Genome-wide association studies revealed genomic regions associated with production and reproduction traits in indicine cattle

Antoon J (2011) Nutritional regulation of stearoyl-CoA desaturase in the bovine mammary gland. Ph.D. Thesis, Wageningen University, Netherland. https://edepot.wur.nl/185325

Arishima T, Sasaki S, Isobe T, Ikebata Y, Shimbara S, Ikeda S, Kawashima K, Suzuki Y, Watanabe M, Sugano S, Mizoshita K, Sugimoto Y. Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle. BMC Genet. 2017;18(1):103. https://doi.org/10.1186/s12863-017-0573-8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Atashi H, Salavati M, De Koster J, Crowe MA, Opsomer G, Hostens M. Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows. J Dairy Sci. 2020;103(7):6392–406. https://doi.org/10.3168/jds.2019-17369.

Article  CAS  PubMed  Google Scholar 

Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Methodol. 1995;57:289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x.

Article  Google Scholar 

Cai Z, Dusza M, Guldbrandtsen B, Lund MS, Sahana G. Distinguishing pleiotropy from linked QTL between milk production traits and mastitis resistance in Nordic Holstein cattle. Genet Sel Evol. 2020;52(1):19. https://doi.org/10.1186/s12711-020-00538-6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen Y, Gondro C, Quinn K, Herd RM, Parnell PF, Vanselow B. Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake. Anim Genet. 2011;42(5):475–90. https://doi.org/10.1111/j.1365-2052.2011.02182.x.

Article  CAS  PubMed  Google Scholar 

Chen Z, Brito LF, Luo H, Shi R, Chang Y, Liu L, Guo G, Wang Y. Genetic and genomic analyses of service sire effect on female reproductive traits in holstein cattle. Front Genet. 2021. https://doi.org/10.3389/fgene.2021.713575.

Article  PubMed  PubMed Central  Google Scholar 

Cole JB, Wiggans GR, Ma L, Sonstegard TS, Lawlor TJ, Crooker BA, Van Tassell CP, Yang J, Wang S, Matukumalli LK, Da Y. Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows. BMC Genomics. 2011. https://doi.org/10.1186/1471-2164-12-408.

Article  PubMed  PubMed Central  Google Scholar 

da Costa BC, de Abreu Santos DJ, Aspilcueta-Borquis RR, de Camargo GMF, de Araújo Neto FR, Tonhati H. Use of single-step genome-wide association studies for prospecting genomic regions related to milk production and milk quality of buffalo. J Dairy Res. 2018;85(4):402–6. https://doi.org/10.1017/s0022029918000766.

Article  Google Scholar 

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. https://doi.org/10.1093/bioinformatics/btr330.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dar AH, Kumar S, Mukesh M, Ahmad SF, Singh DV, Sharma RK, Ghosh AK, Singh B, Rahman JU, Sodhi M. Genetic characterization and population structure of different coat colour variants of Badri cattle. Mol Biol Rep. 2020;47(11):8485–97. https://doi.org/10.1007/s11033-020-05890-w.

Article  CAS  PubMed  Google Scholar 

Dar AH, Kumar S, Sodhi M, Rahman JU, Yadav S, Baba NA. Physical and morphometric characterisation of badri cattle. J Animal Res. 2022. https://doi.org/10.30954/2277-940X.02.2022.9.

Article  Google Scholar 

de Camargo GM, Aspilcueta-Borquis RR, Fortes MR, Porto-Neto R, Cardoso DF, Santos DJ, Lehnert SA, Reverter A, Moore SS, Tonhati H. Prospecting major genes in dairy buffaloes. BMC Genomics. 2015;16:872. https://doi.org/10.1186/s12864-015-1986-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fortes MRS, DeAtley KL, Lehnert SA, Burns BM, Reverter A, Hawken RJ, Boe-Hansen G, Moore SS, Thomas MG. Genomic regions associated with fertility traits in male and female cattle: advances from microsatellites to high-density chips and beyond. Animal Reproduct Sci. 2013;141(1–2):1–19. https://doi.org/10.1016/j.anireprosci.2013.07.002.

Article  CAS  Google Scholar 

Fortes MRS, Reverter A, Zhang Y, Collis E, Nagaraj SH, Jonsson NN, Prayaga KC, Barris W, Hawken RJ. Association weight matrix for the genetic dissection of puberty in beef cattle. Proceed National Acad Sci. 2010;107(31):13642–7. https://doi.org/10.1073/pnas.1002044107.

Article  Google Scholar 

Hayes B, Goddard M. Genome-wide association and genomic selection in animal breeding. Genome. 2010;53(11):876–83.

Article  CAS  PubMed  Google Scholar 

Henderson CR. Applications of Linear Models in Animal Breeding. Guelph, Ontario, Canada: University of Guelph; 1984.

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;6:31109. https://doi.org/10.1038/srep31109.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Iqbal N, Liu X, Yang T, Huang Z, Hanif Q, Asif M, Khan QM, Mansoor S. Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan. PLoS ONE. 2019;14(4): e0215065. https://doi.org/10.1371/journal.pone.0215065.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jardé T, Lloyd-Lewis B, Thomas M, Kendrick H, Melchor L, Bougaret L, Watson PD, Ewan K, Smalley MJ, Dale TC. Wnt and Neuregulin1/ErbB signalling extends 3D culture of hormone responsive mammary organoids. Nat Commun. 2016;7:13207. https://doi.org/10.1038/ncomms13207.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang L, Liu J, Sun D, Ma P, Ding X, Yu Y, Zhang Q. Genome wide association studies for milk production traits in Chinese Holstein population. PLoS ONE. 2010;5(10): e13661. https://doi.org/10.1371/journal.pone.0013661.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jung EJ, Park HB, Lee JB, Yoo CK, Kim BM, Kim HI, Kim BW, Lim HT. Genome-wide association analysis identifies quantitative trait loci for growth in a Landrace purebred population. Anim Genet. 2014;45(3):442–4. https://doi.org/10.1111/age.12117.

Article  CAS  PubMed  Google Scholar 

Khan MZ, Liu L, Zhang Z, Khan A, Wang D, Mi S, Usman T, Liu G, Guo G, Li X, Wang Y, Yu Y. Folic acid supplementation regulates milk production variables, metabolic associated genes and pathways in perinatal Holsteins. J Anim Physiol Anim Nutr (Berl). 2020;104(2):483–92. https://doi.org/10.1111/jpn.13313.

Article  CAS  PubMed  Google Scholar 

Kirkpatrick BW. Genetics of Reproduction in Cattle. In: Garrick DJ, Ruvinsky A, editors. The Genetics of Cattle. Boston: CABI Publishing; 2015. p. 260–83.

Chapter  Google Scholar 

Lai FN, Zhai HL, Cheng M, Ma JY, Cheng SF, Ge W, Zhang GL, Wang JJ, Zhang RQ, Wang X, Min LJ, Song JZ, Shen W. Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus). Sci Rep. 2016;6:38096. https://doi.org/10.1038/srep38096.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laodim T, Elzo MA, Koonawootrittriron S, Suwanasopee T, Jattawa D. Pathway enrichment and protein interaction network analysis for milk yield, fat yield and age at first calving in a Thai multibreed dairy population. Asian-Australas J Anim Sci. 2019;32(4):508–18. https://doi.org/10.5713/ajas.18.0382.

Article  CAS  PubMed  Google Scholar 

Larcombe SD, Kolte SW, Ponnudurai G, Kurkure N, Magar S, Velusamy R, Rani N, Rubinibala B, Rekha B, Alagesan A, Weir W, Shiels BR. The impact of tick-borne pathogen infection in Indian bovines is determined by host type but not the genotype of Theileria annulata. Infect Genet Evol. 2019;75: 103972. https://doi.org/10.1016/j.meegid.2019.103972.

Article  CAS  PubMed  PubMed Central 

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