Linkage disequilibrium and haplotype block structure in six commercial pig lines

Abstract

Linkage disequilibrium (LD) across the genome is critical information for association studies and genomic selection because it determines the number of SNP that should be used for a successful association analysis and genomic selection. Linkage disequilibrium also influences the accuracy of genomic breeding values. Some studies have demonstrated that SNP in strong LD are organized into discrete blocks of haplotypes, which are separated by possibly hot spots of recombination. To reduce the number of markers needed to be genotyped for association mapping, a set of SNP can be selected that labels all haplotype blocks. We estimated the LD, calculated the average haplotype block size for 6 pig lines, and compared the block size between lines. Six commercial pig lines were genotyped using the Illumina PorcineSNP60 (number of markers M = 62,163) Genotyping BeadChip (Illumina Inc.); on average, a panel of 37,623 SNP with an average minor allelic frequency (MAF) of 0.283 was included in the analysis. The LD declined as a function of distance. All pig lines had an average r(2) above 0.3 for markers 100 to 150 apart. The estimated average block size was 394.885 kb, and blocks between 100 and 400 kb were most prominent (49.96%) in all lines. These results showed that the extent of LD in pigs is much larger than in the cattle population, in accordance with the genetic map length of pigs, which is much shorter than cattle. The evaluated lines have 2,640 to 3,037 blocks, covering 45% of the pig genome, on average. Differences in haplotype block size between lines were observed for some chromosomes (i.e., SSC 3, 5, 7, 13, 14, and 18), which provide a direction for future studies of haplotype block conservation or divergence across lines.

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

“…Consistent with our results, Al-Mamun et al (2015) reported that the maximum average LD was located between adjacent SNPs on OAR10 and a higher average LD was seen in meat sheep breeds. Values of r 2 for adjacent SNP pairs were also similar to the values observed in other livestock species such as cattle (r 2 = 0.20 for SNPs with an average distance of 68 Kb) (Bohmanova et al, 2010) and goats (r 2 = 0.11 to 0.29 for SNPs with physical distance ranging from 53 to 73 kb) (Brito et al, 2015), although these were lower than those observed in pigs, where one study reported an average r 2 of 0.41 to 0.46 for SNPs <50 kb apart (Veroneze et al, 2013), and in horses (Corbin et al, 2010), which showed r 2 values remaining >0.3 for distances up to 185 kb. The relatively small number of genotyped Barbaresca individuals may have resulted in an overestimation of r 2 , which could explain the differences in the LD values v. the other Sicilian sheep breeds (Mastrangelo et al, 2014).…”

“…The relatively small number of genotyped Barbaresca individuals may have resulted in an overestimation of r 2 , which could explain the differences in the LD values v. the other Sicilian sheep breeds (Mastrangelo et al, 2014). The same consideration was reported by Veroneze et al (2013) to explain the differences in the r 2 values in pig breeds. However, it should be emphasized that several studies have reported LD analysis in sheep (Kijas et al, 2012;Ciani et al, 2013b) in which, despite a higher number of breeds, the number of individuals per breed was similar to those involved in our study.…”

Genomic selection in pigs: state of the art and perspectives

“…Several studies reported information on the extent of linkage disequilibrium in different pig populations (Table 3). In general, it appears that in pigs the level of linkage disequilibrium is larger than in cattle populations (Veroneze et al 2013). Analyses, based on the use of the 60K Illumina chip, indicated that the averaged linkage disequilibrium levels (r 2 ) between two adjacent SNPs might range from 0.36 to 0.46 in different pig populations (Uimari & Tapio 2011;Badke et al 2012;Veroneze et al 2013).…”

Influence of Gene Interaction on Complex Trait Variation with Multilocus Models

“…In higher organisms most pairs of loci are on different chromosomes or far apart on the same chromosome. Further, even for closely linked loci, LD is likely to be small in populations of large effective size, such as for humans and Drosophila melanogaster, although not so for closely linked loci in domestic livestock (e.g., de Roos et al 2008, Veroneze et al 2013 and laboratory populations of experimental species. A theoretical analysis of variance partition in the presence of LD is problematic because trait effects of different loci are not orthogonal; i.e., fitting locus B after A removes less variance than fitting B alone, and epistatic variance may be confounded with that of average effects.…”