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PMID: 12366868 Published · ppublish English Comparative Study Journal Article

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

BMC genetics ·Vol. 3 ·2002-10-07 ·Pages 19

Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ

Abstract

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. 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. 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.

MeSH Terms
Alleles Animals DNA, Plant/genetics Gene Frequency/genetics Genes, Plant/genetics Genetic Markers/genetics Genetic Variation/genetics Genotype Haplotypes/genetics Linkage Disequilibrium/genetics Mice Molecular Sequence Data Polymorphism, Single Nucleotide/genetics Recombination, Genetic/genetics Sequence Analysis, DNA Zea mays/genetics
Chemicals
DNA, Plant Genetic Markers
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Ching Ada
DuPont Crop Genetics, Delaware Technology Park, Suite 200, P,O, Box 6104, Newark, Delaware 19714, USA. ada.s.ching@usa.dupont.com
Caldwell Katherine S
Jung Mark
Dolan Maurine
Smith Oscar S
Tingey Scott
Morgante Michele
Rafalski Antoni J
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Article Info
Journal
BMC genetics
Abbr.
BMC Genet
ISSN
1471-2156
DOI
10.1186/1471-2156-3-19
Email
ada.s.ching@usa.dupont.com
Published
2002-10-07
Epub
2002-00-07
Pages
19
Language
English
Region
England
NLM ID
100966978
PMCID
PMC130040
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1186/1471-2156-3-19 PMC Full Text View journal details
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