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Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, Wang MS, Jiang L, Dai LH, Wang JR, Chu XH, Zeng YQ, Fang LZ, Wu DD, Zhang Q, Ding XD. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience 2023; 26:106119. [PMID: 36852268 PMCID: PMC9958381 DOI: 10.1016/j.isci.2023.106119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.
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Affiliation(s)
- Yi-Fan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chong-Long Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ru-Hai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wen-Wen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Li-He Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jie-Ru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiao-Hong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Ling-Zhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian 271001, China
| | - Xiang-Dong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Li X, Zhang X, Luo Y, Liu R, Sun Y, Zhao S, Yu M, Cao J. Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells. Genes (Basel) 2022; 13:genes13091515. [PMID: 36140681 PMCID: PMC9498719 DOI: 10.3390/genes13091515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/25/2022] Open
Abstract
The porcine monomyeloid cell line, or 3D4/21 cells, is an effective tool to study the immune characteristics and virus infection mechanism of pigs. Due to the introduction of the neomycin resistance gene and the SV40 large T antigen gene, its genome has undergone essential changes, which are still unknown. Studying the variation in genome structure, especially the large fragments of insertions and deletions (InDels), is one of the proper ways to reveal these issues. In this study, an All-seq method was established by combining Mate-pair and Shotgun sequencing methods, and the detection and verification of large fragments of InDels were performed on 3D4/21 cells. The results showed that there were 844 InDels with a length of more than 1 kb, of which 12 regions were deletions of more than 100 kb in the 3D4/21 cell genome. In addition, compared with porcine primary alveolar macrophages, 82 genes including the CD163 had lost transcription in 3D4/21 cells, and 72 genes gained transcription as well. Further referring to the Hi-C structure, it was found that the fusion of the topologically associated domains (TADs) caused by the deletion may lead to abnormal gene function. The results of this study provide a basis for elaborating the genome structure and functional variation in 3D4/21 cells, provide a method for rapid and convenient detection of large-scale InDels, and provide useful clues for the study of the porcine immune function genome and the molecular mechanism of virus infection.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yandong Luo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianhua Cao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan 430070, China
- 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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Du H, Zheng X, Zhao Q, Hu Z, Wang H, Zhou L, Liu JF. Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing. Front Genet 2021; 12:550676. [PMID: 33613628 PMCID: PMC7890942 DOI: 10.3389/fgene.2021.550676] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.
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Affiliation(s)
- Heng Du
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qiqi Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengzheng Hu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Improving read alignment through the generation of alternative reference via iterative strategy. Sci Rep 2020; 10:18712. [PMID: 33127969 PMCID: PMC7599232 DOI: 10.1038/s41598-020-74526-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 09/30/2020] [Indexed: 11/08/2022] Open
Abstract
There is generally one standard reference sequence for each species. When extensive variations exist in other breeds of the species, it can lead to ambiguous alignment and inaccurate variant calling and, in turn, compromise the accuracy of downstream analysis. Here, with the help of the FPGA hardware platform, we present a method that generates an alternative reference via an iterative strategy to improve the read alignment for breeds that are genetically distant to the reference breed. Compared to the published reference genomes, by using the alternative reference sequences we built, the mapping rates of Chinese indigenous pigs and chickens were improved by 0.61-1.68% and 0.09-0.45%, respectively. These sequences also enable researchers to recover highly variable regions that could be missed using public reference sequences. We also determined that the optimal number of iterations needed to generate alternative reference sequences were seven and five for pigs and chickens, respectively. Our results show that, for genetically distant breeds, generating an alternative reference sequence can facilitate read alignment and variant calling and improve the accuracy of downstream analyses.
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Meng J, Song K, Li C, Liu S, Shi R, Li B, Wang T, Li A, Que H, Li L, Zhang G. Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network. BMC Genomics 2019; 20:625. [PMID: 31366319 PMCID: PMC6670154 DOI: 10.1186/s12864-019-5971-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/11/2019] [Indexed: 02/07/2023] Open
Abstract
Background Oyster is rich in glycogen and free amino acids and is called “the milk of sea”. To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale. Results After association analysis, 168 clustered significant single nucleotide polymorphism (SNP) loci were identified for glycogen content and 17 SNPs were verified with 288 oyster individuals in another wide populations. These were the most important candidate loci for oyster breeding. Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. This might enhance the gluconeogenesis process by the transcriptionally regulating the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose 6-phosphatase (G6Pase). Also, for amino acids content, 417 clustered significant SNPs were identified. After genetic network analysis, three node SNP regions were identified to be associated with glycogen, protein, and Asp content, which might explain their significant correlation. Conclusion Overall, this study provides insights into the genetic correlation among complex traits, which will facilitate future oyster functional studies and breeding through molecular design. Electronic supplementary material The online version of this article (10.1186/s12864-019-5971-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Kai Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chunyan Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Sheng Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ruihui Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Busu Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ting Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Ao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Huayong Que
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China.,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China. .,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China. .,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China. .,National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
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Liu C, Ran X, Yu C, Xu Q, Niu X, Zhao P, Wang J. Whole-genome analysis of structural variations between Xiang pigs with larger litter sizes and those with smaller litter sizes. Genomics 2018; 111:310-319. [PMID: 29481841 DOI: 10.1016/j.ygeno.2018.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 02/08/2018] [Accepted: 02/11/2018] [Indexed: 11/30/2022]
Abstract
To gain a better knowledge of structural variations (SVs) in Xiang pig, we used next-generation sequencing to analyze the Xiang pigs with larger (XL) or smaller litter sizes (XS). Our analysis yielded 28,040 putative SVs in the Xiang pig. These SVs distributed throughout all of chromosomes. Some functional regions including exons and untranslated regions were less varied than introns and intergenic regions. We detected 4637 and 4119 specific SVs, which contained 1697 and 1582 genes in XL and XS group, respectively. These genes were mainly enriched in the well-known pathways involved in development and reproduction processes. Population validation was carried out on 50 SVs candidates using PCR method in 144 Xiang pig crowds. All of 50 SVs were confirmed by PCR method and 14 SVs were associated with the litter size of Xiang pigs. These results may be helpful for the elucidation of growth and reproduction regulation in Xiang pig.
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Affiliation(s)
- Chang Liu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China.
| | - Changyan Yu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Qian Xu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Xi Niu
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Pengju Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing 100083, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering, College of Animal Science, Guizhou University, Guiyang 550025, China; Tongren University, Tongren 554300, China.
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