Genomic clues of association between clinical mastitis and SNPs identified by ddRAD sequencing in Murrah buffaloes

References

• BAHS. Basic Animal Husbandry and Fisheries Statistics. BAHS; Department of Animal Husbandry & Dairying, GOI. 2021.
   Google Scholar
• Hogeveen H, Huijps K, Lam TJGM. Economic aspects of mastitis: new developments. N Z Vet J. 2011;59(1):16–23.
   PubMed Web of Science ®Google Scholar
• Kurz JP, Yang Z, Weiss RB, et al. A genome-wide association study for mastitis resistance in phenotypically well-characterized Holstein dairy cattle using a selective genotyping approach. Immunogenetics. 2019;71(1):35–47.
   PubMed Web of Science ®Google Scholar
• Emanuelson U, Danell B, Philipsson J. Genetic parameters for clinical mastitis, somatic cell count and milk production estimates by multiple-trait restricted maximum likelihood. J Dairy Sci. 1988;71(2):467–476.
   PubMed Web of Science ®Google Scholar
• Koivula M, Mäntysaari E, Negussie E, Serenius T. Genetic and phenotypic relationships among milk yield and somatic cell count before and after clinical mastitis. J Dairy Sci. 2005;88(2):827–833.
   PubMed Web of Science ®Google Scholar
• Vallimont J, Dechow CD, Sattler C, Clay J. Heritability estimates associated with alternative definitions of mastitis and correlations with somatic cell score and yield. J Dairy Sci. 2009;92(7):3402–3410.
   PubMed Web of Science ®Google Scholar
• Yang GQ, Chen YM, Wang JP, et al. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Methods. 2016;12(1):1–17.
   PubMedGoogle Scholar
• Rowe HC, Renaut S, Guggisberg A. RAD in the realm of next‐generation sequencing technologies. Mol Ecol. 2011;20(17):3499–3502.
   PubMed Web of Science ®Google Scholar
• Kirsanova E, Heringstad B, Lewandowska‐Sabat A, Olsaker I. Identification of candidate genes affecting chronic subclinical mastitis in Norwegian Red cattle: combining genome‐wide association study, topologically associated domains and pathway enrichment analysis. Anim Genet. 2020;51(1):22–31.
   PubMed Web of Science ®Google Scholar
• Jaiswal S, Jagannadham J, Kumari J, et al. Genome wide prediction, mapping and development of genomic resources of mastitis associated genes in water buffalo. Front Vet Sci. 2021;8:550.
   Web of Science ®Google Scholar
• Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLOS One. 2012;7(5):e37135.
   PubMed Web of Science ®Google Scholar
• Andrews S, Krueger F, Segonds-Pichon A, Biggins L, Krueger C, Wingett S. FastQC. A quality control tool for high throughput sequence data. https:www.bioinformatics.babraham.ac.uk/projects/fastqc. 2010;370.
   Google Scholar
• Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27(6):863–864.
   PubMed Web of Science ®Google Scholar
• Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. Stacks: building and genotyping loci de novo from short-read sequences. G3. 2011;1(3):171–182.
   Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
   PubMed Web of Science ®Google Scholar
• Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27(21):2987–2993.
   PubMed Web of Science ®Google Scholar
• Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008.
   PubMed Web of Science ®Google Scholar
• Browning BL, Browning SR. Genotype imputation with millions of reference samples. Am J Hum Genet. 2016;98(1):116–126.
   PubMed Web of Science ®Google Scholar
• Cingolani P, Platts A, Wang LL, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80–92.
   PubMed Web of Science ®Google Scholar
• Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575.
   PubMed Web of Science ®Google Scholar
• Mi H, Lazareva-Ulitsky B, Loo R, et al. The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res. 2005;33(Database issue):D284–D288.
   PubMedGoogle Scholar
• Krämer A, Green J, Pollard J Jr., Tugendreich S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014;30(4):523–530.
   PubMed Web of Science ®Google Scholar
• Magotra A, Gupta ID, Verma A, Alex R, Mr V, Ahmad T. Candidate SNP of CACNA2D1 gene associated with clinical mastitis and production traits in Sahiwal (Bos taurus indicus) and Karan Fries (Bos taurus taurus × Bos taurus indicus). Anim Biotechnol. 2019;30(1):75–81.
   PubMed Web of Science ®Google Scholar
• Deb R, Singh U, Kumar S, et al. Genotypic to expression profiling of bovine calcium channel, voltage-dependent, alpha-2/delta subunit 1 gene, and their association with bovine mastitis among Frieswal (HFX Sahiwal) crossbred cattle of Indian origin. Anim Biotechnol. 2014;25(2):128–138.
   PubMed Web of Science ®Google Scholar
• Wu X, Lund MS, Sahana G, et al. Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins. Genet Sel Evol. 2015;47(1):1–14.
   PubMedGoogle Scholar
• Flury C, Boschung C, Denzler M, et al. Genome-wide association study for 13 udder traits from linear type classification in cattle. 10th World Congress on Genetics Applied to Livestock Production; 2014.
   Google Scholar
• Wang X, Fan Y, He Y, et al. Integrative analysis of miRNA and mRNA expression profiles in mammary glands of Holstein cows artificially infected with Staphylococcus aureus. Pathogens. 2021;10(5):506.
   PubMed Web of Science ®Google Scholar
• Lu X, Duan A, Liang S, Ma X, Deng T. Genomic identification, evolution, and expression analysis of collagen genes family in water buffalo during lactation. Genes. 2020;11(5):515.
   PubMed Web of Science ®Google Scholar
• Wang W, Gan J, Fang D, et al. Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan. PLOS One. 2018;13(8):e0201534.
   PubMed Web of Science ®Google Scholar
• Song M, Wei Y, Khan MZ, Wang X, Yu Y. Molecular marker study of inflammatory reaction in bovine mammary epithelium cell line induced by methicillin-resistant Staphylococcus aureus. Acta Vet Zootech Sin. 2016;47(10):1995–2002.
   Google Scholar
• Khan MZ, Khan A, Xiao J, et al. Overview of research development on the role of NF-κB signaling in mastitis. Animals. 2020;10(9):1625.
   Web of Science ®Google Scholar
• Chen Q, He G, Zhang W, et al. Stromal fibroblasts derived from mammary gland of bovine with mastitis display inflammation-specific changes. Sci Rep. 2016;6(1):1–13.
   PubMed Web of Science ®Google Scholar
• Power RA, Parkhill J, de Oliveira T. Microbial genome-wide association studies: lessons from human GWAS. Nat Rev Genet. 2017;18(1):41–50.
   PubMed Web of Science ®Google Scholar
• Fang L, Sahana G, Su G, et al. Integrating sequence-based GWAS and RNA-Seq provides novel insights into the genetic basis of mastitis and milk production in dairy cattle. Sci Rep. 2017;7(1):1–16.
   PubMed Web of Science ®Google Scholar
• Kumar DR, Devadasan MJ, Surya T, et al. Genomic diversity and selection sweeps identified in Indian swamp buffaloes reveals it’s uniqueness with riverine buffaloes. Genomics. 2020;112(3):2385–2392.
   PubMed Web of Science ®Google Scholar
• Wara AB, Kumar A, Singh A, Arthikeyan AK, Dutt T, Mishra BP. Genome wide association study of test days and 305 days milk yield in crossbred cattle. Indian J Anim Sci. 2019;89(8):861–865.
   Web of Science ®Google Scholar
• Ibeagha-Awemu EM, Peters SO, Akwanji KA, Imumorin IG, Zhao X. High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits. Sci Rep. 2016;6(1):1–18.
   PubMedGoogle Scholar
• Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011;12(7):499–510.
   PubMed Web of Science ®Google Scholar
• Patel AB, Subramanian RB, Padh H, et al. Identification of single nucleotide polymorphism from Indian Bubalus bubalis through targeted sequence capture. Curr Sci. 2017;112(6):1230–1239.
   Web of Science ®Google Scholar
• Surya T, Vineeth MR, Sivalingam J, et al. Genomewide identification and annotation of SNPs in Bubalus bubalis. Genomics. 2019;111(6):1695–1698.
   PubMed Web of Science ®Google Scholar
• Smitz N, Van Hooft P, Heller R, et al. Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing. Mamm Biol. 2016;81(6):595–603.
   Web of Science ®Google Scholar
• Vineeth MR, Surya T, Sivalingam J, et al. Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle. Trop Anim Health Prod. 2020;52(4):1707–1715.
   PubMed Web of Science ®Google Scholar
• Devadasan MJ, Kumar DR, Vineeth MR, et al. Reduced representation approach for identification of genome-wide SNPs and their annotation for economically important traits in Indian Tharparkar cattle. 3 Biotech. 2020;10(7):1–6.
   PubMedGoogle Scholar
• Ba H, Jia B, Wang G, Yang Y, Kedem G, Li C. Genome-wide SNP discovery and analysis of genetic diversity in farmed sika deer (Cervus nippon) in northeast China using double-digest restriction site-associated DNA sequencing. G3. 2017;7(9):3169–3176.
   Web of Science ®Google Scholar
• Kraus RH, Kerstens HH, Van Hooft P, et al. Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics. 2011;12(1):1–11.
   Google Scholar
• Sharma U, Banerjee P, Joshi J, Kapoor P, Vijh RK. Identification of QTLs for low somatic cell count in Murrah buffaloes. Indian J Anim Sci. 2019;89(7):758–767.
   Web of Science ®Google Scholar
• da Rosa FT, Moreira CGA, Barbero MMD, et al. Associations between MUC1 gene polymorphism and resistance to mastitis, milk production and fertility traits in Murrah water buffaloes. J Appl Anim Res. 2020;48(1):151–155.
   Web of Science ®Google Scholar
• Kaplan S. Nucleotide sequence variations of lactoferrin gene in Anatolian water buffaloes. Fresenius Environ Bull. 2018;27(9):6427–6432.
   Web of Science ®Google Scholar
• Swanson KM, Stelwagen K, Dobson J, et al. Transcriptome profiling of Streptococcus uberis-induced mastitis reveals fundamental differences between immune gene expression in the mammary gland and in a primary cell culture model. J Dairy Sci. 2009;92(1):117–129.
   PubMed Web of Science ®Google Scholar
• Turk R, Koledić M, Maćešić N, et al. The role of oxidative stress and inflammatory response in the pathogenesis of mastitis in dairy cows. Mljekarstvo/Dairy. 2017;67(2):91–101.
   Web of Science ®Google Scholar
• Moyes KM. TRIENNIAL LACTATION SYMPOSIUM: nutrient partitioning during intramammary inflammation: a key to severity of mastitis and risk of subsequent diseases? J Anim Sci. 2015;93(12):5586–5593.
   PubMed Web of Science ®Google Scholar
• Kong X, Zhai J, Yan C, et al. Recent advances in understanding FOXN3 in breast cancer, and other malignancies. Front Oncol. 2019;9:234.
   PubMed Web of Science ®Google Scholar
• Li W, Zhang Z, Liu X, et al. The FOXN3-NEAT1-SIN3A repressor complex promotes progression of hormonally responsive breast cancer. J Clin Invest. 2017;127(9):3421–3440.
   PubMed Web of Science ®Google Scholar
• Roth S, Rottach A, Lotz-Havla AS, et al. Rad50-CARD9 interactions link cytosolic DNA sensing to IL-1beta production. Nat Immunol. 2014;15(6):538–545.
   PubMed Web of Science ®Google Scholar
• Spanou E, Kalisperati P, Pateras IS, et al. Genetic variability as a regulator of TLR4 and NOD signaling in response to bacterial driven DNA damage response (DDR) and inflammation: focus on the gastrointestinal (GI) tract. Front Genet. 2017;8:65.
   PubMed Web of Science ®Google Scholar
• Niu G, Yang Y, Ren J, et al. Overexpression of CPXM2 predicts an unfavorable prognosis and promotes the proliferation and migration of gastric cancer. Oncol Rep. 2019;42(4):1283–1294.
   PubMed Web of Science ®Google Scholar
• Zhao X, Li R, Wang Q, Wu M, Wang Y. Overexpression of carboxypeptidase X M14 family member 2 predicts an unfavorable prognosis and promotes proliferation and migration of osteosarcoma. Diagn Pathol. 2019;14(1):1–11.
   PubMed Web of Science ®Google Scholar
• Mudaliar M, Tassi R, Thomas FC, et al. Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics. Mol BioSyst. 2016;12(9):2748–2761.
   PubMedGoogle Scholar
• Alomary MN. Functional Characterisation of OPCML Clinical Mutations in Ovarian Cancer and Correlate to OPCML Crystal Structure; Doctoral Dissertation, Imperial College London, 2017.
   Google Scholar