Genome-Wide Association Study and Pathway Analysis for Female Fertility Traits in Iranian Holstein Cattle

Abdoli R, Mirhoseini S.Z., Ghavi Hossein-Zadeh N., Zamani P., Ferdosi M.H., Gondro C. (2019a). Genome-wide association study of four composite reproductive traits in Iranian fat-tailed sheep. Reprod Fert Develop., 31(6): 1127-1133.10.1071/RD1828230958977Search in Google Scholar

Abdoli R, Mirhoseini S.Z., Ghavi Hossein-Zadeh N., Zamani P., Gondro C. (2018). Genome-wide association study to identify genomic regions affecting prolificacy in Lori-Bakhtiari sheep. Anim. Genet., 49: 488-491.10.1111/age.12700Search in Google Scholar

Abdoli R, Mirhoseini S.Z., Ghavi Hossein-Zadeh N., Zamani P., Moradi M.H., Ferdosi M.H., Gondro C. (2019b). Genome-wide association study of first lambing age and lambing interval in sheep. Small Ruminant Res., 178: 43-45.10.1016/j.smallrumres.2019.07.014Search in Google Scholar

Aloisio G.M., Nakada Y., Saatcioglu H.D., Peña C.G., Baker M.D., Tarnawa E.D., Mukherjee J., Manjunath H., Bugde A., Sengupta A.L. (2014). PAX7 expression defines germline stem cells in the adult testis. J. Clin. Invest., 124: 3929-3944.10.1172/JCI75943Search in Google Scholar

Ashwell M., Heyen D., Sonstegard T., Van Tassell C., Da Y., VanRaden P., Ron M., Weller J., Lewin H. (2004). Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle. J. Dairy Sci., 87: 468-475.10.3168/jds.S0022-0302(04)73186-0Search in Google Scholar

Bal R.D. (2005). Experimental designs for reliable detection of linkage disequilibrium in unstructured random population association studies. Genetics, 170: 859-873.10.1534/genetics.103.024752Search in Google Scholar

Bazer F.W., Spencer T.E., Johnson G.A., Burghardt R.C. (2011). Uterine receptivity to implantation of blastocysts in mammals. Front Biosci (Schol Ed)., 3: 745-767.10.2741/s184Search in Google Scholar

Behnia F., Taylor, B.D., Woodson M., Kacerovsky M., Hawkins H., Fortunato S.J., Saade G.R., Menon, R. (2015) Chorioamniotic membrane senescence: a signal for parturition? Am J Obstet Gynecol MFM., 213: 359. e1-359. e16.10.1016/j.ajog.2015.05.041Search in Google Scholar

Bhat S.A., Ahmad S.M., Ibeagha-Awemu E.M., Bhat B.A., Dar M.A., Mumtaz P.T., Shah R.A., Ganai N.A. (2019). Comparative transcriptome analysis of mammary epithelial cells at different stages of lactation reveals wide differences in gene expression and pathways regulating milk synthesis between Jersey and Kashmiri cattle. PloS One., 14: 0211773.10.1371/journal.pone.0211773Search in Google Scholar

Bliss S.P., Navratil A.M., Xie J., Roberson M.S. (2010). GnRH signaling, the gonadotrope and endocrine control of fertility. Front Neuroendocrinol., 31: 322-340.10.1016/j.yfrne.2010.04.002Search in Google Scholar

Breen S.M., Knox R.V. (2012). The impact of dose of FSH (Folltropin) containing LH (Lutropin) on follicular development, estrus and ovulation responses in prepubertal gilts. Anim. Reprod. Sci., 132: 193-200.10.1016/j.anireprosci.2012.05.013Search in Google Scholar

Cai Z., Guldbrandtsen B., Lund M.S., Sahana G. (2019). Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression. BMC Genomics., 20: 255.10.1186/s12864-019-5638-9Search in Google Scholar

Chang K. (2007). Key signalling factors and pathways in the molecular determination of skeletal muscle phenotype. Animal., 1: 681-698.10.1017/S1751731107702070Search in Google Scholar

Cochran S.D., Cole J.B., Null D.J., Hansen P.J. (2013a). Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle. BMC Genetics., 14: 49.10.1186/1471-2156-14-49368657723759029Search in Google Scholar

Cochran S.D., Cole J.B., Null D.J., Hansen P.J. (2013b). Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle. Biol. Reprod., 89 (3): 69.10.1095/biolreprod.113.11126023904513Search in Google Scholar

Costa R.B., Camargo G.M., Diaz I.D., Irano N., Dias M.M., Carvalheiro R., Boligon A.A., Baldi F., Oliveira H.N., Tonhati H. (2015). Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference. Genet. Sel. Evol., 47: 67.10.1186/s12711-015-0146-0Search in Google Scholar

Demiray S.B., Goker E.N.T., Tavmergen E., Yilmaz O., Calimlioglu N., Soykam H.O., Oktem G., Sezerman U. (2019). Differential gene expression analysis of human cumulus cells. Clin Exp Reprod Med., 46: 76.10.5653/cerm.2019.46.2.76Search in Google Scholar

Do D., Bissonnette N., Lacasse P., Miglior F., Sargolzaei M., Zhao X., Ibeagha-Awemu E. (2017). Genome-wide association analysis and pathways enrichment for lactation persistency in Canadian Holstein cattle. J. Dairy Sci., 100(3), 1955-1970.10.3168/jds.2016-1191028088409Search in Google Scholar

Doufas A.G., Mastorakos G. (2000). The hypothalamic-pituitary-thyroid axis and the female reproductive system. Ann. N. Y. Acad. Sci., 900: 65-76.10.1111/j.1749-6632.2000.tb06217.xSearch in Google Scholar

Eghbalsaied S. (2011) Estimation of genetic parameters for 13 female fertility indices in Holstein dairy cows. Trop Anim Health Prod., 43: 811-816.10.1007/s11250-010-9767-zSearch in Google Scholar

Fair T., Lonergan P. (2012). The role of progesterone in oocyte acquisition of developmental competence. Reprod. Domest. Anim., 47: 142-147.10.1111/j.1439-0531.2012.02068.xSearch in Google Scholar

Fang L., Sahana G., Su G., Yu Y., Zhang S., Lund M.S., Sørensen P. (2017). Integrating sequence-based GWAS and RNA-Seq provides novel insights into the genetic basis of mastitis and milk production in dairy cattle. Sci. Rep., 7: 455-460.10.1038/srep45560Search in Google Scholar

Farhadian M., Rafat S.A., Hasanpur K., Ebrahimi M., Ebrahimie E. (2018a). Cross-species meta-analysis of transcriptomic data in combination with supervised machine learning models identifies the common gene signature of lactation process. Front. Genet., 9: 235.10.3389/fgene.2018.00235605212930050559Search in Google Scholar

Farhadian M., Rafat S.A., Hasanpur K., Ebrahimie E. (2018b). Transcriptome signature of the lactation process, identified by meta-analysis of microarray and RNA-Seq data. Biotechnol Acta., 99: 153-163.10.5114/bta.2018.75659Search in Google Scholar

Frischknecht M., Bapst B., Seefried F.R., Signer-Hasler H., Garrick D., Stricker C., Fries R., Russ I., Sölkner J., Bieber A. (2017). Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences. BMC Genomics., 18: 910.10.1186/s12864-017-4308-zSearch in Google Scholar

Ghasemi M., Zamani P., Vatankhah M., Abdoli R. (2019). Genome-wide association study of birth weight in sheep. Animal., 13: 1797-1803.10.1017/S1751731118003610Search in Google Scholar

Ghiasi H., Pakdel A., Nejati-Javaremi A., Mehrabani-Yeganeh H., Honarvar M., González-Recio O., Carabaño M.J., Alenda R. (2011). Genetic variance components for female fertility in Iranian Holstein cows. Livest Sci., 139: 277-280.10.1016/j.livsci.2011.01.020Search in Google Scholar

Goddard M.E., Hayes B.J. (2009). Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet., 10: 381.10.1038/nrg2575Search in Google Scholar

Han B., Kang H.M., Eskin, E. (2009). Rapid and accurate multiple testing correction and power estimation for millions of correlated markers. PLoS Genet., 5 (4): e1000456.10.1371/journal.pgen.1000456Search in Google Scholar

Hirose M., Kamoshita M., Fujiwara K., Kato T., Nakamura A., Wojcikiewicz R.J., Parys J.B., Ito J., Kashiwazaki N. (2013). Vitrification procedure decreases inositol 1, 4, 5-trisphophate receptor expression, resulting in low fertility of pig oocytes. J. Anim. Sci., 84: 693-701.10.1111/asj.12061Search in Google Scholar

Höglund J.K., Buitenhuis B., Guldbrandtsen B., Lund M.S., Sahana G. (2015). Genome-wide association study for female fertility in Nordic Red cattle. BMC Genetics., 16: 110.10.1186/s12863-015-0269-xSearch in Google Scholar

Ibeagha-Awemu E.M., Peters S.O., Akwanji K.A., Imumorin I.G., Zhao X. (2016). 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., 6: 31109.10.1038/srep31109Search in Google Scholar

Institute S. (2014) ‘SAS 9.4 Output delivery system: User’s guide.’ (SAS institute).Search in Google Scholar

Jamrozik J., Fatehi J., Kistemaker G.J., Schaeffer L.R. (2005). Estimates of Genetic Parameters for Canadian Holstein Female Reproduction Traits. J. Dairy Sci., 88: 2199-2208.10.3168/jds.S0022-0302(05)72895-2Search in Google Scholar

Jiang L., Liu X., Yang J., Wang H., Jiang J., Liu L., He S., Ding X., Liu J., Zhang Q. (2014). Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits. BMC Genomics., 15: 1105.10.1186/1471-2164-15-1105Search in Google Scholar

Kadarmideen H., Thompson R., Simm G. (2000). Linear and threshold model genetic parameters for disease, fertility and milk production in dairy cattle. Anim. Sci., 71: 411-419.10.1017/S1357729800055338Search in Google Scholar

Klein R.J., Zeiss C., Chew E.Y., Tsai J.-Y., Sackler R.S., Haynes C., Henning A.K., SanGiovanni J.P., Mane S.M., Mayne S.T. (2005). Complement factor H polymorphism in age-related macular degeneration. Science., 308: 385-389.10.1126/science.1109557Search in Google Scholar

Kolbehdari D., Wang Z., Grant J., Murdoch B., Prasad A., Xiu Z., Marques E., Stothard P., Moore S. (2009). A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls. J. Anim. Breed. Genet., 126: 216-227.10.1111/j.1439-0388.2008.00793.xSearch in Google Scholar

Kominakis A., Hager-Theodorides A.L., Zoidis E., Saridaki A., Antonakos G., Tsiamis G. (2017). Combined GWAS and ‘guilt by association’-based prioritization analysis identifies functional candidate genes for body size in sheep. Genet. Sel. Evol., 49 (1): 41.10.1186/s12711-017-0316-3Search in Google Scholar

Kulak K., Dekkers J., McAllister A., Lee A. (1997). Relationships of early performance traits to lifetime profitability in Holstein cows. Can. J. Anim. Sci., 77: 617-624.10.4141/A96-129Search in Google Scholar

Liu A., Wang Y., Sahana G., Zhang Q., Liu L., Lund M.S., Su G. (2017). Genome-wide association studies for female fertility traits in Chinese and Nordic Holsteins. Sci. Rep., 7 (1): 8487.10.1038/s41598-017-09170-9Search in Google Scholar

Lonergan P. (2011) Influence of progesterone on oocyte quality and embryo development in cows. Theriogenology., 76: 1594-1601.10.1016/j.theriogenology.2011.06.012Search in Google Scholar

Loveland K.L., Klein B., Pueschl D., Indumathy S., Bergmann M., Loveland B.E., Hedger M.P., Schuppe H.-C. (2017). Cytokines in male fertility and reproductive pathologies: Immunoregulation and beyond. Front Endocrinol., 8: 307.10.3389/fendo.2017.00307Search in Google Scholar

Ma K., Liao M., Liu F., Ye B., Sun F., Yue G.H. (2016). Charactering the ZFAND3 gene mapped in the sex-determining locus in hybrid tilapia (Oreochromis spp.). Sci. rep., 6: 25471.10.1038/srep25471Search in Google Scholar

Minozzi G., Nicolazzi E.L., Stella A., Biffani S., Negrini R., Lazzari B., Ajmone-Marsan P., Williams J.L. (2013). Genome wide analysis of fertility and production traits in Italian Holstein cattle. PLoS One., 8 (11): e80219.10.1371/journal.pone.0080219Search in Google Scholar

Misztal I. Auvray B, Druet T, Lee DH. (2002). BLUPF90 and related programs (BGF90). In ‘Proceedings of 7th World Congress on Genetics Applied to Livestock Production, Montpelier, France.Search in Google Scholar

Moore S.G., Pryce J.E., Hayes B.J., Chamberlain A.J., Kemper K.E., Berry D.P., McCabe M., Cormican P., Lonergan P., Fair T. (2016). Differentially expressed genes in endometrium and corpus luteum of Holstein cows selected for high and low fertility are enriched for sequence variants associated with fertility. Biol. Rep., 94: 19, 1-11.10.1095/biolreprod.115.13295126607721Search in Google Scholar

Mungall C.J., Bada M., Berardini T.Z., Deegan J., Ireland A., Harris M.A., Hill D.P., Lomax J. (2011). Cross-product extensions of the Gene Ontology. J Biomed Inform., 44: 80-86.10.1016/j.jbi.2010.02.002Search in Google Scholar

Muñoz-Espín D., Cañamero M., Maraver A., Gómez-López G., Contreras J., Murillo-Cuesta S., Rodríguez-Baeza A., Varela-Nieto I., Ruberte J., Collado M. (2013). Programmed cell senescence during mammalian embryonic development. Cell., 155: 1104-1118.10.1016/j.cell.2013.10.019Search in Google Scholar

Nayeri S., Sargolzaei M., Abo-Ismail M., Miller S., Schenkel F., Moore S., Stothard P. (2017). Genome-wide association study for lactation persistency, female fertility, longevity, and lifetime profit index traits in Holstein dairy cattle. J. Dairy Sci., 100: 1246-1258.10.3168/jds.2016-11770Search in Google Scholar

Nayeri S., Sargolzaei M., Abo-Ismail M.K., May N., Miller S.P., Schenkel F., Moore S.S., Stothard P. (2016). Genome-wide association for milk production and female fertility traits in Canadian dairy Holstein cattle. BMC Genetics., 17 (1): 75.10.1186/s12863-016-0386-1Search in Google Scholar

Neupane M., Geary T.W., Kiser J.N., Burns G.W., Hansen P.J., Spencer T.E., Neibergs H.L. (2017). Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle. PloS One., 12: e0188997.10.1371/journal.pone.0188997Search in Google Scholar

Olsen H., Hayes B., Kent M., Nome T., Svendsen M., Larsgard A., Lien S. (2011). Genome-wide association mapping in Norwegian Red cattle identifies quantitative trait loci for fertility and milk production on BTA12. Anim. Genet., 42: 466-474.10.1111/j.1365-2052.2011.02179.xSearch in Google Scholar

Ortega M.S., Denicol A.C., Cole J.B., Null D.J., Taylor J.F., Schnabel R.D., Hansen P.J. (2017). Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows. J. Dairy Sci., 100: 3725-3734.10.3168/jds.2016-12260Search in Google Scholar

Panahi B., Farhadian M., Dumas J., and Hejazi, M. (2019). Integration of cross species RNA-seq Meta-analysis and Machine Learning Models identifies the most important salt stress responsive pathways in microalga Dunaliella. Front. Genet., 10: 752.10.3389/fgene.2019.00752Search in Google Scholar

Pimentel E., Bauersachs S., Tietze M., Simianer H., Tetens J., Thaller G., Reinhardt F., Wolf E., König S. (2011). Exploration of relationships between production and fertility traits in dairy cattle via association studies of SNPs within candidate genes derived by expression profiling. Anim. Genet., 42: 251-262.10.1111/j.1365-2052.2010.02148.xSearch in Google Scholar

Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Bender D., Maller J., Sklar P., De Bakker P.I., Daly M.J. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. AJHG., 81: 559-575.10.1086/519795Search in Google Scholar

Rempel L.A., Freking B.A., Miles J.R., Nonneman D.J., Rohrer G.A., Vallet J.L., Schneider J.F. (2011). Association of porcine heparanase and hyaluronidase 1 and 2 with reproductive and production traits in a Landrace–Duroc–Yorkshire population. Front. Genet., 2: 20.10.3389/fgene.2011.00020Search in Google Scholar

Reverter A., Fortes M. (2013). Building single nucleotide polymorphism-derived gene regulatory networks: towards functional genomewide association studies. J. Anim. Sci., 91: 530-536.10.2527/jas.2012-5780Search in Google Scholar

Reverter A., Porto-Neto L., Fortes M., McCulloch R., Lyons R., Moore S., Nicol D., Henshall J., Lehnert S. (2016). Genomic analyses of tropical beef cattle fertility based on genotyping pools of Brahman cows with unknown pedigree. J. Anim. Sci., 94: 4096-4108.10.2527/jas.2016-0675Search in Google Scholar

Rezende F., Dietsch G., Peñagaricano F. (2018). Genetic dissection of bull fertility in US Jersey dairy cattle. Anim. Genet., 49: 393-402.10.1111/age.12710Search in Google Scholar

Rolf M., Taylor J., Schnabel R., McKay S., McClure M., Northcutt S., Kerley M., Weaber R. (2012). Genome-wide association analysis for feed efficiency in Angus cattle. Anim. Gen., 43: 367-374.10.1111/j.1365-2052.2011.02273.xSearch in Google Scholar

Royal M., Flint A., Woolliams J. (2002). Genetic and phenotypic relationships among endocrine and traditional fertility traits and production traits in Holstein-Friesian dairy cows. J. Anim. Sci., 85: 958-967.10.3168/jds.S0022-0302(02)74155-6Search in Google Scholar

Sargolzaei M. (2014). SNP1101 User’s guide. (Version1.0.0). Semex Alliance, Ontario, Canada.Search in Google Scholar

Schnabel R., Sonstegard T., Taylor J., Ashwell M. (2005). Whole-genome scan to detect QTL for milk production, conformation, fertility and functional traits in two US Holstein families. Anim. Genet., 36: 408-416.10.1111/j.1365-2052.2005.01337.xSearch in Google Scholar

Seyedsharifi R., Nurafkan F., Hedayat Evrigh N., Seifdavati J. (2017). Estimation of Economic Value for Productive and Reproductive Traits of Moghan Agro-Industrial Holstein Cows by using Simulation and Bio-Economic Model. IJAS., 9 (20): 15. [Persian]Search in Google Scholar

Shook G. (2006). Major advances in determining appropriate selection goals. J. Dairy Sci., 89: 1349-1361.10.3168/jds.S0022-0302(06)72202-0Search in Google Scholar

Storer M., Mas A., Robert-Moreno A., Pecoraro M., Ortells M.C., Di Giacomo V., Yosef R., Pilpel N., Krizhanovsky V., Sharpe J. (2013). Senescence is a developmental mechanism that contributes to embryonic growth and patterning. Cell., 155: 1119-1130.10.1016/j.cell.2013.10.041Search in Google Scholar

Sullivan P.G., Jamrozik J., and Kistemaker G.J. (2015). De-regressing MACE versus domestic EBV for genomics. Interbull Bulletin(49).Search in Google Scholar

Sutovsky P. (2003). Ubiquitin-dependent proteolysis in mammalian spermatogenesis, fertilization, and sperm quality control: killing three birds with one stone. Microsc. Res. Tech., 61: 88-102.10.1002/jemt.10319Search in Google Scholar

Toghiani S. (2012). Genetic relationships between production traits and reproductive performance in Holstein dairy cows. Arch Anim Breed., 55: 458-468.10.5194/aab-55-458-2012Search in Google Scholar

Turner S.D. (2014). qqman: an R package for visualizing GWAS results using QQ and manhattan plots. Biorxiv., 005165.10.1101/005165Search in Google Scholar

VanRaden P.M. (2008). Efficient methods to compute genomic predictions. J. Dairy Sci., 91: 4414-4423.10.3168/jds.2007-0980Search in Google Scholar

Velarde M.C., Menon R. (2016). Positive and negative effects of cellular senescence during female reproductive aging and pregnancy. J. Endocrinol., 230: 59-76.10.1530/JOE-16-0018Search in Google Scholar

Walsh S., Williams E., Evans A. (2011). A review of the causes of poor fertility in high milk producing dairy cows. Anim. Reprod. Sci., 123: 127-138.10.1016/j.anireprosci.2010.12.001Search in Google Scholar

Wang H, Zhang L, Cao J, Wu M, Ma X, Liu Z, Liu R, Zhao F, Wei C, Du L. (2015). Genome-Wide specific selection in three domestic sheep breeds. PLoS One., 10(6): e0128688.10.1371/journal.pone.0128688Search in Google Scholar

Xu S., Gao L., Xie X., Ren Y., Shen Z.,Wang F., Shen M., Eyþórsdóttr E., Hallsson J., Kiseleva T., Juha Kantanen J., Li M. (2018). Genome-Wide association analyses highlight the potential for different genetic mechanisms for litter size among sheep breeds. Front. Genet. 9:118.10.3389/fgene.2018.00118Search in Google Scholar

Xu S., Wang, D., Zho, D., Lin Y., Che L., Fang Z., Wu D. (2015). Reproductive Hormone and Transcriptomic Responses of Pituitary Tissue in Anestrus Gilts Induced by Nutrient Restriction. PloS One., 10 (11): e0143219.10.1371/journal.pone.0143219Search in Google Scholar

Yang J., Weedon M.N., Purcell S., Lettre G., Estrada K., Willer C.J., Smith A.V., Ingelsson E., O’connell J.R., Mangino M. (2011). Genomic inflation factors under polygenic inheritance. AJHG., 19 (7): 807.10.1038/ejhg.2011.39Search in Google Scholar