1
|
Kong Y, Li F, Yue X, Xu Y, Bai J, Fu W. SNPS within the SLC27A6 gene are highly associated with Hu sheep fatty acid content. Gene 2024; 927:148716. [PMID: 38914245 DOI: 10.1016/j.gene.2024.148716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/15/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024]
Abstract
Fatty acids (FA) are an important factor affecting meat quality and human health, and the important role of the solute carrier family 27 member 6 (SLC27A6) in FA metabolism has been demonstrated in several species. However, the expression profile of the SLC27A6 in different tissues and the effect of its polymorphism on FA in sheep are currently unknown. This study aimed to explore the differences in FAs in the longissimus dorsi (LD) of 1,085 Hu sheep, the expression profile of SLC27A6, and confirm the effect of single nucleotide polymorphisms (SNPs) on FA phenotypes. We found that many FA phenotypes differ significantly across different seasons, and winter promoted the deposition of polyunsaturated fatty acids (PUFA). The mRNA expression level of SLC27A6 in the lung was significantly higher than that in the heart, testis, and LD. A total of 16 SNPs were detected in the SLC27A6, and 14 SNPs were successfully genotyped by improved multiplex ligase detection reaction (iMLDR) technology. Correlation analysis showed that 7 SNPs significantly affected at least one FA phenotype. Among them, SNP14 contributes to the selection of lamb with low saturated fatty acid content and high PUFA content. Combined genotypes also significantly affected a variety of beneficial FAs such as C18:3n3, C20:4n6, C22:6n3, and monounsaturated fatty acids. This study suggests that SLC27A6 plays an important role in FA metabolism and SNPs that are significantly associated with FA phenotype could be used as potential molecular markers for later targeted regulation of FA profiles in sheep.
Collapse
Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Yanli Xu
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Science, Urumqi 830057, China
| | - Jingjing Bai
- Animal Husbandry and Veterinary Extension Station of Wuwei City, Wuwei 733000, China
| | - Weiwei Fu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| |
Collapse
|
2
|
Feng R, Zhao J, Zhang Q, Zhu Z, Zhang J, Liu C, Zheng X, Wang F, Su J, Ma X, Mi X, Guo L, Yan X, Liu Y, Li H, Chen X, Deng Y, Wang G, Zhang Y, Liu X, Liu J. Generation of Anti-Mastitis Gene-Edited Dairy Goats with Enhancing Lysozyme Expression by Inflammatory Regulatory Sequence using ISDra2-TnpB System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404408. [PMID: 39099401 DOI: 10.1002/advs.202404408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/29/2024] [Indexed: 08/06/2024]
Abstract
Gene-editing technology has become a transformative tool for the precise manipulation of biological genomes and holds great significance in the field of animal disease-resistant breeding. Mastitis, a prevalent disease in animal husbandry, imposes a substantial economic burden on the global dairy industry. In this study, a regulatory sequence gene editing breeding strategy for the successful creation of a gene-edited dairy (GED) goats with enhanced mastitis resistance using the ISDra2-TnpB system and dairy goats as the model animal is proposed. This included the targeted integration of an innate inflammatory regulatory sequence (IRS) into the promoter region of the lysozyme (LYZ) gene. Upon Escherichia Coli (E. coli) mammary gland infection, GED goats exhibited increased LYZ expression, showing robust anti-mastitis capabilities, mitigating PANoptosis activation, and alleviating blood-milk-barrier (BMB) damage. Notably, LYZ is highly expressed only in E. coli infection. This study marks the advent of anti-mastitis gene-edited animals with exogenous-free gene expression and demonstrates the feasibility of the gene-editing strategy proposed in this study. In addition, it provides a novel gene-editing blueprint for developing disease-resistant strains, focusing on disease specificity and biosafety while providing a research basis for the widespread application of the ISDra2-TnpB system.
Collapse
Affiliation(s)
- Rui Feng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Jianglin Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Qian Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Junyu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Chengyuan Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xiaoman Zheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Fan Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Jie Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xianghai Ma
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xiaoyu Mi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Lin Guo
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xiaoxue Yan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Yayi Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Huijia Li
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xu Chen
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Yi Deng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Guoyan Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Xu Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest Agriculture & Forestry University, Yangling, Shaanxi, 712100, China
| |
Collapse
|
3
|
Lyu Y, Yao T, Chen Z, Huangfu R, Cheng H, Ma W, Qi X, Li F, Chen N, Lei C. Genomic characterization of dryland adaptation in endangered Anxi cattle in China. Anim Genet 2024; 55:352-361. [PMID: 38436096 DOI: 10.1111/age.13416] [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: 02/15/2024] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
Abstract
Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including CERS3 involved in regulating skin permeability and antimicrobial functions, RBFOX2 associated with cardiac development, SLC16A7 participated in the regulation of pancreatic endocrine function, and SPATA3 related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.
Collapse
Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Tingting Yao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhefu Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruiyao Huangfu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan, China
| | - Weidong Ma
- Shaanxi Province Agriculture & Husbandry Breeding Farm, Fufeng, China
| | - Xingshan Qi
- Animal Huabandry Bureau in Biyang County, Biyang, Henan, China
| | - Fuqiang Li
- Hunan Tianhua Industrial Corporation Ltd., Lianyuan, Hunan, 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, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| |
Collapse
|
4
|
Zhao L, Hao R, Chai Z, Fu W, Yang W, Li C, Liu Q, Jiang Y. DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock. Comput Biol Chem 2024; 110:108077. [PMID: 38691895 DOI: 10.1016/j.compbiolchem.2024.108077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
A wealth of experimental evidence has suggested that open chromatin regions (OCRs) are involved in many critical biological activities, such as DNA replication, enhancer activity, and gene transcription. Accurately identifying OCRs in livestock species can provide critical insights into the distribution and characteristics of OCRs for disease treatment in livestock, thereby improving animal welfare. However, most current machine-learning methods for OCR prediction were originally designed for a limited number of model organisms, such as humans and some model organisms, and thus their performance on non-model organisms, specifically livestock, is often unsatisfactory. To bridge this gap, we propose DeepOCR, a lightweight depth-separable residual network model for predicting OCRs in livestock, including chicken, cattle, and sheep. DeepOCR integrates a single convolution layer and two improved residue structure blocks to extract and learn important features from the input DNA sequences. A fully connected layer was also employed to further process the extracted features and improve the robustness of the entire network. Our benchmarking experiments demonstrated superior prediction performance of DeepOCR compared to state-of-the-art approaches on testing datasets of the three species. The source code of DeepOCR is freely available for academic purposes at https://github.com/jasonzhao371/DeepOCR/. We anticipate DeepOCR servers as a practical and reliable computational tool for OCR-related studies in livestock species.
Collapse
Affiliation(s)
- Liangwei Zhao
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Ran Hao
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Ziyi Chai
- College of Information Engineering, Northwest A&F University, Yangling 712100, China
| | - Weiwei Fu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Wei Yang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Chen Li
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
| | - Quanzhong Liu
- College of Information Engineering, Northwest A&F University, Yangling 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 712100, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
5
|
Wang Y, Huang Y, Zhen Y, Wang J, Wang L, Chen N, Wu F, Zhang L, Shen Y, Bi C, Li S, Pool K, Blache D, Maloney SK, Liu D, Yang Z, Li C, Yu X, Zhang Z, Chen Y, Xue C, Gu Y, Huang W, Yan L, Wei W, Wang Y, Zhang J, Zhang Y, Sun Y, Wang S, Zhao X, Luo C, Wang H, Ding L, Yang QY, Zhou P, Wang M. De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 2024; 11:488. [PMID: 38734729 PMCID: PMC11088706 DOI: 10.1038/s41597-024-03338-5] [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: 12/13/2023] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The high-quality filtered RNA-seq raw reads were deposited in a public database which provides approximately 54 billion high-quality paired-end sequencing reads in total, with an average mapping rate of ~93.92%. Transcriptome databases represent valuable resources that can be used to study patterns of gene expression, and pathways that are related to key biological processes, including important economic traits in herbivores.
Collapse
Affiliation(s)
- Yifan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
- College of Life Science, Guizhou University, Guiyang, 550025, P. R. China
| | - Yiming Huang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yongkang Zhen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Jiasheng Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Limin Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Ning Chen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Feifan Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Linna Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071033, P. R. China
| | - Congliang Bi
- College of Life Science, Linyi University, Linyi, 276005, P. R. China
| | - Song Li
- College of Life Science, Guizhou University, Guiyang, 550025, P. R. China
| | - Kelsey Pool
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dominique Blache
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Shane K Maloney
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhiquan Yang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Chuang Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Xiang Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Zhenbin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifei Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Chun Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yalan Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Weidong Huang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Lu Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Wenjun Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yusu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Jinying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifan Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yiquan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Shengbo Wang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xinle Zhao
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Chengfang Luo
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Haodong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China.
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Qing-Yong Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China.
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China.
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China.
| |
Collapse
|
6
|
Zhang G, Wang J, Li Y, Zhang Z, Wang X, Chen F, Shi Q, Huang Y, Wang E, Lyu S. POLB Regulates Proliferation and Apoptosis of Bovine Primary Myocytes. Animals (Basel) 2024; 14:1323. [PMID: 38731327 PMCID: PMC11083859 DOI: 10.3390/ani14091323] [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: 02/06/2024] [Revised: 03/30/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
DNA polymerase β (DNA polymerase beta (POLB)) belongs to a member of the DNA polymerase X family, mainly involved in various biological metabolic processes, such as eukaryotic DNA replication, DNA damage repair, gene recombination, and cell cycle regulation. In this study, the muscle development-related gene POLB was screened by selection signature and RNA-seq analysis and then validated for the proliferation and apoptosis of bovine primary myocytes. It was also found that overexpression of the POLB gene had a pro-apoptosis effect, but interfering with the expression of the gene had no significant effect on cells. Then, the analysis of related apoptotic genes revealed that POLB overexpression affected CASP9 gene expression.
Collapse
Affiliation(s)
- Geyang Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (J.W.); (Y.H.)
| | - Yulong Li
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Xiangnan Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Fuying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (J.W.); (Y.H.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
| |
Collapse
|
7
|
Kong Y, Fu W, Wang L, Li F, Li W, Yue X. Molecular characterization of SPATA6 and association of its SNPs with testicular size in sheep. Theriogenology 2024; 215:205-213. [PMID: 38096624 DOI: 10.1016/j.theriogenology.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024]
Abstract
The testis is an important organ for maintaining fertility in males, and testis size is positively correlated with ejaculate volume, sperm motility, thus fertility. Spermatogenesis-associated 6 (SPATA6) is an evolutionarily conserved testis-specific gene reported in many species. However, the effect of SPATA6 expression levels on testicular development and the effect of single nucleotide polymorphisms (SNPs) on testis and epididymis phenotype in sheep have not been studied. The purpose of the research was to investigate the expression profile of SPATA6 and its effect on testicular development and to confirm the effect of SNPs on the testis and epididymis phenotype. In this study, we detected a 1245bp coding sequence (CDS) of SPATA6 and encoded 414 amino acids. The expression levels of SPATA6 were significantly higher in the testis than in other tissues and gradually increased with testis development. Moreover, the expression level in the large testis was significantly higher than that in the small testis at six months. A total of 11 SNPs were detected in the coding region of SPATA6 by cDNA-pooling sequencing and improved multiplex ligation detection reaction (iMLDR) methods. Correlation analysis showed that SNP2 (c. 3631C > G) significantly affected left epididymis weight (LEW) and right epididymis weight (REW), and SNP10 (c. 937 A > G) significantly affected REW. And the combined genotype of SNP1 (c. 4245 G > A) and SNP2 significantly affected REW. The current study concluded that SPATA6 plays an important role in testicular development and the SNPs significantly associated with the epididymis phenotype can provide molecular markers for the early selection of high-fertility Hu sheep.
Collapse
Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Weiwei Fu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Li Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wanhong Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, China; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, China; Engineering Research Center of Grassland Industry, Ministry of Education, China; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| |
Collapse
|
8
|
Liu X, Chen M, Qu X, Liu W, Dou Y, Liu Q, Shi D, Jiang M, Li H. Cis-Regulatory Elements in Mammals. Int J Mol Sci 2023; 25:343. [PMID: 38203513 PMCID: PMC10779164 DOI: 10.3390/ijms25010343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
In cis-regulatory elements, enhancers and promoters with complex molecular interactions are used to coordinate gene transcription through physical proximity and chemical modifications. These processes subsequently influence the phenotypic characteristics of an organism. An in-depth exploration of enhancers and promoters can substantially enhance our understanding of gene regulatory networks, shedding new light on mammalian development, evolution and disease pathways. In this review, we provide a comprehensive overview of the intrinsic structural attributes, detection methodologies as well as the operational mechanisms of enhancers and promoters, coupled with the relevant novel and innovative investigative techniques used to explore their actions. We further elucidated the state-of-the-art research on the roles of enhancers and promoters in the realms of mammalian development, evolution and disease, and we conclude with forward-looking insights into prospective research avenues.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Mingsheng Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| |
Collapse
|
9
|
Zhang CL, Zhang J, Tuersuntuoheti M, Zhou W, Han Z, Li X, Yang R, Zhang L, Zheng L, Liu S. Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166698. [PMID: 37683864 DOI: 10.1016/j.scitotenv.2023.166698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
Sheep are important livestock animals that have evolved under various ecological pressures. Xinjiang is a region with diverse and harsh environments that have shaped many local sheep breeds with unique characteristics and environmental adaptability. However, these breeds are losing ecological flexibility due to the promotion of intensive farming practices. Here we sequenced 14 local sheep breeds from Xinjiang and analyzed their genetic structure and gene flow with other sheep breeds from neighboring regions. The Tibetan Plateau was the geographic origin of Xinjiang native sheep evolution. We performed genome-environment association analysis and identified Bio9: Mean Temperature of Driest Quarter and Bio15: Precipitation Seasonality as the key environmental factors affecting Xinjiang local sheep and the key genes involved in their survival and adaptation. We classified Xinjiang native sheep breeds into six groups based on their differential genes by pairwise selective sweep analysis and Community Network Analysis. We analyzed transcriptome expression data of 832 sheep tissues and detected tissue-specific enrichment of six group-specific genes in different biological systems. Our results revealed the genetic basis of year-round estrus, drought tolerance, hypoxia resistance, and cold tolerance traits of Xinjiang sheep breeds. Moreover, we proposed conservation strategies for Xinjiang local sheep breeds and provided theoretical guidance for breeding new sheep breeds under global extreme environments.
Collapse
Affiliation(s)
- Cheng-Long Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Jihu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Mirenisa Tuersuntuoheti
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Wen Zhou
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Zhipeng Han
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Xiaopeng Li
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Ruizhi Yang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Lulu Zhang
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Langman Zheng
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China
| | - Shudong Liu
- College of Animal Science and Technology, Tarim University, Xingfu Road, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Xingfu Road, Alar 843300, Xinjiang, China.
| |
Collapse
|
10
|
Kozlova A, Sarygina E, Deinichenko K, Radko S, Ptitsyn K, Khmeleva S, Kurbatov L, Spirin P, Prassolov V, Ilgisonis E, Lisitsa A, Ponomarenko E. Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue. BIOLOGY 2023; 12:1494. [PMID: 38132320 PMCID: PMC10740679 DOI: 10.3390/biology12121494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The long-read RNA sequencing developed by Oxford Nanopore Technologies provides a direct quantification of transcript isoforms, thereby making it possible to present alternative splicing (AS) profiles as arrays of single splice variants with different abundances. Additionally, AS profiles can be presented as arrays of genes characterized by the degree of alternative splicing (the DAS-the number of detected splice variants per gene). Here, we successfully utilized the DAS to reveal biological pathways influenced by the alterations in AS in human liver tissue and the hepatocyte-derived malignant cell lines HepG2 and Huh7, thus employing the mathematical algorithm of gene set enrichment analysis. Furthermore, analysis of the AS profiles as abundances of single splice variants by using the graded tissue specificity index τ provided the selection of the groups of genes expressing particular splice variants specifically in liver tissue, HepG2 cells, and Huh7 cells. The majority of these splice variants were translated into proteins products and appeal to be in focus regarding further insights into the mechanisms underlying cell malignization. The used metrics are intrinsically suitable for transcriptome-wide AS profiling using long-read sequencing.
Collapse
Affiliation(s)
- Anna Kozlova
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Elizaveta Sarygina
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Kseniia Deinichenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Sergey Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Svetlana Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (P.S.); (V.P.)
| | - Vladimir Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (P.S.); (V.P.)
| | - Ekaterina Ilgisonis
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| |
Collapse
|
11
|
Su P, Wu H, Huang Y, Lu X, Yin J, Zhang Q, Lan X. The Hoof Color of Australian White Sheep Is Associated with Genetic Variation of the MITF Gene. Animals (Basel) 2023; 13:3218. [PMID: 37893942 PMCID: PMC10603658 DOI: 10.3390/ani13203218] [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: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Studying the characteristics of mammalian hoof colors is important for genetic improvements in animals. A deeper black hoof color is the standard for breeding purebred Australian White (AUW) sheep and this phenotype could be used as a phenotypic marker of purebred animals. We conducted a genome-wide association study (GWAS) analysis using restriction site associated DNA sequencing (RAD-seq) data from 577 Australian White sheep (black hoof color = 283, grey hoof color = 106, amber hoof color = 186) and performed association analysis utilizing the mixed linear model in EMMAX. The results of GWAS demonstrated that a specific single-nucleotide polymorphism (SNP; g. 33097911G>A) in intron 14 of the microphthalmia-associated transcription factor (MITF) gene was significantly associated with the hoof color in AUW sheep (p = 9.40 × 10-36). The MITF gene plays a key role in the development, differentiation, and functional regulation of melanocytes. Furthermore, the association between this locus and hoof color was validated in a cohort of 212 individuals (black hoof color = 122, grey hoof color = 38, amber hoof color = 52). The results indicated that the hoof color of AUW sheep with GG, AG, and AA genotypes tended to be black, grey, and amber, respectively. This study provided novel insights into hoof color genetics in AUW sheep, enhancing our comprehension of the genetic mechanisms underlying the diverse range of hoof colors. Our results agree with previous studies and provide molecular markers for marker-assisted selection for hoof color in sheep.
Collapse
Affiliation(s)
- Peng Su
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hui Wu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yangming Huang
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaofang Lu
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Jing Yin
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Qingfeng Zhang
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin 301607, China; (P.S.)
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 301607, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Feng H, Feng T, Mo Y, Sun S, Wang L, Lu C, Feng C, Xing K, Su Z. Integrated multi-omics analysis reveals insights into Chinese forest musk deer ( Moschus berezovskii) genome evolution and musk synthesis. Front Cell Dev Biol 2023; 11:1156138. [PMID: 37228656 PMCID: PMC10203155 DOI: 10.3389/fcell.2023.1156138] [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: 02/01/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Among the artiodactyls, male animals belonging to the Family Moschidae have a unique tissue, the musk gland, with the capability of musk synthesis. However, the genetic basis of musk gland formation and musk production are still poorly understood. Here, musk gland tissues from two juvenile and three adult Chinese forest musk deer (Moschus berezovskii) were utilized to analyze genomic evolution events, evaluate mRNA profiles and investigate cell compositions. By performing genome reannotation and comparison with 11 ruminant genomes, three expanded gene families were identified in the Moschus berezovskii genome. Transcriptional analysis further indicated that the musk gland displayed a prostate-like mRNA expression pattern. Single-cell sequencing revealed that the musk gland is composed of seven distinguishable cell types. Among them, sebaceous gland cells and luminal epithelial cells play important roles in musk synthesis, while endothelial cells master the regulation of cell-to-cell communication. In conclusion, our study provides insights into musk gland formation and the musk-synthesizing process.
Collapse
Affiliation(s)
- Hui Feng
- Shaanxi Institute of Zoology, Xi’an, Shaanxi, China
| | - Tingyin Feng
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yidi Mo
- Department of Cell Biology, Jinan University, Guangzhou, China
| | - Suli Sun
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lu Wang
- Shaanxi Institute of Zoology, Xi’an, Shaanxi, China
| | - Chunbin Lu
- Department of Developmental Biology and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Chengli Feng
- Shaanxi Institute of Zoology, Xi’an, Shaanxi, China
| | - Ke Xing
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhijian Su
- Department of Cell Biology, Jinan University, Guangzhou, China
- National Engineering Research Center of Genetic Medicine, Jinan University, Guangzhou, China
| |
Collapse
|
14
|
Li A, Yang Q, Li R, Dai X, Cai K, Lei Y, Jia K, Jiang Y, Zan L. Chromosome-level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity. Mol Ecol 2023; 32:1323-1334. [PMID: 35467052 DOI: 10.1111/mec.16483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/29/2022] [Accepted: 04/17/2022] [Indexed: 11/29/2022]
Abstract
The takin (Budorcas taxicolor) is one of the largest bovid herbivores in the subfamily Caprinae. The takin is at high risk of extinction, but its taxonomic status and genetic diversity remain unclear. In this study, we constructed the first reference genome of Bu. taxicolor using PacBio long High-Fidelity reads and Hi-C technology. The assembled genome is ~2.95 Gb with a contig N50 of 68.05 Mb, which were anchored onto 25+XY chromosomes. We found that the takin was more closely related to muskox than to other Caprinae species. Compared to the common ancestral karyotype of bovidae (2n = 60), we found the takin (2n = 52) experienced four chromosome fusions and one large translocation. Furthermore, we resequenced nine golden takins from the main distribution area, the Qinling Mountains, and identified 3.3 million single nucleotide polymorphisms. The genetic diversity of takin was very low (θπ = 0.00028 and heterozygosity =0.00038), among the lowest detected in domestic and wild mammals. Takin genomes showed a high inbreeding coefficient (FROH =0.217), suggesting severe inbreeding depression. The demographic history showed that the effective population size of takins declined significantly from ~100,000 years ago. Our results provide valuable information for protection of takins and insights into their evolution.
Collapse
Affiliation(s)
- Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qimeng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Xuelei Dai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Keli Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinghu Lei
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Kangsheng Jia
- Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Center for Ruminant Genetic and Evolution, Northwest A&F University, Yangling, Shaanxi, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,Research Center for the Qinling Giant Panda (Shaanxi Rare Wildlife Rescue Base), Shaanxi Academy of Forestry Sciences, Zhouzhi, Shaanxi, China
| |
Collapse
|
15
|
Wang W, Li Z, Xie G, Li X, Wu Z, Li M, Liu A, Xiong Y, Wang Y. Convergent Genomic Signatures of Cashmere Traits: Evidence for Natural and Artificial Selection. Int J Mol Sci 2023; 24:ijms24021165. [PMID: 36674681 PMCID: PMC9860930 DOI: 10.3390/ijms24021165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
Convergent evolution provides powerful opportunities to investigate the genetic basis of complex traits. The Tibetan antelope (Pantholops hodgsonii) and Siberian ibex (Capra sibirica) belong to different subfamilies in Bovidae, but both have evolved similar superfine cashmere characteristics to meet the cold temperature in plateau environments. The cashmere traits of cashmere goats underwent strong artificial selection, and some traces of domestication also remained in the genome. Hence, we investigated the convergent genomic signatures of cashmere traits between natural and artificial selection. We compared the patterns of convergent molecular evolution between Tibetan antelope and Siberian ibex by testing positively selected genes, rapidly evolving genes and convergent amino acid substitutions. In addition, we analyzed the selected genomic features of cashmere goats under artificial selection using whole-genome resequencing data, and skin transcriptome data of cashmere goats were also used to focus on the genes involved in regulating cashmere traits. We found that molecular convergent events were very rare, but natural and artificial selection genes were convergent enriched in similar functional pathways (e.g., ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway) in a variety of gene sets. Type IV collagen family genes (COL4A2, COL4A4, COL4A5, COL6A5, COL6A6) and integrin family genes (ITGA2, ITGA4, ITGA9, ITGB8) may be important candidate genes for cashmere formation and development. Our results provide a comprehensive approach and perspective for exploring cashmere traits and offer a valuable reference for subsequent in-depth research on the molecular mechanisms regulating cashmere development and fineness.
Collapse
Affiliation(s)
- Wei 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
| | - Zhuohui 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
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xinmei 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
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Manman 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
| | - Anguo 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
| | - Yan Xiong
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Yu 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
- Correspondence:
| |
Collapse
|
16
|
Fu Y, Liu H, Dou J, Wang Y, Liao Y, Huang X, Tang Z, Xu J, Yin D, Zhu S, Liu Y, Shen X, Liu H, Liu J, Yang X, Zhang Y, Xiang Y, Li J, Zheng Z, Zhao Y, Ma Y, Wang H, Du X, Xie S, Xu X, Zhang H, Yin L, Zhu M, Yu M, Li X, Liu X, Zhao S. IAnimal: a cross-species omics knowledgebase for animals. Nucleic Acids Res 2022; 51:D1312-D1324. [PMID: 36300629 PMCID: PMC9825575 DOI: 10.1093/nar/gkac936] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/23/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
With the exponential growth of multi-omics data, its integration and utilization have brought unprecedented opportunities for the interpretation of gene regulation mechanisms and the comprehensive analyses of biological systems. IAnimal (https://ianimal.pro/), a cross-species, multi-omics knowledgebase, was developed to improve the utilization of massive public data and simplify the integration of multi-omics information to mine the genetic mechanisms of objective traits. Currently, IAnimal provides 61 191 individual omics data of genome (WGS), transcriptome (RNA-Seq), epigenome (ChIP-Seq, ATAC-Seq) and genome annotation information for 21 species, such as mice, pigs, cattle, chickens, and macaques. The scale of its total clean data has reached 846.46 TB. To better understand the biological significance of omics information, a deep learning model for IAnimal was built based on BioBERT and AutoNER to mine 'gene' and 'trait' entities from 2 794 237 abstracts, which has practical significance for comprehending how each omics layer regulates genes to affect traits. By means of user-friendly web interfaces, flexible data application programming interfaces, and abundant functional modules, IAnimal enables users to easily query, mine, and visualize characteristics in various omics, and to infer how genes play biological roles under the influence of various omics layers.
Collapse
Affiliation(s)
- Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Hong Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jingwen Dou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yue Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yong Liao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin Huang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - JingYa Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Shilin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yangfan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiong Shen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hengyi Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jiaqi Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yi Zhang
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430070, PR China
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Zhuqing Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Haiyan Wang
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Xiaoyong Du
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Haohao Zhang
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430070, PR China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, Hubei 430070, PR China
| | - Xiaolei Liu
- Correspondence may also be addressed to Xiaolei Liu.
| | - Shuhong Zhao
- To whom correspondence should be addressed. Tel: +86 27 87387480;
| |
Collapse
|
17
|
Su P, Luo Y, Huang Y, Akhatayeva Z, Xin D, Guo Z, Pan C, Zhang Q, Xu H, Lan X. Short variation of the sheep PDGFD gene is correlated with litter size. Gene X 2022; 844:146797. [PMID: 35985413 DOI: 10.1016/j.gene.2022.146797] [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: 03/10/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022] Open
Abstract
Platelet-derived growth factor (PDGF) family, exert plays a key role in embryonic development, cell proliferation, cell migration, angiogenesis and reproduction. Related studies about GWAS analyses have found that PDGFD significantly affected deposition of tail fat in sheep, but there are no studies on reproduction in animals. In this study, three breed of sheep were used to find insertion/deletion (indel) fragment polymorphism of PDGFD which including Australian white (AUW) sheep (Meat type, n = 932), Guiqian semi-fine wool (GSFW) sheep (wool type, n = 60) and East Friensian milk (EFM) sheep (dairy type, n = 60). Only a 18-bp variation was polymorphic in the study AUW sheep population and the genotypes of different sheep breed are also specific. Moreover, the association analysis indicated that this variant was associated with litter size of AUW sheep in the first parity (p < 0.05). The litter size of II genotype was significantly lower than other genotypes in the first parity (p < 0.05). We also revealed that the PDGFD gene was relatively conservative in eight species, PDGFD mRNA expression in 832 sheep samples implying this gene was related to reproduction traits. Hence, these finding demonstrated the one-cause multipotency of PDGFD gene. Collectively, these results suggest that this indel can be used as an effective marker for sheep breeding.
Collapse
Affiliation(s)
- Peng Su
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China; Tianjin Aoqun Animal Husbandry Co.Ltd., Tianjin 301607, China.
| | - Yunyun Luo
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Yangming Huang
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China; Tianjin Aoqun Animal Husbandry Co.Ltd., Tianjin 301607, China.
| | - Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Dongyun Xin
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Zhengang Guo
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Chuanying Pan
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China.
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin 300000, China; Tianjin Aoqun Animal Husbandry Co.Ltd., Tianjin 301607, China.
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China.
| | - Xianyong Lan
- Key Laboratory of Animal Genetics Breeding and Reproduction of Shanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shanxi 712100, China.
| |
Collapse
|
18
|
Guo J, Sun X, Mao A, Liu H, Zhan S, Li L, Zhong T, Wang L, Cao J, Liu GE, Zhang H. A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the depigmentation phenotype of non-classic Swiss markings in goats. BMC Genomics 2022; 23:437. [PMID: 35698044 PMCID: PMC9190080 DOI: 10.1186/s12864-022-08672-9] [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: 03/04/2022] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pigmentation phenotype diversity is rich in domestic goats, and identification of the genetic loci affecting coat color in goats has long been of interest. Via the detections of selection signatures, a duplication upstream ASIP was previously reported to be a variant affecting the Swiss markings depigmentation phenotype in goats. RESULTS We conducted a genome-wide association study using whole-genome sequencing (WGS) data to identify the genetic loci and causal variants affecting the pigmentation phenotype in 65 Jintang black (JT) goats (i.e., 48 solid black vs. 17 non-classic Swiss markings). Although a single association peak harboring the ASIP gene at 52,619,845-72,176,538 bp on chromosome 13 was obtained using a linear mixed model approach, all the SNPs and indels in this region were excluded as causal variants for the pigmentation phenotype. We then found that all 17 individuals with non-classic Swiss markings carried a 13,420-bp duplication (CHI13:63,129,198-63,142,617 bp) nearly 101 kb upstream of ASIP, and this variant was strongly associated (P = 1.48 × 10- 12) with the coat color in the 65 JT goats. The copy numbers obtained from the WGS data also showed that the duplication was present in all 53 goats from three European breeds with Swiss markings and absent in 45 of 51 non-Swiss markings goats from four other breeds and 21 Bezoars, which was further validated in 314 samples from seven populations based on PCR amplification. The copy numbers of the duplication vary in different goat breeds with Swiss markings, indicating a threshold effect instead of a dose-response effect at the molecular level. Furthermore, breakpoint flanking repeat analysis revealed that the duplication was likely to be a result of the Bov-B-mediated nonallelic homologous recombination. CONCLUSION We confirmed that a genomic region harboring the ASIP gene is a major locus affecting the coat color phenotype of Swiss markings in goats. Although the molecular genetic mechanisms remain unsolved, the 13,420-bp duplication upstream of ASIP is a necessary but not sufficient condition for this phenotype in goats. Moreover, the variations in the copy number of the duplication across different goat breeds do not lead to phenotypic heterogeneity.
Collapse
Affiliation(s)
- Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xueliang Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ayi Mao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haifeng Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Siyuan Zhan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaxue Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Chen C, Yin Y, Li H, Zhou B, Zhou J, Zhou X, Li Z, Liu G, Pan X, Zhang R, Lin Z, Chen L, Qiu Q, Zhang YE, Wang W. Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution. Sci Bull (Beijing) 2022; 67:825-835. [PMID: 36546235 DOI: 10.1016/j.scib.2022.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/06/2023]
Abstract
Ruminants comprise a highly successful group of mammals with striking morphological innovations, including the presence of a rumen. Many studies have shown that species-specific or lineage-specific genes (referred to as new genes) play important roles in phenotypic evolution. In this study, we identified 1064 ruminant-specific genes based on the newly assembled high-quality genomes of representative members of two ruminant families and other publically available high-quality genomes. Ruminant-specific genes shared similar evolutionary and expression patterns with new genes found in other mammals, such as primates and rodents. Most new genes were derived from gene duplication and tended to be expressed in the testes or immune-related tissues, but were depleted in the adult brain. We also found that most genes expressed in the rumen were genes predating sheep-sperm whale split (referred to as old genes), but some new genes were also involved in the evolution of the rumen, and contributed more during rumen development than in the adult rumen. Notably, expression levels of members of the ruminant-specific PRD-SPRRII gene family, which are subject to positive selection, varied throughout rumen development and may thus play important roles in the development of the keratin-rich surface of the rumen. Overall, this study generated two novel ruminant genomes and also provided novel insights into the evolution of new mammalian organs.
Collapse
Affiliation(s)
- Chunyan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuan Yin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jiong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiaofang Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Guichun Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiangyu Pan
- Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; Guangdong Cardiovascular Institute, Guangzhou 510080, China
| | - Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zeshan Lin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
22
|
Rigden DJ, Fernández XM. The 2022 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Res 2022; 50:D1-D10. [PMID: 34986604 PMCID: PMC8728296 DOI: 10.1093/nar/gkab1195] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.
Collapse
Affiliation(s)
- Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | | |
Collapse
|