[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/RD1828230958977]Search 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.12700]Search 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.2019.07.014]Search 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/JCI75943]Search 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)73186-0]Search 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.103.024752]Search 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/s184]Search 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.2015.05.041]Search 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.0211773]Search 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.2010.04.002]Search 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.2012.05.013]Search 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/s12864-019-5638-9]Search 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/S1751731107702070]Search 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: 49.10.1186/1471-2156-14-49368657723759029]Search 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.113.11126023904513]Search 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/s12711-015-0146-0]Search 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.2019.46.2.76]Search 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.2016-1191028088409]Search 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.x]Search 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-z]Search 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.x]Search 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/srep45560]Search 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.2018.00235605212930050559]Search 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.2018.75659]Search 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-z]Search 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/S1751731118003610]Search 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.2011.01.020]Search 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/nrg2575]Search 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.1000456]Search 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.12061]Search 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-x]Search 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/srep31109]Search 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)72895-2]Search 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: 1105.10.1186/1471-2164-15-1105]Search 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/S1357729800055338]Search 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.1109557]Search 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.x]Search 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/s12711-017-0316-3]Search 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/A96-129]Search 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/s41598-017-09170-9]Search 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.2011.06.012]Search 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.2017.00307]Search 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/srep25471]Search 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.0080219]Search 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.115.13295126607721]Search 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.2010.02.002]Search 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.2013.10.019]Search 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.2016-11770]Search 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/s12863-016-0386-1]Search 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.0188997]Search 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.x]Search 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.2016-12260]Search 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.2019.00752]Search 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.x]Search 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: 559-575.10.1086/519795]Search 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.2011.00020]Search 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.2012-5780]Search 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.2016-0675]Search 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.12710]Search 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.x]Search 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)74155-6]Search 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.x]Search 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)72202-0]Search 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.2013.10.041]Search 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.10319]Search 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-55-458-2012]Search in Google Scholar
[Turner S.D. (2014). qqman: an R package for visualizing GWAS results using QQ and manhattan plots. Biorxiv., 005165.10.1101/005165]Search in Google Scholar
[VanRaden P.M. (2008). Efficient methods to compute genomic predictions. J. Dairy Sci., 91: 4414-4423.10.3168/jds.2007-0980]Search 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-16-0018]Search 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.2010.12.001]Search 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.0128688]Search 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.2018.00118]Search 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.0143219]Search 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.2011.39]Search in Google Scholar