Cargando…

SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

BACKGROUND: Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intens...

Descripción completa

Detalles Bibliográficos
Autores principales: Ching, Ada, Caldwell, Katherine S, Jung, Mark, Dolan, Maurine, Smith, Oscar S (Howie), Tingey, Scott, Morgante, Michele, Rafalski, Antoni J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2002
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC130040/
https://www.ncbi.nlm.nih.gov/pubmed/12366868
http://dx.doi.org/10.1186/1471-2156-3-19
_version_ 1782120379407400960
author Ching, Ada
Caldwell, Katherine S
Jung, Mark
Dolan, Maurine
Smith, Oscar S (Howie)
Tingey, Scott
Morgante, Michele
Rafalski, Antoni J
author_facet Ching, Ada
Caldwell, Katherine S
Jung, Mark
Dolan, Maurine
Smith, Oscar S (Howie)
Tingey, Scott
Morgante, Michele
Rafalski, Antoni J
author_sort Ching, Ada
collection PubMed
description BACKGROUND: Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. RESULTS: We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2–8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. CONCLUSIONS: No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.
format Text
id pubmed-130040
institution National Center for Biotechnology Information
language English
publishDate 2002
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-1300402002-10-25 SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines Ching, Ada Caldwell, Katherine S Jung, Mark Dolan, Maurine Smith, Oscar S (Howie) Tingey, Scott Morgante, Michele Rafalski, Antoni J BMC Genet Research Article BACKGROUND: Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. RESULTS: We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2–8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. CONCLUSIONS: No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry. BioMed Central 2002-10-07 /pmc/articles/PMC130040/ /pubmed/12366868 http://dx.doi.org/10.1186/1471-2156-3-19 Text en Copyright © 2002 Ching et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research Article
Ching, Ada
Caldwell, Katherine S
Jung, Mark
Dolan, Maurine
Smith, Oscar S (Howie)
Tingey, Scott
Morgante, Michele
Rafalski, Antoni J
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
title SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
title_full SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
title_fullStr SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
title_full_unstemmed SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
title_short SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
title_sort snp frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC130040/
https://www.ncbi.nlm.nih.gov/pubmed/12366868
http://dx.doi.org/10.1186/1471-2156-3-19
work_keys_str_mv AT chingada snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT caldwellkatherines snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT jungmark snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT dolanmaurine snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT smithoscarshowie snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT tingeyscott snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT morgantemichele snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines
AT rafalskiantonij snpfrequencyhaplotypestructureandlinkagedisequilibriuminelitemaizeinbredlines