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Peng W, Zhang Y, Gao L, Shi W, Liu Z, Guo X, Zhang Y, Li B, Li G, Cao J, Yang M. Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds. BMC Genomics 2024; 25:420. [PMID: 38684985 PMCID: PMC11057119 DOI: 10.1186/s12864-024-10334-x] [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: 11/29/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.
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Affiliation(s)
- Weifeng Peng
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.
| | - Yiyuan Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Wanlu Shi
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Zi Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Xinyu Guo
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Yunxia Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Bing Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Jingya Cao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Mingsheng Yang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.
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Song X, Bai Y, Yuan R, Zhu H, Lan X, Qu L. InDel and CNV within the AKAP13 Gene Revealing Strong Associations with Growth Traits in Goat. Animals (Basel) 2023; 13:2746. [PMID: 37685010 PMCID: PMC10487263 DOI: 10.3390/ani13172746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
A-kinase-anchoring protein 13 (AKAP13) is a member of the AKAP protein family that has been found to be associated with bone formation. Thus, we investigated the AKAP13 gene as a potential candidate gene for molecular-marker-assisted selection (MAS) in breeding. Our aim was to explore genetic variations (InDel and CNV) within the AKAP13 gene of Shaanbei white cashmere (SBWC) goats and analyze their relationship with growth traits. Ultimately, we identified three InDel loci (16-bp deletion, 15-bp insertion, and 25-bp deletion) and three CNVs, and the 16-bp and 15-bp loci were significantly associated with goat body length (p < 0.05). Both the 16-bp deletion variant and the 15-bp insertion variant facilitated an increase in body length in goats. In addition to this, there was a certain superposition effect between 16-bp and 15-bp loci, although there was no linkage. Additionally, the CNV1 locus was significantly correlated with body height and body length of goats (p < 0.05), and CNV2 was significantly correlated with chest depth, chest circumference, and cannon circumference of goats (p < 0.05). Individuals with gain type showed excellent growth performance. In conclusion, the InDel and CNV loci that we have identified could possibly serve as effective molecular markers in goat breeding, which is very essential for improving efficiency and success of breeding. Moreover, our findings provide a new avenue for further research into the function of the AKAP13 gene.
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Affiliation(s)
- Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Yangyang Bai
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Rongrong Yuan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (X.S.); (Y.B.); (R.Y.); (H.Z.)
- College of Life Sciences, Yulin University, Yulin 719000, China
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3
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Wang Q, Song X, Bi Y, Zhu H, Wu X, Guo Z, Liu M, Pan C. Detection distribution of CNVs of SNX29 in three goat breeds and their associations with growth traits. Front Vet Sci 2023; 10:1132833. [PMID: 37706075 PMCID: PMC10495836 DOI: 10.3389/fvets.2023.1132833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/17/2023] [Indexed: 09/15/2023] Open
Abstract
As a member of the SNX family, the goat sorting nexin 29 (SNX29) is initially identified as a myogenesis gene. Therefore, this study aimed to examine the polymorphism in the SNX29 gene and its association with growth traits. In this study, we used an online platform to predict the structures of the SNX29 protein and used quantitative real-time PCR to detect potential copy number variation (CNV) in Shaanbei white cashmere (SBWC) goats (n = 541), Guizhou black (GB) goats (n = 48), and Nubian (NB) goats (n = 39). The results showed that goat SNX29 protein belonged to non-secretory protein. Then, five CNVs were detected, and their association with growth traits was analyzed. In SBWC goats, CNV1, CNV3, CNV4, and CNV5 were associated with chest width and body length (P < 0.05). Among them, the CNV1 individuals with gain and loss genotypes were superior to those individuals with a median genotype, but CNV4 and CNV5 of individuals with the median genotype were superior to those with the loss and gain genotypes. In addition, individuals with the gain genotype had superior growth traits in CNV3. In brief, this study suggests that the CNV of SNX29 can be used as a molecular marker in goat breeding.
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Affiliation(s)
- Qian Wang
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, China
- Life Science Research Center, Yulin University, Yulin, Shaanxi, China
| | - Yi Bi
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, China
- Life Science Research Center, Yulin University, Yulin, Shaanxi, China
| | - Xianfeng Wu
- Institute of Animal Husbandry and Veterinary, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Zhengang Guo
- Animal Husbandry and Veterinary Science Institute of Bijie City, Bijie, Guizhou, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan, China
| | - Chuanying Pan
- College of Animal Science and Technology, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi, China
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Dou M, Li M, Zheng Z, Chen Q, Wu Y, Wang J, Shan H, Wang F, Dai X, Li Y, Yang Z, Tan G, Luo F, Chen L, Shi YS, Wu JW, Luo XJ, Asadollahpour Nanaei H, Niyazbekova Z, Zhang G, Wang W, Zhao S, Zheng W, Wang X, Jiang Y. A missense mutation in RRM1 contributes to animal tameness. SCIENCE ADVANCES 2023; 9:eadf4068. [PMID: 37352351 PMCID: PMC10289655 DOI: 10.1126/sciadv.adf4068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/18/2023] [Indexed: 06/25/2023]
Abstract
The increased tameness to reduce avoidance of human in wild animals has been long proposed as the key step of animal domestication. The tameness is a complex behavior trait and largely determined by genetic factors. However, the underlying genetic mutations remain vague and how they influence the animal behaviors is yet to be explored. Behavior tests of a wild-domestic hybrid goat population indicate the locus under strongest artificial selection during domestication may exert a huge effect on the flight distance. Within this locus, only one missense mutation RRM1I241V which was present in the early domestic goat ~6500 years ago. Genome editing of RRM1I241V in mice showed increased tameness and sociability and reduced anxiety. These behavioral changes induced by RRM1I241V were modulated by the alternation of activity of glutamatergic synapse and some other synapse-related pathways. This study established a link between RRM1I241V and tameness, demonstrating that the complex behavioral change can be achieved by mutations under strong selection during animal domestication.
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Affiliation(s)
- Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, 830011, China
| | - Yongji Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Huiquan Shan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yunjia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Zhirui Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Guanghui Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Funong Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Medical School, Nanjing University, Nanjing, Jiangsu, 210032, China
| | - Jiang Wei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Xiong-Jian Luo
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1983969412, Iran
| | - Zhannur Niyazbekova
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Guojie Zhang
- Centre for Evolutionary and Organismal Biology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310000, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi, 710072, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Wenxin Zheng
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, 830011, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shannxi, 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Wang Q, Wei Z, Zhu H, Pan C, Akhatayeva Z, Song X, Lan X. Goat Pleomorphic Adenoma Gene 1 ( PLAG1): mRNA Expression, CNV Detection and Associations with Growth Traits. Animals (Basel) 2023; 13:2023. [PMID: 37370533 DOI: 10.3390/ani13122023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/19/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study investigated four aspects: bioinformatics analysis, mRNA expression (n = 6), CNV detection (n = 224), and association analysis. The findings indicated that the gene had a large number of conserved motifs, and the gene expression level was higher in fetal goats than in adult goats. Three CNV loci were selected from the database, among which CNV1 was located in the bidirectional promoter region and was associated with goat growth traits. CNV analysis showed that CNV2 and CNV3 of the PLAG1 gene were associated with growth traits such as body weight, heart girth, height at hip cross, and hip width (p < 0.05), with CNV1 loss genotype being the superior genotype, and CNV2 and CNV3 median and gain genotypes of being superior genotypes. This finding further confirms that the PLAG1 gene is the dominant gene for growth traits, which will serve as theoretical guidance for goat breeding.
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Affiliation(s)
- Qian Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhenyu Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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Gong Y, Li Y, Liu X, Ma Y, Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? J Anim Sci Biotechnol 2023; 14:73. [PMID: 37143156 PMCID: PMC10161434 DOI: 10.1186/s40104-023-00860-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/01/2023] [Indexed: 05/06/2023] Open
Abstract
As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.
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Affiliation(s)
- Ying Gong
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Yefang Li
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xuexue Liu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, 37 allées Jules Guesde, Toulouse, 31000, France
| | - Yuehui Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Lin Jiang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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Gao Y, Jiang G, Yang W, Jin W, Gong J, Xu X, Niu X. Animal-SNPAtlas: a comprehensive SNP database for multiple animals. Nucleic Acids Res 2022; 51:D816-D826. [PMID: 36300636 PMCID: PMC9825464 DOI: 10.1093/nar/gkac954] [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: 08/11/2022] [Revised: 10/06/2022] [Accepted: 10/26/2022] [Indexed: 01/30/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) as the most important type of genetic variation are widely used in describing population characteristics and play vital roles in animal genetics and breeding. Large amounts of population genetic variation resources and tools have been developed in human, which provided solid support for human genetic studies. However, compared with human, the development of animal genetic variation databases was relatively slow, which limits the genetic researches in these animals. To fill this gap, we systematically identified ∼ 499 million high-quality SNPs from 4784 samples of 20 types of animals. On that basis, we annotated the functions of SNPs, constructed high-density reference panels and calculated genome-wide linkage disequilibrium (LD) matrixes. We further developed Animal-SNPAtlas, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/) which includes high-quality SNP datasets and several support tools for multiple animals. In Animal-SNPAtlas, users can search the functional annotation of SNPs, perform online genotype imputation, explore and visualize LD information, browse variant information using the genome browser and download SNP datasets for each species. With the massive SNP datasets and useful tools, Animal-SNPAtlas will be an important fundamental resource for the animal genomics, genetics and breeding community.
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Affiliation(s)
| | | | - Wenqian Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Weiwei Jin
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Jing Gong
- To whom correspondence should be addressed. Tel: +86 27 87285085; Fax: +86 27 87285085;
| | - Xuewen Xu
- Correspondence may also be addressed to Xuewen Xu. Tel: +86 27 87285085; Fax: +86 27 87285085;
| | - Xiaohui Niu
- Correspondence may also be addressed to Xiaohui Niu. Tel: +86 27 87285085; Fax: +86 27 87285085;
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Liu J, Lang K, Tan S, Jie W, Zhu Y, Huang S, Huang W. A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals. BMC Genomics 2022; 23:706. [PMID: 36253723 PMCID: PMC9575303 DOI: 10.1186/s12864-022-08881-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 09/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Livestock animals is of great significance in agricultural production. However, the role of specific gene expression, especially alternative splicing in determining phenotype, is not well understood. The livestock research community needs a gene expression and alternative splicing database contributing to livestock genetic improvement. DESCRIPTION We report the construction of LivestockExp ( https://bioinfo.njau.edu.cn/livestockExp ), a web-based database server for the exploration of gene expression and alternative splicing using 43,710 uniformly processed RNA-seq samples from livestock animals and several relative species across six orders. The database is equipped with basic querying functions and multiple online analysis modules including differential/specific expression analysis, co-expression network analysis, and cross-species gene expression conservation analysis. In addition to the re-analysis of public datasets, users can upload personal datasets to perform co-analysis with public datasets. The database also offers a wide range of visualization tools and diverse links to external databases enabling users to efficiently explore the results and to gain additional insights. CONCLUSION LivestockExp covers by far the largest number of livestock animal species and RNA-seq samples and provides a valuable data resource and analysis platform for the convenient utilization of public RNA-seq datasets.
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Affiliation(s)
- Jinding Liu
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. .,Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
| | - Kun Lang
- College of Information Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Suxu Tan
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Wencai Jie
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, China
| | - Yihua Zhu
- College of Information Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shiqing Huang
- College of Information Management, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
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Yan Y, Chi S, Liu G, Huang Y, Pan D, Jiang X. The c.612A>G mutation of MC4R affects constitutive activity and signaling in domestic goats. Anim Genet 2022; 53:665-675. [PMID: 35727803 DOI: 10.1111/age.13214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/14/2022] [Accepted: 04/22/2022] [Indexed: 12/01/2022]
Abstract
As a key gene for balancing energy and regulating feeding behavior, MC4R is relevant to the growth of ruminants. In this presentation, a highly conserved c.612A>G site in the coding sequence (CDS) of MC4R has been selected during a selective sweep analysis of 35 Yiling goats and 20 other wild goats. This site mutation results in an amino acid change from Ile to Met. The genotyping analysis of the c.612A>G site revealed that the A allele was the dominant allele in the domestic goat populations, while the wild goat individuals only had the G allele. For a better understanding of the biological significance of this site, we examined the protein localization and signal detection to explain the function of the two MC4R receptors. The results showed that both the M204 and I204 receptors can normally localize on the membrane. When stimulating the M204 type without α-MSH, it was defective at the level of basal cAMP and decreased significantly against the I204 type. In contrast, the signaling capacity of the M204 receptor was also lower than that of I204 under the stimulation of α-MSH. In the ERK1/2 pathway, stimulating MC4R with NDP-α-MSH, both the M204 and I204 receptors had normal pERK1/2 levels. These results indicate that the p.I204M mutation may change the function by damaging the constitutive activity and signaling, and thus may regulate goats' appetite. This study has potential application for rearing domestic goats.
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Affiliation(s)
- Yinan Yan
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, China
| | - Shaxuan Chi
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, China
| | - Yongjie Huang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, China
| | - Dongmei Pan
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, China
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Fu W, Wang R, Xu N, Wang J, Li R, Asadollahpour Nanaei H, Nie Q, Zhao X, Han J, Yang N, Jiang Y. Galbase: a comprehensive repository for integrating chicken multi-omics data. BMC Genomics 2022; 23:364. [PMID: 35549894 PMCID: PMC9097087 DOI: 10.1186/s12864-022-08598-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species. Results Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features. Conclusion Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits. Galbase is publicly available at http://animal.nwsuaf.edu.cn/ChickenVar. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08598-2.
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Affiliation(s)
- Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Rui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jinxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ran 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
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Québec, Canada
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China. .,Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, China.
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Zhang S, Xu H, Jiang E, Akhatayeva Z, Jiang F, Song E, Pan C, Chen H, Lan X. Screening of Bovine Tissue-Specific Expressed Genes and Identification of Genetic Variation Within an Adipose Tissue-Specific lncRNA Gene. Front Vet Sci 2022; 9:887520. [PMID: 35647086 PMCID: PMC9130833 DOI: 10.3389/fvets.2022.887520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Global classification of bovine genes is important for studies of biology and tissue-specific gene editing. Herein, we classified the tissue-specific expressed genes and uncovered an important variation in the promoter region of an adipose tissue-specific lncRNA gene. Statistical analysis demonstrated that the number of genes specifically expressed in the brain was the highest, while it was lowest in the adipose tissues. A total of 1,575 genes were found to be significantly higher expressed in adipose tissues. Bioinformatic analysis and qRT-PCR were used to uncover the expression profiles of the 23 adipose tissue-specific and highly expressed genes in 8 tissues. The results showed that most of the 23 genes have higher expression level in adipose tissue. Besides, we detected a 12 bp insertion/deletion (indel) variation (rs720343880) in the promoter region of an adipose tissue-specific lncRNA gene (LOC100847835). The different genotypes of this variation were associated with carcass traits of cattle. Therefore, the outcomes of the present study can be used as a starting point to explore the development of cattle organs and tissues, as well as to improve the quality of cattle products.
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Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Han Xu
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Enhui Jiang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Fugui Jiang
- Institute of Animal Science and Veterinary, Shandong Academy of Agriculture Science, Jinan, China
| | - Enliang Song
- Institute of Animal Science and Veterinary, Shandong Academy of Agriculture Science, Jinan, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- *Correspondence: Xianyong Lan
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