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Simple Summary: Long terminal repeat retrotransposons (LTR-RTNs) are vital in genome evolution and diversity. The compact genomes of Tetraodontiformes provide an excellent model for studying LTR-RTN dynamics. An analysis of the genomes of ten tetraodontiform species revealed a total of 819 full-length LTR retrotransposon sequences classified into nine families spanning four distinct superfamilies. Among them, the Gypsy superfamily displayed the highest level of diversity. Takifugu stood out for having the highest abundance of LTR families and sequences. Evidence of recent LTR-RTN activity and multiple invasions was observed in specific tetraodontiform genomes. This investigation provides valuable insights into the evolution of LTR retrotransposons and their impact on the structure and evolution of compact tetraodontiform genomes. This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes. [ABSTRACT FROM AUTHOR]

Simple Summary: Retrotransposons in pigs account for approximately 37.13% of the genome, while long terminal repeats (LTRs) make up 7.56%. These LTR retrotransposons consist of two identical sequences that flank an internal protein-coding region, known as an endogenous retrovirus (ERV). When an insertion polymorphism integrates into a genomic region that harbors functional ERV elements, such as promoters, enhancers, and insulators, it may contribute to phenotypic variation. In this study, we explored the insertion polymorphisms generated by the mobilization of full-length ERVs (Fl-ERVs). Through comparative genomic analysis, we identified 18 insertion polymorphic sites that were generated by Fl-ERVs, and evaluated the genetic impact of one Fl-ERV insertion polymorphism in the STAB2-like gene. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Lipid metabolism has a substantial impact on the quality of meat in swine farming. PPARγ has a close association with lipid metabolism and displays high expression in adipose tissues. It is of paramount importance to control lipid metabolism to regulate PPARγ expression and activity in pigs. In this study, the association between the expression of the PPARγ gene and the backfat thickness of pigs was investigated. In recent years, retrotransposon insertion polymorphisms (RIPs), a new type of molecular marker, have emerged as a potentially valuable tool for genetic breeding in livestock and poultry. In this study, a combined retrotransposon insertion in the PPARγ gene of pigs was discovered that could be used as an efficient marker in selecting pigs for growth rate and lean percentage. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Carbonic anhydrases (CAs) play a crucial role in numerous physiological and pathological processes in animals. Specifically, carbonic anhydrase VB (CA5B) is integral to both gluconeogenesis and lipogenesis. Structural variations, particularly retrotransposon insertion polymorphisms (RIPs), can contribute significantly to these processes. When an RIP is inserted into a genome region containing functional elements (such as promoters, enhancers, and insulators), it can have an impact on both the expression and phenotypic changes of target genes. In this study, we identified an RIP located in the first intron of the CA5B gene, inserted by the SINE element, which enhanced the core promoter activity of the target gene. Through experimental analysis and growth data provided by the pig breeding farm (Anhui academy of agriculture sciences), we found that the SINE insertion improved the expression of the porcine CA5B gene in adipose tissue. Additionally, the number of (ATTT) repeats within the SINE insertion at this site was inconsistent across breeds and individuals. This study provides insight into the role RIPs play in genetic variation of CA5B genes and its phenotypic expression in pigs. 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. [ABSTRACT FROM AUTHOR]

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. 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. [ABSTRACT FROM AUTHOR]

Furthermore, we found most of the confirmed SVs related to SINE insertion or deletion, while ERV only represented one RIP site (Table 2), which is generally agreed with our previous studies, where SINEs are deduced as the major sources of retrotransposon-derived SVs in the pig genome [[58]], although LINE, LTR, and SINE accounted for 18.52%, 7.56%, and 11.05% of the pig genome, respectively [[32]]. Keywords: coat color; phenotypic trait; pig breeds; SINE; RIPs; molecular marker EN coat color phenotypic trait pig breeds SINE RIPs molecular marker N.PAG N.PAG 13 04/26/22 20220415 NES 220415 1. [Extracted from the article]

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. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Our previous studies suggested that the short interspersed nuclear element (SINE) retrotransposon insertion polymorphisms (RIPs), as a new type of molecular marker developed very recently, are ideal molecular markers and have the potential to be used for population genetic analysis and molecular breeding in pigs and possibly it can be extended to other livestock animals as well. However, no report is available for the application of SINE RIPs in population genetic analysis in livestock, including pigs. Here, we evaluated 30 SINE RIPs in several indigenous Chinese miniature pig breeds, including three subpopulations of Bama pigs (BM-cov, BM-clo, and BM-inb). BM-cov is a subpopulation conserved in the national conservation farm, and BM-clo is a closed population maintained over 30 years with only 2 boars and 14 sows imported from its original area, while BM-inb herd is an 18 generation continuous inbreeding line based on the BM-clo population. To our knowledge, it is the first time to report the genetic diversity, breed differentiation, and population structures for these populations by using SINE RIPs, and which suggests the feasibility of SINE RIPs in pig genetic analysis. RIPs have been developed as effective genetic markers and popularly applied for genetic analysis in plants, but few reports are available for domestic animals. Here, we established 30 new molecular markers based on the SINE RIPs, and applied them for population genetic analysis in seven Chinese miniature pigs. The data revealed that the closed herd (BM-clo), inbreeding herd (BM-inb) of Bama miniature pigs were distinctly different from the BM-cov herds in the conservation farm, and other miniature pigs (Wuzhishan, Congjiang Xiang, Tibetan, and Mingguang small ear). These later five miniature pig breeds can further be classified into two clades based on a phylogenetic tree: one included BM-cov and Wuzhishan, the other included Congjiang Xiang, Tibetan, and Mingguang small ear, which was well-supported by structure analysis. The polymorphic information contents estimated by using SINE RIPs are lower than the predictions based on microsatellites. Overall, the genetic distances and breed-relationships between these populations revealed by 30 SINE RIPs generally agree with their evolutions and geographic distributions. We demonstrated the potential of SINE RIPs as new genetic markers for genetic monitoring and population structure analysis in pigs, which can even be extended to other livestock animals. [ABSTRACT FROM AUTHOR]