Water buffalo genome characterization by the Illumina BovineHD BeadChip

Abstract

ABSTRACT. To define the best strategies for genomic association studies and genomic selection, it is necessary to determine the extent of linkage disequilibrium (LD) and the genetic structure of the study population. The current study evaluated the transference of genomic information contained in the Illumina BovineHD BeadChip from cattle to buffaloes, and assessed the extent of the LD in buffaloes. Of the 688,593 bovine single nucleotide polymorphism (SNP) that were successfully genotyped from the 384 buffalo samples, only 16,580 markers were polymorphic, and had minor allele frequencies greater than 0.05. A total of 16,580 polymorphic SNPs were identified, which were uniformly distributed throughout the autosomes, because the density and mean distance between markers were similar for all autosomes. The average minor allele frequency for the 16,580 SNPs was 0.23. The overall mean LD for pairs of adjacent markers was 0.29 and 0.71, when measured as for r 2 and |D'|, respectively. The 16,580 4203©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (2): 4202-4215 (2014) Water buffalo genome characterization polymorphic SNPs were matched to Bos taurus chromosome in the current bovine genome assembly (Btau 4.2), and could be utilized in association studies. In conclusion, the Illumina BovineHD BeadChip contains approximately 16,580 polymorphic markers for the water buffalo, which are broadly distributed across the genome. These data could be used in genomic association and genomic selection studies; however, it might be necessary to develop a panel with specific SNP markers for water buffaloes.

Genomic differentiation between swamp and river buffalo using a cattle high-density single nucleotide polymorphisms panel

“…In our study, we found a total of 20 479 SNP polymorphic in water buffalo and a call rate of 86%. In a similar study, 16 580 SNPs were found in 384 swamp type samples at a similar call rate (85%; Borquis et al, 2014). Our higher number of SNPs is mostly due to the use of swamp and river buffalo samples in our testing.…”

“…However, water buffalo (B. bubalis) and cattle (Bos taurus) are phylogenetically very close, have an high chromosomal homology between species and share gene order and chromosome banding homology (Borquis et al, 2014). Therefore, buffalo studies can benefit of genomic tools developed for cattle, to gather genome-wide diversity information of the buffalo populations.…”

Polymorphism of the STAT5A and MYF-5 genes in Anatolian water buffalo

“…Since there was no literature regarding the analysis of this polymorphism, it was not possible to comment on the STAT5A-AvaI polymorphism in different buffalo breeds. However, it was thought that it could be compared with the results obtained in different cattle breeds due to the high rate of homology of the water buffalo genome with the cattle genome from many gene aspects [35,36]. On the other hand, it was thought that these genes showed homology in cattle and water buffalo because of obtaining the reported-sized PCR products in cattle at the end of the conducted PCR process and cleaving the obtained PCR products with the reported restriction enzymes in cattle.…”

The Differential Expression of Immune Genes between Water Buffalo and Yellow Cattle Determines Species-Specific Susceptibility to Schistosoma japonicum Infection

“…As water buffalo and yellow cattle are both members of the Bovidae family, they are closely related, and the vast amount of cattle genomic resources might serve as shortcuts for further advances genome science and biotechnology in this species [ 32 ]. In 2014, the water buffalo genome research group also declared that the bovine genome could be utilized in association studies [ 33 ]. In this paper, a Bos taurus genome-wide gene chip was used to analyze and compare the overall gene expression profiles of peripheral blood from water buffalo and yellow cattle, both pre- and post infection with S .…”