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Li W, Wu X, Xiang D, Zhang W, Wu L, Meng X, Huo J, Yin Z, Fu G, Zhao G. Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing. Genes (Basel) 2024; 15:233. [PMID: 38397222 PMCID: PMC10887577 DOI: 10.3390/genes15020233] [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: 01/16/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.
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Affiliation(s)
- Wenjun Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xudong Wu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Decai Xiang
- Institute of Pig and Animal Research, Yunnan Academy of Animal Husbandry and Veterinary Science, Kunming 650201, China;
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230036, China; (X.W.); (W.Z.)
| | - Lingxiang Wu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Xintong Meng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Guowen Fu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
| | - Guiying Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (L.W.); (X.M.); (J.H.); (G.F.)
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Choudhury MP, Wang Z, Zhu M, Teng S, Yan J, Cao S, Yi G, Liu Y, Liao Y, Tang Z. Genome-Wide Detection of Copy Number Variations Associated with Miniature Features in Horses. Genes (Basel) 2023; 14:1934. [PMID: 37895283 PMCID: PMC10606273 DOI: 10.3390/genes14101934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Copy number variations (CNVs) are crucial structural genomic variants affecting complex traits in humans and livestock animals. The current study was designed to conduct a comprehensive comparative copy number variation analysis among three breeds, Debao (DB), Baise (BS), and Warmblood (WB), with a specific focus on identifying genomic regions associated with miniature features in horses. Using whole-genome next-generation resequencing data, we identified 18,974 CNVs across 31 autosomes. Among the breeds, we found 4279 breed-specific CNV regions (CNVRs). Baise, Debao, and Warmblood displayed 2978, 986, and 895 distinct CNVRs, respectively, with 202 CNVRs shared across all three breeds. After removing duplicates, we obtained 1545 CNVRs from 26 horse genomes. Functional annotation reveals enrichment in biological functions, including antigen processing, cell metabolism, olfactory conduction, and nervous system development. Debao horses have 970 genes overlapping with CNVRs, possibly causing their small size and mountainous adaptations. We also found that the genes GHR, SOX9, and SOX11 may be responsible for the miniature features of the Debao horse by analyzing their overlapping CNVRs. Overall, this study offers valuable insights into the widespread presence of CNVs in the horse genome. The findings contribute to mapping horse CNVs and advance research on unique miniature traits observed in the Debao horse.
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Affiliation(s)
- Md. Panir Choudhury
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Bangladesh Livestock Research Institute, Ministry of Fisheries and Livestock, Savar, Dhaka 1341, Bangladesh
| | - Zihao Wang
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Min Zhu
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Shaohua Teng
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Jing Yan
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Shuwei Cao
- Animal Husbandry Research Institute, Guangxi Vocational University of Agriculture, Nanning 530002,China; (Z.W.); (M.Z.); (S.T.); (J.Y.); (S.C.)
| | - Guoqiang Yi
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuying Liao
- Guangxi Veterinary Research Institute, Nanning 530001, China
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 518124, China; (M.P.C.); (G.Y.); (Y.L.)
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Wen X, Luo S, Lv D, Jia C, Zhou X, Zhai Q, Xi L, Yang C. Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses. Front Vet Sci 2022; 9:920080. [PMID: 35968025 PMCID: PMC9366519 DOI: 10.3389/fvets.2022.920080] [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: 04/14/2022] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional prediction analysis. The alpha diversity analysis showed that Thoroughbred horses had a more abundant and diverse gut microbiota, while the diversity of gut microbiota in Hybrid horses was intermediate between Thoroughbred and Mongolian horses. Subsequent cluster analysis showed that Hybrid horses have a microbiota composition more similar to Mongolian horses. LEfSe analysis revealed that the bacterial biomarkers for Thoroughbred horses at the family level were Prevotellaceae, Rikenellaceae, Fibrobacteraceae, p_251_o5, Lactobacillaceae, and uncultured_bacterium_o_WCHB1_41; the bacterial biomarker for Mongolian horses was Planococcaceae; and the bacterial biomarkers for Hybrid horses were Moraxellaceae, Enterobacteriaceae, and Ruminococcaceae. The functional prediction results indicated that the metabolic pathways differ significantly between the breeds. Regarding metabolism, the Hybrid horses had the lowest proportion of the carbohydrate metabolic pathways, while the energy metabolic pathway had the highest proportion. The abundance ratios of the remaining eight metabolic pathways in Hybrid horses were between Thoroughbred and Mongolian horses. In conclusion, the results of this study showed an association between horse breeds and gut microbiota.
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Affiliation(s)
- Xiaohui Wen
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shengjun Luo
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dianhong Lv
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunling Jia
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiurong Zhou
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qi Zhai
- Institute of Animal Health, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Li Xi
- Department of Animal Science, College of Biology and Food, Shangqiu Normal University, Shangqiu, China
- *Correspondence: Li Xi
| | - Caijuan Yang
- National S&T Innovation Center for Modern Agricultural Industry, Guangzhou, China
- Caijuan Yang
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