Assessment of OvineSNP50 in Nigerian and Kenyan sheep populations

Abstract

Deciphering genomic information requires markers that are polymorphic and sufficient enough to capture its vast array of genetic data. Polymorphic loci can differ greatly between breeds of the same species and the exclusion of the Nigerian and some African sheep breeds during the development of the OvineSNP50 chip necessitated the validation of SNPs included on the chip to allow for genomic applications of the excluded breeds. A total of sixty sheep samples were genotyped [10 each of the Balami, Uda, West African Dwarf and Yankasa from Nigeria, Dorper and Red Maasai from Kenya (East Africa)] using the Ovine 50k Illumina SNP bead chip. Results revealed that 33,994 SNPs (97.47%) of the called 34,876 SNPs were validated for downstream analysis. Mean heterozygosity values of 0.154 and 0.153 were obtained for polymorphic SNPs on sex and autosomal chromosomes respectively, while the values of 0.662 and 0.054 were obtained on the sex and autosomal chromosomes respectively for the mean identity-bystate (IBS). Six and three individuals violated the per ID and identity-by-state (IBS) thresholds, respectively. It was observed that the Ovine 50k Illumina SNP bead chip was informative in the Nigerian and East African sheep that were studied, and should be useful in examining the underlying genetic variation.

Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites

“…Many molecular markers such as RAPD (Kunene et al, 2009), AFLP (De Marchi et al, 2006), PCR-RFLP (Kucharski et al, 2019), and mtDNA (Kirikci et al, 2018) have been applied to detect genetic diversity in livestock. Today, SSRs (simple sequence repeats (Demir and Balcioglu, 2019) and SNPs (single nucleotide polymorphisms) (Ilori et al, 2018) and NGS (next-generation sequencing) (Kijas et al, 2009) are preferred to reveal genetic diversity among and within different livestock breeds.…”

“…SSR markers were used to detect genetic diversity or parentage test in different livestock including cattle (Demir and Balcioglu, 2019), sheep (Ocampo et al, 2016), goat (Jawasreh et al, 2018, pigs (Szmatoła et al, 2016), horses (Semik and Zabek, 2013) chickens (Karsli and Balcioglu, 2019), rabbit (Abdel-Kayf et. al., 2016), ducks (Hariyono et al, 2019, and donkeys (Han et al, 2017).…”

Establishment of a novel fetal ovine heart cell line by spontaneous cell fusion

“…The OvineSNP50 BeadChip has been used in many applications which included genome-wide selection, comparative genetic studies, and breed characterization for evaluating biodiversity [35, 36, 37]. It was validated by Illumina for genotyping of more than 3000 samples from diverse Ovis aries domestic and wild breeds [19].…”

Polymorphism of Alpha S1-Casein Gene in Yankasa Sheep Breed of Mubi, Adamawa State of Nigeria

“…It has been shown that ovine genetic polymorphisms affect the physicochemical properties of milk hence, there is need for in-depth knowledge of the genetic polymorphism of indigenous ovine milk proteins for the improvement of the quality of ovine milk for its contribution to the Nigerian dairy industry. The genetic basis for diversity in sheep and its consequences on selection on gene polymorphism within the sheep breeds have not been assayed on a genomic scale worldwide [8]. Similarly, to our knowledge, there are no studies on variation in the alpha-casein gene of yankasa breed of sheep.…”