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Khan MZ, Wang J, Ma Y, Chen T, Ma M, Ullah Q, Khan IM, Khan A, Cao Z, Liu S. Genetic polymorphisms in immune- and inflammation-associated genes and their association with bovine mastitis resistance/susceptibility. Front Immunol 2023; 14:1082144. [PMID: 36911690 PMCID: PMC9997099 DOI: 10.3389/fimmu.2023.1082144] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/06/2023] [Indexed: 02/25/2023] Open
Abstract
Bovine mastitis, the inflammation of the mammary gland, is a contagious disease characterized by chemical and physical changes in milk and pathological changes in udder tissues. Depressed immunity and higher expression of inflammatory cytokines with an elevated milk somatic cell count can be observed during mastitis in dairy cattle. The use of somatic cell count (SCC) and somatic cell score (SCS) as correlated traits in the indirect selection of animals against mastitis resistance is in progress globally. Traditional breeding for mastitis resistance seems difficult because of the low heritability (0.10-0.16) of SCC/SCS and clinical mastitis. Thus, genetic-marker-selective breeding to improve host genetics has attracted considerable attention worldwide. Moreover, genomic selection has been found to be an effective and fast method of screening for dairy cattle that are genetically resistant and susceptible to mastitis at a very early age. The current review discusses and summarizes the candidate gene approach using polymorphisms in immune- and inflammation-linked genes (CD4, CD14, CD46, TRAPPC9, JAK2, Tf, Lf, TLRs, CXCL8, CXCR1, CXCR2, C4A, C5, MASP2, MBL1, MBL2, LBP, NCF1, NCF4, MASP2, A2M, and CLU, etc.) and their related signaling pathways (Staphylococcus aureus infection signaling, Toll-like receptor signaling, NF-kappa B signaling pathway, Cytokine-cytokine receptor, and Complement and coagulation cascades, etc.) associated with mastitis resistance and susceptibility phenotypic traits (IL-6, interferon-gamma (IFN-γ), IL17, IL8, SCS, and SCC) in dairy cattle.
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Affiliation(s)
- Muhammad Zahoor Khan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Faculty of Veterinary and Animal Sciences, The University of Agriculture, Dera Ismail Khan, Pakistan
| | - Jingjun Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yulin Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tianyu Chen
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Mei Ma
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qudrat Ullah
- Faculty of Veterinary and Animal Sciences, The University of Agriculture, Dera Ismail Khan, Pakistan
| | - Ibrar Muhammad Khan
- Anhui Province Key Laboratory of Embryo Development and Reproduction Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Adnan Khan
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuai Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Ali A, Rehman MU, Ahmad SM, Mehraj T, Hussain I, Nadeem A, Mir MUR, Ganie SA. In Silico Tools for Analysis of Single-Nucleotide Polymorphisms in the Bovine Transferrin Gene. Animals (Basel) 2022; 12:ani12060693. [PMID: 35327090 PMCID: PMC8944579 DOI: 10.3390/ani12060693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 02/04/2023] Open
Abstract
Dairy cattle with a high milk yield are susceptible to many infectious diseases, such as mastitis. Subclinical mastitis (SCM) is the most prevalent form of mastitis that predominantly affects animal health, and causes adverse effects on the quality and quantity of milk. In dairy animals, subclinical mastitis often remains undetected, as no gross changes in udder characteristics are visible. In the present study, 135 Holstein Friesian dairy animals were selected and screened as healthy (n = 25) and mastitic (n = 110) based on diagnostic tests such as the California mastitis test, pH, electrical conductivity, and somatic cell count. In this study, the somatic cell count was used as a gold-standard test in differentiating subclinical mastitis animals from healthy ones. The present study was carried out to study polymorphisms in the bovine transferrin gene in cows (with subclinical mastitis and healthy). For the early detection of resistant/or susceptible animals, a useful marker could be provided by the detection of single-nucleotide polymorphisms (SNPs) in the transferrin gene, which are often associated with mammary innate immune response. The sequencing results revealed three nucleotide substitutions: two transversions (230 A > C, 231 C > A) and one transition (294 A > G) in susceptible cows as compared to disease-free subjects. The nucleotide variations at position 230 (GAC > GCA) and 231 (GAC > GCA) were nonsynonymous, and corresponded to an amino acid change from aspartic acid to alanine; whereas at position 294 (GAA > GAG), the mutation was synonymous. In the present study, many in silico tools were taken into consideration to determine the effect of SNPs on protein structure and function. The PROVEAN tool found the amino acid substitution to be neutral and deleterious. PolyPhen-2 revealed the amino acid variations at positions 320 and 321 to most likely be damaging; and at the 341 position, the variations were benign. The I-Mutant and MUpro tools found that the protein stability decreased for nonsynonymous variations. The SIFT tool revealed the protein function was likely to be affected in nonsynonymous variations, with no change in the case of synonymous ones. Phylogenetic analysis of the bovine transferrin gene revealed a close relation of the CA allele with the Bos taurus transferrin, while the G allele was closely related to a cross of Bos indicus × Bos taurus serotransferrins, followed by the Bison bison transferrin. The least relation was shown by both alleles to Capra hircus, Ovis aries, and Bubalus bubalis.
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Affiliation(s)
- Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India;
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Muneeb U. Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (M.U.R.); (S.A.G.)
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India;
| | - Tabish Mehraj
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA;
| | - Ishraq Hussain
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Ahmed Nadeem
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Manzoor Ur Rahman Mir
- Division of Veterinary Biochemistry, Faculty of Veterinary Sciences & Animal Husbandry, SKUAST-Kashmir, Shuhama Campus (Alusteng), Ganderbal 190006, J&K, India; (I.H.); (M.U.R.M.)
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar 190006, J&K, India;
- Correspondence: (M.U.R.); (S.A.G.)
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Xu SS, Gao L, Shen M, Lyu F. Whole-Genome Selective Scans Detect Genes Associated With Important Phenotypic Traits in Sheep (Ovis aries ). Front Genet 2021; 12:738879. [PMID: 34868210 PMCID: PMC8637624 DOI: 10.3389/fgene.2021.738879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Sheep (Ovis aries) is one of the important livestock with diverse phenotypic traits. However, little is known about the molecular mechanism of diverse phenotypic traits in domestic sheep. Using the genome-wide high-density SNP data (600K) in 253 samples from 13 populations, we conducted the tests of selective sweeps (i.e., pairwise FST and XP-CLR) associated with several important phenotypic traits (e.g., tail types, horn morphology, prolificacy, coat pigmentation, ear size, milk production, meat production, body size and wool fineness). We identified strong selective signatures in previously reported (e.g., T, RXFP2, BMPR1B, TYRP1, MSRB3, TF, CEBPA, GPR21 and HOXC8) and novel genes associated with the traits, such as CERS6, BTG1, RYR3, SLC6A4, NNAT and OGT for fat deposition in the tails, FOXO4 for fertility, PTCH1 and EMX2 for ear size, and RMI1 and SCD5 for body size. Further gene annotation analysis showed that these genes were identified to be the most probable genes accounting for the diverse phenotypic traits. Our results provide novel insights into the genetic mechanisms underlying the traits and also new genetic markers for genetic improvement in sheep and other livestock.
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Affiliation(s)
- Song-Song Xu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Shenzhen Branch, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lei Gao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Min Shen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Fenghua Lyu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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Liu Z, Sun H, Lai W, Hu M, Zhang Y, Bai C, Liu J, Ren H, Li F, Yan S. Genome-wide re-sequencing reveals population structure and genetic diversity of Bohai Black cattle. Anim Genet 2021; 53:133-136. [PMID: 34783059 DOI: 10.1111/age.13155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 11/29/2022]
Abstract
Bohai Black (BHB) cattle, one of eight representative indigenous breeds in China, is well known for its high resistance to disease, endurance under unfavorable feeding conditions and excellent meat quality. Over recent, the number of BHB cattle has decreased sharply. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 35 individuals from a conservation farm were obtained using the Illumina 150 bp paired-end platform. The results of the genetic structure and diversity analyses showed that BHB cattle had mixed Bos taurus and Bos indicus ancestry, close phylogenic relationships with Jiaxian Red and Luxi cattle and abundant genetic diversity. The bulls tested here could be divided into six families. This study presents a comprehensive evaluation of the genetic structure and diversity of the BHB cattle, and lays the theoretical basis for conservation and utilization of the valuable germplasm resource.
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Affiliation(s)
- Z Liu
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - H Sun
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - W Lai
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - M Hu
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Y Zhang
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - C Bai
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - J Liu
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600, China
| | - H Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - F Li
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600, China
| | - S Yan
- College of Animal Science, Jilin University, Changchun, 130062, China
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Meng X, Gao Z, Liang Y, Zhang C, Chen Z, Mao Y, Huang B, Kui K, Yang Z. Longissimus Dorsi Muscle Transcriptomic Analysis of Simmental and Chinese Native Cattle Differing in Meat Quality. Front Vet Sci 2020; 7:601064. [PMID: 33385016 PMCID: PMC7770222 DOI: 10.3389/fvets.2020.601064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
With the rapid development of economy, the demand for beef, with regard to quantity and quality, by consumers has been increasing in China. Chinese native cattle are characterized by their abundant genetic resources, unique origins, large breeding stocks, and robust environmental adaptability. Thus, to explore the genetic mechanisms on regulating meat quality in Chinese native cattle is of great importance to satisfy increased requirements for beef production. In this study, we investigated three breeds of cattle, namely Yunling, Wenshan, and Simmental, at the age of 12 months. Animals were classified into three groups (n = 5/breed). Growth traits including body weight and body size and plasma hormone levels were measured. Body weight of Wenshan cattle was significantly lower than that of Yunling and Simmental cattle (P < 0.05). Again, body size indexes, such as withers height, body slanting length, chest circumference, and hip and rump length, were significantly lower in Wenshan cattle than those in Yunling and Simmental cattle (P < 0.05). However, there were no significant differences in those indexes between Yunling and Simmental cattle (P > 0.05). Cattle were slaughtered at the age of 18 months and then meat color, pH, pressing losses, muscle tenderness, and cooking losses were measured at 0, 1, 2, 3, 5, and 7 days. Data revealed differences in meat quality among the three breeds analyzed. Based on transcriptomic sequencing and bioinformatic analysis, we observed 3,198 differentially expressed genes related to meat quality, of which 1,750 genes were upregulated. Moreover, we found two important signaling pathways closely linked to meat quality, namely adipocytokine signaling pathway [e.g., Leptin receptor (LEPR)] and protein processing in the endoplasmic reticulum [e.g., signal transducer and activator of transcription 3 (STAT3), heat shock protein (HSPA12A), and calpain 1 (CAPN1)]. The results of transcripts were further verified by qRT-PCR. Using correlation analysis between gene expression levels and shear force, we also identified two functional genes (e.g., HSPA12A and CAPN1) associated with meat quality. Overall, this study provides new sights into novel targets and underlying mechanisms to modulate meat quality in Chinese native cattle.
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Affiliation(s)
- Xiangren Meng
- School of Tourism and Culinary Science, Yangzhou University, Yangzhou, China.,Jiangsu Huai-yang Cuisine Engineering Center, Yangzhou University, Yangzhou, China
| | - Ziwu Gao
- School of Tourism and Culinary Science, Yangzhou University, Yangzhou, China.,Jiangsu Huai-yang Cuisine Engineering Center, Yangzhou University, Yangzhou, China
| | - Yusheng Liang
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Chenglong Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bizhi Huang
- Academy of Grassland and Animal Science, Yunnan, China
| | - Kaixing Kui
- Academy of Grassland and Animal Science, Yunnan, China
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Gao J, Li T, Lu Z, Wang X, Zhao X, Ma Y. Proteomic Analyses of Mammary Glands Provide Insight into the Immunity and Metabolism Pathways Associated with Clinical Mastitis in Meat Sheep. Animals (Basel) 2019; 9:ani9060309. [PMID: 31159303 PMCID: PMC6617192 DOI: 10.3390/ani9060309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Clinical mastitis is one of the most common diseases in sheep and is of major economic concern due to treatment costs, inadequate lamb growth and premature eliminate of ewes. To preliminarily explore possible regulatory roles of proteins involved in the host-pathogen interactions during intramammary infection triggered by this disease in meat sheep, mammary tissues were harvested from sheep with healthy and clinical mastitis caused by natural infection, and the differentially expressed proteins were identified in an infected group when compared to a healthy group, using comparative proteomics based on two-dimensional electrophoresis. Further enrichment analyses indicated that most of the differentially expressed proteins mainly engaged in regulating immune responses and metabolisms. These findings offer candidate proteins for further studies on molecular mechanisms of host defense response and metabolism in sheep cases. Abstract Clinical mastitis is still an intractable problem for sheep breeding. The natural immunologic mechanisms of the mammary gland against infections are not yet understood. For a better understanding of the disease-associated proteins during clinical mastitis in meat sheep, we performed two-dimensional electrophoresis (2-DE)-based comparative proteomic analyses of mammary tissues, including from healthy mammary tissues (HMTs) and from mammary tissues with clinical mastitis (CMMTs). The 2-DE results showed that a total of 10 up-regulated and 16 down-regulated proteins were identified in CMMTs when compared to HMTs. Of these, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses revealed that most proteins were associated with immune responses or metabolisms. The results of qRT-PCR and Western blot for randomly selected four differentially expressed proteins (DEPs) including superoxide dismutase [Mn] (SOD2), annexin A2 (ANAX2), keratin 10 (KRT10) and endoplasmic reticulum resident protein 29 (ERP29) showed that their expression trends were consistent with 2-DE results except ANXA2 mRNA levels. This is an initial report describing the 2-DE-based proteomics study of the meat sheep mammary gland with clinical mastitis caused by natural infection, which provides additional insight into the immune and metabolic mechanisms during sheep mastitis.
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Affiliation(s)
- Jianfeng Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Taotao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Sheep Breeding Biotechnology Engineering Laboratory of Gansu Province, Minqin 733300, China.
| | - Zengkui Lu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xia Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China.
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
- Sheep Breeding Biotechnology Engineering Laboratory of Gansu Province, Minqin 733300, China.
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Brand B, Scheinhardt MO, Friedrich J, Zimmer D, Reinsch N, Ponsuksili S, Schwerin M, Ziegler A. Adrenal cortex expression quantitative trait loci in a German Holstein × Charolais cross. BMC Genet 2016; 17:135. [PMID: 27716033 PMCID: PMC5053117 DOI: 10.1186/s12863-016-0442-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/28/2016] [Indexed: 12/30/2022] Open
Abstract
Background The importance of the adrenal gland in regard to lactation and reproduction in cattle has been recognized early. Caused by interest in animal welfare and the impact of stress on economically important traits in farm animals the adrenal gland and its function within the stress response is of increasing interest. However, the molecular mechanisms and pathways involved in stress-related effects on economically important traits in farm animals are not fully understood. Gene expression is an important mechanism underlying complex traits, and genetic variants affecting the transcript abundance are thought to influence the manifestation of an expressed phenotype. We therefore investigated the genetic background of adrenocortical gene expression by applying an adaptive linear rank test to identify genome-wide expression quantitative trait loci (eQTL) for adrenal cortex transcripts in cattle. Results A total of 10,986 adrenal cortex transcripts and 37,204 single nucleotide polymorphisms (SNPs) were analysed in 145 F2 cows of a Charolais × German Holstein cross. We identified 505 SNPs that were associated with the abundance of 129 transcripts, comprising 482 cis effects and 17 trans effects. These SNPs were located on all chromosomes but X, 16, 24 and 28. Associated genes are mainly involved in molecular and cellular functions comprising free radical scavenging, cellular compromise, cell morphology and lipid metabolism, including genes such as CYP27A1 and LHCGR that have been shown to affect economically important traits in cattle. Conclusions In this study we showed that adrenocortical eQTL affect the expression of genes known to contribute to the phenotypic manifestation in cattle. Furthermore, some of the identified genes and related molecular pathways were previously shown to contribute to the phenotypic variation of behaviour, temperament and growth at the onset of puberty in the same population investigated here. We conclude that eQTL analysis appears to be a useful approach providing insight into the molecular and genetic background of complex traits in cattle and will help to understand molecular networks involved. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0442-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bodo Brand
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany.,Current affiliation: Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, 18059, Rostock, Germany
| | - Markus O Scheinhardt
- Institute of Medical Biometry and Statistics, University of Lübeck, Ratzeburger Allee, Lübeck, Germany
| | - Juliane Friedrich
- Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, Rostock, Germany
| | - Daisy Zimmer
- Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, Rostock, Germany
| | - Norbert Reinsch
- Institute for Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany
| | - Manfred Schwerin
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee, Dummerstorf, Germany.,Institute for Farm Animal Research and Technology, University of Rostock, Justus-von-Liebig-Weg, Rostock, Germany
| | - Andreas Ziegler
- Institute of Medical Biometry and Statistics, University of Lübeck, Ratzeburger Allee, Lübeck, Germany. .,Center for Clinical Trials, University of Lübeck, Ratzeburger Allee, Lübeck, Germany. .,School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa.
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Ju Z, Zheng X, Huang J, Qi C, Zhang Y, Li J, Zhong J, Wang C. Functional characterization of genetic polymorphisms identified in the promoter region of the bovine PEPS gene. DNA Cell Biol 2012; 31:1038-45. [PMID: 22304649 PMCID: PMC3379527 DOI: 10.1089/dna.2011.1555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 12/19/2011] [Accepted: 12/19/2011] [Indexed: 11/12/2022] Open
Abstract
Peptidase S (PEPS) is a metallopeptidase that cleaves N-terminal residues from proteins and peptides. PEPS is used as a cell maintenance enzyme with critical roles in peptide turnover. The promoter region located upstream of the initiation site plays an important role in regulating gene expression. Polymorphism in the promoter region can alter gene expression and lead to biological changes. In the current study, polymorphisms in the promoter region of the PEPS gene were investigated. Polymerase chain reaction (PCR)-restriction fragment length polymorphism and DNA sequencing methods were used to screen sequence variations in the promoter region of DNA samples from 743 Chinese Holstein cattle. Two polymorphisms (g. -534 T>C and g. -2545 G>A) were identified and eight haplotypes were classified by haplotype analysis. The two genetic polymorphisms and haplotypes were associated with fat percentage and somatic cell score in Chinese Holstein cattle. The results of real-time PCR showed that cow kidneys exhibit the highest PEPS expression level. Moreover, bioinformatics analysis predicted that the single-nucleotide polymorphism g. -534 T>C is located in the core promoter region and in the transcription factor binding sites. The promoter activities of the polymorphism of -543 T>C were measured by luciferase assay in the human kidney epithelial cell line 293T. Transcriptional activity is significantly lower in cell lines transfected with the reporter construct containing 2.5 kb upstream fragments with -543 C than in those with wild-type -543 T. The results indicated that genetic variation at locus -543 influences PEPS promoter activity. The genetic variation in the promoter region of PEPS gene may regulate PEPS gene transcription and might have consequences at a regulatory level.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
| | - Xue Zheng
- College of Animal Science, Jilin Agricultural Science and Technology College, Jilin, P.R. China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
| | - Chao Qi
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
| | - Jianbin Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Science, Jinan, P.R. China
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