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Jiang W, Mooney MH, Shirali M. Unveiling the Genetic Landscape of Feed Efficiency in Holstein Dairy Cows: Insights into Heritability, Genetic Markers, and Pathways via Meta-Analysis. J Anim Sci 2024; 102:skae040. [PMID: 38354297 PMCID: PMC10957122 DOI: 10.1093/jas/skae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/09/2024] [Indexed: 02/16/2024] Open
Abstract
Improving the feeding efficiency of dairy cows is a key component to improve the utilization of land resources and meet the demand for high-quality protein. Advances in genomic methods and omics techniques have made it possible to breed more efficient dairy cows through genomic selection. The aim of this review is to obtain a comprehensive understanding of the biological background of feed efficiency (FE) complex traits in purebred Holstein dairy cows including heritability estimate, and genetic markers, genes, and pathways participating in FE regulation mechanism. Through a literature search, we systematically reviewed the heritability estimation, molecular genetic markers, genes, biomarkers, and pathways of traits related to feeding efficiency in Holstein dairy cows. A meta-analysis based on a random-effects model was performed to combine reported heritability estimates of FE complex. The heritability of residual feed intake, dry matter intake, and energy balance was 0.20, 0.34, and 0.22, respectively, which proved that it was reasonable to include the related traits in the selection breeding program. For molecular genetic markers, a total of 13 single-nucleotide polymorphisms and copy number variance loci, associated genes, and functions were reported to be significant across populations. A total of 169 reported candidate genes were summarized on a large scale, using a higher threshold (adjusted P value < 0.05). Then, the subsequent pathway enrichment of these genes was performed. The important genes reported in the articles were included in a gene list and the gene list was enriched by gene ontology (GO):biological process (BP), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis. Three GO:BP terms and four KEGG terms were statistically significant, which mainly focused on adenosine triphosphate (ATP) synthesis, electron transport chain, and OXPHOS pathway. Among these pathways, involved genes such as ATP5MC2, NDUFA, COX7A2, UQCR, and MMP are particularly important as they were previously reported. Twenty-nine reported biological mechanisms along with involved genes were explained mainly by four biological pathways (insulin-like growth factor axis, lipid metabolism, oxidative phosphorylation pathways, tryptophan metabolism). The information from this study will be useful for future studies of genomic selection breeding and genetic structures influencing animal FE. A better understanding of the underlying biological mechanisms would be beneficial, particularly as it might address genetic antagonism.
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Affiliation(s)
- Wentao Jiang
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, BT9 5DL, UK
- Agri-Food and Biosciences Institute, Large Park, Hillsborough, BT26 6DR, UK
| | - Mark H Mooney
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, BT9 5DL, UK
| | - Masoud Shirali
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, BT9 5DL, UK
- Agri-Food and Biosciences Institute, Large Park, Hillsborough, BT26 6DR, UK
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2
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Identification of Differentially Expressed miRNAs in Porcine Adipose Tissues and Evaluation of Their Effects on Feed Efficiency. Genes (Basel) 2022; 13:genes13122406. [PMID: 36553673 PMCID: PMC9778086 DOI: 10.3390/genes13122406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Feed efficiency (FE) is a very important trait affecting the economic benefits of pig breeding enterprises. Adipose tissue can modulate a variety of processes such as feed intake, energy metabolism and systemic physiological processes. However, the mechanism by which microRNAs (miRNAs) in adipose tissues regulate FE remains largely unknown. Therefore, this study aimed to screen potential miRNAs related to FE through miRNA sequencing. The miRNA profiles in porcine adipose tissues were obtained and 14 miRNAs were identified differentially expressed in adipose tissues of pigs with extreme differences in FE, of which 9 were down-regulated and 5 were up-regulated. GO and KEGG analyses indicated that these miRNAs were significantly related to lipid metabolism and these miRNAs modulated FE by regulating lipid metabolism. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) of five randomly selected DEMs was used to verify the reliability of miRNA-seq data. Furthermore, 39 differentially expressed target genes of these DEMs were obtained, and DEMs-target mRNA interaction networks were constructed. In addition, the most significantly down-regulated miRNAs, ssc-miR-122-5p and ssc-miR-192, might be the key miRNAs for FE. Our results reveal the mechanism by which adipose miRNAs regulate feed efficiency in pigs. This study provides a theoretical basis for the further study of swine feed efficiency improvement.
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Veshkini A, Hammon HM, Lazzari B, Vogel L, Gnott M, Tröscher A, Vendramin V, Sadri H, Sauerwein H, Ceciliani F. Investigating circulating miRNA in transition dairy cows: What miRNAomics tells about metabolic adaptation. Front Genet 2022; 13:946211. [PMID: 36082001 PMCID: PMC9445238 DOI: 10.3389/fgene.2022.946211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
In the current study, we investigated dairy cows’ circulating microRNA (miRNA) expression signature during several key time points around calving, to get insights into different aspects of metabolic adaptation. In a trial with 32 dairy cows, plasma samples were collected on days −21, 1, 28, and 63 relative to calving. Individually extracted total RNA was subjected to RNA sequencing using NovaSeq 6,000 (Illumina, CA) on the respective platform of IGA Technology Services, Udine, Italy. MiRDeep2 was used to identify known and novel miRNA according to the miRbase collection. Differentially expressed miRNA (DEM) were assessed at a threshold of fold-change > 1.5 and false discovery rate < 0.05 using the edgeR package. The MiRWalk database was used to predict DEM targets and their associated KEGG pathways. Among a total of 1,692 identified miRNA, 445 known miRNA were included for statistical analysis, of which 84, 59, and 61 DEM were found between days −21 to 1, 1 to 28, and 28 to 63, respectively. These miRNA were annotated to KEGG pathways targeting the insulin, MAPK, Ras, Wnt, Hippo, sphingolipid, T cell receptor, and mTOR signaling pathways. MiRNA-mRNA network analysis identified miRNA as master regulators of the biological process including miR-138, miR-149-5p, miR-2466-3p, miR-214, miR-504, and miR-6523a. This study provided new insights into the miRNA signatures of transition to the lactation period. Calving emerged as a critical time point when miRNA were most affected, while the following period appeared to be recovering from massive parturition changes. The primarily affected pathways were key signaling pathways related to establishing metabolic and immune adaptations.
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Affiliation(s)
- Arash Veshkini
- Institute of Animal Science, Physiology Unit, University of Bonn, Bonn, Germany
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Department of Veterinary Medicine, Università degli Studi di Milano, Lodi, Italy
| | | | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology of the CNR, Milan, Italy
| | - Laura Vogel
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Martina Gnott
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | | | - Hassan Sadri
- Department of Clinical Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Helga Sauerwein
- Institute of Animal Science, Physiology Unit, University of Bonn, Bonn, Germany
| | - Fabrizio Ceciliani
- Department of Veterinary Medicine, Università degli Studi di Milano, Lodi, Italy
- *Correspondence: Fabrizio Ceciliani,
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Winter E, Cisilotto J, Goetten ALF, Veiga Â, Ramos AT, Zimermann FC, Reck C, Creczynski-Pasa TB. MicroRNAs as serum biomarker for Senecio brasiliensis poisoning in cattle. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 94:103906. [PMID: 35697189 DOI: 10.1016/j.etap.2022.103906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/12/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Senecio spp. is one of the most frequent plant-related poisonings in cattle. Its ingestion generates the disease seneciosis, characterized by hepatic damages. Liver biopsies and serum markers dosage are tools used in diagnosis; however, many breeding cattle are undiagnosed. MicroRNAs are non-coding RNA, stable in biological fluids. Their difference in expression levels may indicate the presence of the poisoning. We analyzed the miRNA profiling to identify potential diagnostic biomarkers for Senecio brasiliensis poisoning. The expression of miR-21, miR-885, miR-122, miR-181b, miR-30a, miR-378, and let-7 f were evaluated in the serum of exposed cattle. At least one histological change was found in liver and lower quantity of albumin and high AST and ALP were also detected. MiRNAs miR-30a, miR-378, miR-21, miR-885, and miR-122 presented significantly higher expression in intoxicated animals than in healthy animals. Furthermore, miR-122, miR-885, and, especially, miR-21 signatures demonstrated high sensitivity and specificity, with potential application for detecting poisoning.
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Affiliation(s)
- Evelyn Winter
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil.
| | - Julia Cisilotto
- Postgraduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - André L F Goetten
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Ângela Veiga
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Adriano T Ramos
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Francielli C Zimermann
- Department of Agriculture, Biodiversity and Forest, Postgraduate Program in Conventional and Integrative Veterinary Medicine, Curitibanos, SC 89520-000, Brazil
| | - Carolina Reck
- VERTÁ, Laboratory of Veterinary Diagnostic, Institute of Veterinary Research and Diagnostic, Curitibanos, SC 89520-000, Brazil
| | - Tânia B Creczynski-Pasa
- Department of Pharmaceutical Sciences, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
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Miao Y, Fu C, Liao M, Fang F. Differences in Liver microRNA profiling in pigs with low and high
feed efficiency. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:312-329. [PMID: 35530409 PMCID: PMC9039951 DOI: 10.5187/jast.2022.e4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 01/09/2022] [Indexed: 11/21/2022]
Abstract
Feed cost is the main factor affecting the economic benefits of pig industry.
Improving the feed efficiency (FE) can reduce the feed cost and improve the
economic benefits of pig breeding enterprises. Liver is a complex metabolic
organ which affects the distribution of nutrients and regulates the efficiency
of energy conversion from nutrients to muscle or fat, thereby affecting feed
efficiency. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate feed
efficiency through the modulation of gene expression at the post-transcriptional
level. In this study, we analyzed miRNA profiling of liver tissues in High-FE
and Low-FE pigs for the purpose of identifying key miRNAs related to feed
efficiency. A total 212~221 annotated porcine miRNAs and 136~281 novel
miRNAs were identified in the pig liver. Among them, 188 annotated miRNAs were
co-expressed in High-FE and Low-FE pigs. The 14 miRNAs were significantly
differentially expressed (DE) in the livers of high-FE pigs and low-FE pigs, of
which 5 were downregulated and 9 were upregulated. Kyoto Encyclopedia of Genes
and Genomes analysis of liver DE miRNAs in high-FE pigs and low-FE pigs
indicated that the target genes of DE miRNAs were significantly enriched in
insulin signaling pathway, Gonadotropin-releasing hormone signaling pathway, and
mammalian target of rapamycin signaling pathway. To verify the reliability of
sequencing results, 5 DE miRNAs were randomly selected for quantitative reverse
transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR results of miRNAs
were confirmed to be consistent with sequencing data. DE miRNA data indicated
that liver-specific miRNAs synergistically acted with mRNAs to improve feed
efficiency. The liver miRNAs expression analysis revealed the metabolic pathways
by which the liver miRNAs regulate pig feed efficiency.
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Affiliation(s)
- Yuanxin Miao
- College of Bioengineering,Jingchu
University of Technology, Jingmen 448000, Hubei, China
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Chuanke Fu
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Mingxing Liao
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Fang Fang
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
- National Center for International Research
on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong
Agricultural University, Wuhan 430070, China
- Corresponding author: Fang Fang, Key Laboratory of
Agricultural Animal Genetics, Breeding and Reproduction of Ministry of
Education, Huazhong Agricultural University, Wuhan 430070, China. Tel:
+86-278-728-2091, E-mail:
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6
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Zhang JS, Xu HY, Fang JC, Yin BZ, Wang BB, Pang Z, Xia GJ. Integrated microRNA-mRNA analysis reveals the roles of microRNAs in the muscle fat metabolism of Yanbian cattle. Anim Genet 2021; 52:598-607. [PMID: 34350996 DOI: 10.1111/age.13126] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 12/16/2022]
Abstract
Fat deposition is an important economic trait in farm animals. However, it is difficult to genetically improve intramuscular fat deposition via trait-based cattle breeding. The main objectives of this study were to analyze the factors about beef flavor, and to detect functional microRNA (miRNA, miR) associated with intramuscular fat deposition in Yanbian cattle. Longissimus dorsi samples from six steers were separated into high- and low-fat groups (n = 3 each) based on the marbling score, and transcriptomic analysis was performed using miRNA sequencing. A total of 33 miRNAs and 38 genes were found to be differentially expressed in the high- and low-fat groups. Quantitative real-time polymerase chain reaction was performed to validate the sequencing results. Integrated miRNA-mRNA analysis revealed that miRNA-associated target genes were primarily associated with skeletal muscle development. However, some of the miRNAs (miR-424 etc.) and genes (ATF3 etc.) were also associated with fat metabolism. A targeted relationship between miR-22-3p and the WFIKKN2 gene and its involvement in adipocyte differentiation were confirmed experimentally. The study findings may provide potential candidate molecular targets for the selection of cattle with improved meat quality.
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Affiliation(s)
- J S Zhang
- College of Agriculture, Yanbian University, Yanji, 133002, China
| | - H Y Xu
- College of Agriculture, Yanbian University, Yanji, 133002, China
| | - J C Fang
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - B Z Yin
- College of Agriculture, Yanbian University, Yanji, 133002, China
| | - B B Wang
- College of Agriculture, Yanbian University, Yanji, 133002, China
| | - Z Pang
- College of Agriculture, Yanbian University, Yanji, 133002, China
| | - G J Xia
- College of Agriculture, Yanbian University, Yanji, 133002, China.,Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Yanbian University, Yanji, 133002, China
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7
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Billa PA, Faulconnier Y, Ye T, Bourdon C, Pires JAA, Leroux C. Nutrigenomic analyses reveal miRNAs and mRNAs affected by feed restriction in the mammary gland of midlactation dairy cows. PLoS One 2021; 16:e0248680. [PMID: 33857151 PMCID: PMC8049318 DOI: 10.1371/journal.pone.0248680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
The objective of this study was to investigate the effects of feed restriction on mammary miRNAs and coding gene expression in midlactation cows. Five Holstein cows and 6 Montbéliarde cows underwent 6 days of feed restriction, during which feed allowance was reduced to meet 50% of their net energy for lactation requirements. Mammary biopsies were performed before and at the end of the restriction period. Mammary miRNA and mRNA analyses were performed using high-throughput sequencing and microarray analyses, respectively. Feed restriction induced a negative energy balance and decreased milk production and fat and protein yields in both breeds. Feed restriction modified the expression of 27 miRNAs and 374 mRNAs in mammary glands from Holstein cows, whereas no significant miRNA change was observed in Montbéliarde cows. Among the 27 differentially expressed miRNAs, 8 miRNAs were associated with dairy QTL. Analysis of target genes indicate that the 8 most abundantly expressed miRNAs control transcripts related to lipid metabolism, mammary remodeling and stress response. A comparison between the mRNAs targeted by the 8 most strongly expressed miRNAs and 374 differentially expressed mRNAs identified 59 mRNAs in common. The bioinformatic analyses of these 59 mRNAs revealed their implication in lipid metabolism and endothelial cell proliferation. These effects of feed restriction on mammary miRNAs and mRNAs observed in Holstein cows suggest a potential role of miRNAs in mammary structure and lipid biosynthesis that could explain changes in milk production and composition.
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Affiliation(s)
- Pierre-Alexis Billa
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Yannick Faulconnier
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, Illkirch, France
| | - Céline Bourdon
- INRAE, AgroParisTech, Université Paris-Saclay, UMR Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - José A. A. Pires
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
| | - Christine Leroux
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, Saint-Genès-Champanelle, France
- * E-mail:
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8
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Hao ZY, Wang JQ, Luo YL, Liu X, Li SB, Zhao ML, Jin XY, Shen JY, Ke N, Song YZ, Qiao LR. Deep small RNA-Seq reveals microRNAs expression profiles in lactating mammary gland of 2 sheep breeds with different milk performance. Domest Anim Endocrinol 2021; 74:106561. [PMID: 33035848 DOI: 10.1016/j.domaniend.2020.106561] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
Micro ribonucleic acid (miRNA) is a type of noncoding RNA, and it has been revealed to play important roles in the activity of the mammary gland (MG) in some species. However, the function of miRNAs in MG of sheep is poorly understood. In the study, Gansu Alpine Merino (GAM; n = 9) and Small-tailed Han sheep (STH; n = 9) with different milk production traits were investigated. Microstructures and the expression profile of miRNAs of MG tissues at peak lactation were studied. Mature alveolar lumens of MG in appearance were larger in STH than GAM. The expression levels of CSN2 and the content of rough endoplasmic reticulum were also higher in STH ewes than GAM ewes. A total of 124 mature miRNAs were expressed, and 18 of these were differentially expressed between the 2 breeds. The KEGG analysis results showed that the targeted genes of differentially expressed miRNAs were mainly involved in some metabolic pathways and signaling pathways related to MG development, milk protein, and fat synthesis. The findings in the study can improve our understanding of the roles of miRNAs in the development and lactation of MG in sheep.
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Affiliation(s)
- Z Y Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - J Q Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
| | - Y L Luo
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - X Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - S B Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - M L Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - X Y Jin
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - J Y Shen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - N Ke
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Y Z Song
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - L R Qiao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, Faculty of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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D’Occhio MJ, Baruselli PS, Campanile G. Metabolic health, the metabolome and reproduction in female cattle: a review. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1600385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Michael J. D’Occhio
- School of Life and Environmental Sciences, The University of Sydney, Camden, Australia
| | - Pietro S. Baruselli
- Departamento de Reproducao Animal (VRA), University of Sao Paulo, Sao Paulo, Brazil
| | - Giuseppe Campanile
- Dipartimento di Medicina Veterinaria e Produzioni Animali, University of Naples Federico II, Napoli, Italy
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10
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The sinister face of heme oxygenase-1 in brain aging and disease. Prog Neurobiol 2019; 172:40-70. [DOI: 10.1016/j.pneurobio.2018.06.008] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/19/2018] [Accepted: 06/30/2018] [Indexed: 11/23/2022]
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Association of plasma microRNA expression with age, genetic background and functional traits in dairy cattle. Sci Rep 2018; 8:12955. [PMID: 30154501 DOI: 10.1038/s41598-018-31099-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023] Open
Abstract
A number of blood circulating microRNAs (miRNAs) are proven disease biomarkers and have been associated with ageing and longevity in multiple species. However, the role of circulating miRNAs in livestock species has not been fully studied. We hypothesise that plasma miRNA expression profiles are affected by age and genetic background, and associated with health and production traits in dairy cattle. Using PCR arrays, we assessed 306 plasma miRNAs for effects of age (calves vs mature cows) and genetic background (control vs select lines) in 18 animals. We identified miRNAs which were significantly affected by age (26 miRNAs) and genetic line (5 miRNAs). Using RT-qPCR in a larger cow population (n = 73) we successfully validated array data for 12 age-related miRNAs, one genetic line-related miRNA, and utilised expression data to associate their levels in circulation with functional traits in these animals. Plasma miRNA levels were associated with telomere length (ageing/longevity indicator), milk production and composition, milk somatic cell count (mastitis indicator), fertility, lameness, and blood metabolites linked with body energy balance and metabolic stress. In conclusion, circulating miRNAs could provide useful selection markers for dairy cows to help improve health, welfare and production performance.
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12
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Comparative transcriptome analysis to investigate the potential role of miRNAs in milk protein/fat quality. Sci Rep 2018; 8:6250. [PMID: 29674689 PMCID: PMC5908868 DOI: 10.1038/s41598-018-24727-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/14/2018] [Indexed: 01/06/2023] Open
Abstract
miRNAs play an important role in the processes of cell differentiation, biological development, and physiology. Here we investigated the molecular mechanisms regulating milk secretion and quality in dairy cows via transcriptome analyses of mammary gland tissues from dairy cows during the high-protein/high-fat, low-protein/low-fat or dry periods. To characterize the important roles of miRNAs and mRNAs in milk quality and to elucidate their regulatory networks in relation to milk secretion and quality, an integrated analysis was performed. A total of 25 core miRNAs were found to be differentially expressed (DE) during lactation compared to non-lactation, and these miRNAs were involved in epithelial cell terminal differentiation and mammary gland development. In addition, comprehensive analysis of mRNA and miRNA expression between high-protein/high-fat group and low-protein/low-fat groups indicated that, 38 miRNAs and 944 mRNAs were differentially expressed between them. Furthermore, 38 DE miRNAs putatively negatively regulated 253 DE mRNAs. The putative genes (253 DE mRNAs) were enriched in lipid biosynthetic process and amino acid transmembrane transporter activity. Moreover, putative DE genes were significantly enriched in fatty acid (FA) metabolism, biosynthesis of amino acids, synthesis and degradation of ketone bodies and biosynthesis of unsaturated FAs. Our results suggest that DE miRNAs might play roles as regulators of milk quality and milk secretion during mammary gland differentiation.
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13
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Ioannidis J, Donadeu FX. Comprehensive analysis of blood cells and plasma identifies tissue-specific miRNAs as potential novel circulating biomarkers in cattle. BMC Genomics 2018; 19:243. [PMID: 29636028 PMCID: PMC5894187 DOI: 10.1186/s12864-018-4646-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/03/2018] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The potential of circulating miRNAs as biomarkers of tissue function, both in health and disease, has been extensively demonstrated in humans. In addition, circulating miRNA biomarkers offer significant potential towards improving the productivity of livestock species, however, such potential has been hampered by the absence of information on the nature and source of circulating miRNA populations in these species. In addition, many miRNAs originally proposed as robust biomarkers of a particular tissue or disease in humans have been later shown not to be tissue specific and thus to actually have limited biomarker utility. In this study, we comprehensively analysed miRNA profiles in plasma and cell fractions of blood from cattle with the aim to identify tissue-derived miRNAs which may be useful as biomarkers of tissue function in this important food animal species. RESULTS Using small RNA sequencing, we identified 92 miRNAs with significantly higher expression in plasma compared to paired blood cell samples (n = 4 cows). Differences in miRNA levels between plasma and cell fractions were validated for eight out of 10 miRNAs using RT-qPCR (n = 10 cows). Among miRNAs found to be enriched in plasma, we confirmed miR-122 (liver), miR-133a (muscle) and miR-215 (intestine) to be tissue-enriched, as reported for other species. Profiling of additional miRNAs across different tissues identified the human homologue, miR-802, as highly enriched specifically in liver. CONCLUSIONS These results provide novel information on the source of bovine circulating miRNAs and could significantly facilitate the identification of production-relevant tissue biomarkers in livestock. In particular, miR-802, a circulating miRNA not previously identified in cattle, can reportedly regulate insulin sensitivity and lipid metabolism, and thus could potentially provide a specific biomarker of liver function, a key parameter in the context of post-partum negative energy balance in dairy cows.
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Affiliation(s)
- Jason Ioannidis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
| | - F. Xavier Donadeu
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
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14
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Integrated regulatory network reveals novel candidate regulators in the development of negative energy balance in cattle. Animal 2017; 12:1196-1207. [PMID: 29282162 DOI: 10.1017/s1751731117003524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Negative energy balance (NEB) is an altered metabolic state in modern high-yielding dairy cows. This metabolic state occurs in the early postpartum period when energy demands for milk production and maintenance exceed that of energy intake. Negative energy balance or poor adaptation to this metabolic state has important effects on the liver and can lead to metabolic disorders and reduced fertility. The roles of regulatory factors, including transcription factors (TFs) and micro RNAs (miRNAs) have often been separately studied for evaluating of NEB. However, adaptive response to NEB is controlled by complex gene networks and still not fully understood. In this study, we aimed to discover the integrated gene regulatory networks involved in NEB development in liver tissue. We downloaded data sets including mRNA and miRNA expression profiles related to three and four cows with severe and moderate NEB, respectively. Our method integrated two independent types of information: module inference network by TFs, miRNAs and mRNA expression profiles (RNA-seq data) and computational target predictions. In total, 176 modules were predicted by using gene expression data and 64 miRNAs and 63 TFs were assigned to these modules. By using our integrated computational approach, we identified 13 TF-module and 19 miRNA-module interactions. Most of these modules were associated with liver metabolic processes as well as immune and stress responses, which might play crucial roles in NEB development. Literature survey results also showed that several regulators and gene targets have already been characterized as important factors in liver metabolic processes. These results provided novel insights into regulatory mechanisms at the TF and miRNA levels during NEB. In addition, the method described in this study seems to be applicable to construct integrated regulatory networks for different diseases or disorders.
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15
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Selected microRNA-192 mutant indicates association with several function genes in bovine cells. Genes Genomics 2017; 40:361-371. [PMID: 29892841 DOI: 10.1007/s13258-017-0635-3] [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: 07/30/2017] [Accepted: 11/13/2017] [Indexed: 10/18/2022]
Abstract
MicroRNAs are implicated in many cellular processes such as cell differentiation and development, tumorigenesis, and immune regulation. In this study, miR192 was detected using quantitative real-time polymerase chain reaction (qRT-PCR) when MDBK cells were exposed to Escherichia coli. Cells with malfunction of bta-miR-192 were established using transcription activator-like effector nuclease (TALEN) technology. Finally, bta-miR-192 mutant cells were screened for differentially expressed genes using RNA-sequencing (RNA-seq). The results showed that miR192 significantly decreased in cells exposed to E. coli F18ac and E. coli K88ac. The RNA-seq results showed that 1673 differentially expressed transcripts were identified; 890 genes were upregulated and 775 genes were downregulated. With the gene ontology enrichment analysis, 431 differentially expressed genes (DEGs) were classified into 937 gene ontology terms. The pathway enrichment analysis showed that 535 genes were involved in 254 pathway terms. Interestingly, most of these DEGs were associated with the pathways in cancers or infectious diseases. When the selected DEGs (n = 162) in these pathways were intersected with 120 differential transcripts, 11 DEGs were identified. Subsequently, several genes associated with regulation, cancers, or viral infections, such as LEF1, AXIN2, MX1, and FCGR2B, were identified among the DEGs using functional analysis. Furthermore, associations between bta-miR-192 and DEGs were detected by intersecting the bta-miR-192's target genes with the DEGs, indicating that three genes including CBL, DICER1 and TRERF1 were involved in this relationship. These findings provided useful guidance for investigating the role played by bta-miR-192 in cellular functionality in bovine cells.
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16
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Du X, Yang Y, Xu C, Peng Z, Zhang M, Lei L, Gao W, Dong Y, Shi Z, Sun X, Wang Z, Li X, Li X, Liu G. Upregulation of miR-181a impairs hepatic glucose and lipid homeostasis. Oncotarget 2017; 8:91362-91378. [PMID: 29207650 PMCID: PMC5710930 DOI: 10.18632/oncotarget.20523] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/06/2017] [Indexed: 01/20/2023] Open
Abstract
The contributions of altered post-transcriptional gene silencing to the development of metabolic disorders remain poorly understood thus far. The objective of this study was to evaluate the roles of miR-181a in the regulation of hepatic glucose and lipid metabolism. MiR-181a is abundantly expressed in the liver, and we found that blood and hepatic miR-181a levels were significantly increased in patients and dairy cows with non-alcoholic fatty liver disease, as well as in high-fat diet and ob/ob mice. We determined that sirtuin1 is a target of miR-181a. Moreover, we found that hepatic sirtuin1 and peroxisome proliferator-activated receptor-γ coactivator-1α expression levels are downregulated, and acetylated peroxisome proliferator-activated receptor-γ coactivator-1α expression levels are upregulated in patients and dairy cows with non-alcoholic fatty liver disease, as well as in high-fat diet and ob/ob mice. MiR-181a overexpression inhibits the sirtuin1-peroxisome proliferator-activated receptor-γ coactivator-1α pathway, reduces insulin sensitivity, and increases gluconeogenesis and lipid synthesis in dairy cow hepatocytes and HepG2 cells. Conversely, silencing of miR-181a over-activates the sirtuin1-peroxisome proliferator-activated receptor-γ coactivator-1α pathway, increases insulin sensitivity and glycogen content, and decreases gluconeogenesis and lipid synthesis in hepatocytes, even under non-esterified fatty acids treatment conditions. Furthermore, miR-181a overexpression or sirtuin1 knockdown in mice increases lipid accumulation and decreases insulin sensitivity and glycogen content in the liver. Taken together, these findings indicate that increased hepatic miR-181a impairs glucose and lipid homeostasis by silencing sirtuin1 in non-alcoholic fatty liver disease.
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Affiliation(s)
- Xiliang Du
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yuchen Yang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chuang Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Zhicheng Peng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Min Zhang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Lin Lei
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenwen Gao
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yuhao Dong
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhen Shi
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xudong Sun
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhe Wang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiaobing Li
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xinwei Li
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Guowen Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, China
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Liu A, Wang Y, Sahana G, Zhang Q, Liu L, Lund MS, Su G. Genome-wide Association Studies for Female Fertility Traits in Chinese and Nordic Holsteins. Sci Rep 2017; 7:8487. [PMID: 28814769 PMCID: PMC5559619 DOI: 10.1038/s41598-017-09170-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/20/2017] [Indexed: 12/18/2022] Open
Abstract
Reduced female fertility could cause considerable economic loss and has become a worldwide problem in the modern dairy industry. The objective of this study was to detect quantitative trait loci (QTL) for female fertility traits in Chinese and Nordic Holsteins using various strategies. First, single-trait association analyses were performed for female fertility traits in Chinese and Nordic Holsteins. Second, the SNPs with P-value < 0.005 discovered in Chinese Holsteins were validated in Nordic Holsteins. Third, the summary statistics from single-trait association analyses were combined into meta-analyses to: (1) identify common QTL for multiple fertility traits within each Holstein population; (2) detect SNPs which were associated with a female fertility trait across two Holstein populations. A large numbers of QTL were discovered or confirmed for female fertility traits. The QTL segregating at 31.4~34.1 Mb on BTA13, 48.3~51.9 Mb on BTA23 and 34.0~37.6 Mb on BTA28 shared between Chinese and Nordic Holsteins were further ascertained using a validation approach and meta-analyses. Furthermore, multiple novel variants identified in Chinese Holsteins were validated with Nordic data as well as meta-analyses. The genes IL6R, SLC39A12, CACNB2, ZEB1, ZMIZ1 and FAM213A were concluded to be strong candidate genes for female fertility in Holsteins.
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Affiliation(s)
- Aoxing Liu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.,Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Qin Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.
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18
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Hanging Drop, A Best Three-Dimensional (3D) Culture Method for Primary Buffalo and Sheep Hepatocytes. Sci Rep 2017; 7:1203. [PMID: 28446763 PMCID: PMC5430879 DOI: 10.1038/s41598-017-01355-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/27/2017] [Indexed: 02/07/2023] Open
Abstract
Livestock, having close resemblance to humans, could be a better source of primary hepatocytes than rodents. Herein, we successfully developed three-dimensional (3D) culturing system for primary sheep and buffalo hepatocytes. The 3D-structures of sheep hepatocytes were formed on the fifth-day and maintained until the tenth-day on polyHEMA-coated plates and in hanging drops with William’s E media (HDW). Between the cultured and fresh cells, we observed a similar expression of GAPDH, HNF4α, ALB, CYP1A1, CK8 and CK18. Interestingly, a statistically significant increase was noted in the TAT, CPS, AFP, AAT, GSP and PCNA expression. In buffalo hepatocytes culture, 3D-like structures were formed on the third-day and maintained until the sixth-day on polyHEMA and HDW. The expression of HNF4α, GSP, CPS, AFP, AAT, PCNA and CK18 was similar between cultured and fresh cells. Further, a statistically significant increase in the TAT and CK8 expression, and a decrease in the GAPDH, CYP1A1 and ALB expression were noted. Among the culture systems, HDW maintained the liver transcript markers more or less similar to the fresh hepatocytes of the sheep and buffalo for ten and six days, respectively. Taken together, hanging drop is an efficient method for 3D culturing of primary sheep and buffalo hepatocytes.
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19
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Chuammitri P, Srikok S, Saipinta D, Boonyayatra S. The effects of quercetin on microRNA and inflammatory gene expression in lipopolysaccharide-stimulated bovine neutrophils. Vet World 2017; 10:403-410. [PMID: 28507412 PMCID: PMC5422244 DOI: 10.14202/vetworld.2017.403-410] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/28/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate gene expression of microRNA (miRNA) milieus (MIRLET7E, MIR17, MIR24-2, MIR146A, and MIR181C), inflammatory cytokine genes (interleukin 1β [IL1B], IL6, CXCL8, and tumor necrosis factor [TNF]), and the pathogen receptor toll-like receptor (TLR4) in bovine neutrophils under quercetin supplementation. MATERIALS AND METHODS Isolated bovine neutrophils were incubated with bacterial lipopolysaccharide under quercetin treatment or left untreated. Real-time polymerase chain reaction was performed to determine the expression of the miRNAs and messenger RNA (mRNA) transcripts in neutrophils. RESULTS Quercetin-treated neutrophils exhibited a remarkable suppression in MIR24-2, MIR146A, and MIR181C expression. Similarly, mRNA expression of IL1B, IL6, CXCL8, TLR4, and TNF genes noticeably declined in the quercetin group. Many proinflammatory genes (IL1B, IL6, and CXCL8) and the pathogen receptor TLR4 had a negative correlation with MIR146A and MIR181C as revealed by Pearson correlation. CONCLUSIONS Interaction between cognate mRNAs and miRNAs under quercetin supplementation can be summarized as a positive or negative correlation. This finding may help understand the effects of quercetin either on miRNA or gene expression during inflammation, especially as a potentially applicable indicator in bovine mastitis.
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Affiliation(s)
- Phongsakorn Chuammitri
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Suphakit Srikok
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Duanghathai Saipinta
- Dairy Cow Hospital, Faculty of Veterinary Medicine, Chiang Mai University, Mae On, Chiang Mai 50130, Thailand
| | - Sukolrat Boonyayatra
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
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20
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Zhang M, Wei F, Guo K, Hu Z, Li Y, Xie G, Wang Y, Cai X, Peng L, Wang L. A Novel FC116/ BC10 Mutation Distinctively Causes Alteration in the Expression of the Genes for Cell Wall Polymer Synthesis in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1366. [PMID: 27708650 PMCID: PMC5030303 DOI: 10.3389/fpls.2016.01366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/29/2016] [Indexed: 05/11/2023]
Abstract
We report isolation and characterization of a fragile culm mutant fc116 that displays reduced mechanical strength caused by decreased cellulose content and altered cell wall structure in rice. Map-based cloning revealed that fc116 was a base substitution mutant (G to A) in a putative beta-1,6-N-acetylglucosaminyltransferase (C2GnT) gene (LOC_Os05g07790, allelic to BC10). This mutation resulted in one amino acid missing within a newly-identified protein motif "R, RXG, RA." The FC116/BC10 gene was lowly but ubiquitously expressed in the all tissues examined across the whole life cycle of rice, and slightly down-regulated during secondary growth. This mutant also exhibited a significant increase in the content of hemicelluloses and lignins, as well as the content of pentoses (xylose and arabinose). But the content of hexoses (glucose, mannose, and galactose) was decreased in both cellulosic and non-cellulosic (pectins and hemicelluloses) fractions of the mutant. Transcriptomic analysis indicated that the typical genes in the fc116 mutant were up-regulated corresponding to xylan biosynthesis, as well as lignin biosynthesis including p-hydroxyphenyl (H), syringyl (S), and guaiacyl (G). Our results indicate that FC116 has universal function in regulation of the cell wall polymers in rice.
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Affiliation(s)
- Mingliang Zhang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Feng Wei
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Kai Guo
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Zhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yuyang Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Guosheng Xie
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Xiwen Cai
- Department of Plant Science, North Dakota State UniversityFargo, ND, USA
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Lingqiang Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural UniversityWuhan, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
- College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
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21
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Al-Husseini W, Chen Y, Gondro C, Herd RM, Gibson JP, Arthur PF. Characterization and Profiling of Liver microRNAs by RNA-sequencing in Cattle Divergently Selected for Residual Feed Intake. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 29:1371-82. [PMID: 26954124 PMCID: PMC5003961 DOI: 10.5713/ajas.15.0605] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/10/2015] [Accepted: 12/14/2015] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying variation in this measure of feed efficiency in bovines.
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Affiliation(s)
- Wijdan Al-Husseini
- The Centre for Genetics Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Yizhou Chen
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Cedric Gondro
- The Centre for Genetics Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Robert M Herd
- NSW Department of Primary Industries, Beef Industry Centre, Armidale, NSW 2351, Australia
| | - John P Gibson
- The Centre for Genetics Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Paul F Arthur
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
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Bionaz M, Osorio J, Loor JJ. TRIENNIAL LACTATION SYMPOSIUM: Nutrigenomics in dairy cows: Nutrients, transcription factors, and techniques1,2. J Anim Sci 2015; 93:5531-53. [DOI: 10.2527/jas.2015-9192] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- M. Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis 97333
| | - J. Osorio
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis 97333
| | - J. J. Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
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23
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Mahmoudi A, Zargaran A, Amini HR, Assadi A, Vajdi Hokmabad R, Eghbalsaied S. A SNP in the 3′-untranslated region of AMPKγ1 may associate with serum ketone body and milk production of Holstein dairy cows. Gene 2015; 574:48-52. [DOI: 10.1016/j.gene.2015.07.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/23/2015] [Indexed: 12/21/2022]
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24
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Identification of a Novel Hepacivirus in Domestic Cattle from Germany. J Virol 2015; 89:7007-15. [PMID: 25926652 DOI: 10.1128/jvi.00534-15] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Hepatitis C virus (HCV) continues to represent one of the most significant threats to human health. In recent years, HCV-related sequences have been found in bats, rodents, horses, and dogs, indicating a widespread distribution of hepaciviruses among animals. By applying unbiased high-throughput sequencing, a novel virus of the genus Hepacivirus was discovered in a bovine serum sample. De novo assembly yielded a nearly full-length genome coding for a polyprotein of 2,779 amino acids. Phylogenetic analysis confirmed that the virus represents a novel species within the genus Hepacivirus. Viral RNA screening determined that 1.6% (n = 5) of 320 individual animals and 3.2% (n = 5) of 158 investigated cattle herds in Germany were positive for bovine hepacivirus. Repeated reverse transcription-PCR (RT-PCR) analyses of animals from one dairy herd proved that a substantial percentage of cows were infected, with some of them being viremic for over 6 months. Clinical and postmortem examination revealed no signs of disease, including liver damage. Interestingly, quantitative RT-PCR from different organs and tissues, together with the presence of an miR-122 binding site in the viral genome, strongly suggests a liver tropism for bovine hepacivirus, making this novel virus a promising animal model for HCV infections in humans. IMPORTANCE Livestock animals act as important sources for emerging pathogens. In particular, their large herd size and the existence of multiple ways of direct and food-borne infection routes emphasize their role as virus reservoirs. Apart from the search for novel viruses, detailed characterization of these pathogens is indispensable in the context of risk analysis. Here, we describe the identification of a novel HCV-like virus in cattle. In addition, determination of the prevalence and of the course of infection in cattle herds provides valuable insights into the biology of this novel virus. The results presented here form a basis for future studies targeting viral pathogenesis of bovine hepaciviruses and their potential to establish zoonotic infections.
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25
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Lin SH, Song W, Cressatti M, Zukor H, Wang E, Schipper HM. Heme oxygenase-1 modulates microRNA expression in cultured astroglia: implications for chronic brain disorders. Glia 2015; 63:1270-84. [PMID: 25820186 DOI: 10.1002/glia.22823] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/02/2015] [Indexed: 01/03/2023]
Abstract
BACKGROUND Over-expression of the heme-degrading enzyme, heme oxygenase-1 (HO-1) promotes iron deposition, mitochondrial damage, and autophagy in astrocytes and enhances the vulnerability of nearby neuronal constituents to oxidative injury. These neuropathological features and aberrant brain microRNA (miRNA) expression patterns have been implicated in the etiopathogeneses of various neurodevelopmental and aging-related neurodegenerative disorders. OBJECTIVE To correlate glial HO-1 overexpression with altered miRNA patterns, which have been linked to the aforementioned "core" neuropathological features. METHODS miRNA microchip assays were performed on HMOX1- and sham-transfected primary rat astroglia and affected miRNAs were further validated by qPCR. The roles of the heme degradation products, carbon monoxide (CO), iron (Fe) and bilirubin on miRNA expression were assessed and salient mRNA targets of the impacted miRNAs were ascertained. RESULTS In HMOX1-transfected astrocytes, rno-miR-140*, rno-miR-17, and rno-miR-16 were significantly up-regulated, and rno-miR-297, rno-miR-206, rno-miR-187, rno-miR-181a, rno-miR-138 and rno-miR-29c were down-regulated, compared to sham-transfected controls. CO and Fe were implicated in the HMOX1 effects, whereas bilirubin was inert or counteracted the HMOX1-related changes. mRNA levels of Ngfr, Vglut1, Mapk3, Tnf-α, and Sirt1, known targets of the down-regulated miRNAs and abnormal in various human brain disorders, were significantly increased in the HMOX-1-transfected astrocytes. CONCLUSIONS In chronic CNS disorders, altered expression of salient miRNAs and their mRNA targets may contribute to the neural damage accruing from the over-expression of glial HO-1.
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Affiliation(s)
- Shih-Hsiung Lin
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
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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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