jul 2019; Accepted: 28 Oct 2019.

Copyright: © 2019 Prunier, Lemaçon, Bastien, Jafarikia, Porth, Robert and Droit. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
PhD. Julien Prunier, Research Center of the CHU de Québec, Québec City, G1V 4G2, Quebec, Canada, jprunier.1@gmail.com
Prof. Arnaud Droit, Research Center of the CHU de Québec, Québec City, G1V 4G2, Quebec, Canada, Arnaud.Droit@crchudequebec.ulaval.ca