Characterizing Milk Production Related Genes in Holstein Using RNA-seq |
Seo, Minseok
(Interdisciplinary Program in Bioinformatics, Seoul National University)
Lee, Hyun-Jeong (Interdisciplinary Program in Bioinformatics, Seoul National University) Kim, Kwondo (Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University) Caetano-Anolles, Kelsey (Department of Animal Sciences, University of Illinois) Jeong, Jin Young (Division of Animal Products R&D, National Institute of Animal Science) Park, Sungkwon (Animal Nutritional & Physiology Team, National Institute of Animal Science) Oh, Young Kyun (Animal Nutritional & Physiology Team, National Institute of Animal Science) Cho, Seoae (CHO&KIM genomics) Kim, Heebal (Interdisciplinary Program in Bioinformatics, Seoul National University) |
1 | Accorsi, P. A., B. Pacioni, C. Pezzi, M. Forni, D. J. Flint, and E. Seren. 2002. Role of prolactin, growth hormone and insulinlike growth factor 1 in mammary gland involution in the dairy cow. J. Dairy Sci 85:507-513. DOI |
2 | Canovas, A., G. Rincon, A. Islas-Trejo, S. Wickramasinghe, and J. F. Medrano. 2010. SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm. Genome 21:592-598. DOI |
3 | Chauhan, V. and J. Hayes. 1991. Genetic parameters for first lactation milk production and composition traits for Holsteins using multivariate restricted maximum likelihood. J Dairy Sci 74:603-610. DOI |
4 | Constantin, A. and C. Csatlos. 2010. Research on the influence of microwave treatment on milk composition. Bulletin of the Transilvania University of Brasov 3:52. |
5 | Cui, X. G., Y. L. Hou, S. H. Yang, Y. Xie, S. L. Zhang, Y. Zhang, Q. Zhang, X. M. Lu, G. E. Liu, and D. X. Sun. 2014. Transcriptional profiling of mammary gland in Holstein cows with extremely different milk protein and fat percentage using RNA sequencing. BMC Genomics 15:226. DOI |
6 | Glasser, F., A. Ferlay, and Y. Chilliard. 2008. Oilseed lipid supplements and fatty acid composition of cow milk: A metaanalysis. J. Dairy Sci. 91:4687-4703. DOI |
7 | Hennighausen, L. and G. W. Robinson. 2001. Signaling pathways in mammary gland development. Dev. Cell 1:467-475. DOI |
8 | Hill, P. D., J. C. Aldag, and R. T. Chatterton. 1999. Effects of pumping style on milk production in mothers of non-nursing preterm infants. J. Hum. Lact. 15:209-216. DOI |
9 | McDonald, T. L., M. A. Larson, D. R. Mack, and A. Weber. 2001. Elevated extrahepatic expression and secretion of mammaryassociated serum amyloid A 3 (M-SAA3) into colostrum. Vet. Immunol. Immunopathol. 83:203-211. DOI |
10 | Mensink, R. P., P. L. Zock, A. D. Kester, and M. B. Katan. 2003. Effects of dietary fatty acids and carbohydrates on the ratio of serum total to HDL cholesterol and on serum lipids and apolipoproteins: a meta-analysis of 60 controlled trials. Am. J. Clin. Nutr. 77:1146-1155. DOI |
11 | Neale, B. M., S. E. Medland, S. Ripke, P. Asherson, B. Franke, K.-P. Lesch, S. V. Faraone, T. T. Nguyen, H. Schafer, and P. Holmans et al. 2010. Meta-analysis of genome-wide association studies of attention-deficit/hyperactivity disorder. J. Am. Acad. Child Adolesc. Psychiatry 49:884-897. DOI |
12 | Minozzi, G., J. L. Williams, A. Stella, F. Strozzi, M. Luini, M. L. Settles, J. F. Taylor, R. H. Whitlock, R. Zanella, and H. L. Neibergs. 2012. Meta-analysis of two genome-wide association studies of bovine paratuberculosis. Plos One 7:e32578. DOI |
13 | Mizoguchi, Y., T. Hirano, T. Itoh, H. Aso, A. Takasuga, Y. Sugimoto, and T. Watanabe. 2010. Differentially expressed genes during bovine intramuscular adipocyte differentiation profiled by serial analysis of gene expression. Anim. Genet. 41:436-441. |
14 | Molenaar, A. J., D. P. Harris, G. H. Rajan, M. L. Pearson, M. R. Callaghan, L. Sommer, V. C. Farr, K. E. Oden, M. C. Miles, and R. S. Petrova et al. 2009. The acute-phase protein serum amyloid A3 is expressed in the bovine mammary gland and plays a role in host defence. Biomarkers 14:26-37. DOI |
15 | Onetti, S. G. and R. R. Grummer. 2004. Response of lactating cows to three supplemental fat sources as affected by forage in the diet and stage of lactation: A meta-analysis of literature. Anim. Feed Sci. Technol. 115:65-82. DOI |
16 | Park, D. S., H. Lee, P. G. Frank, B. Razani, A. V. Nguyen, A. F. Parlow, R. G. Russell, J. Hulit, R. G. Pestell, and M. P. Lisanti. 2002. Caveolin-1-deficient mice show accelerated mammary gland development during pregnancy, premature lactation, and hyperactivation of the Jak-2/STAT5a signaling cascade. Mol. Biol. Cell 13:3416-3430. DOI |
17 | Pepe, G., G. C. Tenore, R. Mastrocinque, P. Stusio, and P. Campiglia. 2013. Potential anticarcinogenic peptides from bovine milk. J. Amino Acids Article ID 939804. |
18 | Sorensen, M., J. V. Norgaard, P. K. Theil, M. Vestergaard, and K. Sejrsen. 2006. Cell turnover and activity in mammary tissue during lactation and the dry period in dairy cows. J. Dairy Sci. 89:4632-4639. DOI |
19 | Renehan, A. G., M. Tyson, M. Egger, R. F. Heller, and M. Zwahlen. 2008. Body-mass index and incidence of cancer: a systematic review and meta-analysis of prospective observational studies. Lancet 371:569-578. DOI |
20 | Seo, M., J. Yoon, and T. Park. 2015. GRACOMICS: software for graphical comparison of multiple results with omics data. BMC Genomics 16:256. DOI |
21 | Sugimoto, K., N. Ichikawa-Tomikawa, S. Satohisa, Y. Akashi, R. Kanai, T. Saito, N. Sawada, and H. Chiba. 2013. The tightjunction protein claudin-6 induces epithelial differentiation from mouse F9 and embryonic stem cells. PloS one 8:e75106. DOI |
22 | Takasuga, A., T. Watanabe, Y. Mizoguchi, T. Hirano, N. Ihara, A. Takano, K. Yokouchi, A. Fujikawa, K. Chiba, and N. Kobayashi et al. 2007. Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping. Mamm. Genome 18:125-136. DOI |
23 | Tao, S., J. W. Bubolz, B. C. Do Amaral, I. M. Thompson, M. J. Hayen, S. E. Johnson, and G. E. Dahl. 2011. Effect of heat stress during the dry period on mammary gland development. J. Dairy Sci. 94:5976-5986. DOI |
24 | Tezer, M., Y. Ozluk, O. Sanli, O. Asoglu, and A. Kadioglu. 2012. Nitric oxide may mediate nipple erection. J. Androl. 33:805-810. DOI |
25 | Thompson, S. G. and J. Higgins. 2002. How should metaregression analyses be undertaken and interpreted? Stat. Med. 21:1559-1573. DOI |
26 | Yarus, S., J. M. Rosen, A. M. Cole, and G. Diamond. 1996. Production of active bovine tracheal antimicrobial peptide in milk of transgenic mice. Proc. Nat. Acad. Sci. 93:14118-14121. DOI |
27 | Vargas, B., A. F. Groen, M. Herrero, and J. A. Van Arendonk. 2002. Economic values for production and functional traits in Holstein cattle of Costa Rica. Livest. Prod. Sci. 75:101-116. DOI |
28 | Wang, Z., M. Gerstein, and M. Snyder. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63. DOI |
29 | Wickramasinghe, S., G. Rincon, A. Islas-Trejo, and J. F. Medrano. 2012. Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics 13:45. DOI |
30 | Yoon, J. T., J. H. Lee, C. K. Kim, Y. C. Chung, and C.-H. Kim. 2004. Effects of milk production, season, parity and lactation period on variations of milk urea nitrogen concentration and milk components of Holstein dairy cows. Asian Australas. J. Anim. Sci. 17:479-484. DOI |