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Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res 2024; 31:dsae008. [PMID: 38447059 PMCID: PMC11090087 DOI: 10.1093/dnares/dsae008] [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: 12/23/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chenyu Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Li Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuping Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Du Z, Chen C, Zheng Y, Wang X, Song C. Retroviral Insertion Polymorphism (RIP) of Porcine Endogenous Retroviruses (PERVs) in Pig Genomes. Animals (Basel) 2024; 14:621. [PMID: 38396589 PMCID: PMC10886097 DOI: 10.3390/ani14040621] [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: 12/25/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Endogenous retroviruses (ERVs) are one of the superfamilies of long terminal repeat retrotransposons (LTRs) in mice and humans. Approximately 8% of the pig genome is composed of sequences derived from LTRs. While the majority of ERVs in pigs have decayed, a small number of full-length copies can still mobilize within the genome. This study investigated the unexplored retroviral insertion polymorphisms (RIPs) generated by the mobilization of full-length ERVs (Fl-ERVs), and evaluated their impact on phenotypic variation to gain insights into the biological role of Fl-ERVs in pigs. Overall, 39 RIPs (insertions or deletions relative to the pig reference genome) generated by Fl-ERVs were predicted by comparative genomic analysis, and 18 of them were confirmed by PCR detection. Four RIP sites (D5, D14, D15, and D18) were further evaluated by population analysis, and all of them displayed polymorphisms in multiple breeds. The RIP site of ERV-D14, which is a Fl-ERV inserted in the STAB2-like gene, was further confirmed by sequencing. Population analysis of the polymorphic site of ERV-D14 reveals that it presents moderate polymorphism information in the Large White pig breed, and the association analysis reveals that the RIP of ERV-D14 is associated with age variations at 30 kg body weight (p < 0.05) and 100 kg body weight (p < 0.01) in the population of Large White pigs (N = 480). Furthermore, the ERV-D14 RIP is associated with changes in the expression of the target gene STAB2-like in the liver, backfat, and leaf fat in Sushan pigs. These data suggest that some Fl-ERVs are still mobilizing in the pig's genome, and contribute to genomic and phenotypic variations.
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Affiliation(s)
- Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (C.C.); (Y.Z.); (X.W.)
- College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610225, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (C.C.); (Y.Z.); (X.W.)
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (C.C.); (Y.Z.); (X.W.)
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (C.C.); (Y.Z.); (X.W.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (C.C.); (Y.Z.); (X.W.)
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Kosushkin S, Korchagin V, Vergun A, Ryskov A. Interspecific Comparison of Orthologous Short Interspersed Elements Loci Using Whole-Genome Data. Genes (Basel) 2023; 14:2089. [PMID: 38003031 PMCID: PMC10670947 DOI: 10.3390/genes14112089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The polymorphism of SINE-containing loci reflects the evolutionary processes that occurred both during the period before the divergence of the taxa and after it. Orthologous loci containing SINE in two or more genomes indicate the relatedness of the taxa, while different copies may have a specific set of mutations and degree of difference. Polymorphic insertion can be interpreted with a high degree of confidence as a shared derived character in the phylogenetic reconstruction of the history of the taxon. The computational comparison of the entire set of SINE-containing loci between genomes is a challenging task, and we propose to consider it in detail using the genomes of representatives of squamate reptiles (lizards) as an example. Our approach allows us to extract copies of SINE from the genomes, find pairwise orthologous loci by using flanking genomic sequences, and analyze the resulting sets of loci for the presence or absence of SINE, the degree of similarity of the flanks, and the similarity of the SINE themselves. The workflow we propose allows us to efficiently extract and analyze orthologous SINE loci for the downstream analysis, as shown in our comparison of species- and genus-level taxa in lacertid lizards.
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Affiliation(s)
- Sergei Kosushkin
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia; (V.K.)
| | - Vitaly Korchagin
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia; (V.K.)
| | - Andrey Vergun
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia; (V.K.)
- Department of Biochemistry, Molecular Biology and Genetics, Moscow Pedagogical State University, 1/1 M. Pirogovskaya Str., Moscow 119991, Russia
| | - Alexey Ryskov
- Laboratory of Genome Organization, Institute of Gene Biology of the Russian Academy of Sciences, Vavilova Str., 34/5, Moscow 119334, Russia; (V.K.)
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Zong W, Wang J, Zhao R, Niu N, Su Y, Hu Z, Liu X, Hou X, Wang L, Wang L, Zhang L. Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs. J Anim Sci Biotechnol 2023; 14:136. [PMID: 37805653 PMCID: PMC10559557 DOI: 10.1186/s40104-023-00929-x] [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: 05/23/2023] [Accepted: 08/03/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted. RESULTS Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. CONCLUSIONS: We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanfang Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ziping Hu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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He J, Yu M, Chi C, Du Z, Zheng Y, Chen C, Moawad AS, Song C, Wang X. Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs. Animals (Basel) 2023; 13:2355. [PMID: 37508132 PMCID: PMC10376311 DOI: 10.3390/ani13142355] [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: 06/07/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPARα and a combined retrotransposon in intron 2 of PPARγ, designated as PPARα-ERV-RIP and PPARγ-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPARα-ERV-RIP+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPARγ-COM-RIP-/- genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARγ gene expression in the backfat of those with the PPARγ-COM-RIP-/- genotype (-/- indicated homozygous without insertion) was significantly greater (p < 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p < 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPARγ, making PPARγ-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding.
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Affiliation(s)
- Jia He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Miao Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chenglin Chi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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Zheng Y, Chen C, Wang M, Moawad AS, Wang X, Song C. SINE Insertion in the Pig Carbonic Anhydrase 5B (CA5B) Gene Is Associated with Changes in Gene Expression and Phenotypic Variation. Animals (Basel) 2023; 13:1942. [PMID: 37370452 DOI: 10.3390/ani13121942] [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: 03/20/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Transposons are genetic elements that are present in mammalian genomes and occupy a large proportion of the pig genome, with retrotransposons being the most abundant. In a previous study, it was found that a SINE retrotransposon was inserted in the 1st intron of the CA5B gene in pigs, and the present study aimed to investigate the SINE insertion polymorphism in this gene in different pig breeds. Polymerase chain reaction (PCR) was used to confirm the polymorphism in 11 pig breeds and wild boars), and it was found that there was moderate polymorphism information content in 9 of the breeds. Further investigation in cell experiments revealed that the 330 bp SINE insertion in the RIP-CA5B site promoted expression activity in the weak promoter region of this site. Additionally, an enhancer verification vector experiment showed that the 330 bp SINE sequence acted as an enhancer on the core promoter region upstream of the CA5B gene region. The expression of CA5B in adipose tissue (back fat and leaf fat) in individuals with the (SINE+/+) genotype was significantly higher than those with (SINE+/-) and (SINE-/-) genotypes. The association analysis revealed that the (SINE+/+) genotype was significantly associated with a higher back fat thickness than the (SINE-/-) genotype. Moreover, it was observed that the insertion of SINE at the RIP-CA5B site carried ATTT repeats, and three types of (ATTT) repeats were identified among different individuals/breeds (i.e., (ATTT)4, (ATTT)6 and (ATTT)9). Overall, the study provides insights into the genetic basis of adipose tissue development in pigs and highlights the role of a SINE insertion in the CA5B gene in this process.
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Affiliation(s)
- Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory, Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
| | - Mengli Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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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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10
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Tardiolo G, Romeo O, Zumbo A, Di Marsico M, Sutera AM, Cigliano RA, Paytuví A, D’Alessandro E. Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet. Animals (Basel) 2023; 13:642. [PMID: 36830429 PMCID: PMC9951753 DOI: 10.3390/ani13040642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3-V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.
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Affiliation(s)
- Giuseppe Tardiolo
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
| | - Orazio Romeo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Alessandro Zumbo
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
| | - Marco Di Marsico
- Sequentia Biotech SL, Carrer del Dr. Trueta 179, 08005 Barcelona, Spain
| | - Anna Maria Sutera
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
| | | | - Andreu Paytuví
- Sequentia Biotech SL, Carrer del Dr. Trueta 179, 08005 Barcelona, Spain
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell’Annunziata, Via Palatucci snc, 98168 Messina, Italy
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11
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D'Alessandro E, Arfuso F, Floridia V, Tardiolo G, Fazio F, Giannetto C, Piccione G, Zumbo A. Different genotype and a liquid whey-supplemented diet influence the resilience of pigs through immune-modulation and anti-inflammatory response. Front Vet Sci 2022; 9:1046101. [PMID: 36439344 PMCID: PMC9683634 DOI: 10.3389/fvets.2022.1046101] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/13/2022] [Indexed: 07/30/2023] Open
Abstract
This study evaluated (i) whether weight gain and levels of inflammatory and immune markers including white blood cells (WBC), serum haptoglobin, C-reactive protein, albumin, and globulin fractions change between the Nero Siciliano pig breed and the crossbreed Landrace x Large White (LxLW) reared under the same environmental and farming conditions; and (ii) whether a liquid whey diet supplementation affects the investigated parameters in both genotypes. In this study, 10 crossbreed LxLW and 10 Nero Siciliano pigs were given control feed, representing the control groups (CTRC and CTRNS), whereas 10 crossbreed LxLW and 10 Nero Siciliano pigs were given control feed supplemented with liquid whey for 2 months, representing the experimental groups (WC and WNS). From each pig, body weight and blood were collected before experimental diet supplementation (T0), and one (T1) and two (T2) months after the start of the diet supplemented with whey. The white blood cell count (WBC), serum haptoglobin, C-reactive protein, total proteins, albumin and globulin fraction concentration were assessed. Two-way analysis of variance showed an increasing trend of body weight both in the control and experimental groups of the two pig genotypes throughout the monitoring period (p < 0.01) without a significant effect of genotype and diet (p > 0.05). The concentration of haptoglobin, β1- and β2-globulins was affected by pig genotype, diet supplementation, and time (p < 0.01). The values of WBC, C-reactive protein, albumin, α-globulins, and A/G ratio were affected by diet supplementation (p < 0.01) and time (p < 0.01) without an influence of genotype (p > 0.05). Nero Siciliano pigs showed lower levels of haptoglobin, β1-globulin, and β2-globulin compared to crossbreed LxLW. Nero Siciliano pigs and crossbred LxLW fed with liquid whey showed lower levels of WBC, haptoglobin, C-reactive protein, α-, β1-, and β2-globulins and higher values of albumin compared to control groups. The results reinforced the hypothesis that autochthonous breeds possess higher resilience to farming conditions when compared to allochthonous breeds. Moreover, an immune-modulatory and an anti-inflammatory power of liquid whey dietary supplementation is suggested probably thanks to its content in natural bioactive substances including anti-inflammatory cytokines and anti-oxidative factors.
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12
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Blaj I, Tetens J, Bennewitz J, Thaller G, Falker-Gieske C. Structural variants and tandem repeats in the founder individuals of four F 2 pig crosses and implications to F 2 GWAS results. BMC Genomics 2022; 23:631. [PMID: 36057580 PMCID: PMC9440560 DOI: 10.1186/s12864-022-08716-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/23/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study. RESULTS A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. Interestingly, a common pattern on how structural variants or tandem repeats regulate the phenotypic traits emerged. Many of the significant variants were embedded or nearby long non-coding RNAs drawing attention to their functional importance. Through which specific mechanisms the identified long non-coding RNAs and their associated structural variants or tandem repeats contribute to quantitative trait variation will need further investigation. CONCLUSIONS The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation.
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Affiliation(s)
- Iulia Blaj
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany.
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | - Jörn Bennewitz
- Institute of Animal Husbandry and Breeding, University of Hohenheim, Stuttgart, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Kiel University, Kiel, Germany
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13
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SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits. Genes (Basel) 2022; 13:genes13081422. [PMID: 36011333 PMCID: PMC9407865 DOI: 10.3390/genes13081422] [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: 07/08/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 12/03/2022] Open
Abstract
Retrotransposon is an important component of the mammalian genome. Previous studies have shown that the expression of protein-coding genes was affected by the insertion of retrotransposon into the proximal genes, and the phenotype variations would be related to the retrotransposon insertion polymorphisms (RIPs). In this study, leptin (LEP), leptin receptor (LEPR), and leptin receptor overlapping transcript (LEPROT), which play important roles in the regulation of fat synthesis and body weight, were screened to search for the RIPs and their effect on phenotype and gene expression, as well as to further study the function of the insertion. The results showed that three RIPs located in intron 1 of LEPROT and intron 2 and 21 of LEPR were identified, and they were all SINEA1, which was one type of retrotransposon. The SINE insertion at the LEPROT was the dominant allele in native pig breeds. The age of 100 kg body weight of SINE+/+ Large White individuals was significantly higher than those of SINE+/− and SINE−/− individuals (p < 0.05). The LEPROT gene expression in the liver and suet of 30-day-old SINE−/− Sujiang piglets were significantly higher than those of SINE+/+ and SINE+/− piglets (p < 0.01). The dual-luciferase reporter gene assay showed that SINE insertion in PK15 and 3T3-L1 cells significantly reduced the promoter activity of the LEPROT gene (p < 0.01). Therefore, SINE insertion can be a repressor to reduce the expression of LEPROT and could be a useful molecular marker for assisted selection of growth traits in pig breeding.
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14
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Becker D, Weikard R, Heimes A, Hadlich F, Hammon HM, Meyerholz MM, Petzl W, Zerbe H, Schuberth HJ, Hoedemaker M, Schmicke M, Engelmann S, Kühn C. Allele-biased expression of the bovine APOB gene associated with the cholesterol deficiency defect suggests cis-regulatory enhancer effects of the LTR retrotransposon insertion. Sci Rep 2022; 12:13469. [PMID: 35931741 PMCID: PMC9355974 DOI: 10.1038/s41598-022-17798-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/31/2022] [Indexed: 11/09/2022] Open
Abstract
The insertion of an endogenous retroviral long terminal repeat (LTR) sequence into the bovine apolipoprotein B (APOB) gene is causal to the inherited genetic defect cholesterol deficiency (CD) observed in neonatal and young calves. Affected calves suffer from developmental abnormalities, symptoms of incurable diarrhoea and often die within weeks to a few months after birth. Neither the detailed effects of the LTR insertion on APOB expression profile nor the specific mode of inheritance nor detailed phenotypic consequences of the mutation are undisputed. In our study, we analysed German Holstein dairy heifers at the peak of hepatic metabolic load and exposed to an additional pathogen challenge for clinical, metabolic and hepatic transcriptome differences between wild type (CDF) and heterozygote carriers of the mutation (CDC). Our data revealed that a divergent allele-biased expression pattern of the APOB gene in heterozygous CDC animals leads to a tenfold higher expression of exons upstream and a decreased expression of exons downstream of the LTR insertion compared to expression levels of CDF animals. This expression pattern could be a result of enhancer activity induced by the LTR insertion, in addition to a previously reported artificial polyadenylation signal. Thus, our data support a regulatory potential of mobile element insertions. With regard to the phenotype generated by the LTR insertion, heterozygote CDC carriers display significantly differential hepatic expression of genes involved in cholesterol biosynthesis and lipid metabolism. Phenotypically, CDC carriers show a significantly affected lipomobilization compared to wild type animals. These results reject a completely recessive mode of inheritance for the CD defect, which should be considered for selection decisions in the affected population. Exemplarily, our results illustrate the regulatory impact of mobile element insertions not only on specific host target gene expression but also on global transcriptome profiles with subsequent biological, functional and phenotypic consequences in a natural in-vivo model of a non-model mammalian organism.
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Affiliation(s)
- Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Annika Heimes
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Frieder Hadlich
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Harald M Hammon
- Institute of Nutritional Physiology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Marie M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, Germany
- Institute for Immunology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfram Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, Germany
| | - Holm Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, Germany
| | | | - Martina Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Marion Schmicke
- Faculty of Natural Sciences III, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technical University Braunschweig, Brunswick, Germany
- Microbial Proteomics, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
- Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany.
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15
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Firsov SY, Kosherova KA, Mukha DV. Identification and functional characterization of the German cockroach, Blattella germanica, short interspersed nuclear elements. PLoS One 2022; 17:e0266699. [PMID: 35696390 PMCID: PMC9191728 DOI: 10.1371/journal.pone.0266699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/24/2022] [Indexed: 11/18/2022] Open
Abstract
In recent decades, experimental data has accumulated indicating that short interspersed nuclear elements (SINEs) can play a significant functional role in the regulation of gene expression in the host genome. In addition, molecular markers based on SINE insertion polymorphisms have been developed and are widely used for genetic differentiation of populations of eukaryotic organisms. Using routine bioinformatics analysis and publicly available genomic DNA and small RNA-seq data, we first described nine SINEs in the genome of the German cockroach, Blattella germanica. All described SINEs have tRNA promoters, and the start of their transcription begins 11 bp upstream of an "A" box of these promoters. The number of copies of the described SINEs in the B. germanica genome ranges from several copies to more than a thousand copies in a SINE-specific manner. Some of the described SINEs and their degenerate copies can be localized both in the introns of genes and loci known as piRNA clusters. piRNAs originating from piRNA clusters are shown to be mapped to seven of the nine types of SINEs described, including copies of SINEs localized in gene introns. We speculate that SINEs, localized in the introns of certain genes, may regulate the level of expression of these genes by a PIWI-related molecular mechanism.
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Affiliation(s)
- Sergei Yu. Firsov
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Karina A. Kosherova
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V. Mukha
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
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16
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Wang X, D’Alessandro E, Chi C, Moawad AS, Zong W, Chen C, Song C. Genetic Evaluation and Population Structure of Jiangsu Native Pigs in China Revealed by SINE Insertion Polymorphisms. Animals (Basel) 2022; 12:ani12111345. [PMID: 35681812 PMCID: PMC9179424 DOI: 10.3390/ani12111345] [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: 03/30/2022] [Revised: 05/04/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary In a previous study, 30 SINE-RIPs were applied for population genetic analysis in 7 Chinese miniature pig populations and approved effectively in the genetic distances and breed-relationships between these populations. There are abundant indigenous pigs famous across the world for their prolificacy in the Jiangsu Province of eastern China, such as Meishan, Erhualian. Since pork production relies on limited commercial breeds such as Landrace, Large White, and Duroc pigs, characterized by maximizing productivity in intensive production systems, these indigenous pigs are nowadays decrease sharply. The genetic characterizations of these resources are essential requirements for the development of conservation, selection, and sustainable utilizations. Therefore, SINE-RIPs were selected to evaluate the genetic variation and population structure of Jiangsu pig populations and the results may assist with the conservation and utilization of these native pig populations. Abstract Short interspersed nuclear elements (SINEs), one type of retrotransposon, are considered to be ideal molecular markers due to their wide distribution in the genome, high copy number, and high polymorphism. Preliminary studies have identified more than 35,000 SINE-retrotransposon insertion polymorphisms (RIPs) in the pig genome. In this study, 18 SINE-RIPs were used to evaluate the genetic variation and population structure of seven native pig populations and two crossbreeds in the Jiangsu Province of China. Two commercial pig breeds (Duroc and Large White) and one Italian native breed (Sicilian Black pig) were selected as the control. The results showed that all 18 SINE-RIPs were polymorphic among these pigs. The Jiangsu native pig populations (Erhualian, Fengjing, Middle Meishan, Mi, Shawutou, Small Meishan, and Huai) were shown to be more polymorphic than the crossbreeds (Sushan and Sujiang) and external breeds (Sicilian Black pig, Large White, and Duroc) based on the expected heterozygosity and polymorphic information content values. Some native pigs, including Small Meishan, Mi, Middle Meishan, and Erhualian, had a higher degree of inbreeding according to the FIS values. Based on the neighbor-joining tree, all of the Jiangsu native pig populations formed one branch, while the three external pig breeds formed the other branches, with the two crossbreeds containing more than 50% external pig ancestry. The Huai pigs were independent of the other Jiangsu native pigs but shared a common ancestor with Sujiang and Mi. The results provide a new perspective on the population structure of these native pig breeds and will assist with the conservation and utilization of Chinese native pigs.
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Affiliation(s)
- Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Enrico D’Alessandro
- Unit of Animal Production, Department of Veterinary Science, University of Messina, 98168 Messina, Italy;
| | - Chenglin Chi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Ali Shoaib Moawad
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China; (X.W.); (C.C.); (A.S.M.); (W.Z.); (C.C.)
- Correspondence: ; Tel./Fax: +86-514-87979034
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17
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Du Z, D’Alessandro E, Zheng Y, Wang M, Chen C, Wang X, Song C. Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes. Animals (Basel) 2022; 12:ani12080969. [PMID: 35454216 PMCID: PMC9031378 DOI: 10.3390/ani12080969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 12/17/2022] Open
Abstract
The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.
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Affiliation(s)
- Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, University of Messina, Via Palatucci, 98168 Messina, Italy;
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Mengli Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Z.D.); (Y.Z.); (M.W.); (C.C.); (X.W.)
- Correspondence:
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18
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Yang N, Zhao B, Chen Y, D'Alessandro E, Chen C, Ji T, Wu X, Song C. Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus). Genome Biol Evol 2021; 13:6322960. [PMID: 34270728 PMCID: PMC8346653 DOI: 10.1093/gbe/evab168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Although the rabbit genome has already been annotated, it is mobilome remains largely unknown. Here, multiple pipelines were used to de novo mine and annotate the mobilome in rabbit. Four families and 19 subfamilies of LINE1s, two families and nine subfamilies of SINEs, and 12 ERV families were defined in rabbit based on sequence identity, structural organization, and phylogenetic tree. The analysis of insertion age and polymerase chain reaction suggests that a number of families are very young and may remain active, such as L1B, L1D, OcuSINEA, and OcuERV1. RepeatMasker annotation revealed a distinct transposable element landscape within the genome, with approximately two million copies of SINEs, representing the greatest proportion of the genome (19.61%), followed by LINEs (15.44%), and LTRs (4.11%), respectively, considerably different from most other mammal mobilomes except hedgehog and tree shrew, in which LINEs have the highest proportion. Furthermore, a very high rate of insertion polymorphisms (>85%) for the youngest subfamily (OcuSINEA1) was identified by polymerase chain reaction. The majority of retrotransposon insertions overlapped with protein-coding regions (>80%) and lncRNA (90%) genes. Genomic distribution bias was observed for retrotransposons, with those immediately upstream (-1 kb) and downstream (1 kb) of genes significantly depleted. Local GC content in 50-kb widows had significantly negative correlations with LINE (rs=-0.996) and LTR (rs=-0.829) insertions. The current study revealed a distinct mobilome landscape in rabbit, which will assist in the elucidation of the evolution of the genome of lagomorphs, and even other mammals.
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Affiliation(s)
- Naisu Yang
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Bohao Zhao
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Yang Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | | | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Ting Ji
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Xinsheng Wu
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Jiangsu, China
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SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor. Animals (Basel) 2021; 11:ani11071871. [PMID: 34201672 PMCID: PMC8300111 DOI: 10.3390/ani11071871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary GH/IGF axis genes play a central role in the regulation of skeletal accretion during development and growth, and thus represent candidate genes for growth traits. Retrotransposon insertion polymorphisms are major contributors to structural variations. They tend to generate large effect mutations resulting in variations in target gene activity and phenotype due to the fact that they carry functional elements, such as enhancers, insulators, or promoters. In the present study, RIPs in four GH/IGF axis genes (GH, GHR, IGF1, and IGF1R) were investigated by comparative genomics and PCR. Four RIPs in the GHR gene and one RIP in the IGF1 gene were identified. Further analysis revealed that one RIP in the first intron of GHR might play a role in the regulation of GHR expression by acting as a repressor. These findings contribute to the understanding of the role of RIPs in the genetic variation of GH/IGF axis genes and phenotypic variation in pigs. Abstract The genetic diversity of the GH/IGF axis genes and their association with the variation of gene expression and phenotypic traits, principally represented by SNPs, have been extensively reported. Nevertheless, the impact of retrotransposon insertion polymorphisms (RIPs) on the GH/IGF axis gene activity has not been reported. In the present study, bioinformatic prediction and PCR verification were performed to screen RIPs in four GH/IGF axis genes (GH, GHR, IGF1 and IGF1R). In total, five RIPs, including one SINE RIP in intron 3 of IGF1, one L1 RIP in intron 7 of GHR, and three SINE RIPs in intron 1, intron 5 and intron 9 of GHR, were confirmed by PCR, displaying polymorphisms in diverse breeds. Dual luciferase reporter assay revealed that the SINE insertion in intron 1 of GHR significantly repressed the GHR promoter activity in PK15, Hela, C2C12 and 3T3-L1 cells. Furthermore, qPCR results confirmed that this SINE insertion was associated with a decreased expression of GHR in the leg muscle and longissimus dorsi, indicating that it may act as a repressor involved in the regulation of GHR expression. In summary, our data revealed that RIPs contribute to the genetic variation of GH/IGF axis genes, whereby one SINE RIP in the intron 1 of GHR may decrease the expression of GHR by acting as a repressor.
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