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Luo J, Min Q, Sun X, Guo X, Song M, Zeng X, Guo J, Zhang H, Han Y, Li L. Comparative Whole-Genome Analysis of Production Traits and Genetic Structure in Baiyu and Chuanzhong Black Goats. Animals (Basel) 2024; 14:3616. [PMID: 39765520 PMCID: PMC11672699 DOI: 10.3390/ani14243616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Revised: 12/10/2024] [Accepted: 12/13/2024] [Indexed: 01/11/2025] Open
Abstract
Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. This study aimed to systematically elucidate the differences in production performance and genetic traits between Baiyu black goats and Chuanzhong black goats. We quantified growth and reproductive attributes for both breeds. Furthermore, we conducted a comprehensive analysis of genetic diversity, population structure, and selection signatures using whole-genome resequencing data. This dataset included 30 individuals from the Baiyu black goat breed, 41 from the Chuanzhong black goat breed, and an additional 59 individuals representing Chengdu grey goats, Tibetan cashmere goats, and Jianchang black goats, totaling 130 individuals across five goat breeds. The comparative analysis of production performance revealed that the weight and body size of Chuanzhong black goats were significantly higher than those of Baiyu black goats (p < 0.01). At the same time, the average kidding rate and kid-weaning survival rate of Chuanzhong black goats were also notably superior to those of Baiyu black goats (p < 0.01). The Baiyu black goats exhibited a more abundant genetic diversity and distinct genetic differences compared to the Chuanzhong black goat, according to an analysis grounded on genomic variation. The Baiyu black goats are more closely related to Tibetan cashmere goats, whereas Chuanzhong black goats share a closer genetic relationship with Chengdu grey goats. Additionally, we employed the π, Fst, and XP-EHH methodologies to identify genes related to immunity (TRIM10, TRIM15, TRIM26, and TRIM5), neurodevelopment (FOXD4L1, PCDHB14, PCDHB4, PCDHB5, PCDHB6, and PCDHB7), reproduction (BTNL2 and GABBR1), body size (NCAPG, IBSP, and MKNK1), and meat quality traits (SUCLG2 and PGM5). These results provide a theoretical basis for further resource conservation and breeding improvement of the Baiyu black goat and Chuanzhong black goat.
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Affiliation(s)
- Jing Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Qi Min
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Xueliang Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Xinyu Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Meijun Song
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Xuehui Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
| | - Yanguo Han
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.L.); (Q.M.); (X.S.); (X.G.); (M.S.); (X.Z.); (J.G.); (H.Z.)
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Ogweng P, Bowden CF, Smyser TJ, Muwanika VB, Piaggio AJ, Masembe C. Ancestry and genome-wide association study of domestic pigs that survive African swine fever in Uganda. Trop Anim Health Prod 2024; 56:366. [PMID: 39467944 PMCID: PMC11519200 DOI: 10.1007/s11250-024-04195-5] [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: 05/06/2024] [Accepted: 09/17/2024] [Indexed: 10/30/2024]
Abstract
African swine fever (ASF) is endemic to Uganda and causes annual outbreaks. Some pigs survive these outbreaks and remain asymptomatic but are African swine fever virus (ASFV) positive. The potential heritability and genetic disparities in disease susceptibility among Ugandan pigs are not fully understood. In a 12-year study, whole blood and tissue samples were collected from 212 pigs across 19 districts in Uganda. Polymerase chain reaction (PCR) assays were used to determine ASFV infection status and genotyping was completed using a commercial porcine array. The point prevalence of ASF was calculated for each district, and breed composition origins were quantified for the sampled pigs by implementing established ancestry analyses. Genome-wide associated studies (GWAS) were conducted using all available domestic swine samples (full study population; n = 206) as well as a reduced dataset (farm-level study population; n = 129). This study revealed a greater number of ASFV-positive pigs in border districts than in non-border districts, a high level of admixture among domestic pigs sampled from Ugandan smallholder farms, and 48 loci that were associated with ASFV infection status. The discovery of 48 significant SNPs and 28 putative candidate genes may imply the possibility of heritability for resistance to ASFV. However, additional investigations in ASFV-endemic regions are required to fully elucidate the heritability of ASFV susceptibility among surviving pigs in Uganda.
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Affiliation(s)
- Peter Ogweng
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda.
| | - Courtney F Bowden
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, 80521, USA
| | - Timothy J Smyser
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, 80521, USA
| | - Vincent B Muwanika
- Department of Environmental Management, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Antoinette J Piaggio
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, CO, 80521, USA
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
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Miao J, Wei X, Cao C, Sun J, Xu Y, Zhang Z, Wang Q, Pan Y, Wang Z. Pig pangenome graph reveals functional features of non-reference sequences. J Anim Sci Biotechnol 2024; 15:32. [PMID: 38389084 PMCID: PMC10882747 DOI: 10.1186/s40104-023-00984-4] [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: 08/29/2023] [Accepted: 12/22/2023] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. RESULTS In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs. CONCLUSIONS Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.
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Affiliation(s)
- Jian Miao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xingyu Wei
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Caiyun Cao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jiabao Sun
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yuejin Xu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Zhe Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
- Yazhou Bay Science and Technology City, Hainan Institute of Zhejiang University, Yazhou District, Building 11, Yongyou Industrial Park, Sanya, 572025, Hainan, China.
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Yang X, Li X, Bao Q, Wang Z, He S, Qu X, Tang Y, Song B, Huang J, Yi G. Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses. Genes (Basel) 2024; 15:166. [PMID: 38397156 PMCID: PMC10888464 DOI: 10.3390/genes15020166] [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: 11/20/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
In the Suidae family, warthogs show significant survival adaptability and trait specificity. This study offers a comparative genomic analysis between the warthog and other Suidae species, including the Luchuan pig, Duroc pig, and Red River hog. By integrating the four genomes with sequences from the other four species, we identified 8868 single-copy orthologous genes. Based on 8868 orthologous protein sequences, phylogenetic assessments highlighted divergence timelines and unique evolutionary branches within suid species. Warthogs exist on different evolutionary branches compared to DRCs and LCs, with a divergence time preceding that of DRC and LC. Contraction and expansion analyses of warthog gene families have been conducted to elucidate the mechanisms of their evolutionary adaptations. Using GO, KEGG, and MGI databases, warthogs showed a preference for expansion in sensory genes and contraction in metabolic genes, underscoring phenotypic diversity and adaptive evolution direction. Associating genes with the QTLdb-pigSS11 database revealed links between gene families and immunity traits. The overlap of olfactory genes in immune-related QTL regions highlighted their importance in evolutionary adaptations. This work highlights the unique evolutionary strategies and adaptive mechanisms of warthogs, guiding future research into the distinct adaptability and disease resistance in pigs, particularly focusing on traits such as resistance to African Swine Fever Virus.
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Affiliation(s)
- Xintong Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Qi Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Sang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Xiaolu Qu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Yueting Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama 547500, China
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