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Kusza S, Badaoui B, Wanjala G. Insights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity. Sci Rep 2024; 14:16515. [PMID: 39019985 PMCID: PMC11255268 DOI: 10.1038/s41598-024-67558-w] [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: 04/22/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024] Open
Abstract
Numerous studies have indicated that Morocco's indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D'man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24-48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1-6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13, and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco. Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds' genomic landscapes and adaptive mechanisms.
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Affiliation(s)
- Szilvia Kusza
- Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary.
| | - Bouabid Badaoui
- Faculty of Sciences, Centre de Biotechnologies Végétales et Microbiennes, Biodiversité et Environnement, Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI),, Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - George Wanjala
- Faculty of Agricultural and Food Sciences and Environmental Management, Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
- Doctoral School of Animal Science, University of Debrecen, Böszörményi út 138., 4032, Debrecen, Hungary
- Institute of Animal Sciences and Wildlife Management, University of Szeged, Andrássy út 15., 6800, Hódmezővásárhely, Hungary
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Hu R, Shah AM, Han Q, Ma J, Dai P, Meng Y, Peng Q, Jiang Y, Kong X, Wang Z, Zou H. Proteomics Reveals the Obstruction of Cellular ATP Synthesis in the Ruminal Epithelium of Growth-Retarded Yaks. Animals (Basel) 2024; 14:1243. [PMID: 38672391 PMCID: PMC11047487 DOI: 10.3390/ani14081243] [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: 02/17/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Growth-retarded yaks are of a high proportion on the Tibetan plateau and reduce the economic income of farmers. Our previous studies discovered a maldevelopment in the ruminal epithelium of growth-retarded yaks, but the molecular mechanisms are still unclear. This study aimed to reveal how the proteomic profile in the ruminal epithelium contributed to the growth retardation of yaks. The proteome of the ruminal epithelium was detected using a high-resolution mass spectrometer. There were 52 proteins significantly differently expressed between the ruminal epithelium of growth-retarded yaks and growth-normal yaks, with 32 downregulated and 20 upregulated in growth-retarded yaks. Functional analysis showed the differently expressed proteins involved in the synthesis and degradation of ketone bodies (p = 0.012), propanoate metabolism (p = 0.018), pyruvate metabolism (p = 0.020), and mineral absorption (p = 0.024). The protein expressions of SLC26A3 and FTH1, enriched in the mineral absorption, were significantly downregulated in growth-retarded yaks. The key enzymes ACAT2 and HMGCS2 enriched in ketone bodies synthesis and key enzyme PCCA enriched in propanoate metabolism had lower protein expressions in the ruminal epithelium of growth-retarded yaks. The ATP concentration and relative mitochondrial DNA copy number in the ruminal epithelium of growth-normal yaks were dramatically higher than those of growth-retarded yaks (p < 0.05). The activities of citrate synthase (CS), the α-ketoglutarate dehydrogenase complex (α-KGDHC), isocitrate dehydrogenase (ICD) in the tricarboxylic acid cycle (TCA), and the mitochondrial respiratory chain complex (MRCC) were significantly decreased in ruminal epithelium of growth-retarded yaks compared to growth-normal yaks (p < 0.05). The mRNA expressions of COQ9, COX4, and LDHA, which are the encoding genes in MRCC I, IV and anaerobic respiration, were also significantly decreased in the ruminal epithelium of growth-retarded yaks (p < 0.05). Correlation analysis revealed that the average daily gain (ADG) was significantly positively correlated to the relative mitochondrial DNA copy number (p < 0.01, r = 0.772) and ATP concentration (p < 0.01, r = 0.728) in the ruminal epithelium, respectively. The ruminal weight was positively correlated to the relative mitochondrial DNA copy number (p < 0.05, r = 0.631) and ATP concentration in ruminal epithelium (p < 0.01, r = 0.957), respectively. The ruminal papillae had a significant positive correlation with ATP concentration in ruminal epithelium (p < 0.01, r = 0.770). These results suggested that growth-retarded yaks had a lower VFA metabolism, ketone bodies synthesis, ion absorption, and ATP synthesis in the ruminal epithelium; it also indicated that the growth retardation of yaks is related to the obstruction of cellular ATP synthesis in rumen epithelial cells.
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Affiliation(s)
- Rui Hu
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
| | - Ali Mujtaba Shah
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (Y.J.)
| | - Qiang Han
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
| | - Jian Ma
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
| | - Peng Dai
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
| | - Yukun Meng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (Y.J.)
| | - Quanhui Peng
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
| | - Yahui Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.M.); (Y.J.)
| | - Xiangying Kong
- Haibei Demonstration Zone of Plateau Modern Ecological Animal Husbandry Science and Technology, Haibei 810299, China;
| | - Zhisheng Wang
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
| | - Huawei Zou
- Low Carbon Breeding Cattle and Safety Production University Key Laboratory of Sichuan Province, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, China; (R.H.); (A.M.S.); (Q.H.); (J.M.); (P.D.); (Q.P.); (Z.W.)
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Chai J, Liu Z, Wu J, Kang Y, Abdelsattar MM, Zhao W, Wang S, Yang S, Deng F, Li Y, Zhuang Y, Zhang N. Dietary β-hydroxybutyric acid improves the growth performance of young ruminants based on rumen microbiota and volatile fatty acid biosynthesis. Front Microbiol 2024; 14:1296116. [PMID: 38260877 PMCID: PMC10801009 DOI: 10.3389/fmicb.2023.1296116] [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: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction The ketone body β-hydroxybutyric acid (BHB) plays critical roles in cellular proliferation and metabolic fuel utilization; however, its effects on the rumen microbiota remain unknown. Methods Here, three doses of BHB (low, medium, and high) were supplemented to early-weaned goat kids. Results Compared with controls, the beneficial effects of BHB on growth and rumen development were observed in goats at 90 days of age (d). The low dose of dietary BHB increased the concentration of rumen acetate, propionate, and butyrate on d90. The sequencing results of the rumen microbiota revealed marked shifts in rumen microbial community structure after early-weaned goat kids consumed BHB for 2 months. The signature bacterial ASVs for each treatment were identified and were the main drivers contributing to microbial interactions in the rumen. The bacteria associated with rumen weight were also correlated with body weight. Some classified bacterial signatures, including Prevotella, Olsenella umbonate, and Roseburia faecis, were related to rumen volatile fatty acids and host development. Conclusion Overall, dietary BHB altered rumen microbiota and environments in young goats, which contributed to rumen development and growth.
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Affiliation(s)
- Jianmin Chai
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, NC, United States
| | - Zeyue Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Jun Wu
- Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Yuan Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Mahmoud M. Abdelsattar
- Department of Animal and Poultry Production, Faculty of Agriculture, South Valley University, Qena, Egypt
| | - Wei Zhao
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shiqin Wang
- Anhui Province Key Laboratory of Animal Nutritional Regulation and Health, College of Animal Science, Anhui Science and Technology University, Chuzhou, China
| | - Shuli Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Feilong Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
| | - Yimin Zhuang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Naifeng Zhang
- Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Institute of Feed Research of Chinese Academy of Agricultural Sciences, Beijing, China
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