An<i>in silico</i>evaluation of non-synonymous single nucleotide polymorphisms of mastitis resistance genes in cattle

Jacob, Kala K; Radhika, G.; Aravindakshan, T. V.

doi:10.1080/10495398.2018.1524770

Cited by 12 publications

(9 citation statements)

References 27 publications

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“…The substitution Glu341Glu was tolerated and did not affect the protein function. A similar study reported the use of three different in silico computational tools (PROVEAN, SIFT, and I-Mutant) [30]. The same study identified 14 variants as deleterious using the PROVEAN tool, while SIFT identified 15 variants that affected the protein function, and I-Mutant found 16 variants that were deleterious and were efficient in destabilizing proteins [30].…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we found that the variation in the AC > CA allele caused an amino acid change that likely would affect the protein structure and function. Nonsynonymous SNPs that generate variants modify not only the protein's tertiary structure, but also affect its function and stability, and also may form deleterious phenotypes [30]. The possible reasons for this are fourfold.…”

Section: Discussionmentioning

confidence: 99%

“…A similar study reported the use of three different in silico computational tools (PROVEAN, SIFT, and I-Mutant) [30]. The same study identified 14 variants as deleterious using the PROVEAN tool, while SIFT identified 15 variants that affected the protein function, and I-Mutant found 16 variants that were deleterious and were efficient in destabilizing proteins [30]. In another in silico study with an A122V substitution, the effect on the bovine CXCR1 protein was determined, and it was found to have a tolerable (SIFT), (PolyPhen-2) and nondeleterious (I-Mutant) effect [37].…”

Section: Discussionmentioning

confidence: 99%

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In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene

Ali

Rehman

Ahmad

et al. 2022

Animals

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Dairy cattle with a high milk yield are susceptible to many infectious diseases, such as mastitis. Subclinical mastitis (SCM) is the most prevalent form of mastitis that predominantly affects animal health, and causes adverse effects on the quality and quantity of milk. In dairy animals, subclinical mastitis often remains undetected, as no gross changes in udder characteristics are visible. In the present study, 135 Holstein Friesian dairy animals were selected and screened as healthy (n = 25) and mastitic (n = 110) based on diagnostic tests such as the California mastitis test, pH, electrical conductivity, and somatic cell count. In this study, the somatic cell count was used as a gold-standard test in differentiating subclinical mastitis animals from healthy ones. The present study was carried out to study polymorphisms in the bovine transferrin gene in cows (with subclinical mastitis and healthy). For the early detection of resistant/or susceptible animals, a useful marker could be provided by the detection of single-nucleotide polymorphisms (SNPs) in the transferrin gene, which are often associated with mammary innate immune response. The sequencing results revealed three nucleotide substitutions: two transversions (230 A > C, 231 C > A) and one transition (294 A > G) in susceptible cows as compared to disease-free subjects. The nucleotide variations at position 230 (GAC > GCA) and 231 (GAC > GCA) were nonsynonymous, and corresponded to an amino acid change from aspartic acid to alanine; whereas at position 294 (GAA > GAG), the mutation was synonymous. In the present study, many in silico tools were taken into consideration to determine the effect of SNPs on protein structure and function. The PROVEAN tool found the amino acid substitution to be neutral and deleterious. PolyPhen-2 revealed the amino acid variations at positions 320 and 321 to most likely be damaging; and at the 341 position, the variations were benign. The I-Mutant and MUpro tools found that the protein stability decreased for nonsynonymous variations. The SIFT tool revealed the protein function was likely to be affected in nonsynonymous variations, with no change in the case of synonymous ones. Phylogenetic analysis of the bovine transferrin gene revealed a close relation of the CA allele with the Bos taurus transferrin, while the G allele was closely related to a cross of Bos indicus × Bos taurus serotransferrins, followed by the Bison bison transferrin. The least relation was shown by both alleles to Capra hircus, Ovis aries, and Bubalus bubalis.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene

Ali

Rehman

Ahmad

et al. 2022

Animals

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“…Though exonic variations are very limited in number, they do play an important role in population differentiation at the genetic level (86). Nonsynonymous SNP polymorphism in the genic region of mastitis genes is very valuable for mastitis disease resistance breeding in bovines (87).…”

Section: Evaluation Of Mastitis Tgp Based Variant Mining (Snps and Indels)mentioning

confidence: 99%

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

et al. 2021

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Water buffalo (Bubalus bubalis) are an important animal resource that contributes milk, meat, leather, dairy products, and power for plowing and transport. However, mastitis, a bacterial disease affecting milk production and reproduction efficiency, is most prevalent in populations having intensive selection for higher milk yield, especially where the inbreeding level is also high. Climate change and poor hygiene management practices further complicate the issue. The management of this disease faces major challenges, like antibiotic resistance, maximum residue level, horizontal gene transfer, and limited success in resistance breeding. Bovine mastitis genome wide association studies have had limited success due to breed differences, sample sizes, and minor allele frequency, lowering the power to detect the diseases associated with SNPs. In this work, we focused on the application of targeted gene panels (TGPs) in screening for candidate gene association analysis, and how this approach overcomes the limitation of genome wide association studies. This work will facilitate the targeted sequencing of buffalo genomic regions with high depth coverage required to mine the extremely rare variants potentially associated with buffalo mastitis. Although the whole genome assembly of water buffalo is available, neither mastitis genes are predicted nor TGP in the form of web-genomic resources are available for future variant mining and association studies. Out of the 129 mastitis associated genes of cattle, 101 were completely mapped on the buffalo genome to make TGP. This further helped in identifying rare variants in water buffalo. Eighty-five genes were validated in the buffalo gene expression atlas, with the RNA-Seq data of 50 tissues. The functions of 97 genes were predicted, revealing 225 pathways. The mastitis proteins were used for protein-protein interaction network analysis to obtain additional cross-talking proteins. A total of 1,306 SNPs and 152 indels were identified from 101 genes. Water Buffalo-MSTdb was developed with 3-tier architecture to retrieve mastitis associated genes having genomic coordinates with chromosomal details for TGP sequencing for mining of minor alleles for further association studies. Lastly, a web-genomic resource was made available to mine variants of targeted gene panels in buffalo for mastitis resistance breeding in an endeavor to ensure improved productivity and the reproductive efficiency of water buffalo.

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“…Therefore, there is increasing interest in developing mastitis-resistant herds. ( Asaf et al, 2014a;Asaf et al, 2014b;Jacob et al, 2018;Rupp et al, 2007;Tolone et al, 2016;Youngerman et al, 2004). Breast cancer 1 (BRCA1) gene is one of those genes that has been reported to be associated with hereditary breast cancer risk in humans (Friedman et al, 1994) as well as mastitis in cattle (Yuan et al, 2012b).…”

Section: Introductionmentioning

confidence: 99%

Association of BRCA1 (G22231T, T25025A, C28300A) polymorphisms with subclinical mastitis and milk yields in Holstein Cattle

Daldaban¹,

Arslan²,

Akçay³

et al. 2021

Harran Üniversitesi Veteriner Fakültesi Dergisi

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In this study, it was aimed to investigate the relationship between three SNP on the BRCA1 gene and subclinical mastitis, as well as milk yields during four lactation periods in Holstein breed cattle. The animal material of the study consisted of 151 Holstein cows reared under the same care and feeding conditions. Complete DNA was isolated from blood samples by using phenol: chloroform: isoamyl alcohol method. Genotyping of G22231T, T25025A and C28300A SNPs on the BRCA1 was done by the PCR-RFLP method. Subclinical mastitis of animals was determined in milk samples by California Mastitis Test (CMT). In the study, CMT data, four lactation periods' milk yields, and proportional distributions of SNP genotypes were calculated. Statistical significance of the data was determined by the Pearson chi-square test. The relationship between C28300A SNP, which was monomorphic, and subclinical mastitis has not been analyzed. In the samples examined, the difference between the proportional distribution of SNP genotypes of G22231T and T25025A in subclinical mastitis and healthy groups was not found statistically significant (P>0.05). As a result of the Chi-square (χ2) analysis conducted, it was observed that the Holstein cattle were in the Hardy-Weinberg equilibrium in terms of G22231T and T25025A SNPs. Considering the physiological processes in which the BRCA1 gene is involved, it was thought that these genes and SNPs should be evaluated with more samples in studies on resistance to mastitis.

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Anin silicoevaluation of non-synonymous single nucleotide polymorphisms of mastitis resistance genes in cattle

Cited by 12 publications

References 27 publications

In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene

In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene

Genome Wide Prediction, Mapping and Development of Genomic Resources of Mastitis Associated Genes in Water Buffalo

Association of BRCA1 (G22231T, T25025A, C28300A) polymorphisms with subclinical mastitis and milk yields in Holstein Cattle

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