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The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping

With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and g...

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Autores principales: Cui, Bo, Guo, Zhongxu, Cao, Hongbo, Calus, Mario, Zhang, Qianqian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903072/
https://www.ncbi.nlm.nih.gov/pubmed/36761695
http://dx.doi.org/10.3389/fgene.2022.1028662
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author Cui, Bo
Guo, Zhongxu
Cao, Hongbo
Calus, Mario
Zhang, Qianqian
author_facet Cui, Bo
Guo, Zhongxu
Cao, Hongbo
Calus, Mario
Zhang, Qianqian
author_sort Cui, Bo
collection PubMed
description With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and genes that are highly preferred or pruned during the process of adaptive introgression or long-term hybridization. To the best of our knowledge, we are the first to develop a platform with computational integration of a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping. The rIBD algorithm is designed for mapping the fine-scaled genomic regions under adaptive introgression between the source breeds and the admixed breed. Our rIBD calculation platform provides compact functions including reading input information and uploading of files, rIBD calculation, and presentation of the rIBD scores. We analyzed the simulated data using the rIBD calculation platform and calculated the average IBD score of 0.061 with a standard deviation of 0.124. The rIBD scores generally follow a normal distribution, and a cut-off of 0.432 and −0.310 for both positive and negative rIBD scores is derived to enable the identification of genomic regions showing significant introgression signals from the source breed to the admixed breed. A list of genomic regions with detailed calculated rIBD scores is reported, and all the rIBD scores for each of the considered windows are presented in plots on the rIBD calculation platform. Our rIBD calculation platform provides a user-friendly tool for the calculation of fine-scaled rIBD scores for each of the genomic regions to map possible functional genomic variants due to adaptive introgression or long-term hybridization.
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spelling pubmed-99030722023-02-08 The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping Cui, Bo Guo, Zhongxu Cao, Hongbo Calus, Mario Zhang, Qianqian Front Genet Genetics With the development of genotyping and sequencing technology, researchers working in the area of conservation genetics are able to obtain the genotypes or even the sequences of a representative sample of individuals from the population. It is of great importance to examine the genomic variants and genes that are highly preferred or pruned during the process of adaptive introgression or long-term hybridization. To the best of our knowledge, we are the first to develop a platform with computational integration of a relative identity-by-descent (rIBD) scores algorithm for introgressive mapping. The rIBD algorithm is designed for mapping the fine-scaled genomic regions under adaptive introgression between the source breeds and the admixed breed. Our rIBD calculation platform provides compact functions including reading input information and uploading of files, rIBD calculation, and presentation of the rIBD scores. We analyzed the simulated data using the rIBD calculation platform and calculated the average IBD score of 0.061 with a standard deviation of 0.124. The rIBD scores generally follow a normal distribution, and a cut-off of 0.432 and −0.310 for both positive and negative rIBD scores is derived to enable the identification of genomic regions showing significant introgression signals from the source breed to the admixed breed. A list of genomic regions with detailed calculated rIBD scores is reported, and all the rIBD scores for each of the considered windows are presented in plots on the rIBD calculation platform. Our rIBD calculation platform provides a user-friendly tool for the calculation of fine-scaled rIBD scores for each of the genomic regions to map possible functional genomic variants due to adaptive introgression or long-term hybridization. Frontiers Media S.A. 2023-01-24 /pmc/articles/PMC9903072/ /pubmed/36761695 http://dx.doi.org/10.3389/fgene.2022.1028662 Text en Copyright © 2023 Cui, Guo, Cao, Calus and Zhang. https://creativecommons.org/licenses/by/4.0/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.
spellingShingle Genetics
Cui, Bo
Guo, Zhongxu
Cao, Hongbo
Calus, Mario
Zhang, Qianqian
The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
title The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
title_full The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
title_fullStr The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
title_full_unstemmed The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
title_short The computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
title_sort computational implementation of a platform of relative identity-by-descent scores algorithm for introgressive mapping
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9903072/
https://www.ncbi.nlm.nih.gov/pubmed/36761695
http://dx.doi.org/10.3389/fgene.2022.1028662
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