Linkage disequilibrium and haplotype block patterns in popcorn populations

Abstract

Linkage disequilibrium (LD) analysis provides information on evolutionary aspects of the populations and allows selecting populations and single nucleotide polymorphisms (SNPs) for association studies. Recently, haplotype blocks have been used to increase the power of quantitative trait loci detection in genome-wide association studies and the prediction accuracy with genomic selection. The objectives of this study were to compare the degree of LD, the LD decay, the LD decay extent, and the number and length of haplotype blocks in the populations and to elaborate the first LD map for maize, for elucidating if the maize chromosomes also had a pattern of interspaced regions of high and low rates of recombination. We used a biparental temperate population, a tropical synthetic, and a tropical breeding population, genotyped for approximately 75,000 SNPs. The level of LD expressed by the r2 values is surprisingly low (0.02, 0.04, and 0.04), but comparable to some non-isolated human populations. The general evidence is that the synthetic is the population with higher LD. It is not expected a significant advantage of haplotype-based association study and along generations genomic selection due to the reduced number of SNPs in the haplotype blocks (2 to 3). The results concerning LD decay (rapid decay after 5-10 kb) and LD decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. Our most important result is that maize chromosomes had a pattern of regions of extensive LD interspaced with regions of low LD. However, our simple simulated LD map provides evidence that this pattern can reflect regions with differences of allele frequencies and LD level (expressed by D) and not regions with high and low rates of recombination.