Linkage disequilibrium and haplotype block structure in a composite beef cattle breed

Abstract

Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.

Results: The maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.

Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.

Figure 1

Average r² values for CA, MA and CAN animals, and persistence of LD phase (PL) between CA and MA animals with respect to physical genomic distance (kb).

Figure 2

Mean values of linkage disequilibrium (r²) per chromosome (chr:1-29) according to distance (in kb) between markers for CA, MA, and CAN animals.

Figure 3

Maximum and average haplotype block length per chromosome.

Figure 4

Haplotype block distributions for chromosomes (chrs) 7, 10, 12, 15, 16, 21, 23, 24, 25 and 29 (red ellipses for highlighted area of uncommon haplotype block distribution: gaps without any haplotype - chrs10, 12, 23; areas with higher frequencies of larger haplotypes - chrs 7, 12, 16, 24, 29; and uncommon haplotype pattern distributions at the extreme ends - chrs 15, 21, 25).