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Du M, Liu Y, Cao J, Li X, Wang N, He Q, Zhang L, Zhao B, Dugarjaviin M. Food from Equids-Commercial Fermented Mare's Milk (Koumiss) Products: Protective Effects against Alcohol Intoxication. Foods 2024; 13:2344. [PMID: 39123538 PMCID: PMC11312395 DOI: 10.3390/foods13152344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Fermented mare's milk (koumiss), a traditional Central Asian dairy product derived from fermented mare's milk, is renowned for its unique sour taste and texture. It has long been consumed by nomadic tribes for its nutritional and medicinal benefits. This study aimed to comprehensively analyze the protective effects of koumiss against alcohol-induced harm across behavioral, hematological, gastrointestinal, hepatic, and reproductive dimensions using a mouse model. Optimal intoxicating doses of alcohol and koumiss doses were determined, and their effects were explored through sleep tests and blood indicator measurements. Pretreatment with koumiss delayed inebriation, accelerated sobering, and reduced mortality in mice, mitigating alcohol's impact on blood ethanol levels and various physiological parameters. Histopathological and molecular analyses further confirmed koumiss's protective role against alcohol-induced damage in the liver, stomach, small intestine, and reproductive system. Transcriptomic studies on reproductive damage indicated that koumiss exerts its benefits by influencing mitochondrial and ribosomal functions and also shows promise in mitigating alcohol's effects on the reproductive system. In summary, koumiss emerges as a potential natural agent for protection against alcohol-induced harm, opening avenues for future research in this field.
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Affiliation(s)
- Ming Du
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuanyi Liu
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jialong Cao
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xinyu Li
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Na Wang
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qianqian He
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lei Zhang
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bilig Zhao
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Manglai Dugarjaviin
- Key Laboratory of Equus Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (M.D.); (Y.L.); (J.C.); (X.L.); (N.W.); (Q.H.); (L.Z.); (B.Z.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, Inner Mongolia Agricultural University, Hohhot 010018, China
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Kumar H, Yadav A, Hanah SS, Devi LS, Khate K, P S G. Genetic parameters of body weight traits in Mithun (Bos frontalis) using animal model. Trop Anim Health Prod 2024; 56:204. [PMID: 38995429 DOI: 10.1007/s11250-024-04069-w] [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] [Received: 02/29/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Mithun (Bos frontalis), a domestically raised herbivore, holds significant economic importance for the farming community of Northeast India. This study aimed to elucidate the genetic parameters governing Mithun body weight traits across different ages using data from the sole organized semi-intensive Mithun farm in India. Information was gathered from 110 Mithuns born over a period spanning from 2011 to 2022. Body weight taken at week 1 (W1), 1-month (M1), 3-months (M3), 6-months (M6), 9-months (M9), 12-months (M12), 30-months (M30) and 45-months (M45) were considered for the study. The genetic parameters estimation employed the BLUPF90 suite of programs, incorporating univariate Gibbs sampler animal model with fixed effects; season and period of birth, and sex of the animal. Variance and covariance components, including direct additive genetic effects, were estimated. Heritability estimates for the eight body weight traits ranged from 0.47 ± 0.0050 to 0.50 ± 0.0043, indicating varying genetic influence across growth stages. Results revealed that Mithun herd has a substantial genetic variability for growth traits and therefore there is ample scope to select for a better growth rate. Here, we conclude that Month 12 (M12) and Month 9 (M9) body weights exhibit higher heritability, indicating potential for genetic improvement through selective breeding.
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Affiliation(s)
- Harshit Kumar
- ICAR - National Research Centre on Mithun, 797106, Medziphema, Nagaland, India
| | - Ashish Yadav
- ICAR - National Dairy Research Institute, 132001, Karnal, Haryana, India
| | | | - L Sunitibala Devi
- ICAR - National Research Centre on Mithun, 797106, Medziphema, Nagaland, India
| | - Kobu Khate
- ICAR - National Research Centre on Mithun, 797106, Medziphema, Nagaland, India
| | - Girish P S
- ICAR - National Research Centre on Mithun, 797106, Medziphema, Nagaland, India.
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Rehman SU, Zhen Y, Ding L, Saleh AA, Zhang Y, Zhang J, He F, Husien HM, Zhou P, Wang M. Integrative Meta-Analysis: Unveiling Genetic Factors in Meat Sheep Growth and Muscular Development through QTL and Transcriptome Studies. Animals (Basel) 2024; 14:1679. [PMID: 38891726 PMCID: PMC11171046 DOI: 10.3390/ani14111679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
OBJECTIVE The study aimed to investigate the effects of castration on performance, carcass characteristics, and meat quality in sheep, as well as explore the expression of key genes related to metabolic pathways and muscle growth following castration. METHODS A meta-analysis approach was utilized to analyze data from multiple studies to compare the performance, carcass characteristics, and meat quality of castrated sheep (wethers) with intact rams. Additionally, protein-protein interaction (PPI) networks, differential gene expression (DEG) interactions, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify molecular mechanisms associated with fat metabolism and muscle development in sheep tails. RESULTS The analysis revealed that castrated sheep (wethers) exhibited improved average daily gain, increased tenderness, lower backfat thickness, and a tendency for greater loin muscle area compared to intact rams. This suggests that castration promotes faster growth and results in leaner carcasses with potentially higher muscle content. Furthermore, the identification of downregulated DEGs like ACLY, SLC27A2, and COL1A1 and upregulated DEGs such as HOXA9, PGM2L1, and ABAT provides insights into the molecular mechanisms underlying fat deposition and muscle development in sheep. CONCLUSIONS The findings support the practice of castration in sheep production as it enhances growth performance, leads to leaner carcasses with higher muscle content, and improves meat tenderness. The identified changes in gene expression offer valuable insights for further research into understanding the impact of castration on muscle development and fat metabolism in sheep. This meta-analysis contributes to the knowledge of molecular mechanisms involved in fat deposition in sheep, opening avenues for future investigations in livestock fat metabolism research.
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Affiliation(s)
- Shahab Ur Rehman
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Yongkang Zhen
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Luoyang Ding
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
- Animal and Fish Production Department, Faculty of Agriculture (Al-Shatby), Alexandria University, Alexandria City 11865, Egypt
| | - Yifan Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Jinying Zhang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Feiyang He
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Hosameldeen Mohamed Husien
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
| | - Mengzhi Wang
- Laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (S.U.R.); (L.D.); (F.H.)
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
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Sun Y, Wang Y, Li Y, Li H, Wang C, Zhang Q. Comparative transcriptome and proteome analyses of the longissimus dorsi muscle for explaining the difference between donkey meat and other meats. Anim Biotechnol 2023; 34:3085-3098. [PMID: 36271875 DOI: 10.1080/10495398.2022.2134883] [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
Domestic donkeys (Equus asinus) have been maintained mainly for service purposes in the past. Nowadays, there is an increasing interest in donkey milk and meat production in several countries, including China. Donkey meat is highly consumed because of its nutritional value and unique flavor. However, genomic studies on donkey meat are limited. Therefore, in this study, we aimed to examine the molecular difference of longissimus dorsi muscles of donkey, cow, and goat. RNA sequencing and Proteome sequencing technology were used to analyze the transcriptome and proteome of the longissimus dorsi muscle of donkey, cow, and goat. A total of 1338 and 1780 differentially expressed genes (DEGs) were identified in donkey meat compared with that in cow and goat meat, respectively. Most of the DEGs were involved in biological processes, including small GTPase-mediated signal transduction, protein ubiquitination, protein glycosylation, and MAP kinase tyrosine/serine/threonine phosphatase activity. Additionally, 764 and 1024 differentially expressed proteins (DEPs) were identified in cow vs. donkey, and goat vs. donkey, respectively; these DEPs were mainly involved in metabolism. Genetic variation and regulatory factors can combine as a database to provide more valuable molecular information for further analysis.
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Affiliation(s)
- Yan Sun
- Shandong Provincial Key Laboratory of Animal Biotochnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Yonghui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yuhua Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotochnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
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Chung Y, Jang SS, Kang DH, Kim YK, Kim HJ, Chung KY, Choi I, Lee SH. Identification of potential biomarkers associated with meat tenderness in Hanwoo (Korean cattle): An expression quantitative trait loci analysis. Anim Genet 2023; 54:786-791. [PMID: 37828654 DOI: 10.1111/age.13360] [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: 08/29/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023]
Abstract
Meat tenderness is considered the most important trait contributing to beef quality, level of consumer satisfaction, willingness to pay premium prices and industry profit. Genomic selection method would be helpful for genetic improvement of traits with low heritability and that are difficult to measure. The identification of core genes can aid genomic selection for complex traits with low heritability that are difficult to measure. We performed statistical analysis of associations between longissimus dorsi muscle tenderness and gene expression in 20 Hanwoo cattle, using Warner-Bratzler shear force and RNAseq data, respectively. We found a total of 166 core genes, from which six (ASAP1, CAPN5, ELN, SUMF2, TTC8 and MGAT4A) were regulated by 16 cis-expression quantitative trait loci (eQTL) SNPs. Notably, we found that a cis-eQTL SNP of the ELN gene contained an MFZ-1 binding site in its putative promoter region. These findings provide useful information for genomic prediction of beef tenderness in Hanwoo cattle.
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Affiliation(s)
- Yoonji Chung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
| | - Sun Sik Jang
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, South Korea
| | - Dong Hun Kang
- Department of Beef Science, Korea National University of Agriculture and Fisheries, Wanju, South Korea
| | - Yeong Kuk Kim
- Quantomic Research and Solution, Daejeon, South Korea
| | - Hyun Joo Kim
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang, South Korea
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Ki Yong Chung
- Department of Beef Science, Korea National University of Agriculture and Fisheries, Wanju, South Korea
| | - Inchul Choi
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, South Korea
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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Pezeshkian Z, Mirhoseini SZ, Ghovvati S, Ebrahimie E. Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys. Animals (Basel) 2022; 12:1240. [PMID: 35625086 PMCID: PMC9138110 DOI: 10.3390/ani12101240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
Feed efficiency is important due to the high cost of food, which accounts for about 70% of the total cost of a turkey breeding system. Native poultry are an important genetic resource in poultry breeding programs. This study aimed to conduct a global transcriptome analysis of native male turkeys which have been phenotyped for high and low feed efficiency. Feed efficiency traits were recorded during the experimental period. After slaughter, the three most efficient and three least efficient male turkeys were selected for RNA-Seq analysis. A total of 365 genes with different expressions in muscle tissue were identified between turkeys with a high feed efficiency compared to turkeys with a low feed efficiency. In the pathway analysis of up-regulated genes, major pathways included the "metabolism of glycine, serine, and threonine"; the "adipocytokine signaling pathway" and the "biosynthesis of amino acids". In the pathway analysis of down-regulated genes, the major pathways included "dorso-ventral axis formation" and "actin cytoskeleton regulation". In addition, gene set enrichment analyses were performed, which showed that high feed efficiency birds exhibit an increased expression of genes related to the biosynthesis of amino acids and low feed efficiency birds an increased expression of genes related to the immune response. Furthermore, functional analysis and protein network interaction analysis revealed that genes including GATM, PSAT1, PSPH, PHGDH, VCAM1, CD44, KRAS, SRC, CAV3, NEDD9, and PTPRQ were key genes for feed efficiency. These key genes may be good potential candidates for biomarkers of feed efficiency in genetic selection in turkeys.
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Affiliation(s)
- Zahra Pezeshkian
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht 41635-1314, Guilan, Iran; (Z.P.); (S.G.)
| | - Seyed Ziaeddin Mirhoseini
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht 41635-1314, Guilan, Iran; (Z.P.); (S.G.)
| | - Shahrokh Ghovvati
- Department of Animal Sciences, Faculty of Agriculture, University of Guilan, Rasht 41635-1314, Guilan, Iran; (Z.P.); (S.G.)
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, SA 5371, Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Ma J, Zhang T, Wang W, Chen Y, Cai W, Zhu B, Xu L, Gao H, Zhang L, Li J, Gao X. Comparative Transcriptome Analyses of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation. Front Genet 2022; 12:778788. [PMID: 35087567 PMCID: PMC8789257 DOI: 10.3389/fgene.2021.778788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Gayal and yak are well adapted to their local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analyses were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3,020 and 1,995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expressed regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found that UQCRC1 and COX5A are the shared differentially expressed hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differential hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expressed hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expressed hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Junya Li
- *Correspondence: Junya Li, ; Xue Gao,
| | - Xue Gao
- *Correspondence: Junya Li, ; Xue Gao,
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10
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Fraik AK, Margres MJ, Epstein B, Barbosa S, Jones M, Hendricks S, Schönfeld B, Stahlke AR, Veillet A, Hamede R, McCallum H, Lopez-Contreras E, Kallinen SJ, Hohenlohe PA, Kelley JL, Storfer A. Disease swamps molecular signatures of genetic-environmental associations to abiotic factors in Tasmanian devil (Sarcophilus harrisii) populations. Evolution 2020; 74:1392-1408. [PMID: 32445281 DOI: 10.1111/evo.14023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
Abstract
Landscape genomics studies focus on identifying candidate genes under selection via spatial variation in abiotic environmental variables, but rarely by biotic factors (i.e., disease). The Tasmanian devil (Sarcophilus harrisii) is found only on the environmentally heterogeneous island of Tasmania and is threatened with extinction by a transmissible cancer, devil facial tumor disease (DFTD). Devils persist in regions of long-term infection despite epidemiological model predictions of species' extinction, suggesting possible adaptation to DFTD. Here, we test the extent to which spatial variation and genetic diversity are associated with the abiotic environment (i.e., climatic variables, elevation, vegetation cover) and/or DFTD. We employ genetic-environment association analyses using 6886 SNPs from 3287 individuals sampled pre- and post-disease arrival across the devil's geographic range. Pre-disease, we find significant correlations of allele frequencies with environmental variables, including 365 unique loci linked to 71 genes, suggesting local adaptation to abiotic environment. The majority of candidate loci detected pre-DFTD are not detected post-DFTD arrival. Several post-DFTD candidate loci are associated with disease prevalence and were in linkage disequilibrium with genes involved in tumor suppression and immune response. Loss of apparent signal of abiotic local adaptation post-disease suggests swamping by strong selection resulting from the rapid onset of DFTD.
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Affiliation(s)
- Alexandra K Fraik
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Mark J Margres
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164.,Plant Biology, University of Minnesota, Minneapolis, Minnesota, 55455
| | - Soraia Barbosa
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Menna Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Sarah Hendricks
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Barbara Schönfeld
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Amanda R Stahlke
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Anne Veillet
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Rodrigo Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Hamish McCallum
- School of Environment, Griffith University Nathan, Nathan, QLD, 4111, Australia
| | - Elisa Lopez-Contreras
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Samantha J Kallinen
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Paul A Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Drive, Moscow, Idaho, 83844
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164
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11
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Liu S, Yue T, Ahmad MJ, Hu X, Zhang X, Deng T, Hu Y, He C, Zhou Y, Yang L. Transcriptome Analysis Reveals Potential Regulatory Genes Related to Heat Tolerance in Holstein Dairy Cattle. Genes (Basel) 2020; 11:genes11010068. [PMID: 31936116 PMCID: PMC7017222 DOI: 10.3390/genes11010068] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/24/2019] [Accepted: 01/03/2020] [Indexed: 01/08/2023] Open
Abstract
Heat stress affects the physiology and production performance of Chinese Holstein dairy cows. As such, the selection of heat tolerance in cows and elucidating its underlying mechanisms are vital to the dairy industry. This study aimed to investigate the heat tolerance associated genes and molecular mechanisms in Chinese Holstein dairy cows using a high-throughput sequencing approach and bioinformatics analysis. Heat-induced physiological indicators and milk yield changes were assessed to determine heat tolerance levels in Chinese Holstein dairy cows by Principal Component Analysis method following Membership Function Value Analysis. Results indicated that rectal temperature (RT), respiratory rate (RR), and decline in milk production were significantly lower (p < 0.05) in heat tolerant (HT) cows while plasma levels of heat shock protein (HSP: HSP70, HSP90), and cortisol were significantly higher (p < 0.05) when compared to non-heat tolerant (NHT) Chinese Holstein dairy cows. By applying RNA-Seq analysis, we identified 200 (81 down-regulated and 119 up-regulated) significantly (|log2fold change| ≥ 1.4 and p ≤ 0.05) differentially expressed genes (DEGs) in HT versus NHT Chinese Holstein dairy cows. In addition, 14 of which were involved in protein–protein interaction (PPI) network. Importantly, several hub genes (OAS2, MX2, IFIT5 and TGFB2) were significantly enriched in immune effector process. These findings might be helpful to expedite the understanding for the mechanism of heat tolerance in Chinese Holstein dairy cows.
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Affiliation(s)
- Shenhe Liu
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Tingting Yue
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Muhammad Jamil Ahmad
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Xiangwei Hu
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Xinxin Zhang
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China;
| | - Yan Hu
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Changjiu He
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Yang Zhou
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
| | - Liguo Yang
- Ministry of Education, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (S.L.); (T.Y.); (M.J.A.); (X.H.); (X.Z.); (Y.H.); (C.H.); (Y.Z.)
- Correspondence:
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12
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Grajales SMB, Zuluaga JJE, Herrera AL, Osorio NR, Vergara DMB. RNA-seq differential gene expression analysis in mammary tissue from lactating dairy cows supplemented with sunflower oil. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an19107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Context
Nutrition is the main environmental factor that regulates the composition and secretion of milk fat. For this reason, supplementation of ruminant feed with lipid sources is proposed as a strategy to improve the milk fatty acid profile. However, incorporation of these compounds in milk depends not only on the structure of the diet but also on the efficient capture of nutrients by the mammary tissue and the coordination in the expression and regulation of multiple genes.
Aim
To evaluate the effect of supplementation with sunflower oil, on gene expression in the mammary gland of Holstein cows under grazing and in the first third of lactation, by using RNA sequencing technology.
Methods
Six Holstein cows were divided into two groups: a control group, and a group supplemented with 700 g/day of sunflower oil (unsaturated fatty acid) for 25 days. On the last day, a sample of mammary tissue was taken for RNA-seq analysis. Raw data were analysed by using the CLC Genomics Workbench software.
Key results
Milk protein genes CSN1S1, CSN2, PAEP (LGB), CSN3, CSN1S2 and LALBA were the most abundant in all samples. In the supplemented group, 13 genes were differentially expressed with a false discovery rate <0.15 of which six were upregulated (PRSS2, BEST3, LOC618633, ASB5, NTS and C2CD4B) and seven downregulated (BOLA, DEFB, CLIC6, ATP6V1B1, DCHS2, EYA4 and CYP4B1). These were related to immune-response processes, cell differentiation and membrane transport.
Conclusions
Supplementation with sunflower oil affects metabolism and other cellular functions in mammary tissue, influencing the expression of genes associated with lipid metabolism, and genes involved in cell–cell interactions, cell morphology, cell death and immune response.
Implications
These results help to highlight the mechanisms underlying in vivo responses to dietary factors such as supplementation with seed oil in lactating cows. This will serve as a basis for the future development of strategies that improve the fatty acid profile of milk.
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Mukherjee S, Cai Z, Mukherjee A, Longkumer I, Mech M, Vupru K, Khate K, Rajkhowa C, Mitra A, Guldbrandtsen B, Lund MS, Sahana G. Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). BMC Genomics 2019; 20:617. [PMID: 31357931 PMCID: PMC6664528 DOI: 10.1186/s12864-019-5980-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun. RESULTS We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle. CONCLUSION Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.
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Affiliation(s)
- Sabyasachi Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Anupama Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
- Present address: Dairy Cattle Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Imsusosang Longkumer
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Moonmoon Mech
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Kezhavituo Vupru
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Kobu Khate
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Chandan Rajkhowa
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Abhijit Mitra
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
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