Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)

Abstract

BackgroundThe availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.MethodsThe genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K.ResultsThis 90K “SNP-Chip” was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production.ConclusionThe 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.

Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds

“…The assumption was supported by previous reports that utilized microsatellite markers [38–40] and mtDNA [41, 42]. This can be explained by the current buffalo 90K array is optimized for use in four river buffalo breeds (Mediterranean, Murrah, Nili-Ravi, and Jaffarabadi buffaloes) and has the lower representation of swamp breeds [43]. The disproportionate distribution of MAF between river and swamp groups is another reason to influence the SNP ascertainment bias.…”

“…To date, high-throughput SNP genotyping has been extensively applied to various domestic animals [19–21] and plants [22]. The first SNP genotyping platform (Axiom® buffalo genotyping array; 90K Affymetrix) designed explicitly for river buffalo has recently been developed [23] and used for the genome-wide analysis study (GWAS) in different buffalo breeds [24–26]. This SNP90K array provides a viable choice for buffalo scientific research such as molecular breeding, complex traits, conservation, and biodiversity.…”

Asian water buffalo: domestication, history and genetics

“…The Axiom ® Buffalo Genotyping Array was developed by Affymetrix as a water buffalo specific genotyping tool (Iamartino et al ). The array contains 89 988 SNPs, together with 5799 probes for Quality Control and 1784 probes for gender determination (Iamartino et al ).…”

“…The Axiom ® Buffalo Genotyping Array was developed by Affymetrix as a water buffalo specific genotyping tool (Iamartino et al ). The array contains 89 988 SNPs, together with 5799 probes for Quality Control and 1784 probes for gender determination (Iamartino et al ). The candidate SNPs for the array design were selected to be evenly distributed genome‐wide with respect to the bovine UMD 3.1 genome, but have been recently remapped after the release of the current version of the buffalo reference genome (Low et al ).…”

“…Also, SNP numbers were weighted with respect to the significance of the breeds included in the discovery panel as follows: Mediterranean, 30%; Murrah, 30%; Jafarabadi, 20%; Nili‐Ravi, 20%. When the array was tested on a set of 15 river buffalo breeds, a total of 67 330 and 9229 SNP probes were validated as polymorphic and monomorphic high‐quality SNPs respectively (Iamartino et al ). However, owing to the over‐representation of river buffalo breeds in the SNP discovery panel, this 90K SNP chip is affected by a moderate‐to‐high ascertainment bias, with only about 22.74% of the markers being polymorphic in swamp buffalo populations (Colli et al ).…”