Single nucleotide polymorphisms identified in exons 5–6 of cattle HSP90AB1 gene
A total number of 9 SNPs were detected in exons 5–6 and the surrounding introns of the HSP90AB1 gene in all the three cattle breeds used for the study (presented in Table ii). Two (2) SNPs were identified in the Muturu, two (2) were identified in the White Fulani and five (5) was also identified in the N’Dama. The White Fulani had two transitions (353G > A, 1G > A), Muturu had two transversions (1C > G, 85A > C,) while N’Dama had four transversions (827A > C, 852A > T, 870A > T, 861A > C) and one transition (190G > A). One of the SNPs was shared between white Fulani and muturu and majority of the SNPs identified were mostly transversion type
Table iia: Single Nucleotide Polymorphisms in Exons 5–6
Breed Number of SNPs Positions Types of Mutation
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White Fulani 2 1, 353 Transitions (G353A)
Muturu 2 1, 85 Transversions (A85C)
N’Dama 5 190,827,852,861,870 Transitions and Transversions
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Table iib: Single Nucleotide Polymorphisms Identified in Exon 5–6 of HSP90AB1 and type of Mutations for the breeds studied.
Genetic diversity Indices of exons 5–6 of HSP90AB1 gene of the three cattle breeds
The genetic diversity indices of Exons 5–6 in HSP90AB1 genes of the three locally adapted cattle breeds are shown in Table iii.
For exons 5–6, the total number of sequences used for White Fulani and N’Dama breeds were seventeen (17) each while N’Dama had fourteen (14) sequences. The singleton variable site for Muturu and N’Dama were two (2) and four (4) respectively while White Fulani had none, with N’Dama breed having the highest singleton variable site for the region of HSP90AB1 gene. The parsimony informative sites for White Fulani and N’Dama were two (2) and four (4) respectively while Muturu breed had none, with the N’Dama breed possessing the highest (4) parsimony informative site and muturu having the least (0) for the region of HSP90AB1. The number of haplotypes (h) for White Fulani, Muturu and N’Dama were four (4), four (4) and seven (7) respectively, with the N’Dama having the highest (7) haplotypes (h). The haplotype diversity (Hd) for White Fulani, Muturu and N’dama were 0.684, 0.331 and 0.846 respectively, also here N’Dama possessing the highest (0.846) haplotype diversity (Hd ) and Muturu having the least value (0.331). Each of White Fulani, Muturu and N’Dama had Nucleotide diversity (ᴫ) of 9.8 x10− 4, 4.0 x 10− 4, and 2.40 x 10− 3 respectively, with N’Dama having the highest (2.40 x 10− 3) and Muturu having the least nucleotide diversity value (4.0 x 10− 4 ) for the region of the HSP90AB1 gene. It was also observed that there was a very high sequence conservation across the three breeds with White Fulani and Muturu possessing the highest (9.98×10− 1) same number of sequence conservation, while N’Dama had the least value (9.91x10− 1).
Table iii: Genetic Diversity Indices of Exons 5–6 in HSP90AB1 gene of the three cattle Breeds studied (White Fulani, Muturu and N’Dama).
Results for Exons 12-13
Single nucleotide polymorphisms identified in exons 12–13 of cattle HSP90AB1 gene
A total number of 11 SNPs were detected in exons 12–13 and the surrounding introns of the HSP90AB1 gene in all the three cattle breeds used for the study (presented in Table v). One (1) SNP was identified in the Muturu, seven (7) were identified in the White Fulani and three (3) was also identified in the N’Dama. The White Fulani had seven transversions, Muturu had one transition (700C > T,) while N’Dama had three transversions (287G > T, 2G > T, 4G > C). Majority of the SNPs identified were mostly transversion type.
Table v: Single Nucleotide Polymorphisms in Exons 12–13
Genetic diversity Indices of exons 12–13 of HSP90AB1 gene of the three cattle breeds
The genetic diversity indices of Exons 5–6 in HSP90AB1 genes of the three locally adapted cattle breeds are shown in Table vi.
The total number of sequences used for Muturu and N’Dama were seventeen (17) each while White Fulani had sixteen (16) sequences. The singleton variable sites for White Fulani, Muturu and N’Dama were Nine (9), Zero (0) and one (1) respectively, with white Fulani having the highest (9) and Muturu having the least (0). The parsimony informative sites for White Fulani, Muturu and N’Dama breeds were six (6), one (1) and two (2) respectively, with White Fulani having the highest (6), and Muturu having the least (1). The number of haplotypes (h) for White Fulani, Muturu and N’Dama were nine (9), two (2) and four (4) respectively, White Fulani having the highest (9) and Muturu having the least (2). The haplotype diversity (Hd ) for White Fulani, Muturu and N’Dama were 8.58 x10− 1, 5.29 x 10− 1 and 7.28 x 10− 1 respectively, with White Fulani having the highest value (8.58 x10− 1 ) and Muturu having the least value (5.29 x 10− 1 ). Each of White Fulani, Muturu and N’Dama had nucleotide diversity (ᴫ) of 4.5 x 10− 3, 7.6 x 10− 4 and 1.58 x 10− 3 respectively. This showed that White Fulani breed possessed the highest (4.5 x 10− 3) nucleotide diversity value while Muturu had the least value (7.6 x 10− 4). White Fulani, Muturu and N’Dama had high sequence conservation of 9.78 x 10− 1, 9.99 x 10− 1 and 9.91 x 10− 1 respectively, with Muturu having the highest value (9.99 x 10− 1) and the white Fulani having the least value (9.78 x 10− 1).
Table vi: Genetic Diversity of Exons 12–13 in HSP90AB1 gene of the three Cattle Breeds (White Fulani, Muturu and N’Dama).