Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm
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Linkage disequilibrium (LD) at the adh1 locus was examined in two sets of maize inbreds. A set of 32 was chosen to represent most of the genetic diversity in the cultivated North American elite maize breeding pool. A second set of 192 inbreds was chosen to sample more deeply the two major heterotic groups in elite maize germplasm. Analysis of several loci in the vicinity of the adh1 gene shows that LD as measured by D′ and r2 extends greater than 500 kbp in this germplasm. The presence of this exceptionally long segment of high LD may be suggestive of selection acting on one of the genes in the vicinity of adh1 or of a locally reduced rate of recombination.
Supplementary Table 1 List of maize inbred lines. Heterotic group classification, assignment to Structure groups and Figure 3 key are included.
Supplementary Table 2 List of PCR primer sequences, listed in the 5’-3’ direction. Primers PS37, PS38, PS39-40 are identical to those used by Ching A. et al. (2002). Information on the use of primer pair for the analysis of the 32 inbred set and 192 inbred set is included.
Supplementary Table 3 Identity and location of SNPs and Indels in the Adh1 region
Supplementary Table 4
NEXUS data table