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PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species

The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP...

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Detalles Bibliográficos
Autores principales: Shook, Johnathon M., Lourenco, Daniela, Singh, Asheesh K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8562157/
https://www.ncbi.nlm.nih.gov/pubmed/34737757
http://dx.doi.org/10.3389/fpls.2021.676269
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author Shook, Johnathon M.
Lourenco, Daniela
Singh, Asheesh K.
author_facet Shook, Johnathon M.
Lourenco, Daniela
Singh, Asheesh K.
author_sort Shook, Johnathon M.
collection PubMed
description The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present “Parental Allele Tracing, Recombination Identification, and Optimal predicTion” (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs.
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spelling pubmed-85621572021-11-03 PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species Shook, Johnathon M. Lourenco, Daniela Singh, Asheesh K. Front Plant Sci Plant Science The lowering genotyping cost is ushering in a wider interest and adoption of genomic prediction and selection in plant breeding programs worldwide. However, improper conflation of historical and recent linkage disequilibrium between markers and genes restricts high accuracy of genomic prediction (GP). Multiple ancestors may share a common haplotype surrounding a gene, without sharing the same allele of that gene. This prevents parsing out genetic effects associated with the underlying allele of that gene among the set of ancestral haplotypes. We present “Parental Allele Tracing, Recombination Identification, and Optimal predicTion” (i.e., PATRIOT) approach that utilizes marker data to allow for a rapid identification of lines carrying specific alleles, increases the accuracy of genomic relatedness and diversity estimates, and improves genomic prediction. Leveraging identity-by-descent relationships, PATRIOT showed an improvement in GP accuracy by 16.6% relative to the traditional rrBLUP method. This approach will help to increase the rate of genetic gain and allow available information to be more effectively utilized within breeding programs. Frontiers Media S.A. 2021-09-29 /pmc/articles/PMC8562157/ /pubmed/34737757 http://dx.doi.org/10.3389/fpls.2021.676269 Text en Copyright © 2021 Shook, Lourenco and Singh. 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 Plant Science
Shook, Johnathon M.
Lourenco, Daniela
Singh, Asheesh K.
PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species
title PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species
title_full PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species
title_fullStr PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species
title_full_unstemmed PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species
title_short PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species
title_sort patriot: a pipeline for tracing identity-by-descent for chromosome segments to improve genomic prediction in self-pollinating crop species
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8562157/
https://www.ncbi.nlm.nih.gov/pubmed/34737757
http://dx.doi.org/10.3389/fpls.2021.676269
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