Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

Analysis of genetic structure and identification of important genes associated with muscle growth in Fujian Muscovy duck

Fujian Muscovy duck is a well-known meat waterfowl in Fujian Province due to its high meat production, superior breeding potential, and strong resistance. To fully explore the genetic characteristics of these advantages, Fujian black Muscovy duck and white Muscovy duck were used for whole-genome re-sequencing and transcriptome analyses. Population structure analysis showed significant differentiation between the two feather strains. Runs of homozygosity analysis indicated a stronger artificial influence on the black-feathered strain, with ROH island genes notably enriched in muscle tissue-related terms and pathways. Selective sweep and transcriptome analysis revealed a significant enrichment of genes linked to muscle tissue and muscle fiber-related terms and pathways. Key candidate genes identified, such as MEF2C, MYOZ2, and METTL21C, are believed to play crucial roles in meat production in Fujian Muscovy duck. This study offers a new perspective on improving meat production in Fujian Muscovy duck, which can benefit breeding strategies and production management.

Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs

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.

The power of retrotransposons in high-throughput genotyping and sequencing

The use of molecular markers has become an essential part of molecular genetics through their application in numerous fields, which includes identification of genes associated with targeted traits, operation of backcrossing programs, modern plant breeding, genetic characterization, and marker-assisted selection. Transposable elements are a core component of all eukaryotic genomes, making them suitable as molecular markers. Most of the large plant genomes consist primarily of transposable elements; variations in their abundance contribute to most of the variation in genome size. Retrotransposons are widely present throughout plant genomes, and replicative transposition enables them to insert into the genome without removing the original elements. Various applications of molecular markers have been developed that exploit the fact that these genetic elements are present everywhere and their ability to stably integrate into dispersed chromosomal localities that are polymorphic within a species. The ongoing development of molecular marker technologies is directly related to the deployment of high-throughput genotype sequencing platforms, and this research is of considerable significance. In this review, the practical application to molecular markers, which is a use of technology of interspersed repeats in the plant genome were examined using genomic sources from the past to the present. Prospects and possibilities are also presented.

Feeding and meat qualities of young pigs of different genotypes according to melanocortin 4 receptor (Mc4r) gene and interbreed differentiation according to the coefficient of decrease in growth intensity in early ontogenesis

The paper presents the results of studies of fattening and meat qualities of young large white pigs of different genotypes for the melanocortin receptor 4 (Mc4r) gene and the decline in growth intensity in early ontogeny. The research was carried out in the agricultural formations of the Dnipropetrovsk region, the Jazz meat processing plant, the laboratory of the genetics of the Institute of Pig Breeding and APV of the National Academy of Sciences, and the laboratory of animal husbandry of the State Institution “Institute of Grain Crops of the National Academy of Sciences”. The work was carried out following the scientific research program of the National Academy of Sciences No. 30, “Innovative technologies of breeding, industrial and organic production of pig farming products” (“Pig farming”). Assessment of animals for fattening and meat quality was carried out taking into account the following characteristics: average daily gain of live weight during the period of control fattening, g; the age of reaching 100 kg live weight, days, length of the chilled carcass, cm; length of the bacon half of the cooled carcass, cm; thickness of lard at the level of 6–7 thoracic vertebrae, mm. The coefficient of decline in growth intensity was calculated according to the method of Yu. K. Sviechin. Biometric research results were processed using generally accepted methods. It was established that according to live weight at 4 and 6 months of age, fattening and meat qualities (age of reaching a live weight of 100 kg, days; lard thickness at the level of 6–7 thoracic vertebrae, mm; length of the chilled carcass, cm) young pigs the controlled population belongs to the I class and the elite class. The coefficient of growth decline in animals of the controlled population ranges from 108.57 to 142.51 points. The data analysis shows that according to the live weight at 4 and 6 months of age, the age of reaching the live weight of 100 kg, the fat thickness at the level of 6–7 thoracic vertebrae, and the length of the chilled carcass, the young pigs of the controlled population belong to the I class and the elite class. Animals of the Mc4r АГ genotype prevail over peers of the Mc4r AA genotype in terms of fattening and meat qualities by an average of 5.90 %. The interbreed differentiation of young pigs by the coefficient of the intensity of growth decline (∆K) shows that the difference between the animals of the experimental groups in terms of the average daily gain in live weight is 23.3 g (td = 2.62), the age of reaching 100 kg live weight is 2.7 days (td = 1.59), the length of the cooled carcass is 1.4 mm (td = 2.12). The number of reliable correlations between fattening and meat qualities, coefficient of the intensity of growth decline (∆K), and Tyler B. index is 75.0 %, which indicates the possibility of their use in selection and breeding work. The use of young pigs of the Mc4r АG genotype and animals of the I group, in which the coefficient of the intensity of growth decline (∆K) ranges from 115.61 to 123.27 points, provides additional production at the level of +3.68 – +1.75 % respectively.

Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation

It has been established that through binding to bone morphogenetic proteins (BMPs), bone morphogenetic protein receptor I B (BMPR1B) can mediate transforming growth factor β (TGF-β) signal transduction, and is involved in the regulation of several biological processes, such as bone and muscle formation and homeostasis, as well as folliculogenesis. Also known as FecB, BMPR1B has been reported as the major gene for sheep prolificacy. A number of previous studies have analyzed the relationship between single nucleotide polymorphisms (SNPs) in this gene and its related performance. In recent years, with the illustration of the effect of retrotransposon insertion on the expression of the proximal genes or phenotypic variation, retrotransposon insertion polymorphisms (RIPs) have been used as a novel type of molecular marker in the evaluation of evolution, population structure and breeding of plant and domestic animals. In this study, the RIPs in porcine BMPR1B gene were excavated, and thereafter verified using a comparative genome and polymerase chain reaction (PCR). The potential effects of phenotype, gene expression and functions related to RIPs were also explored. The results showed that 13 distinct RIPs were identified in introns of porcine BMPR1B. Among these, only BMPR1B-SINE-RIP9 and BMPR1B-LINE-RIP13 displayed a close relationship with the growth traits of Large White pigs. Moreover, the total number of BMPR1B-SINE+/+-RIP9 individuals born was found to be significantly higher than that of SINE−/− (p < 0.05). These two RIPs showed an obvious distribution pattern among Chinese indigenous breeds and Western commercial breeds. The expression of BMPR1B in ovaries of adult BMPR1B-SINE+/+-RIP9 Sushan pigs was found to be significantly higher in comparison to those of BMPR1B-SINE−/−-RIP9 (p < 0.05). SINE insertion of BMPR1B-SINE-RIP9 and LINE insertion of BMPR1B-LINE-RIP13 were observed to significantly increase the activity of Octamer binding transcription factor 4 (OCT4) minipromoter in CHO and C2C12 cells (p < 0.01). Therefore, these two RIPs could serve as useful molecular markers for modulating the growth or reproductive traits in assisted selection of pig breeding, while the mechanisms of the insertion function should be studied further.