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

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.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.Direct analysis of genetic variation at the DNA sequence level at many loci became possible in recent years due to improvements in sequencing technology. High throughput genotyping methods, including DNA chips, allele-specific PCR and primer extension approaches make single nucleotide polymorphisms (SNPs) especially attractive as genetic markers [1-3].If a whole-genome scan is to be undertaken, trait mapping by allele association requires high marker density [4-7] which could be provided by SNPs. Recent detailed analysis of allelic diversity at the maize Dwarf8 gene, which indicated association with flowering time [8], is an example of association approach using candidate genes. SNPs may also be used for mapping expressed sequence tags (ESTs) in defined segregating populations and for the integration of genetic and physical (contig) maps, which contain EST-derived landmarks.While po