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Record information and status
Record ID
103414
Status
Published
Date of creation
2012-05-09 17:59 UTC (dina.abdelhakim@cbd.int)
Date of publication
2012-05-09 17:59 UTC (dina.abdelhakim@cbd.int)

General Information
Title
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
Author
Ada Ching, Katherine S Caldwell, Mark Jung, Maurine Dolan, Oscar S (Howie) Smith, Scott Tingey, Michele Morgante and Antoni J Rafalski
Author’s contact information
Antoni J Rafalski
Email: j-antoni.rafalski@usa.dupont.com

DuPont Crop Genetics, Delaware Technology Park,
Suite 200, P.O. Box 6104,
Newark, Delaware 19714, USA
Language(s)
  • English
Publication date
2002-10-07
Subject
Summary, abstract or table of contents
Abstract:

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 noncoding 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.
Thematic areas
  • Scientific and technical issues
    • Risk assessment
Background material to the “Guidance on risk assessment of living modified organisms”
Is this document is recommend as background material for the “Guidance on Risk Assessment of Living Modified Organisms”
Yes
Section(s) of the “Guidance on Risk Assessment of Living Modified Organisms” this background material is relevant
Additional Information
Type of resource
  • Article (journal / magazine / newspaper)
Identifier
doi:10.1186/1471-2156-3-19
Publisher and its location
BioMed Central (BMC)
Rights
© 2002 Ching et al
Format
14 page PDF
Source
BMC Genetics
Keywords and any other relevant information
Citation: BMC Genetics 2002, 3:19