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Tecku PKM, Zhao Z, Wang K, Ji X, Chen D, Shen Q, Yu Y, Cui S, Wang J, Chen Z, Xue J, Tang G. Transcriptomic and Proteomic Analyses of the Liver and Ileum Identify Key Genes and Pathways Associated with Low and High Groups of Social Genetic Effect of Residual Feed Intake. Animals (Basel) 2025; 15:1345. [PMID: 40362160 PMCID: PMC12070873 DOI: 10.3390/ani15091345] [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: 03/24/2025] [Revised: 04/28/2025] [Accepted: 04/29/2025] [Indexed: 05/15/2025] Open
Abstract
Social genetic effects (SGEs) refer to how the genotypes of other individuals impact an individual's phenotype within a population. These effects significantly influence the feeding behavior and production performance in pigs, though their mechanisms are not well understood. This study examined two pig groups with extreme SGE values for residual feed intake (RFI), analyzing their feeding behavior and the molecular mechanisms involved using transcriptomics and proteomics analysis of liver and ileum tissues. Pigs with higher SGE values exhibited distinct feeding patterns, spending more time at the feeder but making fewer visits. They consumed less overall feed but had a higher intake per visit. Differentially expressed genes and proteins were identified in the liver and ileum and were associated with processes such as mitochondrial functions, oxidative phosphorylation, and cholesterol metabolism. Integrated analysis supported these findings. Combined transcriptome and proteome analysis identified potential key genes that were associated with processes including mitochondrial processes, oxidative phosphorylation, fat digestion and absorption, and cholesterol metabolism. The results showed that pigs with differing SGE values display different feeding behaviors and utilize distinct molecular pathways affecting RFI. These findings offer valuable insights into how SGEs influence feed efficiency and shed light on the fundamental mechanisms underlying it.
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Affiliation(s)
- Patrick Kofi Makafui Tecku
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenjian Zhao
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Wang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Digital Intelligent Breeding Technology Innovation for Swine and Poultry, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd., Chengdu 610023, China
| | - Xiang Ji
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Dong Chen
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Shen
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Yu
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengdi Cui
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Junge Wang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyang Chen
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia Xue
- Chengdu Animal Disease Prevention and Control Center, Chengdu 610041, China;
| | - Guoqing Tang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (P.K.M.T.); (Z.Z.); (K.W.); (X.J.); (D.C.); (Q.S.); (Y.Y.); (S.C.); (J.W.); (Z.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Cai B, Kang Y, Ding Z, Guo S, Cao M, Hu L, Zhang B, Wang X, Pei J, Ge Q, Xiong L, Wu X, Guo X. Genomic Characterization of Crossbred-Driven Adaptation in the Endangered Yangba Cattle of China. Animals (Basel) 2025; 15:1065. [PMID: 40218458 PMCID: PMC11987921 DOI: 10.3390/ani15071065] [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: 02/24/2025] [Revised: 03/26/2025] [Accepted: 04/04/2025] [Indexed: 04/14/2025] Open
Abstract
This study unveils the unique origins, evolution, and genetic variations of the Yangba cattle, an endangered breed in China, through a comparative genomic analysis involving 202 individuals from 21 domestic and international breeds. Genetic component analysis revealed that the Yangba cattle comprise four ancestral lineages: Eurasian taurine (18%), East Asian taurine (26%), Chinese indicine (39%), and Indian indicine (17%). Their high genetic diversity and low inbreeding coefficient set them apart significantly from mainstream commercial breeds. Gene introgression analysis indicated that the influx of genetic material from East Asian taurine has enhanced the Yangba cattle's adaptability to environmental stress, while the introgression from Chinese indicine has endowed them with unique advantages in muscle development and tissue repair. A genome-wide selection scan identified strong positive selection signals for genes such as ABCC2, which is involved in immune regulation, and NCOA3, which plays a role in growth regulation, in the Yangba cattle. This study systematically elucidates, for the first time, the composite ancestral composition and mechanisms of adaptive evolution in Yangba cattle. These findings offer critical insights into the conservation and sustainable utilization of endangered cattle resources and underscore the importance of implementing effective breeding programs.
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Affiliation(s)
- Bao Cai
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Yandong Kang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Shaoke Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Mengli Cao
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Liyan Hu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Ben Zhang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Xingdong Wang
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
| | - Jie Pei
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Qianyun Ge
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (B.C.); (Y.K.); (Z.D.); (S.G.); (M.C.); (L.H.); (B.Z.); (X.W.); (J.P.); (Q.G.); (L.X.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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Wang Q, Lu Y, Li M, Gao Z, Li D, Gao Y, Deng W, Wu J. Leveraging Whole-Genome Resequencing to Uncover Genetic Diversity and Promote Conservation Strategies for Ruminants in Asia. Animals (Basel) 2025; 15:831. [PMID: 40150358 PMCID: PMC11939356 DOI: 10.3390/ani15060831] [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: 01/24/2025] [Revised: 02/28/2025] [Accepted: 03/12/2025] [Indexed: 03/29/2025] Open
Abstract
Whole-genome resequencing (WGRS) is a critical branch of whole-genome sequencing (WGS), primarily targeting species with existing reference genomes. By aligning sequencing data to the reference genome, WGRS enables precise detection of genetic variations in individuals or populations. As a core technology in genomic research, WGS holds profound significance in ruminant studies. It not only reveals the intricate structure of ruminant genomes but also provides essential data for deciphering gene function, variation patterns, and evolutionary processes, thereby advancing the exploration of ruminant genetic mechanisms. However, WGS still faces several challenges, such as incomplete and inaccurate genome assembly, as well as the incomplete annotation of numerous unknown genes or gene functions. Although WGS can identify a vast number of genomic variations, the specific relationships between these variations and phenotypes often remain unclear, which limits its potential in functional studies and breeding applications. By performing WGRS on multiple samples, these assembly challenges can be effectively addressed, particularly in regions with high repeat content or complex structural variations. WGRS can accurately identify subtle variations among different individuals or populations and further elucidate their associations with specific traits, thereby overcoming the limitations of WGS and providing more precise genetic information for functional research and breeding applications. This review systematically summarizes the latest applications of WGRS in the analysis of ruminant genetic structures, genetic diversity, economic traits, and adaptive traits, while also discussing the challenges faced by this technology. It aims to provide a scientific foundation for the improvement and conservation of ruminant genetic resources.
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Affiliation(s)
| | | | | | | | | | | | - Weidong Deng
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China (Y.L.); (M.L.); (Z.G.); (D.L.); (Y.G.)
| | - Jiao Wu
- Yunnan Provincial Key Laboratory of Animal Nutrition and Feed, Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China (Y.L.); (M.L.); (Z.G.); (D.L.); (Y.G.)
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Cheng H, Lyu Y, Liu Z, Li C, Qu K, Li S, Ahmed Z, Ma W, Qi X, Chen N, Lei C. A Whole-Genome Scan Revealed Genomic Features and Selection Footprints of Mengshan Cattle. Genes (Basel) 2024; 15:1113. [PMID: 39336704 PMCID: PMC11431585 DOI: 10.3390/genes15091113] [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: 07/29/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
(1) Background: Mengshan cattle from the Yimeng mountainous region in China stand out as a unique genetic resource, known for their adaptive traits and environmental resilience. However, these cattle are currently endangered and comprehensive genomic characterization remains largely unexplored. This study aims to address this gap by investigating the genomic features and selection signals in Mengshan cattle. (2) Methods: Utilizing whole-genome resequencing data from 122 cattle, including 37 newly sequenced Mengshan cattle, we investigated population structure, genetic diversity, and selection signals. (3) Results: Our analyses revealed that current Mengshan cattle primarily exhibit European taurine cattle ancestry, with distinct genetic characteristics indicative of adaptive traits. We identified candidate genes associated with immune response, growth traits, meat quality, and neurodevelopment, shedding light on the genomic features underlying the unique attributes of Mengshan cattle. Enrichment analysis highlighted pathways related to insulin secretion, calcium signaling, and dopamine synapse, further elucidating the genetic basis of their phenotypic traits. (4) Conclusions: Our results provide valuable insights for further research and conservation efforts aimed at preserving this endangered genetic resource. This study enhances the understanding of population genetics and underscores the importance of genomic research in informing genetic resources and conservation initiatives for indigenous cattle breeds.
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Affiliation(s)
- Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
- Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
| | - Ziao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
| | - Chuanqing Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675099, China;
| | - Shuang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot 12350, Pakistan;
| | - Weidong Ma
- Shaanxi Province Agriculture & Husbandry Breeding Farm, Baoji 722203, China;
| | - Xingshan Qi
- Animal Husbandry Bureau in Biyang County, Zhumadian 463700, China;
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (H.C.); (Y.L.); (Z.L.); (C.L.); (S.L.); (N.C.)
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Hu M, Shi L, Yi W, Li F, Yan S. Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data. Anim Biosci 2024; 37:461-470. [PMID: 38271971 PMCID: PMC10915192 DOI: 10.5713/ab.23.0304] [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: 08/15/2023] [Revised: 10/13/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. METHODS To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. RESULTS The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. CONCLUSION In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.
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Affiliation(s)
- Mingyue Hu
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Lulu Shi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Wenfeng Yi
- Department of Animal Science, Jilin University, Changchun 130062,
China
| | - Feng Li
- Shandong Binzhou Animal Science & Veterinary Medicine Academy, Binzhou, 256600,
China
| | - Shouqing Yan
- Department of Animal Science, Jilin University, Changchun 130062,
China
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Chen J, Zhang L, Gao L, Wei Z, Dang D, Yang L. Population Structure and Genetic Diversity of Yunling Cattle Determined by Whole-Genome Resequencing. Genes (Basel) 2023; 14:2141. [PMID: 38136963 PMCID: PMC10742670 DOI: 10.3390/genes14122141] [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: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
The Yunling cattle breed, a three-breed crossbreed, which comprises 50% Brahman cattle, 25% Murray Grey cattle and 25% Yunnan Yellow cattle, has several advantageous traits, including rapid growth, superior meat quality, ability to improve tolerance in hot and humid climates, tick resistance and rough feed. It can be rightfully stated that Yunling cattle serve as vital genetic repositories of the local Yunnan cattle. Gaining insights into the genetic information of Yunling cattle plays a significant role in the formulation of sound breeding strategies for this breed, safeguarding genetic resources and mitigating the risks associated with inbreeding depression. In this study, we constructed the Yunling cattle standard reference genome and aligned the whole genomes of 129 Yunling cattle individuals to the constructed reference genome to estimate the current genetic status of Yunling cattle in Yunnan Province, China. The average alignment rate and the average percentage of properly paired are both 99.72%. The average nucleotide diversity in Yunling cattle is 0.000166, which indicates a lower level of diversity. Population structure analysis classified Yunling cattle into two subgroups. Inbreeding analysis revealed that inbreeding events did occur in the Yunling cattle, which may have contributed to the low genetic diversity observed. This study presents a comprehensive assessment of the genetic structure and diversity among the Yunling cattle and provides a theoretical foundation for the preservation and exploitation of these precious germplasm resources.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Lilian Zhang
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Lutao Gao
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Zaichao Wei
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
- School of Data Science, Baoshan University, Baoshan 678000, China
| | - Dong Dang
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
| | - Linnan Yang
- State Key Laboratory of Agricultural Big Data, Academy of Big Data, Yunnan Agricultural University, Kunming 655508, China (Z.W.)
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Hu M, Yi W, Liu Z, Lai W, Shi L, Ren Y, Li F, Yan S. Assessing the current genetic status of Lubei white goat based on the whole-genome data. Anim Genet 2023. [PMID: 37015738 DOI: 10.1111/age.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023]
Affiliation(s)
- Mingyue Hu
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, 130062, China
| | - Yanling Ren
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, 256600, China
| | - Feng Li
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, 256600, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, 130062, China
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Ma X, Cheng H, Liu Y, Sun L, Chen N, Jiang F, You W, Yang Z, Zhang B, Song E, Lei C. Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12050665. [PMID: 35268233 PMCID: PMC8909316 DOI: 10.3390/ani12050665] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/16/2022] [Accepted: 03/05/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Bohai Black cattle are one of the indigenous black coat cattle breeds in China, which are famous for their excellent meat quality. Whole-genome sequencing technology has been extensively developed to study species genome genetic diversity, population structure, selection pressure, demographic events, etc. However, a limited number of studies have reported genomic diversity and selection pressures in Bohai Black cattle. The purpose of this study is to analyze population structure and genomic differences between Bohai Black cattle and five “core” cattle populations from all over the world, mainly oriented on the identification of selection signatures using whole-genome sequencing data. In addition, we identify a series of candidate genes that can potentially be related to black coat color, meat quality, immunity, and reproduction in this breed. This study provides valuable genomic resources and theoretical basis for the future breeding of Bohai Black cattle. Abstract Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.
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Affiliation(s)
- Xiaohui Ma
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Haijian Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
| | - Yangkai Liu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Luyang Sun
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Fugui Jiang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
| | - Wei You
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
| | - Zhangang Yang
- HuaXing Bohai Black Cattle Co., Ltd., Binzhou 256600, China;
| | - Baoheng Zhang
- Wudi Animal Husbandry and Veterinary Service Management Center of Binzhou City, Binzhou 256600, China;
| | - Enliang Song
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
- Correspondence: (E.S.); (C.L.); Tel.: +86-138-6415-6955 (E.S.); +86-135-7299-2159 (C.L.)
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
- Correspondence: (E.S.); (C.L.); Tel.: +86-138-6415-6955 (E.S.); +86-135-7299-2159 (C.L.)
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