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Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approac...

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Autores principales: Arca, Mariangela, Mary-Huard, Tristan, Gouesnard, Brigitte, Bérard, Aurélie, Bauland, Cyril, Combes, Valérie, Madur, Delphine, Charcosset, Alain, Nicolas, Stéphane D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817617/
https://www.ncbi.nlm.nih.gov/pubmed/33488638
http://dx.doi.org/10.3389/fpls.2020.568699
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author Arca, Mariangela
Mary-Huard, Tristan
Gouesnard, Brigitte
Bérard, Aurélie
Bauland, Cyril
Combes, Valérie
Madur, Delphine
Charcosset, Alain
Nicolas, Stéphane D.
author_facet Arca, Mariangela
Mary-Huard, Tristan
Gouesnard, Brigitte
Bérard, Aurélie
Bauland, Cyril
Combes, Valérie
Madur, Delphine
Charcosset, Alain
Nicolas, Stéphane D.
author_sort Arca, Mariangela
collection PubMed
description Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.
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spelling pubmed-78176172021-01-22 Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array Arca, Mariangela Mary-Huard, Tristan Gouesnard, Brigitte Bérard, Aurélie Bauland, Cyril Combes, Valérie Madur, Delphine Charcosset, Alain Nicolas, Stéphane D. Front Plant Sci Plant Science Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species. Frontiers Media S.A. 2021-01-07 /pmc/articles/PMC7817617/ /pubmed/33488638 http://dx.doi.org/10.3389/fpls.2020.568699 Text en Copyright © 2021 Arca, Mary-Huard, Gouesnard, Bérard, Bauland, Combes, Madur, Charcosset and Nicolas. http://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
Arca, Mariangela
Mary-Huard, Tristan
Gouesnard, Brigitte
Bérard, Aurélie
Bauland, Cyril
Combes, Valérie
Madur, Delphine
Charcosset, Alain
Nicolas, Stéphane D.
Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array
title Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array
title_full Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array
title_fullStr Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array
title_full_unstemmed Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array
title_short Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array
title_sort deciphering the genetic diversity of landraces with high-throughput snp genotyping of dna bulks: methodology and application to the maize 50k array
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7817617/
https://www.ncbi.nlm.nih.gov/pubmed/33488638
http://dx.doi.org/10.3389/fpls.2020.568699
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