Alignment of Chromosomal Structures in Water Buffalo By Linkage Disequilibrium

A reference genome mapping is important for studies that need the exact position of the markers, such as GWAS and/or to build linkage phases, such as signature selection and imputation. Although the buffalo genome is sequenced, it is available in scaffolds and genes are not annotated. Because of this, the cattle genome is used as a reference for SNP position. The aim of the present study was to align homologue chromosomal structure blocks between cattle and buffalo using linkage disequilibrium (LD). A total of 352 buffaloes were genotyped with the 90K Axiom Buffalo Genotyping (Affymetrix) (buffalo specific) and 363 buffaloes, with Bovine HD BeadChip (Illumina) (cattle specific) (call rate> 0.90 for samples). A total of 46,378 and 13,142 SNPs were considered for Affymetrix and Illumina panels respectively (call rate>0.95, MAF>5% and p-value for HWE <10^-6). Only autosomal markers with known position at the cattle genome reference (UMD3.1) were used in the analyses. The LD between the pairs of markers was calculated by r² statistics using the PLINK software. Only r²>0.2 among the markers (intra and inter-chromosome) were used to establish the groups and align the structures. As expected, the chromosomes that have the biggest numbers of markers in LD were 1 and 27 (230 and 67); 2 and 23 (232 and 47); 5 and 28 (199 and 49); 8 and 19 (307 and 64); 16 e 29 (303 and 80) by Affymetrix and and Illumina panels respectively. The results using the Affymetrix panel also indicated a segment, 21:59,800,00-60-500,00 bp, is possibly translocated to a region between chromosomes 1 and 27. Moreover, the structures were aligned by the initial extremities of the cattle chromosomes. It is possible to observe a higher level of LD in these regions (centromeres) than other region, indicating that there was a process of fusion of the chromosomes of the ancestral species to form the buffalo chromosomes.