Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers

Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence...

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Autores principales: Van Inghelandt, Delphine, Melchinger, Albrecht E., Lebreton, Claude, Stich, Benjamin
Formato: Texto
Lenguaje:English
Publicado: Springer-Verlag 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854351/
https://www.ncbi.nlm.nih.gov/pubmed/20063144
http://dx.doi.org/10.1007/s00122-009-1256-2
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author Van Inghelandt, Delphine
Melchinger, Albrecht E.
Lebreton, Claude
Stich, Benjamin
author_facet Van Inghelandt, Delphine
Melchinger, Albrecht E.
Lebreton, Claude
Stich, Benjamin
author_sort Van Inghelandt, Delphine
collection PubMed
description Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-009-1256-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-28543512010-04-21 Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers Van Inghelandt, Delphine Melchinger, Albrecht E. Lebreton, Claude Stich, Benjamin Theor Appl Genet Original Paper Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of our study were to (a) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (b) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (c) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. Our study was based on 1,537 elite maize inbred lines genotyped with 359 SSR and 8,244 SNP markers. The average number of alleles per locus, of group specific alleles, and the gene diversity (D) were higher for SSRs than for SNPs. Modified Roger’s distance (MRD) estimates and membership probabilities of the STRUCTURE matrices were higher for SSR than for SNP markers but the germplasm organization in four heterotic pools was consistent with STRUCTURE results based on SSRs and SNPs. MRD estimates calculated for the two marker systems were highly correlated (0.87). Our results suggested that the same conclusions regarding the structure and the diversity of heterotic pools could be drawn from both markers types. Furthermore, although our results suggested that the ratio of the number of SSRs and SNPs required to obtain MRD or D estimates with similar precision is not constant across the various precision levels, we propose that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-009-1256-2) contains supplementary material, which is available to authorized users. Springer-Verlag 2010-01-10 2010 /pmc/articles/PMC2854351/ /pubmed/20063144 http://dx.doi.org/10.1007/s00122-009-1256-2 Text en © The Author(s) 2010 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
spellingShingle Original Paper
Van Inghelandt, Delphine
Melchinger, Albrecht E.
Lebreton, Claude
Stich, Benjamin
Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
title Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
title_full Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
title_fullStr Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
title_full_unstemmed Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
title_short Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
title_sort population structure and genetic diversity in a commercial maize breeding program assessed with ssr and snp markers
topic Original Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854351/
https://www.ncbi.nlm.nih.gov/pubmed/20063144
http://dx.doi.org/10.1007/s00122-009-1256-2
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