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Yao H, Dou Z, Zhao Z, Liang X, Yue H, Ma W, Su Z, Wang Y, Hao Z, Yan H, Wu Z, Wang L, Chen G, Yang J. Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits. BMC Genomics 2023; 24:660. [PMID: 37919661 PMCID: PMC10621195 DOI: 10.1186/s12864-023-09703-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, we aimed to identify candidate genes and metabolic pathways that affect milk production traits in Bactrian camels. METHODS We classified camels (fourth parity) as low- or high-yield, examined pregnant camels using B-mode ultrasonography, observed the microscopic changes in the mammary gland using hematoxylin and eosin (HE) staining, and used RNA sequencing to identify differentially expressed genes (DEGs) and pathways. RESULTS The average standard milk yield over the 300 days during parity was recorded as 470.18 ± 9.75 and 978.34 ± 3.80 kg in low- and high-performance camels, respectively. Nine female Junggar Bactrian camels were subjected to transcriptome sequencing, and 609 and 393 DEGs were identified in the low-yield vs. high-yield (WDL vs. WGH) and pregnancy versus colostrum period (RSQ vs. CRQ) comparison groups, respectively. The DEGs were compared with genes associated with milk production traits in the Animal Quantitative Trait Loci database and in Alashan Bactrian camels, and 65 and 46 overlapping candidate genes were obtained, respectively. Functional enrichment and protein-protein interaction network analyses of the DEGs and candidate genes were conducted. After comparing our results with those of other livestock studies, we identified 16 signaling pathways and 27 core candidate genes associated with maternal parturition, estrogen regulation, initiation of lactation, and milk production traits. The pathways suggest that emerged milk production involves the regulation of multiple complex metabolic and cellular developmental processes in camels. Finally, the RNA sequencing results were validated using quantitative real-time PCR; the 15 selected genes exhibited consistent expression changes. CONCLUSIONS This study identified DEGs and metabolic pathways affecting maternal parturition and milk production traits. The results provides a theoretical foundation for further research on the molecular mechanism of genes related to milk production traits in camels. Furthermore, these findings will help improve breeding strategies to achieve the desired milk yield in camels.
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Affiliation(s)
- Huaibing Yao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Zhihua Dou
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Zhongkai Zhao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Xiaorui Liang
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Haitao Yue
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Wanpeng Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhanqiang Su
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Yuzhuo Wang
- Xinjiang Altai Regional Animal Husbandry Veterinary Station, Altay, 836500, Xinjiang, China
| | - Zelin Hao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Hui Yan
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
| | - Zhuangyuan Wu
- Xinjiang Altai Regional Animal Husbandry Veterinary Station, Altay, 836500, Xinjiang, China
| | - Liang Wang
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
- Bactrian Camel Academy of Xinjiang, Xinjiang Wangyuan Camel Milk Limited Company, Altay, 836500, Xinjiang, China
| | - Gangliang Chen
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China
- Bactrian Camel Academy of Xinjiang, Xinjiang Wangyuan Camel Milk Limited Company, Altay, 836500, Xinjiang, China
| | - Jie Yang
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, 777 Huarui Street, Urumqi, 830017, Xinjiang, PR China.
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi, 830017, China.
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Do DN, Suravajhala P. Editorial: Role of Non-Coding RNAs in Animals. Animals (Basel) 2023; 13:ani13050805. [PMID: 36899662 PMCID: PMC10000048 DOI: 10.3390/ani13050805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
The importance of non-coding RNAs (ncRNAs), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation is increasingly being appreciated in many species [...].
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Affiliation(s)
- Duy Ngoc Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: (D.N.D.); (P.S.)
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, India
- Correspondence: (D.N.D.); (P.S.)
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RNA-Seq Reveals the Roles of Long Non-Coding RNAs (lncRNAs) in Cashmere Fiber Production Performance of Cashmere Goats in China. Genes (Basel) 2023; 14:genes14020384. [PMID: 36833312 PMCID: PMC9956036 DOI: 10.3390/genes14020384] [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: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in cashmere fiber production in cashmere goats. In this study, Liaoning cashmere (LC) goats (n = 6) and Ziwuling black (ZB) goats (n = 6) with remarkable divergences in cashmere yield, cashmere fiber diameter, and cashmere color were selected for the construction of expression profiles of lncRNAs in skin tissue using RNA sequencing (RNA-seq). According to our previous report about the expression profiles of mRNAs originated from the same skin tissue as those used in the study, the cis and trans target genes of differentially expressed lncRNAs between the two caprine breeds were screened, resulting in a lncRNA-mRNA network. A total of 129 lncRNAs were differentially expressed in caprine skin tissue samples between LC goats and ZB goats. The presence of 2 cis target genes and 48 trans target genes for the differentially expressed lncRNAs resulted in 2 lncRNA-cis target gene pairs and 93 lncRNA-trans target gene pairs. The target genes concentrated on signaling pathways that were related to fiber follicle development, cashmere fiber diameter, and cashmere fiber color, including PPAR signaling pathway, metabolic pathways, fatty acid metabolism, fatty acid biosynthesis, tyrosine metabolism, and melanogenesis. A lncRNA-mRNA network revealed 22 lncRNA-trans target gene pairs for seven differentially expressed lncRNAs selected, of which 13 trans target genes contributed to regulation of cashmere fiber diameter, while nine trans target genes were responsible for cashmere fiber color. This study brings a clear explanation about the influences of lncRNAs over cashmere fiber traits in cashmere goats.
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Xuan R, Zhao X, Li Q, Zhao Y, Wang Y, Du S, Duan Q, Guo Y, Ji Z, Chao T, Wang J. Characterization of long noncoding RNA in nonlactating goat mammary glands reveals their regulatory role in mammary cell involution and remodeling. Int J Biol Macromol 2022; 222:2158-2175. [DOI: 10.1016/j.ijbiomac.2022.09.291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
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Potential Novel Biomarkers for Mastitis Diagnosis in Sheep. Animals (Basel) 2021; 11:ani11102783. [PMID: 34679803 PMCID: PMC8532728 DOI: 10.3390/ani11102783] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Inflammation of the mammary gland (mastitis) is an important disease of dairy sheep. Mastitis management depends mainly on the diagnosis. Conventional diagnostic methods including somatic cell count, California Mastitis Test, and microbial culture have limitations. Therefore researchers are looking for new diagnostic biomarkers of mastitis including specific proteins produced by the liver in case of disease (acute phase proteins), unique genetic sequences (miRNAs), or antimicrobial peptides produced by immune cells during inflammation (cathelicidines). Abstract This review aims to characterize promising novel markers of ovine mastitis. Mastitis is considered as one of the primary factors for premature culling in dairy sheep and has noticeable financial, productional, and animal welfare-related implications. Furthermore, clinical, and subclinical mammary infections negatively affect milk yield and alter the milk composition, thereby leading to lowered quality of dairy products. It is, therefore, crucial to control and prevent mastitis through proper diagnosis, treatment or culling, and appropriate udder health management particularly at the end of the lactation period. The clinical form of mastitis is characterized by abnormalities in milk and mammary gland tissue alteration or systemic symptoms consequently causing minor diagnostic difficulties. However, to identify ewes with subclinical mastitis, laboratory diagnostics is crucial. Mastitis control is primarily dependent on determining somatic cell count (SCC) and the California Mastitis Test (CMT), which aim to detect the quantity of cells in the milk sample. The other useful diagnostic tool is microbial culture, which complements SCC and CMT. However, all mentioned diagnostic methods have their limitations and therefore novel biomarkers of ovine subclinical mastitis are highly desired. These sensitive indicators include acute-phase proteins, miRNA, and cathelicidins measurements, which could be determined in ovine serum and/or milk and in the future may become useful in early mastitis diagnostics as well as a preventive tool. This may contribute to increased detection of ovine mammary gland inflammation in sheep, especially in subclinical form, and consequently improves milk quality and quantity.
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Michailidou S, Gelasakis A, Banos G, Arsenos G, Argiriou A. Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds. Front Genet 2021; 12:700489. [PMID: 34349787 PMCID: PMC8326974 DOI: 10.3389/fgene.2021.700489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
In dairy sheep industry, milk production dictates the value of a ewe. Milk production is directly related to the morphology and physiology of the mammary gland; both being designated targets of breeding strategies. Although within a flock breeding parameters are mutual, large differences in milk production among individual ewes are usually observed. In this work, we tested two of the most productive dairy sheep breeds reared intensively in Greece, one local the Chios breed and one foreign the Lacaune breed. We used transcriptome sequencing to reveal molecular mechanisms that render the mammary gland highly productive or not. While highly expressed genes (caseins and major whey protein genes) were common among breeds, differences were observed in differentially expressed genes. ENSOARG00000008077, as a member of ribosomal protein 14 family, together with LPCAT2, CCR3, GPSM2, ZNF131, and ASIP were among the genes significantly differentiating mammary gland's productivity in high yielding ewes. Gene ontology terms were mainly linked to the inherent transcriptional activity of the mammary gland (GO:0005524, GO:0030552, GO:0016740, GO:0004842), lipid transfer activity (GO:0005319) and innate immunity (GO:0002376, GO:0075528, GO:0002520). In addition, clusters of genes affecting zinc and iron trafficking into mitochondria were highlighted for high yielding ewes (GO:0071294, GO:0010043). Our analyses provide insights into the molecular pathways involved in lactation between ewes of different performances. Results revealed management issues that should be addressed by breeders in order to move toward increased milk yields through selection of the desired phenotypes. Our results will also contribute toward the selection of the most resilient and productive ewes, thus, will strengthen the existing breeding systems against a spectrum of environmental threats.
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Affiliation(s)
- Sofia Michailidou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Gelasakis
- Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Athens, Greece
| | - Georgios Banos
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Scotland’s Rural College, Easter Bush, Edinburgh, United Kingdom
| | - George Arsenos
- Laboratory of Animal Husbandry, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anagnostis Argiriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece
- Department of Food Science and Nutrition, University of the Aegean, Lemnos, Greece
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