Genetic Diversity Determined within and among CIMMYT Maize Populations of Tropical, Subtropical, and Temperate Germplasm by SSR Markers

Genetic diversity in maize (Zea mays L.) plays a key role for future breeding progress. The main objectives of our study were to (i) investigate the genetic diversity within and among CIMMYT maize populations by simple sequence repeat (SSR) markers, (ii) examine genotype frequencies for deviations from Hardy-Weinberg equilibrium (HWE) at individual loci, and (iii) test for linkage disequilibrium (LD) between pairs of loci. Twenty-three maize populations and pools established in 1974, which mostly comprise germplasm from different racial complexes adapted to tropical, subtropical intermediate-maturity, subtropical early-maturity, and temperate megaenvironments (ME), were fingerprinted by 83 SSR markers covering the entire maize genome. Across all populations, 27% of the SSR markers deviated significantly from HWE with an excess of homozygosity in 99% of the cases. We observed no evidence for genome-wide LD among pairs of loci within each of the seven tropical populations analyzed. Estimates of genetic differentiation (G_ST) between populations within MEs averaged 0.09 and revealed that most of the molecular variation was found within the populations. Principal coordinate analysis based on allele frequencies of the populations revealed that populations adapted to the same ME clustered together and, thus, supported clearly the ME structure.