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Jahan N, Wasim M, Rubaya R, Radeen KR, Alim MA, Hossain MMK, Zohora FT, Das KC, Salimullah M, Bhuyan AA, Alam J. Sequence variability of CatSper1 and TNP2 gene in indigenous and crossbred cattle in Bangladesh. Anim Biotechnol 2023; 34:2007-2016. [PMID: 35446730 DOI: 10.1080/10495398.2022.2063729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
CatSper1 and TNP2 genes are known to affect semen quality and fertility parameters, including sperm motility and maturation. However, studies are yet to examine the genes in indigenous and crossbred cattle in Bangladesh. Therefore, this study was conducted to determine the genetic variants of CatSper1 and TNP2 in indigenous and crossbred cattle in Bangladesh. Blood samples were collected from 130 indigenous and 70 crossbred (Holstein Friesian × indigenous) cattle. Nucleotide variation was evaluated by PCR-RFLP and sequencing. The results of the study showed that the indigenous cattle possessed only TT genotype (1.0), whereas the crossbreds possessed both TT (0.91) and CT (0.09) genotypes, which was validated by gene sequencing. Additionally, the CatSper1 was conserved in both the indigenous and crossbred cattle, suggesting good semen quality and fertility. However, the TNP2 was conserved in the indigenous breeds and mostly conserved in the crossbreds. The findings of this study reveal the diversity of CatSper1 and TNP2 genes in indigenous and crossbred cattle.
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Affiliation(s)
- Nusrat Jahan
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Muhammad Wasim
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Rubaya Rubaya
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Kazi Rafsan Radeen
- Environmental Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Md Abdul Alim
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - M M Kamal Hossain
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Fatama Tous Zohora
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Anjuman Ara Bhuyan
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Jahangir Alam
- Animal Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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Mukherjee A, Gali J, Kar I, Datta S, Roy M, Acharya AP, Patra AK. Candidate genes and proteins regulating bull semen quality: a review. Trop Anim Health Prod 2023; 55:212. [PMID: 37208528 DOI: 10.1007/s11250-023-03617-0] [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: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Poor semen profile reflected by suboptimum fertility statistics is a concern in bulls reared for breeding purpose. A critical review of research on candidate genes and proteins associated with semen quality traits will be useful to understand the progress of molecular marker development for bull semen quality traits. Here, we have tabulated and classified candidate genes and proteins associated with bull semen quality based on a literature survey. A total of 175 candidate genes are associated with semen quality traits in various breeds of cattle. Several studies using candidate gene approach have identified 26 genes carrying a total of 44 single nucleotide polymorphisms. Furthermore, nine genome-wide association studies (GWASes) have identified 150 candidate genes using bovine single nucleotide polymorphisms (SNP) chips. Three genes, namely membrane-associated ring-CH-type finger 1 (MARCH1), platelet-derived growth factor receptor beta, and phosphodiesterase type 1, were identified commonly in two GWASes, which, especially MARCH1, are required to explore their regulatory roles in bull semen quality in in-depth studies. With the advancement of high-throughput-omic technologies, more candidate genes associated with bull semen quality may be identified in the future. Therefore, the functional significance of candidate genes and proteins need to be delved further into future investigations to augment bull semen quality.
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Affiliation(s)
- Ayan Mukherjee
- Department of Veterinary Biotechnology, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Jaganmohanarao Gali
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Indrajit Kar
- Department of Avian Science, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Sanjoy Datta
- Department of Animal Genetics and Breeding, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Manoranjan Roy
- Department of Animal Genetics and Breeding, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Aditya Pratap Acharya
- Department of Veterinary Biotechnology, West Bengal University of Animal and Fishery Sciences, Mohanpur, Nadia, West Bengal, India
| | - Amlan Kumar Patra
- Department of Animal Nutrition, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India.
- American Institute for Goat Research, Langston University, Langston, Oklahoma, USA.
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Indriastuti R, Pardede BP, Gunawan A, Ulum MF, Arifiantini RI, Purwantara B. Sperm Transcriptome Analysis Accurately Reveals Male Fertility Potential in Livestock. Animals (Basel) 2022; 12:2955. [PMID: 36359078 PMCID: PMC9657999 DOI: 10.3390/ani12212955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 08/13/2023] Open
Abstract
Nowadays, selection of superior male candidates in livestock as a source of frozen semen based on sperm quality at the cellular level is not considered accurate enough for predicting the potential of male fertility. Sperm transcriptome analysis approaches, such as messenger RNA levels, have been shown to correlate with fertility rates. Using this technology in livestock growth has become the principal method, which can be widely applied to predict male fertility potential in the livestock industry through the analysis of the sperm transcriptome. It provides the gene expression to validate the function of sperm in spermatogenesis, fertilization, and embryo development, as the parameters of male fertility. This review proposes a transcriptomic analysis approach as a high-throughput method to predict the fertility potential of livestock more accurately in the future.
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Affiliation(s)
- Rhesti Indriastuti
- Reproductive Biology Study Program, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
- Tuah Sakato Technology and Resource Development Center, Department of Animal Husbandry and Animal Health of West Sumatra, Payakumbuh 26229, Indonesia
| | - Berlin Pandapotan Pardede
- Department of Veterinary Clinic, Reproduction, and Pathology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
| | - Asep Gunawan
- Department of Animal Production and Technology, Faculty of Animal Science, IPB University, Bogor 16680, Indonesia
| | - Mokhamad Fakhrul Ulum
- Department of Veterinary Clinic, Reproduction, and Pathology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
| | - Raden Iis Arifiantini
- Department of Veterinary Clinic, Reproduction, and Pathology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
| | - Bambang Purwantara
- Department of Veterinary Clinic, Reproduction, and Pathology, School of Veterinary Medicine and Biomedical Sciences, IPB University, Bogor 16680, Indonesia
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Peng C, Cheng Q, Liu Y, Zhang Z, Wang Z, Ma H, Liu D, Wang L, Wang C. Marginal Zinc Deficiency in Mice Increased the Number of Abnormal Sperm and Altered the Expression Level of Spermatogenesis-Related Genes. Biol Trace Elem Res 2022; 200:3738-3749. [PMID: 34676520 DOI: 10.1007/s12011-021-02979-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/17/2021] [Indexed: 12/27/2022]
Abstract
Marginal zinc deficiency is more common than severe zinc deficiency, and the effect of marginal zinc deficiency on male reproduction is unknown. This study investigated the effect of marginal zinc deficiency on spermatogenesis and its mechanism. Male ICR mice were fed normal zinc (30 mg/kg) and marginal zinc deficiency (10 mg/kg) diets for 35 days. Zinc-dependent proteins and enzymes were measured as biomarkers of zinc levels in the body. Metallothionein and Cu-Zn SOD levels in the control group were higher than those in the marginal zinc deficiency group. Hematoxylin and eosin staining showed that the marginal zinc deficiency diet caused histopathological changes in the testis and destruction of the sperm head under scanning electron microscopy. Sperm parameters and sex hormone levels were also affected by marginal zinc deficiency. In addition, marginal zinc deficiency led to alter expression level of several important spermatogenesis-related genes in the epididymis and testes. These results indicate that although zinc intake in marginal zinc deficiency is close to the recommended reference value, low zinc intake interferes with the expression of genes related to spermatogenesis and may lead to sperm abnormalities in mice.
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Affiliation(s)
- Cheng Peng
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Qian Cheng
- Angel Nutritech Company Limited, Yichang, 443000, Hubei Province, People's Republic of China
| | - Youjiao Liu
- Angel Nutritech Company Limited, Yichang, 443000, Hubei Province, People's Republic of China
| | - Zhaoyu Zhang
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Ziqiong Wang
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Haitao Ma
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Duanya Liu
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Lei Wang
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China
| | - Chunhong Wang
- Department of Preventive Medicine, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei Province, People's Republic of China.
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Search for Associations of FSHR, INHA, INHAB, PRL, TNP2 and SPEF2 Genes Polymorphisms with Semen Quality in Russian Holstein Bulls (Pilot Study). Animals (Basel) 2021; 11:ani11102882. [PMID: 34679903 PMCID: PMC8532936 DOI: 10.3390/ani11102882] [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: 08/10/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of the study was to search for new mutations in the previously studied gene loci of follicle-stimulating hormone receptor (FSHR), inhibin α (INHA), inhibin β A (INHAB), prolactin (PRL), transition protein 2 (TNP2), and sperm flagella 2 (SPEF2) by sequencing, as well as the search for associations of previously identified mutations at these loci with fresh semen quality in Russian Holstein bulls. Phenotypic data from 189 bulls was collected. Data was analyzed for most bulls for three years of semen collection. The maximum value of each semen quality indicator (doublet ejaculate volume, sperm concentration, progressive motility and total number of spermatozoa) were selected. SNPs were identified in the FSHR, INHA, INHAB, TNP2, SPEF2 genes. The PRL gene did not have polymorphism. Significant (p < 0.05) associations of polymorphisms in the FSHR gene with double ejaculate volume, concentration and total number of spermatozoa were identified. Polymorphism in the INHA gene was significantly associated (p < 0.05) with sperm concentration. Polymorphism in the INHAB gene was significantly associated (p < 0.05) with doublet ejaculate volume and total number of spermatozoa. Polymorphisms in the TNP2 and SPEF2 genes did not have significant associations with semen quality. The SNPs studied in our pilot work may be considered as candidate genetic markers in the selection of bulls.
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de Sousa MAP, de Athayde FRF, Maldonado MBC, de Lima AO, Fortes MRS, Lopes FL. Single nucleotide polymorphisms affect miRNA target prediction in bovine. PLoS One 2021; 16:e0249406. [PMID: 33882076 PMCID: PMC8059806 DOI: 10.1371/journal.pone.0249406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/17/2021] [Indexed: 02/06/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) can have significant effects on phenotypic characteristics in cattle. MicroRNAs (miRNAs) are small, non-coding RNAs that act as post-transcriptional regulators by binding them to target mRNAs. In the present study, we scanned ~56 million SNPs against 1,064 bovine miRNA sequences and analyzed, in silico, their possible effects on target binding prediction, primary miRNA formation, association with QTL regions and the evolutionary conservation for each SNP locus. Following target prediction, we show that 71.6% of miRNA predicted targets were altered as a consequence of SNPs located within the seed region of the mature miRNAs. Next, we identified variations in the Minimum Free Energy (MFE), which represents the capacity to alter molecule stability and, consequently, miRNA maturation. A total of 48.6% of the sequences analyzed showed values within those previously reported as sufficient to alter miRNA maturation. We have also found 131 SNPs in 46 miRNAs, with altered target prediction, occurring in QTL regions. Lastly, analysis of evolutionary conservation scores for each SNP locus suggested that they have a conserved biological function through the evolutionary process. Our results suggest that SNPs in microRNAs have the potential to affect bovine phenotypes and could be of great value for genetic improvement studies, as well as production.
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Affiliation(s)
- Marco Antônio Perpétuo de Sousa
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Flavia Regina Florêncio de Athayde
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
| | - Marina Rufino S. Fortes
- School of Chemistry and Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Flavia Lombardi Lopes
- Department of Production and Animal Health, São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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Islam S, Reddy UK, Natarajan P, Abburi VL, Bajwa AA, Imran M, Zahoor MY, Abdullah M, Bukhari AM, Iqbal S, Ashraf K, Nadeem A, Rehman H, Rashid I, Shehzad W. Population demographic history and population structure for Pakistani Nili-Ravi breeding bulls based on SNP genotyping to identify genomic regions associated with male effects for milk yield and body weight. PLoS One 2020; 15:e0242500. [PMID: 33232358 PMCID: PMC7685427 DOI: 10.1371/journal.pone.0242500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/03/2020] [Indexed: 11/20/2022] Open
Abstract
The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.
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Affiliation(s)
- Saher Islam
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Lakshmi Abburi
- Department of Biology, West Virginia State University, Institute, West Virginia, United States of America
| | - Amna Arshad Bajwa
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Imran
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Yasir Zahoor
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Abdullah
- Department of Livestock Production, University of Veterinary and Animal Sciences, Pattoki, Pakistan
| | - Aamir Mehmood Bukhari
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Sajid Iqbal
- Semen Production Unit, Qadirabad, District Sahiwal, Pakistan
- Livestock and Dairy Development Department, Government of the Punjab, Lahore, Pakistan
| | - Kamran Ashraf
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habibur Rehman
- Department of Physiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Rashid
- Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Wasim Shehzad
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
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Nazarizadeh A, Mohammadi F, Alian F, Faraji P, Nourbakhsh M, Alizadeh-Fanalou S. MicroRNA-154: A Novel Candidate for Diagnosis and Therapy of Human Cancers. Onco Targets Ther 2020; 13:6603-6615. [PMID: 32753896 PMCID: PMC7354082 DOI: 10.2147/ott.s249268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/31/2020] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous, non-coding, single-stranded, tiny RNAs with 21–23 nucleotides that regulate several biological functions through binding to target mRNAs and modulating gene expression at post-transcriptional levels. Recent studies have described crucial roles for miRNAs in pathophysiology of numerous human cancers. They can act as an oncogene and promote cancer or as a tumor suppressor and alleviate the disease. Recently discovered microRNA-154 (miR-154) has been proposed to be involved in multiple physiological and pathological processes including cancer. With this aspect, aberrant expression of miR-154 has been demonstrated in variety of human malignancies, suggesting an important role for miR-154 in tumorigenesis. To be specific, it is considered as a tumor suppressor miRNA and exerts its beneficial effects by targeting several genes. This review systematically summarizes the recent advances done on the role of miR-154 in different cancers and discusses its potential prognostic, diagnostic and therapeutic values.
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Affiliation(s)
- Ali Nazarizadeh
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Forogh Mohammadi
- Department of Veterinary, Agriculture Faculty, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Fatemeh Alian
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Parisa Faraji
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mitra Nourbakhsh
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahin Alizadeh-Fanalou
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
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9
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Ju Z, Jiang Q, Wang J, Wang X, Yang C, Sun Y, Zhang Y, Wang C, Gao Y, Wei X, Hou M, Huang J. Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows. BMC Genomics 2020; 21:102. [PMID: 32000686 PMCID: PMC6993440 DOI: 10.1186/s12864-020-6526-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
Background Neutrophils are the first effectors of inflammatory response triggered by mastitis infection, and are important defense cells against pathogenic Escherichia coli (E. coli). DNA methylation, as a critical epigenetic mechanism for regulating gene function, is involved in bovine mastitis. Results In this study, we sequenced the blood neutrophils of healthy and E. coli-infected mastitic half-sib cows for the overall DNA methylation levels using transcriptome sequencing and reduced representation bisulfite sequencing. The methylation levels in the mastitis cows (MCs) were decreased compared with healthy cows (HCs). A total of 494 differentially methylated regions were identified, among which 61 were up-methylated and 433 were down-methylated (MCs vs. HCs). The expression levels of 1094 differentially expressed genes were up-regulated, and 245 genes were down-regulated. Twenty-nine genes were found in methylation and transcription data, among which seven genes’ promoter methylation levels were negatively correlated with expression levels, and 11 genes were differentially methylated in the exon regions. The bisulfite sequencing PCR and quantitative real-time PCR validation results demonstrated that the promoter methylation of CITED2 and SLC40A1 genes affected differential expression. The methylation of LGR4 exon 5 regulated its own alternative splicing. The promoter methylation of bta-miR-15a has an indirect effect on the expression of its target gene CD163. The CITED2, SLC40A1, and LGR4 genes can be used as candidates for E. coli-induced mastitis resistance. Conclusions This study explored the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-induced mastitis, thereby helping explain the function of DNA methylation in the pathogenesis of mastitis and provided new target genes and epigenetic markers for mastitis resistance breeding in dairy cattle.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yaran Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yaping Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Xiaochao Wei
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Minghai Hou
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China.,Engineering Center of Animal Breeding and Reproduction, Jinan, Shandong, 250100, People's Republic of China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China. .,Engineering Center of Animal Breeding and Reproduction, Jinan, Shandong, 250100, People's Republic of China.
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Pasquini G, Kunej T. A Map of the microRNA Regulatory Networks Identified by Experimentally Validated microRNA-Target Interactions in Five Domestic Animals: Cattle, Pig, Sheep, Dog, and Chicken. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:448-456. [PMID: 31381467 DOI: 10.1089/omi.2019.0082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Domestic animals are members of the broader ecological context, in which humans are situated. Yet, genomics and systems science research have lagged behind and been relatively underappreciated in domestic animals compared to human genetics/genomics. Harnessing big data calls for omics data mapping studies in a broad range of mammals. To this end, microRNAs (miRNAs) regulate posttranscriptional expression of target genes, hence, governing different biological pathways and physiological processes. The knowledge of miRNA regulatory networks and maps is important for understanding regulation of gene expression and functions in both humans and domestic animals. However, complete miRNA regulatory networks have not yet been described in all species, particularly in domestic animals. We report here an original analysis so as to map the miRNA regulatory networks in domestic animals based on miRNA-target interactions (MTIs). Validated MTIs for five species; cattle, pig, sheep, dog, and chicken were extracted from the miRTarBase. miRNA regulomes were visualized using the Cytoscape software. The data in cattle, chicken, and pig were sufficient to visualize networks, identify central molecules, and subnetworks associated with the same phenotype; however, the MTI data in dog and sheep are still limited. We found several hub genes with large number of interactions, for example, 1 miRNA (bta-miR-17-5p) interacting with 27 genes and 7 miRNAs interacting with the same gene (tumor necrosis factor [TNF]) in cattle. In addition, two single-nucleotide polymorphisms were identified within the seed region of a previously demonstrated MTI, namely, between HMGB3 (high mobility group box 3) gene and bta-miR-17-5p. In summary, this miRNA regulome mapping study will enable and guide further studies of genome function in mammals with a view to applications in human as well as veterinary medicine. Furthermore, these miRNA regulomes can help to clarify fundamental pathways in cell biology and reveal molecular insights on phenotypic trait variability in common complex diseases and response phenotypes of drugs or other health interventions for precision medicine in the future.
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Affiliation(s)
- Giacomo Pasquini
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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11
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Malovrh Š, Kunej T, Kovač M, Dovč P. The microRNA gene <i>bta-mir-2313</i> in cattle: an atlas of regulatory elements and an association analysis with growth and carcass traits in the Slovenian Simental cattle breed. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-271-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Abstract. MicroRNAs (miRNA) are a class of non-coding RNAs important in
posttranscriptional regulation of target genes. Regulation requires
complementarity between the target mRNA and the miRNA region responsible for
their recognition and binding, also called the seed region. Previous studies
have proven that expression profiles and genetic variations of miRNA genes
(miR-SNP; SNP – single nucleotide polymorphism) and their target sites
(miR-TS-SNPs) have an impact on phenotypic variation and disease
susceptibility in human, animal models, and livestock. MicroRNA-associated
polymorphisms therefore represent biomarker potential for phenotypic traits
in livestock. Effects of miRNA gene polymorphisms on phenotypic traits have
been studied in several animal species but much less in cattle. The aim of
the present study was therefore to analyze the genetic variability in the
bta-mir-2313 gene and test associations with growth and carcass
traits of the Slovenian Simmental cattle breed. Additionally, validated and
predicted genomic information related to the miRNA gene bta-mir-2313
has been obtained and presented as an atlas of miRNA regulatory elements.
Sanger sequencing has been used for biomarker development and genotyping of
145 animals of Slovenian dual-purpose Simmental cattle. Out of nine known
polymorphisms located within pre-miRNA regions, one mature miRNA seed SNP was
polymorphic in the Slovenian Simmental cattle breed. An additional three
polymorphisms were identified within the flanking pri-miRNA regions. There
was no significant effect of polymorphisms on 18 tested fattening and carcass
traits; however, validated polymorphisms could now be tested in association
with other traits in other cattle populations. The microRNA gene
bta-mir-2313 warrants further genetic and functional analyses since
it overlaps with a large number of quantitative trait loci (QTL), has over
3100 predicted targets and highly polymorphic mature seed regions, and is
located within protein-coding gene GRAMD1B, previously associated
with production traits in cattle. Mature miRNA seed SNPs present important
genomic loci for functional studies because they could affect the gain/loss
of downstream targets and should be systematically studied in cattle.
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12
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Zhang Y, Wang X, Jiang Q, Hao H, Ju Z, Yang C, Sun Y, Wang C, Zhong J, Huang J, Zhu H. DNA methylation rather than single nucleotide polymorphisms regulates the production of an aberrant splice variant of IL6R in mastitic cows. Cell Stress Chaperones 2018; 23:617-628. [PMID: 29353404 PMCID: PMC6045551 DOI: 10.1007/s12192-017-0871-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/28/2022] Open
Abstract
Interleukin-6 receptor-alpha (IL6R) interacts with IL6 and forms a ligand-receptor complex, which can stimulate various cellular responses, such as cell proliferation, cell differentiation, and activation of inflammatory processes. Both genetic mutation and epigenetic modification regulate gene transcription. We identified a novel splice variant of bovine IL6R, designated as IL6R-TV, which is characterized by the skipping of exon 2 of the NCBI-referenced IL6R gene (IL6R-reference). The expression levels of IL6R-TV and IL6R-reference transcripts were lower in normal mammary gland tissues. These transcripts play a potential role during inflammatory infection. We also detected two putative functional SNPs (g.19711 T > C and g.19731 G > C) located within the upstream 100 bp of exon 2. These SNPs formed two haplotypes (T-G and C-C). Two mutant pSPL3 exon-trapping plasmids (pSPL3-T-G and pSPL3-C-C) were transferred into the bovine mammary epithelial cells (MAC-T) and human embryonic kidney 293 T cells (HEK293T) to investigate the relationship between the two SNPs and the aberrant splicing of IL6R. DNA methylation levels of the alternatively spliced exon in normal and mastitis-infected mammary gland tissues were quantified through nested bisulfate sequencing PCR (BSP) and cloning sequencing. We found that DNA methylation regulated IL6R transcription. The DNA methylation level was high in mastitis-infected mammary gland tissues and stimulated IL6R expression, thereby promoting the inclusion of the alternatively spliced exon. The upregulated expression of the two transcripts was due to DNA methylation modification rather than genetic mutations.
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Affiliation(s)
- Yan Zhang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Haisheng Hao
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China
| | - Jinming Huang
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, People's Republic of China.
| | - Huabin Zhu
- Institute of Animal Sciences (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, People's Republic of China.
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Ju Z, Wang C, Wang X, Yang C, Zhang Y, Sun Y, Jiang Q, Li R, Li J, Zhong J, Huang J. The effect of the SNP g.18475 A>G in the 3'UTR of NCF4 on mastitis susceptibility in dairy cattle. Cell Stress Chaperones 2018; 23:385-391. [PMID: 29476341 PMCID: PMC5904081 DOI: 10.1007/s12192-017-0848-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 01/02/2023] Open
Abstract
Neutrophil cytosolic factor 4 (NCF4) is a member of the nicotinamide adenine dinucleotide phosphate oxidase subunit. This protein functions as an essential factor in the host defense against the progression of bacterial infection. To explore the variability of the NCF4 gene and the susceptibility of cows to mastitis, NCF4 functional single nucleotide polymorphism (SNP) of the 3' untranslated region (3'UTR) and its targeted microRNA (miRNA) were identified. One SNP g.18475 A>G in the 3'UTR of NCF4 was found within the binding seed region of bta-miR-2426. We constructed two recombinant pMIR-REPORT™ vectors with the A or G allele in the g.18475 locus and transiently co-transfected the vectors in human embryo kidney 293T (HEK 293T) cells, along with bta-miR-2426 mimics. A luciferase assay indicated that this SNP affects the binding of NCF4 and bta-miR-2426. In addition, the association analysis results showed that cows with the GG genotype in SNP g.18475 A>G had a relatively lower SCS value than cows with the AA genotype. Finally, quantitative real-time PCR (RT-qPCR) results showed that the cows with genotype GG had a relatively higher expression of NCF4 mRNA compared to the cows with genotype AA. NCF4 expression was regulated by the miRNA-mRNA interaction mechanism, and an important role for NCF4 in mastitis susceptibility in dairy cow was suggested.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Rongling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Jianbin Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China.
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong, 250131, China.
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14
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Liu S, Yin H, Li C, Qin C, Cai W, Cao M, Zhang S. Genetic effects of PDGFRB and MARCH1 identified in GWAS revealing strong associations with semen production traits in Chinese Holstein bulls. BMC Genet 2017; 18:63. [PMID: 28673243 PMCID: PMC5496367 DOI: 10.1186/s12863-017-0527-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 06/19/2017] [Indexed: 11/11/2022] Open
Abstract
Background Using a genome-wide association study strategy, our previous study discovered 19 significant single-nucleotide polymorphisms (SNPs) related to semen production traits in Chinese Holstein bulls. Among them, three SNPs were within or close to the phosphodiesterase 3A (PDE3A), membrane associated ring-CH-type finger 1 (MARCH1) and platelet derived growth factor receptor beta (PDGFRB) genes. The present study was designed with the objectives of identifying genetic polymorphism of the PDE3A, PDGFRB and MARCH1 genes and their effects on semen production traits in a Holstein bull population. Results A total of 20 SNPs were detected and genotyped in 730 bulls. Association analyses using de-regressed estimated breeding values of each semen production trait revealed four statistically significant SNPs for one or more semen production traits (P < 0.05): one SNP was located downstream of PDGFRB and three SNPs were located in the promoter of MARCH1. Interestingly, for MARCH1, haplotype-based analysis revealed significant associations of haplotypes with semen volume per ejaculate. Furthermore, high expression of the MARCH1 gene was observed in sperm cells. One SNP (rs43445726) in the regulatory region of MARCH1 had a significant effect on gene expression. Conclusion Our study demonstrated the significant associations of genetic variants of the PDGFRB and MARCH1 genes with semen production traits. The identified SNPs may serve as genetic markers to optimize breeding programs for semen production traits in Holstein bull populations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0527-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuli Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongwei Yin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Cong Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Chunhua Qin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Wentao Cai
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Mingyue Cao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Shengli Zhang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
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15
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Wang X, Cui X, Zhang Y, Hao H, Ju Z, Liu D, Jiang Q, Yang C, Sun Y, Wang C, Huang J, Zhu H. Splicing-related single nucleotide polymorphism of RAB, member of RAS oncogene family like 2B (RABL2B) jeopardises semen quality in Chinese Holstein bulls. Reprod Fertil Dev 2017; 29:2411-2418. [DOI: 10.1071/rd17111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/18/2017] [Indexed: 11/23/2022] Open
Abstract
RAB, member of RAS oncogene family like 2B (RABL2B) is a member of a poorly characterised clade of the RAS GTPase superfamily, which plays an essential role in male fertility, sperm intraflagellar transport and tail assembly. In the present study, we identified a novel RABL2B splice variant in bovine testis and spermatozoa. This splice variant, designated RABL2B-TV, is characterised by exon 2 skipping. Moreover, a single nucleotide polymorphism (SNP), namely c.125G>A, was found within the exonic splicing enhancer (ESE) motif, indicating that the SNP caused the production of the RABL2B-TV aberrant splice variant. This was demonstrated by constructing a pSPL3 exon capturing vector with different genotypes and transfecting these vectors into murine Leydig tumour cell line (MLTC-1) cells. Expression of the RABL2B-TV transcript was lower in semen from high- versus low-performance bulls. Association analysis showed that sperm deformity rate was significantly lower in Chinese Holstein bulls with the GG or GA genotype than in bulls with the AA genotype (P < 0.05). In addition, initial sperm motility was significantly higher in individuals with the GG or GA genotype than in individuals with the AA genotype (P < 0.05). The findings of the present study suggest that the difference in semen quality in bulls with different RABL2B genotypes is generated via an alternative splicing mechanism caused by a functional SNP within the ESE motif.
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16
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Qin C, Yin H, Zhang X, Sun D, Zhang Q, Liu J, Ding X, Zhang Y, Zhang S. Genome-wide association study for semen traits of the bulls in Chinese Holstein. Anim Genet 2016; 48:80-84. [PMID: 27610941 DOI: 10.1111/age.12433] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2016] [Indexed: 11/30/2022]
Abstract
A genome-wide association study (GWAS) was performed to identify markers and candidate genes for five semen traits in the Holstein bull population in China. The analyzed dataset consisted of records from 692 bulls from eight bull stations; each bull was genotyped using the Illumina BovineSNP50 BeadChip. Association tests between each trait and the 41 188 informative high-quality SNPs were achieved with gapit software. In total, 19 suggestive significant SNPs, partly located within the reported QTL regions or within or close to the reported candidate genes, associated with five semen traits were detected. By combining our GWAS results with the biological functions of these genes, eight novel promising candidate genes, including ETNK1, PDE3A, PDGFRB, CSF1R, WT1, DSCAML1, SOD1 and RUNX2, were identified that potentially relate to semen traits. Our findings may provide a basis for further research on the genetic mechanism of semen traits and marker-assisted selection of such traits in Holstein bulls.
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Affiliation(s)
- Chunhua Qin
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongwei Yin
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xu Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Dongxiao Sun
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Qin Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Jianfeng Liu
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiangdong Ding
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Yi Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Shengli Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory of Animal Breeding, China Agricultural University, Beijing, 100193, China
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17
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An X, Song Y, Bu S, Ma H, Gao K, Hou J, Wang S, Lei Z, Cao B. Association of polymorphisms at the microRNA binding site of the caprine KITLG 3'-UTR with litter size. Sci Rep 2016; 6:25691. [PMID: 27168023 PMCID: PMC4863368 DOI: 10.1038/srep25691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/21/2016] [Indexed: 01/23/2023] Open
Abstract
This study identified three novel single nucleotide polymorphisms (SNPs) (c.1389C > T, c.1457A > C and c.1520G > A) in the caprine KITLG 3'-UTR through DNA sequencing. The three SNP loci were closely linked in Guanzhong dairy (GD) goats. Two alleles of the c.1457A > C SNP introduced two miRNA sites (chi-miR-204-5p and chi-miR-211). Individuals with combined genotype TT-CC-AA had a higher litter size compared with those with combined genotypes CC-AA-GG, TC-CC-GA and CC-AC-GG (P < 0.05). Luciferase assays showed that chi-miR-204-5p and chi-miR-211 suppressed luciferase expression in the presence of allele 1457A compared with negative control (NC) and allele 1457C (P < 0.05). Western blot revealed that KITLG significantly decreased in the granulosa cells (GCs) of genotype AA compared with that in the GCs of genotype CC and NC (P < 0.05). The KITLG mRNA levels of the CC-AA-GG carriers significantly decreased compared with those of the TT-CC-AA, TC-CC-GA and CC-AC-GG carriers. In addition, cell proliferation was reduced in haplotype C-A-G GCs compared with that in haplotype T-C-A GCs. These results suggest that SNPs c.1389C > T, c.1457A > C and c.1520G > A account for differences in the litter size of GD goats because chi-miR-204-5p and chi-miR-211 could change the expression levels of the KITLG gene and reduce GC proliferation.
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Affiliation(s)
- Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shuhai Bu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Haidong Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Kexin Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jinxing Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Shan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhang Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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18
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Cui X, Sun Y, Wang X, Yang C, Ju Z, Jiang Q, Zhang Y, Huang J, Zhong J, Yin M, Wang C. A g.-1256 A>C in the promoter region of CAPN1 is associated with semen quality traits in Chinese Holstein bulls. Reproduction 2016; 152:101-9. [PMID: 27107033 DOI: 10.1530/rep-15-0535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/21/2016] [Indexed: 02/04/2023]
Abstract
The micromolar calcium-activated neutral protease gene (CAPN1) is a physiological candidate gene for sperm motility. However, the molecular mechanisms involved in regulating the expression of the CAPN1 gene in bulls remain unknown. In this study, we investigated the expression pattern of CAPN1 in testis, epididymis, and sperm at the RNA and protein levels by qRT-PCR, western blot, immunohistochemistry, and immunofluorescence assay. Results revealed that the expression of CAPN1 levels was higher in the sperm head compared with that in other tissues. Moreover, we identified a novel single-nucleotide polymorphism (g.-1256 A>C, ss 1917715340) in the noncanonical core promoter of the CAPN1 gene between base g.-1306 and g.-1012. Additionally, we observed greater sperm motility in bulls with the genotype CC than in those with the genotype AA (P<0.01), indicating that different genotypes were associated with the bovine semen trait. Furthermore, a higher fluorescence intensity of the C allele than that of the A allele at g. -1256 A>C was revealed by transient transfection in MLTC-1 cells and luciferase report assay. Finally, CAPN1 was highly expressed in the spermatozoa with the CC genotype compared with that with the AA genotype by qRT-PCR. This study is the first report on genetic variant g.-1256 A>C in the promoter region of CAPN1 gene association with the semen quality of Chinese Holstein bulls by influencing its expression. g.-1256 A>C can be a functional molecular marker in cattle breeding.
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Affiliation(s)
- Xiaohui Cui
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China College of Life ScienceShandong Normal University, Jinan, People's Republic of China
| | - Yan Sun
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Chunhong Yang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Zhihua Ju
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Qiang Jiang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Yan Zhang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Jinming Huang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Jifeng Zhong
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
| | - Miao Yin
- College of Life ScienceShandong Normal University, Jinan, People's Republic of China
| | - Changfa Wang
- Dairy Cattle Research CenterShandong Academy of Agricultural Science, Jinan, People's Republic of China
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19
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An X, Song Y, Hou J, Wang S, Gao K, Cao B. Identification of a functional SNP in the 3′-UTR of caprineMTHFRgene that is associated with milk protein levels. Anim Genet 2016; 47:499-503. [PMID: 27062401 DOI: 10.1111/age.12425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Xiaopeng An
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 P.R. China
| | - Yuxuan Song
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 P.R. China
| | - Jinxing Hou
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 P.R. China
| | - Shan Wang
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 P.R. China
| | - Kexin Gao
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 P.R. China
| | - Binyun Cao
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 P.R. China
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20
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Huang J, Guo F, Zhang Z, Zhang Y, Wang X, Ju Z, Yang C, Wang C, Hou M, Zhong J. PCK1
is negatively regulated by bta-miR-26a, and a single-nucleotide polymorphism in the 3′ untranslated region is involved in semen quality and longevity of Holstein bulls. Mol Reprod Dev 2016; 83:217-25. [DOI: 10.1002/mrd.22613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 12/29/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Jinming Huang
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Fang Guo
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Zebin Zhang
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Yuanpei Zhang
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Xiuge Wang
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Zhihua Ju
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Chunhong Yang
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Changfa Wang
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Minghai Hou
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
| | - Jifeng Zhong
- Dairy Cattle Research Center; Shandong Academy of Agricultural Sciences; Shandong China
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21
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Ju Z, Wang C, Wang X, Yang C, Sun Y, Jiang Q, Wang F, Li M, Zhong J, Huang J. Role of an SNP in Alternative Splicing of Bovine NCF4 and Mastitis Susceptibility. PLoS One 2015; 10:e0143705. [PMID: 26600390 PMCID: PMC4658021 DOI: 10.1371/journal.pone.0143705] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023] Open
Abstract
Neutrophil cytosolic factor 4 (NCF4) is component of the nicotinamide dinucleotide phosphate oxidase complex, a key factor in biochemical pathways and innate immune responses. In this study, splice variants and functional single-nucleotide polymorphism (SNP) of NCF4 were identified to determine the variability and association of the gene with susceptibility to bovine mastitis characterized by inflammation. A novel splice variant, designated as NCF4-TV and characterized by the retention of a 48 bp sequence in intron 9, was detected in the mammary gland tissues of infected cows. The expression of the NCF4-reference main transcript in the mastitic mammary tissues was higher than that in normal tissues. A novel SNP, g.18174 A>G, was also found in the retained 48 bp region of intron 9. To determine whether NCF4-TV could be due to the g.18174 A>G mutation, we constructed two mini-gene expression vectors with the wild-type or mutant NCF4 g.18174 A>G fragment. The vectors were then transiently transfected into 293T cells, and alternative splicing of NCF4 was analyzed by reverse transcription-PCR and sequencing. Mini-gene splicing assay demonstrated that the aberrantly spliced NCF4-TV with 48 bp retained fragment in intron 9 could be due to g.18174 A>G, which was associated with milk somatic count score and increased risk of mastitis infection in cows. NCF4 expression was also regulated by alternative splicing. This study proposes that NCF4 splice variants generated by functional SNP are important risk factors for mastitis susceptibility in dairy cows.
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Affiliation(s)
- Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
- * E-mail: (ZJ); (JH)
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Chunhong Yang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Yan Sun
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Fei Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Mengjiao Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250131, China
- * E-mail: (ZJ); (JH)
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Hou J, An X, Song Y, Gao T, Lei Y, Cao B. Two Mutations in the Caprine MTHFR 3'UTR Regulated by MicroRNAs Are Associated with Milk Production Traits. PLoS One 2015; 10:e0133015. [PMID: 26186555 PMCID: PMC4505847 DOI: 10.1371/journal.pone.0133015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 06/22/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND 5,10-Methylenetetrahydrofolate reductase (MTHFR) plays a central role in folate metabolism by irreversibly converting 5,10-methylenetetrahydrofolate to 5-methylenetetrahydrofolate, a predominant circulating form of folate. Folate is reportedly important for milk protein synthesis, and MTHFR may be a key regulatory point of folate metabolism for milk protein synthesis in mammary epithelial cells. Prior to this study, polymorphisms of the MTHFR gene were not associated with milk production traits from a breeding perspective. Single nucleotide polymorphisms (SNPs) at microRNA (miRNA) binding sites (miR-SNPs) can affect gene expression. This study aimed to identify the effects of miR-SNPs (g.2244A>G and g.2264A>G) in the caprine MTHFR 3' UTR on the milk production traits of dairy goats. RESULTS Guanzhong dairy (GD, n = 325) goats were used to detect SNPs in the caprine MTHFR 3' UTR by DNA sequencing. Two novel SNPs (g.2244A>G and g.2264A>G) were identified in the said region. The homozygous haplotype A-G of the SNPs g.2244A>G and g.2264A>G was significantly associated with milk yield and milk protein levels in GD goats (P < 0.05). Functional assays indicated that the MTHFR 2244 A → G substitution could increase the binding activity of hsa-miR-1266 with the MTHFR 3' UTR. The MTHFR 2264 A → G substitution could decrease the binding activity of hsa-miR-616 with the MTHFR 3' UTR. In addition, we observed a significant increase in the MTHFR mRNA levels of homozygous haplotype A-G carriers relative to those of homozygous haplotype G-A carriers. These results indicated that both SNPs altered the MTHFR mRNA levels. These altered levels of MTHFR mRNA may account for the association of SNPs with milk production traits. CONCLUSIONS This study is the first to report that the g.2244A>G and g.2264A>G polymorphisms were associated with milk production traits in GD goats. Further investigations should explore the underlying miRNA-mediated mechanisms that are modified by the g.2244A>G and g.2264A>G SNPs. The current study evaluated these SNPs as potential genetic markers in goats, with potential applications in breeding programs.
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Affiliation(s)
- Jinxing Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Teyang Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Yingnan Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
- * E-mail:
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The g.-165 T>C Rather than Methylation Is Associated with Semen Motility in Chinese Holstein Bulls by Regulating the Transcriptional Activity of the HIBADH Gene. PLoS One 2015; 10:e0127670. [PMID: 26133183 PMCID: PMC4489673 DOI: 10.1371/journal.pone.0127670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 04/17/2015] [Indexed: 12/05/2022] Open
Abstract
The 3-hydroxyisobutyrate dehydrogenase (HIBADH) is regarded as a human sperm-motility marker. However, the molecular mechanisms involved in the regulation of expression of the HIBADH gene in bulls remain largely unknown. HIBADH was detected in the testis, epididymis, and sperm via reverse transcription polymerase chain reaction and Western blot analysis. It is also expressed in the seminiferous epithelium, spermatids, and the entire epididymis, as detected by immunohistochemistry. Furthermore, HIBADH was expressed in the neck-piece and mid-piece of bull spermatids, as shown in the immunofluorescence assay. Using serially truncated bovine HIBADH promoters and luciferase constructs, we discovered an 878 bp (-703 bp to +175 bp) fragment that constitutes the core promoter region. One SNP g.-165 T>C of HIBADH was identified and genotyped in 307 Chinese Holstein bulls. Correlation analysis revealed that bulls with the TT genotype had higher initial sperm motility than those with the CC genotype (P < 0.05). Furthermore, the T- or C-containing loci (designated as pGL3-T and pGL3-C) were transiently transfected into MLTC-1 to test the effect of SNP on HIBADH expression. The luciferase reporter assay showed that the pGL3-T genotype exhibited 58% higher transcriptional activity than the pGL3-C genotype (P < 0.05). The bisulfite sequencing analysis revealed that the methylation pattern of the core promoter presented hypomethylation in the ejaculated semen in high-motility and low-motility bulls. The results demonstrated for the first time that the g.-165 T>C rather than methylation in the 5'-flanking region could affect the bovine sperm motility through the regulation of HIBADH gene transcriptional activity.
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An X, Hou J, Gao T, Lei Y, Li G, Song Y, Wang J, Cao B. Single-nucleotide polymorphisms g.151435C>T and g.173057T>C in PRLR gene regulated by bta-miR-302a are associated with litter size in goats. Theriogenology 2015; 83:1477-1483.e1. [DOI: 10.1016/j.theriogenology.2015.01.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 01/19/2015] [Accepted: 01/24/2015] [Indexed: 01/22/2023]
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Zhang S, Zhang Y, Yang C, Zhang W, Ju Z, Wang X, Jiang Q, Sun Y, Huang J, Zhong J, Wang C. TNP1 Functional SNPs in bta-miR-532 and bta-miR-204 Target Sites Are Associated with Semen Quality Traits in Chinese Holstein Bulls1. Biol Reprod 2015; 92:139. [DOI: 10.1095/biolreprod.114.126672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/13/2015] [Indexed: 12/25/2022] Open
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26
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Yudin NS, Voevoda MI. Molecular genetic markers of economically important traits in dairy cattle. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415050087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Li R, Zhang CL, Liao XX, Chen D, Wang WQ, Zhu YH, Geng XH, Ji DJ, Mao YJ, Gong YC, Yang ZP. Transcriptome microRNA profiling of bovine mammary glands infected with Staphylococcus aureus. Int J Mol Sci 2015; 16:4997-5013. [PMID: 25749476 PMCID: PMC4394461 DOI: 10.3390/ijms16034997] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/19/2015] [Accepted: 02/23/2015] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs are small non-coding RNA molecules that are important regulators of gene expression at the post-transcriptional level. miRNAs impact the processes of cell proliferation, differentiation and apoptosis. Thus, the regulation of miRNA expression profiles associated with mastitis will be conducive for its control. In this study, Staphylococcus aureus (S. aureus) was administered to the mammary gland of Chinese Holstein cows to construct a bacteria-type mastitis model. Total RNA was isolated from bovine mammary gland tissue samples from the S. aureus-induced mastitis group and controls. miRNAs were analyzed using Solexa sequencing and bioinformatics processing for the experimental group and control group. Two miRNA libraries were constructed respectively. A total of 370 known bovine miRNAs and 341 novel mi RNAs were detected for the S. aureus and 358 known bovine miRNAs and 232 novel miRNAs for control groups. A total of 77 miRNAs in the S. aureus group showed significant differences compared to the control group. GO (Gene Ontology) analysis showed these target genes were involved in the regulation of cells, binding, etc., while KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that these genes were enriched in endocytosis, and olfactory transduction pathways involved in cancer. These results provide an experimental basis to reveal the cause and regulatory mechanism of mastitis and also suggest the potential of miRNAs to serve as biomarkers for the diagnosis of mastitis in dairy cows.
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Affiliation(s)
- Rui Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Cheng-Long Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Xiang-Xiang Liao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Dan Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Wen-Qiang Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yi-Hui Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Xiao-Han Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - De-Jun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yong-Jiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yun-Chen Gong
- The Centre for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, Toronto, ON M5S 2J7, Canada.
| | - Zhang-Ping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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