title: Characterizing Milk Production Related Genes in Holstein Using RNA-seq.
abstract: 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.
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Korea ; CHO&KIM genomics, Seoul 151-919, Korea .
authors.forename: Minseok
authors.initials: M
authors.lastname: Seo
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Korea ; Animal Nutritional & Physiology Team, National Institute of Animal Science, Jeonju 565-851, Korea .
authors.forename: Hyun-Jeong
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea .
authors.forename: Kwondo
authors.initials: K
authors.lastname: Kim
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA .
authors.forename: Kelsey
authors.initials: K
authors.lastname: Caetano-Anolles
authors.affiliation: Division of Animal Products R&D, National Institute of Animal Science, Jeonju 565-851, Korea .
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Jeong
authors.affiliation: Animal Nutritional & Physiology Team, National Institute of Animal Science, Jeonju 565-851, Korea . ; Department of Food Science and Technology, Sejong University, Seoul 143-747, Korea .
authors.forename: Sungkwon
authors.initials: S
authors.lastname: Park
authors.affiliation: Animal Nutritional & Physiology Team, National Institute of Animal Science, Jeonju 565-851, Korea .
authors.forename: Young Kyun
authors.initials: YK
authors.lastname: Oh
authors.affiliation: CHO&KIM genomics, Seoul 151-919, Korea .
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Korea ; CHO&KIM genomics, Seoul 151-919, Korea . ; Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA .
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
keywords: Differentially Expressed Gene; Holstein; Meta-analysis; Milk Production; Milk Yield; RNA-seq