Suitability of BovineSNP50 BeadChip for the evaluation of the Cervidae family diversity

Abstract

Polymorphic SNPs were identified using BovineSNP50 BeadChip in three groups of cervids: farmed Red deer (n = 3), and free range Red deer (n = 5) and Fallow deer (n = 2). From the total of 54 609 SNPs, 53.85% could be genotyped. Out of 28 502 successfully genotyped autosomal SNPs only 5.3% were polymorphic. The average minor allele frequency within cervids was 0.23 (number of polymorphic SNPs ranged from 467 to 686). Results of the molecular variance analysis showed that 67.38% of variation occurred within individuals and the rest was explained by a species difference (F ST = 0.32). The value of F IT (0.33) indicated a higher proportion of homozygote genotypes in the analyzed dataset. Pairwise F ST values showed very clearly the genetic differentiation between Red and Fallow deer which ranged from 0.06 (farmed and free range deer) to 0.74 (farmed Red and Fallow deer). A similar result was found for Nei's genetic distances that ranged from 0.01 (among Fallow deer) to 0.79 (among farmed Red and Fallow deer). The genetic differentiation of the analyzed cervid species was evaluated also by the principal component analysis with the involvement of 6 other species from the family Cervidae, which showed a division of the Cervidae cluster into 7 subpopulations. The panels of SNPs primarily produced for a model species are becoming the marker of choice for the application in other species, but the best methods of their discovery, validation, and genotyping in non-model species need further investigations.

From Wisent to the Lab and Back Again—A Complex SNP Set for Population Management as an Effective Tool in European Bison Conservation

“…In a preliminary study [6], it was shown that of the markers available on the microarrays Bovine50SNP and BovineHD, as many as 94.5% of SNPs were genotyped in European bison (with call rates equal to or greater than 90%), A similar call rate was reported for American bison in a study by Decker et al [26], whereas lower values were obtained by the same author for Water buffalo Bubalus bubalis 86.4%, or Kudu Tragelaphus strepsiceros 76.6%. For other species, such as deer, by using BovineSNP50 it was possible to successfully genotype a much lower number of SNPs, 38.7-53.8% of markers [27,28]. Nevertheless, microarrays have been successfully used in wildlife research.…”

An Assessment of Applicability of SNP Chip Developed for Domestic Goats in Genetic Studies of Caucasian Tur (Capra caucasica)

“…Tokarska et al [15] used the BovineSNP50 BeadChip created for cattle (Bos taurus) to infer the population structure of European bison (Bos bonasus). Kasarda et al [16] have demonstrated suitability of the above-mentioned SNP microarray for the evaluation of the Cervidae family diversity. Kharzinova et al [17,18] have shown the applicability of the BovineSNP50 BeadChip and BovineHD BeadChip for genome-wide studies of reindeer (Rangifer tarandus).…”