SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines - PubMed (original) (raw)

Comparative Study

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

Ada Ching et al. BMC Genet. 2002.

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 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.

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Figures

Figure 1

Figure 1

Distribution of insertion /deletion sizes Number of observed insertion / deletion polymorphisms (indels) of each size class is shown.

Figure 2

Figure 2

Neighbor-joining trees representing Adh1 haplotype relationships. Level of support for branch points is indicated in %, and branch length expressed as nucleotide differences are shown in parentheses. Genotypes correspond to those of Table 1, and color indicates major heterotic groups: stiff stalk (blue), non stiff stalk (green) and Lancaster (red).

Figure 3

Figure 3

Neighbor-joining trees representing stearoyl-ACP desaturase haplotype relationships. Level of support for branch points is indicated in %, and branch length expressed as nucleotide differences are shown in parentheses. Genotypes correspond to those of Table 1, and color indicates major heterotic groups: stiff stalk (blue), non stiff stalk (green) and Lancaster (red).

Figure 4

Figure 4

Neighbor-joining trees representing acetyl-CoA C-acyltransferase haplotype relationships. Level of support for branch points is indicated in %, and branch length expressed as nucleotide differences are shown in parentheses. Genotypes correspond to those of Table 1, and color indicates major heterotic groups: stiff stalk (blue), non stiff stalk (green) and Lancaster (red).

Figure 5

Figure 5

Composite plot of linkage disequilibrium as a function of distance. Two measures of linkage disequilibrium, absolute value of D' (A) and r2 (B) are shown as a function of distance for all loci examined. LD values between all pairs of SNP were plotted. Logarithmic trend line is included in plot (B). Of the 344 pairwise comparisons, 161 were significant at P < 0.01, with Bonferroni correction, and 126 were significant at P < 0.001 level.

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