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Gebreselase HB, Nigussie H, Wang C, Luo C. Genetic Diversity, Population Structure and Selection Signature in Begait Goats Revealed by Whole-Genome Sequencing. Animals (Basel) 2024; 14:307. [PMID: 38254476 PMCID: PMC10812714 DOI: 10.3390/ani14020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Goats belong to a group of animals called small ruminants and are critical sources of livelihood for rural people. Genomic sequencing can provide information ranging from basic knowledge about goat diversity and evolutionary processes that shape genomes to functional information about genes/genomic regions. In this study, we exploited a whole-genome sequencing data set to analyze the genetic diversity, population structure and selection signatures of 44 individuals belonging to 5 Ethiopian goat populations: 12 Aberegalle (AB), 5 Afar (AF), 11 Begait (BG), 12 Central highlands (CH) and 5 Meafure (MR) goats. Our results revealed the highest genetic diversity in the BG goat population compared to the other goat populations. The pairwise genetic differentiation (FST) among the populations varied and ranged from 0.011 to 0.182, with the closest pairwise value (0.003) observed between the AB and CH goats and a distant correlation (FST = 0.182) between the BG and AB goats, indicating low to moderate genetic differentiation. Phylogenetic tree, ADMIXTURE and principal component analyses revealed a classification of the five Ethiopian goat breeds in accordance with their geographic distribution. We also found three top genomic regions that were detected under selection on chromosomes 2, 5 and 13. Moreover, this study identified different candidate genes related to milk characteristics (GLYCAM1 and SRC), carcass (ZNF385B, BMP-7, PDE1B, PPP1R1A, FTO and MYOT) and adaptive and immune response genes (MAPK13, MAPK14, SCN7A, IL12A, EST1 DEFB116 and DEFB119). In conclusion, this information could be helpful for understanding the genetic diversity and population structure and selection scanning of these important indigenous goats for future genetic improvement and/or as an intervention mechanism.
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Affiliation(s)
- Haile Berihulay Gebreselase
- State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Key Laboratory of Animal Breeding and Nutrition Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Department of Biotechnology, College of Natural and Computational Science, Aksum University, Aksum 1010, Tigray, Ethiopia
| | | | - Changfa Wang
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng 252000, China;
| | - Chenglong Luo
- State Key Laboratory of Swine and Poultry Breeding Industry Guangdong Key Laboratory of Animal Breeding and Nutrition Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Xiong J, Bao J, Hu W, Shang M, Zhang L. Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat. Front Genet 2023; 13:1044017. [PMID: 36685859 PMCID: PMC9852865 DOI: 10.3389/fgene.2022.1044017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.
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Ahlawat S, Choudhary V, Singh T, Arora R, Kumar A, Kaur M, Chhabra P, Sharma R, Kumar Vijh R. First report on delineation of differentially expressed genes and pathways in milk somatic cells of mastitic and healthy Murrah buffaloes. Gene X 2022; 831:146575. [PMID: 35568339 DOI: 10.1016/j.gene.2022.146575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/20/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
Despite immense contribution of buffaloes as dairy species, limited studies have addressed the bubaline mastitis as compared to cattle. This was the first differential transcriptomic study investigating the alterations induced by clinical mastitis in buffalo milk relative to healthy controls. Comparative gene expression profiling of three biological replicates of each group identified 1014 up-regulated and 999 down-regulated genes in the diseased buffaloes (Fold change > 2, FDR < 0.05). Activation of immune and inflammatory responses were the most enriched GO terms in the mastitic animals, with higher transcript abundance of many genes coding for anti-microbial proteins such as β-defensins, perforin, granzymes, granulysin, cathelicidins etc. Analysis of the gene regulatory interactions of the up-regulated DEGs identified many hub genes that govern the cellular and macromolecular metabolic processes (E2F4, E2F1, RBL2, FOXM1, IRF1 and MYB). This study contributes to an insightful understanding of molecular mechanisms governing immune response of buffaloes to mastitis.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Vikas Choudhary
- District Disease Diagnostic Laboratory, Karnal, Department of Animal Husbandry and Dairying, Haryana, India
| | - Tersem Singh
- District Disease Diagnostic Laboratory, Karnal, Department of Animal Husbandry and Dairying, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
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5
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Asselstine V, Miglior F, Suárez-Vega A, Fonseca PAS, Mallard B, Karrow N, Islas-Trejo A, Medrano JF, Cánovas A. Genetic mechanisms regulating the host response during mastitis. J Dairy Sci 2019; 102:9043-9059. [PMID: 31421890 DOI: 10.3168/jds.2019-16504] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
Mastitis is a very costly and common disease in the dairy industry. The study of the transcriptome from healthy and mastitic milk somatic cell samples using RNA-Sequencing technology can provide measurements of transcript levels associated with the immune response to the infection. The objective of this study was to characterize the Holstein milk somatic cell transcriptome from 6 cows to determine host response to intramammary infections. RNA-Sequencing was performed on 2 samples from each cow from 2 separate quarters, one classified as healthy (n = 6) and one as mastitic (n = 6). In total, 449 genes were differentially expressed between the healthy and mastitic quarters (false discovery rate <0.05, fold change >±2). Among the differentially expressed genes, the most expressed genes based on reads per kilobase per million mapped reads (RPKM) in the healthy group were associated with milk components (CSN2 and CSN3), and in the mastitic group they were associated with immunity (B2M and CD74). In silico functional analysis was performed using the list of 449 differentially expressed genes, which identified 36 significantly enriched metabolic pathways (false discovery rate <0.01), some of which were associated with the immune system, such as cytokine-cytokine interaction and cell adhesion molecules. Seven functional candidate genes were selected, based on the criteria of being highly differentially expressed between healthy and mastitic groups and significantly enriched in metabolic pathways that are relevant to the inflammatory process (GLYCAM1, B2M, CD74, BoLA-DRA, FCER1G, SDS, and NFKBIA). Last, we identified the differentially expressed genes that are located in quantitative trait locus regions previously known to be associated with mastitis, specifically clinical mastitis, somatic cell count, and somatic cell score. It was concluded that multiple genes within quantitative trait locus regions could potentially affect host response to mastitis-causing agents, making some cows more susceptible to intramammary infections. The identification of potential candidate genes with functional, statistical, biological, and positional relevance associated with host defense to infection will contribute to a better understanding of the underlying genetic architecture associated with mastitis. This in turn will improve the sustainability of agricultural practices by facilitating the selection of cows with improved host defense leading to increased resistance to mastitis.
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Affiliation(s)
- V Asselstine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - A Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - B Mallard
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - N Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - A Islas-Trejo
- Department of Animal Science, University of California-Davis, Davis 95616
| | - J F Medrano
- Department of Animal Science, University of California-Davis, Davis 95616
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
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Mol P, Kannegundla U, Dey G, Gopalakrishnan L, Dammalli M, Kumar M, Patil AH, Basavaraju M, Rao A, Ramesha KP, Prasad TSK. Bovine Milk Comparative Proteome Analysis from Early, Mid, and Late Lactation in the Cattle Breed, Malnad Gidda (Bos indicus). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:223-235. [PMID: 29389253 DOI: 10.1089/omi.2017.0162] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Bovine milk is important for both veterinary medicine and human nutrition. Understanding the bovine milk proteome at different stages of lactation has therefore broad significance for integrative biology and clinical medicine as well. Indeed, different lactation stages have marked influence on the milk yield, milk constituents, and nourishment of the neonates. We performed a comparative proteome analysis of the bovine milk obtained at different stages of lactation from the Indian indigenous cattle Malnad Gidda (Bos indicus), a widely available breed. The milk differential proteome during the lactation stages in B. indicus has not been investigated to date. Using high-resolution mass spectrometry-based quantitative proteomics of the bovine whey proteins at early, mid, and late lactation stages, we identified a total of 564 proteins, out of which 403 proteins were found to be differentially abundant at different lactation stages. As is expected of any body fluid proteome, 51% of the proteins identified in the milk were found to have signal peptides. Gene ontology analyses were carried out to categorize proteins altered across different lactation stages based on biological process and molecular function, which enabled us to correlate their significance in each lactation stage. We also investigated the potential pathways enriched in different lactation stages using bioinformatics pathway analysis tools. To the best of our knowledge, this study represents the first and largest inventory of milk proteins identified to date for an Indian cattle breed. We believe that the current study broadly informs both veterinary omics research and the emerging field of nutriproteomics during lactation stages.
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Affiliation(s)
- Praseeda Mol
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,2 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | | | - Gourav Dey
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 Centre for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University) , Mangalore, India .,5 Manipal Academy of Higher Education , Manipal, Karnataka, India
| | - Lathika Gopalakrishnan
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 Centre for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University) , Mangalore, India .,5 Manipal Academy of Higher Education , Manipal, Karnataka, India
| | - Manjunath Dammalli
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,6 Department of Biotechnology, Siddaganga Institute of Technology , Tumkur, India
| | - Manish Kumar
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,5 Manipal Academy of Higher Education , Manipal, Karnataka, India
| | - Arun H Patil
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 Centre for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University) , Mangalore, India .,7 School of Biotechnology, KIIT University , Bhubaneswar, India
| | | | - Akhila Rao
- 3 National Dairy Research Institute , Bangalore, India
| | | | - Thottethodi Subrahmanya Keshava Prasad
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,4 Centre for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University) , Mangalore, India
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Ji X, Li X, Ma Y, Li D. Differences in proteomic profiles of milk fat globule membrane in yak and cow milk. Food Chem 2017; 221:1822-1827. [DOI: 10.1016/j.foodchem.2016.10.097] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 01/01/2023]
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Bu D, Bionaz M, Wang M, Nan X, Ma L, Wang J. Transcriptome difference and potential crosstalk between liver and mammary tissue in mid-lactation primiparous dairy cows. PLoS One 2017; 12:e0173082. [PMID: 28291785 PMCID: PMC5349457 DOI: 10.1371/journal.pone.0173082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 02/15/2017] [Indexed: 12/15/2022] Open
Abstract
Liver and mammary gland are among the most important organs during lactation in dairy cows. With the purpose of understanding both the different and the complementary roles and the crosstalk of those two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4×44K Bovine Agilent microarray chip. The transcriptome difference between the two tissues was analyzed using SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR). The analysis uncovered >9,000 genes differentially expressed (DEG) between the two tissues with a FDR<0.001. The functional analysis of the DEG uncovered a larger metabolic (especially related to lipid) and inflammatory response capacity in liver compared with mammary tissue while the mammary tissue had a larger protein synthesis and secretion, proliferation/differentiation, signaling, and innate immune system capacity compared with the liver. A plethora of endogenous compounds, cytokines, and transcription factors were estimated to control the DEG between the two tissues. Compared with mammary tissue, the liver transcriptome appeared to be under control of a large array of ligand-dependent nuclear receptors and, among endogenous chemical, fatty acids and bacteria-derived compounds. Compared with liver, the transcriptome of the mammary tissue was potentially under control of a large number of growth factors and miRNA. The in silico crosstalk analysis between the two tissues revealed an overall large communication with a reciprocal control of lipid metabolism, innate immune system adaptation, and proliferation/differentiation. In summary the transcriptome analysis confirmed prior known differences between liver and mammary tissue, especially considering the indication of a larger metabolic activity in liver compared with the mammary tissue and the larger protein synthesis, communication, and proliferative capacity in mammary tissue compared with the liver. Relatively novel is the indication by the data that the transcriptome of the liver is highly regulated by dietary and bacteria-related compounds while the mammary transcriptome is more under control of hormones, growth factors, and miRNA. A large crosstalk between the two tissues with a reciprocal control of metabolism and innate immune-adaptation was indicated by the network analysis that allowed uncovering previously unknown crosstalk between liver and mammary tissue for several signaling molecules.
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Affiliation(s)
- Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
- CAAS-ICRAF Joint Laboratory on Agroforestry and Sustainable Animal Husbandry, World Agroforestry Centre, East and Central Asia, Beijing, China
- Synergetic Innovation Center of Food Safety and Nutrition, Harbin, China
| | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, United States of America
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, P.R. China
| | - Xuemei Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
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9
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Crisà A, Ferrè F, Chillemi G, Moioli B. RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk. BMC Vet Res 2016; 12:264. [PMID: 27884183 PMCID: PMC5123407 DOI: 10.1186/s12917-016-0881-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/07/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism. RESULTS A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB). CONCLUSIONS To our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.
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Affiliation(s)
- Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy.
| | - Fabrizio Ferrè
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126, Bologna, Italy
| | - Giovanni Chillemi
- Applications and Innovation Department, CINECA, SCAI SuperComputing, Via dei Tizii 6, 00185, Rome, Italy
| | - Bianca Moioli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy
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Characterisation of the immune compounds in koala milk using a combined transcriptomic and proteomic approach. Sci Rep 2016; 6:35011. [PMID: 27713568 PMCID: PMC5054531 DOI: 10.1038/srep35011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/16/2016] [Indexed: 01/15/2023] Open
Abstract
Production of milk is a key characteristic of mammals, but the features of lactation vary greatly between monotreme, marsupial and eutherian mammals. Marsupials have a short gestation followed by a long lactation period, and milk constituents vary greatly across lactation. Marsupials are born immunologically naïve and rely on their mother’s milk for immunological protection. Koalas (Phascolarctos cinereus) are an iconic Australian species that are increasingly threatened by disease. Here we use a mammary transcriptome, two milk proteomes and the koala genome to comprehensively characterise the protein components of koala milk across lactation, with a focus on immune constituents. The most abundant proteins were well-characterised milk proteins, including β-lactoglobulin and lactotransferrin. In the mammary transcriptome, 851 immune transcripts were expressed, including immunoglobulins and complement components. We identified many abundant antimicrobial peptides, as well as novel proteins with potential antimicrobial roles. We discovered that marsupial VELP is an ortholog of eutherian Glycam1, and likely has an antimicrobial function in milk. We also identified highly-abundant koala endogenous-retrovirus sequences, identifying a potential transmission route from mother to young. Characterising the immune components of milk is key to understanding protection of marsupial young, and the novel immune compounds identified may have applications in clinical research.
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11
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Gassi JY, Blot M, Beaucher E, Robert B, Leconte N, Camier B, Rousseau F, Bourlieu C, Jardin J, Briard-Bion V, Lambert S, Gésan-Guiziou G, Lopez C, Gaucheron F. Preparation and characterisation of a milk polar lipids enriched ingredient from fresh industrial liquid butter serum: Combination of physico-chemical modifications and technological treatments. Int Dairy J 2016. [DOI: 10.1016/j.idairyj.2015.08.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing. Sci Rep 2015; 5:18399. [PMID: 26677795 PMCID: PMC4683406 DOI: 10.1038/srep18399] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/17/2015] [Indexed: 11/08/2022] Open
Abstract
This study presents a dynamic characterization of the sheep milk transcriptome aiming at achieving a better understanding of the sheep lactating mammary gland. Transcriptome sequencing (RNA-seq) was performed on total RNA extracted from milk somatic cells from ewes on days 10, 50, 120 and 150 after lambing. The experiment was performed in Spanish Churra and Assaf breeds, which differ in their milk production traits. Nearly 67% of the annotated genes in the reference genome (Oar_v3.1) were expressed in ovine milk somatic cells. For the two breeds and across the four lactation stages studied, the most highly expressed genes encoded caseins and whey proteins. We detected 573 differentially expressed genes (DEGs) across lactation points, with the largest differences being found, between day 10 and day 150. Upregulated GO terms at late lactation stages were linked mainly to developmental processes linked to extracellular matrix remodeling. A total of 256 annotated DEGs were detected in the Assaf and Churra comparison. Some genes selectively upregulated in the Churra breed grouped under the endopeptidase and channel activity GO terms. These genes could be related to the higher cheese yield of this breed. Overall, this study provides the first integrated overview on sheep milk gene expression.
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Lin J, Bao ZK, Zhang Q, Hu WW, Yu QH, Yang Q. Transcriptome analysis of the mammary gland from GH transgenic goats during involution. Gene 2015; 565:228-34. [PMID: 25865296 DOI: 10.1016/j.gene.2015.04.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 03/11/2015] [Accepted: 04/07/2015] [Indexed: 11/26/2022]
Abstract
Mammary glands are organs for milk production in female mammals. Growth hormone (GH) is known to affect the growth and development of the mammary gland, as well as to increase milk production in dairy goats. This study performed a comprehensive expression profiling of genes expressed in the mammary gland of early involution GH transgenic (n=4) and non-transgenic goats (n=4) by RNA sequencing. RNA was extracted from mammary gland tissues collected at day 3 of involution. Gene expression analysis was conducted by Illumina RNA sequencing and sequence reads were assembled and analyzed using TopHat. FPKM (fragments per kilobase of exon per million) values were analyzed for differentially expressed genes using the Cufflinks package. Gene ontology analysis of differentially expressed genes was categorized using agriGO, while KEGG pathway analysis was performed with the online KEGG automatic annotation server. Our results revealed that 75% of NCBI goat annotated genes were expressed during early involution. A total of 18,323 genes were expressed during early involution in GH transgenic goats, compared with 18,196 expressed genes during early involution of non-transgenic goats. In these expressed genes, the majority (17,589) were ubiquitously expressed in GH transgenic and non-transgenic goats. However, there were 745 differentially expressed genes, 421 of which were upregulated and 324 were downregulated in GH transgenic goats. GO and KEGG pathway analysis showed that these genes were involved in mammary gland physiology, including cell adhesion molecules, ECM-receptor interaction, Jak-STAT signaling pathway, and fat metabolism. Our results demonstrated that the GH receptor was strongly affected in GH transgenic goats, which may activate the IGF-1/Stat3 signaling pathway. Overall, our study provided a global view of the transcriptome during involution of GH transgenic and non-transgenic goats, which increases our understanding of the biology of involution in the goat.
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Affiliation(s)
- Jian Lin
- College of Veterinary, Nanjing Agricultural University, Weigang 1, Jiangsu, PR China
| | - Ze Kun Bao
- College of Veterinary, Nanjing Agricultural University, Weigang 1, Jiangsu, PR China
| | - Qiang Zhang
- College of Veterinary, Nanjing Agricultural University, Weigang 1, Jiangsu, PR China
| | - Wei Wei Hu
- College of Veterinary, Nanjing Agricultural University, Weigang 1, Jiangsu, PR China
| | - Qing Hua Yu
- College of Veterinary, Nanjing Agricultural University, Weigang 1, Jiangsu, PR China
| | - Qian Yang
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, PR China.
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14
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Ferreira AM, Bislev SL, Bendixen E, Almeida AM. The mammary gland in domestic ruminants: a systems biology perspective. J Proteomics 2013; 94:110-23. [PMID: 24076120 DOI: 10.1016/j.jprot.2013.09.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/04/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022]
Abstract
UNLABELLED Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. BIOLOGICAL SIGNIFICANCE Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance.
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Affiliation(s)
- Ana M Ferreira
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal; BCV Laboratory, Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
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