Advanced SearchSearch Tips
Characterizing Milk Production Related Genes in Holstein Using RNA-seq
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Characterizing Milk Production Related Genes in Holstein Using RNA-seq
Seo, Minseok; Lee, Hyun-Jeong; Kim, Kwondo; Caetano-Anolles, Kelsey; Jeong, Jin Young; Park, Sungkwon; Oh, Young Kyun; Cho, Seoae; Kim, Heebal;
  PDF(new window)
Although the chemical, physical, and nutritional properties of bovine milk have been extensively studied, only a few studies have attempted to characterize milk-synthesizing genes using RNA-seq data. RNA-seq data was collected from 21 Holstein samples, along with group information about milk production ability; milk yield; and protein, fat, and solid contents. Meta-analysis was employed in order to generally characterize genes related to milk production. In addition, we attempted to investigate the relationship between milk related traits, parity, and lactation period. We observed that milk fat is highly correlated with lactation period; this result indicates that this effect should be considered in the model in order to accurately detect milk production related genes. By employing our developed model, 271 genes were significantly (false discovery rate [FDR] adjusted p-value<0.1) detected as milk production related differentially expressed genes. Of these genes, five (albumin, nitric oxide synthase 3, RNA-binding region (RNP1, RRM) containing 3, secreted and transmembrane 1, and serine palmitoyltransferase, small subunit B) were technically validated using quantitative real-time polymerase chain reaction (qRT-PCR) in order to check the accuracy of RNA-seq analysis. Finally, 83 gene ontology biological processes including several blood vessel and mammary gland development related terms, were significantly detected using DAVID gene-set enrichment analysis. From these results, we observed that detected milk production related genes are highly enriched in the circulation system process and mammary gland related biological functions. In addition, we observed that detected genes including caveolin 1, mammary serum amyloid A3.2, lingual antimicrobial peptide, cathelicidin 4 (CATHL4), cathelicidin 6 (CATHL6) have been reported in other species as milk production related gene. For this reason, we concluded that our detected 271 genes would be strong candidates for determining milk production.
RNA-seq;Holstein;Milk Production;Meta-analysis;Milk Yield;Differentially Expressed Gene;
 Cited by
Genome-wide association studies to identify quantitative trait loci affecting milk production traits in water buffalo, Journal of Dairy Science, 2017, 00220302  crossref(new windwow)
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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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.

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. crossref(new window)

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. crossref(new window)

Hennighausen, L. and G. W. Robinson. 2001. Signaling pathways in mammary gland development. Dev. Cell 1:467-475. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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.

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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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.

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. crossref(new window)

Seo, M., J. Yoon, and T. Park. 2015. GRACOMICS: software for graphical comparison of multiple results with omics data. BMC Genomics 16:256. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

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. crossref(new window)

Tezer, M., Y. Ozluk, O. Sanli, O. Asoglu, and A. Kadioglu. 2012. Nitric oxide may mediate nipple erection. J. Androl. 33:805-810. crossref(new window)

Thompson, S. G. and J. Higgins. 2002. How should metaregression analyses be undertaken and interpreted? Stat. Med. 21:1559-1573. crossref(new window)

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. crossref(new window)

Wang, Z., M. Gerstein, and M. Snyder. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63. crossref(new window)

Wickramasinghe, S., G. Rincon, A. Islas-Trejo, and J. F. Medrano. 2012. Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics 13:45. crossref(new window)

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. crossref(new window)

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. crossref(new window)