ArticleBMC genetics2002
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines.
Article in BMC genetics, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers.
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163 citing papers in PubMed.
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- Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel.Food and energy security · 2021Article
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- Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA.Scientific reports · 2021Article
- Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing.Biomolecules · 2021Article
- Identification, Association of Natural Variation and Expression Analysis ofPlants (Basel, Switzerland) · 2020Article
- Development and validation of high-throughput and low-cost STARP assays for genes underpinning economically important traits in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome.BMC plant biology · 2020Article
- Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.Molecular plant pathology · 2020Article
103 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
backgroundRecent 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.
resultsWe 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.
conclusionsNo 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.
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