1
|
Pedrosa VB, Schenkel FS, Chen SY, Oliveira HR, Casey TM, Melka MG, Brito LF. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes (Basel) 2021; 12:genes12111830. [PMID: 34828436 PMCID: PMC8624223 DOI: 10.3390/genes12111830] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.
Collapse
Affiliation(s)
- Victor B. Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, Brazil
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Theresa M. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
| | - Melkaye G. Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI 54022, USA;
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Correspondence:
| |
Collapse
|
2
|
Going further post-RNA-seq: In silico functional analyses revealing candidate genes and regulatory elements related to mastitis in dairy cattle. J DAIRY RES 2021; 88:286-292. [PMID: 34372953 DOI: 10.1017/s0022029921000571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study aimed to obtain a better understanding of the regulatory genes and molecules involved in the development of mastitis. For this purpose, the transcription factors (TF) and MicroRNAs (miRNA) related to differentially expressed genes previously found in extracorporeal udders infected with Streptococcus agalactiae were investigated. The Gene-TF network highlighted LOC515333, SAA3, CD14, NFKBIA, APOC2 and LOC100335608 and genes that encode the most representative transcription factors STAT3, PPARG, EGR1 and NFKB1 for infected udders. In addition, it was possible to highlight, through the analysis of the gene-miRNA network, genes that could be post-transcriptionally regulated by miRNAs, such as the relationship between the CCL5 gene and the miRNA bta-miR-363. Overall, our data demonstrated genes and regulatory elements (TF and miRNA) that can play an important role in mastitis resistance. The results provide new insights into the first functional pathways and the network of genes that orchestrate the innate immune responses to infection by Streptococcus agalactiae. Our results will increase the general knowledge about the gene networks, transcription factors and miRNAs involved in fighting intramammary infection and maintaining tissue during infection and thus enable a better understanding of the pathophysiology of mastitis.
Collapse
|
3
|
Pegolo S, Momen M, Morota G, Rosa GJM, Gianola D, Bittante G, Cecchinato A. Structural equation modeling for investigating multi-trait genetic architecture of udder health in dairy cattle. Sci Rep 2020; 10:7751. [PMID: 32385377 PMCID: PMC7210309 DOI: 10.1038/s41598-020-64575-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 04/15/2020] [Indexed: 02/04/2023] Open
Abstract
Mastitis is one of the most prevalent and costly diseases in dairy cattle. It results in changes in milk composition and quality which are indicators of udder inflammation in absence of clinical signs. We applied structural equation modeling (SEM) - GWAS aiming to explore interrelated dependency relationships among phenotypes related to udder health, including milk yield (MY), somatic cell score (SCS), lactose (%, LACT), pH and non-casein N (NCN, % of total milk N), in a cohort of 1,158 Brown Swiss cows. The phenotypic network inferred via the Hill-Climbing algorithm was used to estimate SEM parameters. Integration of multi-trait models-GWAS and SEM-GWAS identified six significant SNPs for SCS, and quantified the contribution of MY and LACT acting as mediator traits to total SNP effects. Functional analyses revealed that overrepresented pathways were often shared among traits and were consistent with biological knowledge (e.g., membrane transport activity for pH and MY or Wnt signaling for SCS and NCN). In summary, SEM-GWAS offered new insights on the relationships among udder health phenotypes and on the path of SNP effects, providing useful information for genetic improvement and management strategies in dairy cattle.
Collapse
Affiliation(s)
- Sara Pegolo
- Department of Agronomy, Food Natural resources, Animals and Environment, University of Padua, Legnaro, (PD), Italy.
| | - Mehdi Momen
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Guilherme J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, WI, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Daniel Gianola
- Department of Animal Sciences, University of Wisconsin, Madison, WI, USA.,Department of Dairy Science, University of Wisconsin, Madison, WI, USA
| | - Giovanni Bittante
- Department of Agronomy, Food Natural resources, Animals and Environment, University of Padua, Legnaro, (PD), Italy
| | - Alessio Cecchinato
- Department of Agronomy, Food Natural resources, Animals and Environment, University of Padua, Legnaro, (PD), Italy
| |
Collapse
|
4
|
Isolated perfused udder model for transcriptome analysis in response to Streptococcus agalactiae. J DAIRY RES 2020; 86:307-314. [PMID: 31451129 DOI: 10.1017/s0022029919000451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This study aimed to evaluate the transcriptional changes occurring in isolated perfused mammary alveolar tissue in response to inoculation with S. agalactiae and to identify the most affected biological functions and pathways after 3 h. Four udders taken at slaughter from cows with healthy mammary gland were perfused ex situ with warmed and gassed Tyrode's solution. Mammary alveolar tissue samples were taken from the left fore and rear quarters (IQ-inoculated quarters) before inoculation (hour 0) and at 3 h post inoculation (hpi) and at the same times from control right fore and rear quarters (not inoculated: NIQ). A total of 1756 differentially expressed genes (DEGs) were identified between IQ and NIQ at 3 hpi using edgeR package. Within this set of DEGs, 952 were up regulated and mainly involved with innate immune response and inflammatory response, e.g., CD14, CCL5, TLR2, IL-8, SAA3, as well as in transcriptional regulation such as FOS, STAT3 and NFKBIA. Genes down-regulated (804) included those involved with lipid synthesis e.g., APOC2, SCD, FABP3 and FABP4. The most affected pathways were chemokine signaling, Wnt signaling and complement and coagulation cascades, which likely reflects the early stage response of mammary tissue to S. agalactiae infection. No significant gene expression changes were detected by RNA-Seq in the others contrasts. Real time-PCR confirmed the increase in mRNA abundance of immune-related genes: TLR2, TLR4, IL-1β, and IL-10 at 3 hpi between IQ and NIQ. The expression profiles of Casp1 and Bax for any contrasts were unaffected whereas Bcl2 was increased in IQ, which suggests no induction of apoptosis during the first hours after infection. Results provided novel information regarding the early functional pathways and gene network that orchestrate innate immune responses to S. agalactiae infection. This knowledge could contribute to new strategies to enhance resistance to this disease, such as genomic selection.
Collapse
|
5
|
Alhussien MN, Dang AK. Potential roles of neutrophils in maintaining the health and productivity of dairy cows during various physiological and physiopathological conditions: a review. Immunol Res 2019; 67:21-38. [PMID: 30644032 DOI: 10.1007/s12026-019-9064-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Neutrophils represent the first line of innate immunity and are the most prominent line of cellular defence against invading microorganisms. On stimulation, they can quickly move through the walls of veins and into the tissues of the body to immediately attack or monitor the foreign antigens. Neutrophils are highly versatile and sophisticated cells which are endowed with highly sensitive receptor-based perception systems. They were traditionally classified as short-lived phagocytes actively involved during infection and inflammation, but recently, it has been seen that neutrophils are capable of detecting the presence of sperms during insemination as well as an implanting embryo in the female reproductive tract. These specialised phagocytes play a major role in tissue remodelling and wound healing, and maintain homeostasis during parturition, expulsion of placenta, folliculogenesis, corpus luteum formation and luteolysis. Here, we review the role played by neutrophils in maintaining homeostasis during normal and inflammatory conditions of dairy cattle. We have summarised the alteration in the expression of some cell adhesion molecules and cytokines on bovine neutrophils during different physiological and physiopathological conditions. Some emerging issues in the field of neutrophil biology and the possible strategies to strengthen their activity during the period of immunosuppression have also been discussed.
Collapse
Affiliation(s)
- Mohanned Naif Alhussien
- Animal Production Division, Agricultural College, Aleppo University, Aleppo, Syrian Arab Republic. .,Lactation and Immuno-Physiology Laboratory, ICAR-National Dairy Research Institute, Karnal, Haryana, 132 001, India.
| | - Ajay Kumar Dang
- Lactation and Immuno-Physiology Laboratory, ICAR-National Dairy Research Institute, Karnal, Haryana, 132 001, India
| |
Collapse
|
6
|
Differential expression of immune response genes associated with subclinical mastitis in dairy buffaloes. Animal 2019; 13:1651-1657. [DOI: 10.1017/s1751731118003324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
7
|
Zhang H, Jiang H, Fan Y, Chen Z, Li M, Mao Y, Karrow NA, Loor JJ, Moore S, Yang Z. Transcriptomics and iTRAQ-Proteomics Analyses of Bovine Mammary Tissue with Streptococcus agalactiae-Induced Mastitis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11188-11196. [PMID: 30096236 DOI: 10.1021/acs.jafc.8b02386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Mastitis is a highly prevalent disease in dairy cows that causes large economic losses. Streptococcus agalactiae is a common contagious pathogen and a major cause of bovine mastitis. The immune response to intramammary infection with S. agalactiae in dairy cows is a very complex biological process. To understand the host immune response to S. agalactiae-induced mastitis, mammary gland of lactating Chinese Holstein cows was challenged with S. agalactiae via nipple tube perfusion. Visual inspection, analysis of milk somatic cell counts, histopathology, and transmission electron microscopy of mammary tissue were performed to confirm S. agalactiae-induced mastitis. Microarray and isobaric tags for relative and absolute quantitation (iTRAQ) were used to compare the transcriptomes and proteomes of healthy and mastitic mammary tissue. Compared with healthy tissue, a total of 129 differentially expressed genes (DEGs, fold change >2, p < 0.05) and 144 differentially expressed proteins (DEPs, fold change >1.2, p < 0.05) were identified in mammary tissue from S. agalactiae-challenged cows. Among the concordant 18 DEGs/DEPs, immunoglobulin M precursor, cathelicidin-7 precursor, integrin alpha-5, and complement C4-A-like isoform X1 were associated with mastitis. Intramammary infection with S. agalactiae triggered a complex host innate immune response that involved complement and coagulation cascades, ECM-receptor interaction, focal adhesion, and phagosome and bacterial invasion of epithelial cells pathways. These results provide candidate genes or proteins for further studies in the context of prevention and targeted treatment of bovine mastitis.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Niel A Karrow
- Department of Animal Biosciences , University of Guelph , Guelph N1G 2W1 , Canada
| | - Juan J Loor
- Department of Animal Sciences & Division of Nutritional Sciences , University of Illinois , Urbana , Illinois 61801 , United States
| | - Stephen Moore
- Centre for Animal Science , University of Queensland , Saint Luci , Queensland 4072a , Australia
| | | |
Collapse
|
8
|
Stella AAS, Fonseca LFS, Gimenez DFJ, Tanamati F, do Nascimento AV, Cardoso DF, Tonhati H. Expression profile of the CSF3 and LPO genes in milk from buffalo (Bubalus bubalis) with and without mastitis. Mol Cell Probes 2018; 41:39-42. [PMID: 30217657 DOI: 10.1016/j.mcp.2018.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/05/2018] [Accepted: 09/11/2018] [Indexed: 11/15/2022]
Abstract
This study compared the expression profile of the candidate genes, CSF3 and LPO, by investigating the immune response mechanisms involved in the phenotype of resistance and susceptibility to mastitis of healthy and infected buffaloes. The Granulocyte Colony Stimulating Factor 3 (CSF3) and Lactoperoxidase (LPO) genes expression profiles were determined in 24 milk samples from buffaloes with (N = 12) and without (N = 12) mastitis, using the quantitative real-time PCR (qRT-PCR) technique. CSF3 and LPO expressions were 5.14 (P = 0.001) and 2.41 (P = 0.097) times higher in animals with mastitis compared to healthy animals, respectively, evidencing a trend toward different expressions of this gene in the studied groups. Our finding suggests that LPO and CSF3 genes are an important defense mechanism against mastitis in dairy buffaloes, and may be putative genes for selecting healthier animals in buffalo breeding programs.
Collapse
Affiliation(s)
- Aline Aparecida Silva Stella
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Larissa Fernanda Simielli Fonseca
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Daniele Fernanda Jovino Gimenez
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Fernanda Tanamati
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - André Vieira do Nascimento
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Diercles Francisco Cardoso
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, SP, Brazil.
| |
Collapse
|
9
|
Behdani E, Bakhtiarizadeh MR. Construction of an integrated gene regulatory network link to stress-related immune system in cattle. Genetica 2017; 145:441-454. [PMID: 28825201 DOI: 10.1007/s10709-017-9980-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023]
Abstract
The immune system is an important biological system that is negatively impacted by stress. This study constructed an integrated regulatory network to enhance our understanding of the regulatory gene network used in the stress-related immune system. Module inference was used to construct modules of co-expressed genes with bovine leukocyte RNA-Seq data. Transcription factors (TFs) were then assigned to these modules using Lemon-Tree algorithms. In addition, the TFs assigned to each module were confirmed using the promoter analysis and protein-protein interactions data. Therefore, our integrated method identified three TFs which include one TF that is previously known to be involved in immune response (MYBL2) and two TFs (E2F8 and FOXS1) that had not been recognized previously and were identified for the first time in this study as novel regulatory candidates in immune response. This study provides valuable insights on the regulatory programs of genes involved in the stress-related immune system.
Collapse
Affiliation(s)
- Elham Behdani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Ramin University, Khozestan, Iran
| | | |
Collapse
|