Table 1.
Summary of SNPs used in this study.
Table 2.
Properties of SNPs and SNP haplotypes.
Table 3.
Number of haplotypes (alleles) observed in each locus from which one or more SNPs were amplified.
Figure 1.
Allele frequency for total SNPs.
SNPs scored as biallelic markers are in the top panel, and scored as SNP haplotypes are in the bottom panel.
Figure 2.
Estimated ln(probability of the data).
Ln(probability of the data) was calculated for K ranging from 1 to 10 (top panel) and delta K values for SNPs and SNP haplotypes for K from 2 to 9 (bottom panel).
Figure 3.
Estimated population structure of the diverse inbred maize lines in the study.
Each of the 632 individuals is represented by a thin vertical line, which is partitioned into k colored segments that represent the individual estimated membership to the k clusters.
Figure 4.
Distribution of pairwise relative kinship values.
Values equal to or greater than 0.40 were gouped as 0.40.
Table 4.
Diversity comparison of tropical (A) and temperate (B) and subgroups.
Table 5.
Alleles captured by subsets of the data for SNP haplotypes.
Table 6.
Comparison of the 21 “CML” lines with the same name stored at CIMMYT and North Carolina State University, respectively.
Figure 5.
Linkage disequillibrium across the maize 10 chromosomes measured with 914 SNPs.
Only SNPs with a minor allele frequency greater than 0.05 are shown.
Table 7.
Mean LD among all SNPs with a minimum allelic frequency greater than 0.05, over different map distances and across 10 chromosomes.
Table 8.
Average LD decay distance of the 10 chromosomes for r2 greater than 0.1.
Figure 6.
Mean LD estimates at different physical distances for three different minimum threshold cutoff levels for minimum allele frequency.
Mean LD estimates are pooled over all chromosomes, and three different minimum threshold cutoff levels for minimum allele frequency are shown.
Figure 7.
Mean LD estimates for different physical distances for six different sample sizes.
Mean LD estimates are pooled over all chromosomes, and six different sample sizes using SNPs with minor allele frequency greater than 0.05 are shown.
Table 9.
Correlations between pairwise estimates of LD obtained from different sample sizes compared to the entire sample of 632 lines.
Figure 8.
Mean LD estimates at different physical distances for tropical and temperate subgroups.
Mean LD estimates are pooled over all chromosomes, and two subgroups (A = tropical, B = temperate) at sample size = 80 are shown, using SNPs with a minor allele frequency of 0.05.