Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci wa...

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Autores principales:	Jianbing Yan, Trushar Shah, Marilyn L Warburton, Edward S Buckler, Michael D McMullen, Jonathan Crouch
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/117367037f8348dba6e3f8e9796285b6
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spelling	oai:doaj.org-article:117367037f8348dba6e3f8e9796285b62021-11-25T06:27:10ZGenetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.1932-620310.1371/journal.pone.0008451https://doaj.org/article/117367037f8348dba6e3f8e9796285b62009-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20041112/?tool=EBIhttps://doaj.org/toc/1932-6203A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.Jianbing YanTrushar ShahMarilyn L WarburtonEdward S BucklerMichael D McMullenJonathan CrouchPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 12, p e8451 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jianbing Yan Trushar Shah Marilyn L Warburton Edward S Buckler Michael D McMullen Jonathan Crouch Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
description	A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection. Linkage disequilibrium (LD) was measured overall and within chromosomes, allelic frequency groups, subgroups related by geographic origin, and subgroups of different sample sizes. The LD decay distance differed among chromosomes and ranged between 1 to 10 kb. The LD distance increased with the increase of minor allelic frequency (MAF), and with smaller sample sizes, encouraging caution when using too few lines in a study. The LD decay distance was much higher in temperate than in tropical and subtropical lines, because tropical and subtropical lines are more diverse and contain more rare alleles than temperate lines. A core set of inbreds was defined based on haplotypes, and 60 lines capture 90% of the haplotype diversity of the entire panel. The defined core sets and the entire collection can be used widely for different research targets.
format	article
author	Jianbing Yan Trushar Shah Marilyn L Warburton Edward S Buckler Michael D McMullen Jonathan Crouch
author_facet	Jianbing Yan Trushar Shah Marilyn L Warburton Edward S Buckler Michael D McMullen Jonathan Crouch
author_sort	Jianbing Yan
title	Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
title_short	Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
title_full	Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
title_fullStr	Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
title_full_unstemmed	Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.
title_sort	genetic characterization and linkage disequilibrium estimation of a global maize collection using snp markers.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/117367037f8348dba6e3f8e9796285b6
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Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.

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