Performance of bovine high density SNPs genotyping array in indigenous Pakistani cattle breeds

Abstract

The bovine high density SNPs genotyping array has a wide range of applications including detection of selection signatures, identification of copy number variants (CNVs), genome wide association studies, and dendrogram relationships. This array can also be used to improve the accuracy of genomic predictions for low heritable traits viz. reproductive traits. The effectiveness of this array for genomic selection mainly depends on polymorphism level. In this study, we used 136 individuals from ten different Pakistani cattle breeds, include Achi (18), Bhagnari (14), Cholistani (13), Dajal (10), Dhanni (10), Kankraj (12), Lohani (19), Red Sindhi (13), Sahiwal (14), and Tharparkar (13) using high density SNPs genotyping and this array contained approximately 777, 962 SNPs. The results of this study revealed that approximately 500, 939 SNPs were found polymorphic in these breeds. The results indicate that high density SNPs bead chip would offer an informative genotyping platform for quantitative trait loci (QTL) mapping in indigenous Pakistani cattle breeds.

Single Nucleotide Polymorphisms of ALDH18A1 and MAT2A Genes and Their Genetic Associations with Milk Production Traits of Chinese Holstein Cows

“…On the other hand, considering cost-effectiveness, low-density gene chips can also be constructed by selecting loci such as SNPs of ALDH18A1 and MAT2A that are closely associated with milk production traits, focusing on estimating the breeding value of the target traits [ 30 , 31 ]. At present, many studies use low-density SNP chipsets to genotype animals, and then accurately interpolate them into high-density groups to improve the accuracy of breeding value estimation [ 32 , 33 , 34 ]. However, the application in this direction still needs in-depth verification.…”

Causes, types, etiological agents, prevalence, diagnosis, treatment, prevention, effects on human health and future aspects of bovine mastitis

“…Identifying specific high-density SNPs associated with mastitis traits together with genomic breeding values, it would be expected that resistance to mastitis could be increased over consecutive generations of breeding (Deb et al ., 2012; Mustafa et al ., 2018). Further progress in genomic selection technology will allow genetic improvement in terms of mastitis-resistant animals (Vukasinovic et al ., 2017).…”

Seroprevalence of hemorrhagic septicemia in buffalo and cattle in flood, irrigated and sandy areas of Punjab, Pakistan

“…Muzaffargarh is situated in Southern Punjab Province, almost exact center of Pakistan. The area is spread over 8435 km 2 , it forms a strip between river Chenab in the east and river Indus in west district Multan and Khanewal are present on the eastern side of the district M. Garh while on western side D. G. Khan district, on north side district Layyah and south side district Bahawalpur is present. District M. Garh has four tehsils as Kot Addu, Ali Pur, Jatoi and M. Garh and in the study different UC's of all these tehsils were randomly selected.…”

“…Pakistan is an agricultural country, livestock and dairy farming plays a major role in the economy of Pakistan [1,2]. Livestock is the sub-sector of agriculture and its share in agriculture's GDP is round about 58.3% and 11.4% of the total GDP of Pakistan during the year 2016-17 compared to 58.3% and 11.6% during the corresponding last year respectively.…”

“…The prevalent serotyping of Pasteurella multocida causing Hemorrhagic Septicemia (HS) is listed as B disease i.e B2 (Asian Type) E2 (African Type). Other serotypes reported are A (1), A (1, 3), A (4), B (1), B (2,5) District Muzaffar Garh (M. Garh) have cattle (1.436), buffalo (0.647), sheep (0.441), goat (0.994) Million respectively [14]. District M. Garh is situated B/w River Chanab, and River Indus in the form of a strip and these rivers pass along the eastern and western borders of the district respectively.…”