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Simple Summary: The low developmental efficiency of cloned pig embryos limits the application of the pig cloning technique. In this study, a small molecule drug called CPI was added to the culture medium of nuclear donor cells to enhance the developmental capacity of subsequent cloned pig embryos. CPI treatment of nuclear donor cells changed the cellular energy metabolism status from oxidative phosphorylation to glycolysis, and significantly improved the developmental competence of subsequent cloned pig embryos. This study provides a simple approach to facilitate the development and application of pig cloning technology. Somatic cell nuclear transfer (SCNT) technology holds great promise for livestock industry, life science and human biomedicine. However, the development and application of this technology is limited by the low developmental potential of SCNT embryos. The developmental competence of cloned embryos is influenced by the energy metabolic status of donor cells. The purpose of this study was to investigate the effects of CPI, an oxidative phosphorylation inhibitor, on the energy metabolism pathways of pig fibroblasts and the development of subsequent SCNT embryos. The results showed that treatment of porcine fibroblasts with CPI changed the cellular energy metabolic pathways from oxidative phosphorylation to glycolysis and enhanced the developmental ability of subsequent SCNT embryos. The present study establishes a simple, new way to improve pig cloning efficiency, helping to promote the development and application of pig SCNT technology. [ABSTRACT FROM AUTHOR]

Simple Summary: In China, soup is widely perceived as a nutritional tonic, and pig bones are a primary ingredient in its preparation. Consequently, the market price of pig bones, even when of equal weight, surpasses that of pork, particularly in southern China. Despite this economic significance, the trait of pig bone weight has not been a focus in pig breeding programs due to the inherent challenges associated with in vivo measurement. The genetic selection method stands out as an effective approach for targeting the trait of pig bone weight in pig breeding. Recognizing its significance, our research endeavors have delved into molecular genetics to gain insights into the genetic aspects of pig bone weight. In order to unravel the genetic underpinnings of specific traits, we employed bioinformatics methodologies to conduct an analysis on three-way hybrid commercial pigs. Our primary objective was to identify genetic markers and genes associated with four distinct bone weight traits. Utilizing genome-wide association studies (GWAS), we scrutinized a population comprising 571 three-way hybrid commercial pigs to pinpoint single nucleotide polymorphisms (SNPs) and genes linked to these traits. The results identified twelve genes, namely OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9, that were related to four bone weight traits. This comprehensive genetic insight provides valuable information on the mechanisms governing bone growth and weight in the context of pig breeding. The pig bone weight trait holds significant economic importance in southern China. To expedite the selection of the pig bone weight trait in pig breeding, we conducted molecular genetic research on these specific traits. These traits encompass the bone weight of the scapula (SW), front leg bone weight (including humerus and ulna) (FLBW), hind leg bone weight (including femur and tibia) (HLBW), and spine bone weight (SBW). Up until now, the genetic structure related to these traits has not been thoroughly explored, primarily due to challenges associated with obtaining the phenotype data. In this study, we utilized genome-wide association studies (GWAS) to discern single nucleotide polymorphisms (SNPs) and genes associated with four bone weight traits within a population comprising 571 Duroc × (Landrace × Yorkshire) hybrid pigs (DLY). In the analyses, we employed a mixed linear model, and for the correction of multiple tests, both the false discovery rate and Bonferroni methods were utilized. Following functional annotation, candidate genes were identified based on their proximity to the candidate sites and their association with the bone weight traits. This study represents the inaugural application of GWAS for the identification of SNPs associated with individual bone weight in DLY pigs. Our analysis unveiled 26 SNPs and identified 12 promising candidate genes (OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, GLP1R, TGFB3, PLCB1, TLR4, KCNJ2, ABCA6, and ABCA9) associated with the four bone weight traits. Furthermore, our findings on the genetic mechanisms influencing pig bone weight offer valuable insights as a reference for the genetic enhancement of pig bone traits. [ABSTRACT FROM AUTHOR]

Simple Summary: By integrating prior biological information into genomic selection methods using appropriate models, it is possible to improve prediction accuracy for complex traits. In this context, we conducted a comparative assessment of two genomic prediction models, namely, genomic best linear unbiased prediction and genomic feature best linear unbiased prediction. The accuracy of these models in predicting the growth traits of backfat thickness and loin muscle area was evaluated. Our results revealed that the genomic feature best linear unbiased prediction model can effectively integrate prior information into the model, which is superior to the genomic best linear unbiased prediction model in some cases. These findings provide valuable ideas for enhancing the genomic prediction accuracy of growth traits in pigs. Enhancing the accuracy of genomic prediction is a key goal in genomic selection (GS) research. Integrating prior biological information into GS methods using appropriate models can improve prediction accuracy for complex traits. Genome-wide association study (GWAS) is widely utilized to identify potential candidate loci associated with complex traits in livestock and poultry, offering essential genomic insights. In this study, a GWAS was conducted on 685 Duroc × Landrace × Yorkshire (DLY) pigs to extract significant single-nucleotide polymorphisms (SNPs) as genomic features. We compared two GS models, genomic best linear unbiased prediction (GBLUP) and genomic feature BLUP (GFBLUP), by using imputed whole-genome sequencing (WGS) data on 651 Yorkshire pigs. The results revealed that the GBLUP model achieved prediction accuracies of 0.499 for backfat thickness (BFT) and 0.423 for loin muscle area (LMA). By applying the GFBLUP model with GWAS-based SNP preselection, the average prediction accuracies for BFT and LMA traits reached 0.491 and 0.440, respectively. Specifically, the GFBLUP model displayed a 4.8% enhancement in predicting LMA compared to the GBLUP model. These findings suggest that, in certain scenarios, the GFBLUP model may offer superior genomic prediction accuracy when compared to the GBLUP model, underscoring the potential value of incorporating genomic features to refine GS models. [ABSTRACT FROM AUTHOR]

Simple Summary: Tenderloin and rib weight are important components of the economic value of pig carcasses, and selling them separately after fine segmentation further enhances the economic value of the carcasses. This study represents one of the rare attempts to conduct a genome-wide analysis focused on the economic value of pig carcasses, utilizing post-slaughter carcass phenotype values and genotype data to identify genetic variation regions. Through our investigation, we have identified several promising candidate regions and genes that have the potential to contribute valuable insights for breeding strategies and marker-assisted selection in pig production. During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)—important components of pig carcass economic value—remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs. [ABSTRACT FROM AUTHOR]

Simple Summary: Improving the reproductive performance of sows is a paramount goal in breeding programs. The number of teats is significantly associated with the reproductive performance of sows, with quantitative trait loci (QTL) related to porcine papilla number traits identified across almost all chromosomes, and with candidate genes proposed. In this study, we analyzed the total teat number traits of 1518 Duroc × (Landrace × Yorkshire) (DLY) pigs and performed genotyping using a 50K chip. By screening SNP loci and related genes, this study aimed to identify genetic factors affecting the number of teats in DLY pigs and to facilitate future breeding programs aimed at improving this trait. The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits. [ABSTRACT FROM AUTHOR]

Simple Summary: In this study, bioinformatics approaches were used to better understand the genetic architecture of internal organ weights in three-way crossbred commercial pigs and to map genetic markers and genes. For this purpose, we used single-trait and multi-trait genome-wide association studies (GWASs) followed by a haplotype block analysis. We explored the key genetic markers and genes from the internal organ weight genome-wide association study results of three-way crossbred commercial pigs. In this manner, five genes, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, were defined as central in affecting internal organ weight in pigs. Moreover, APK1, ANO6, and UNC5C were identified to be pleiotropic in multi-trait GWASs. These results can be applied to various types of genomic studies of pigs. Internal organ weight is an essential indicator of growth status as it reflects the level of growth and development in pigs. However, the associated genetic architecture has not been well explored because phenotypes are difficult to obtain. Herein, we performed single-trait and multi-trait genome-wide association studies (GWASs) to map the genetic markers and genes associated with six internal organ weight traits (including heart weight, liver weight, spleen weight, lung weight, kidney weight, and stomach weight) in 1518 three-way crossbred commercial pigs. In summation, single-trait GWASs identified a total of 24 significant single- nucleotide polymorphisms (SNPs) and 5 promising candidate genes, namely, TPK1, POU6F2, PBX3, UNC5C, and BMPR1B, as being associated with the six internal organ weight traits analyzed. Multi-trait GWAS identified four SNPs with polymorphisms localized on the APK1, ANO6, and UNC5C genes and improved the statistical efficacy of single-trait GWASs. Furthermore, our study was the first to use GWASs to identify SNPs associated with stomach weight in pigs. In conclusion, our exploration of the genetic architecture of internal organ weights helps us better understand growth traits, and the key SNPs identified could play a potential role in animal breeding programs. [ABSTRACT FROM AUTHOR]

Simple Summary: The cloning technique is important for animal husbandry and biomedicine because it can be used to clone superior breeding livestock and produce multipurpose genetically modified animals. However, the success rate of cloning currently is very low due to the low developmental efficiency of cloned embryos, which limits the application of cloning. The low developmental competence is related to the excessive cell death in cloned embryos. Interleukin 17D (IL17D) is required for the normal development of mouse embryos by inhibiting cell death. This study aimed to investigate whether IL17D can improve cloned pig embryo development by inhibiting cell death. Addition of IL17D protein to culture medium decreased the cell death level and improved the developmental ability of cloned pig embryos. IL17D treatment enhanced cloned pig embryo development by regulating cell death-associated gene pathways and promoting genome-wide gene expression, which is probably via up-regulating the expression of a gene called GADD45B. This study provided a new approach to improve the pig cloning efficiency by adding IL17D protein to the culture medium of cloned pig embryos. Cloned animals generated by the somatic cell nuclear transfer (SCNT) approach are valuable for the farm animal industry and biomedical science. Nevertheless, the extremely low developmental efficiency of cloned embryos hinders the application of SCNT. Low developmental competence is related to the higher apoptosis level in cloned embryos than in fertilization-derived counterparts. Interleukin 17D (IL17D) expression is up-regulated during early mouse embryo development and is required for normal development of mouse embryos by inhibiting apoptosis. This study aimed to investigate whether IL17D plays roles in regulating pig SCNT embryo development. Supplementation of IL17D to culture medium improved the developmental competence and decreased the cell apoptosis level in cloned porcine embryos. The transcriptome data indicated that IL17D activated apoptosis-associated pathways and promoted global gene expression at embryonic genome activation (EGA) stage in treated pig SCNT embryos. Treating pig SCNT embryos with IL17D up-regulated expression of GADD45B, which is functional in inhibiting apoptosis and promoting EGA. Overexpression of GADD45B enhanced the developmental efficiency of cloned pig embryos. These results suggested that IL17D treatment enhanced the developmental ability of cloned pig embryos by suppressing apoptosis and promoting EGA, which was related to the up-regulation of GADD45B expression. This study demonstrated the roles of IL17D in early development of porcine SCNT embryos and provided a new approach to improve the developmental efficiency of cloned porcine embryos. [ABSTRACT FROM AUTHOR]

Simple Summary: Somatic cell nuclear transfer (SCNT) is a potential and promising technique for preserving and enlarging superior livestock genetic resources. Here, we investigated the effects of cloning on Pietrain boars, which are widely used to produce lean-type swine because of their high growth rate and lean fat rate. Our data revealed that SCNT manipulation caused some defects in growth performance, but the clones had normal semen quality and reproductive performance. Furthermore, the progeny of clones exhibited better growth performance than non-clones. These results indicated that the cloning of superior boars can be applied to produce more commercial pigs with increased economic benefit in practical breeding and production. How to maximize the use of the genetic merits of the high-ranking boars (also called superior ones) is a considerable question in the pig breeding industry, considering the money and time spent on selection. Somatic cell nuclear transfer (SCNT) is one of the potential ways to answer the question, which can be applied to produce clones with genetic resources of superior boar for the production of commercial pigs. For practical application, it is essential to investigate whether the clones and their progeny keep behaving better than the "normal boars", considering that in vitro culture and transfer manipulation would cause a series of harmful effects to the development of clones. In this study, 59,061 cloned embryos were transferred into 250 recipient sows to produce the clones of superior Pietrain boars. The growth performance of 12 clones and 36 non-clones and the semen quality of 19 clones and 28 non-clones were compared. The reproductive performance of 21 clones and 25 non-clones were also tested. Furthermore, we made a comparison in the growth performance between 466 progeny of the clones and 822 progeny of the non-clones. Our results showed that no significant difference in semen quality and reproductive performance was observed between the clones and the non-clones, although the clones grew slower and exhibited smaller body size than the non-clones. The F1 progeny of the clones showed a greater growth rate than the non-clones. Our results demonstrated through the large animal population showed that SCNT manipulation resulted in a low growth rate and small body size, but the clones could normally produce F1 progeny with excellent growth traits to bring more economic benefits. Therefore, SCNT could be effective in enlarging the merit genetics of the superior boars and increasing the economic benefits in pig reproduction and breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: Feed efficiency is one of the most valuable economic traits in the pig industry. The small intestine is the site where most of the nutrients are absorbed from ingested food. Here, we studied the relationship between small intestinal proteomics and feed efficiency in Duroc × (Landrace × Yorkshire) pigs, which is the most popular commercial pig in the Chinese pork market. Exploring the molecular mechanisms of feed efficiency will create great value for the pig industry. Our research provided a reference for further understanding of the key proteins that affect small intestinal microvilli formation and the important pathways related to feed efficiency in pigs. Feed efficiency is an economically important trait controlled by multiple genes in pigs. The small intestine is the main organ of digestion and nutrient absorption. To explore the biological processes by which small intestine proteomics affects feed efficiency (FE), we investigated the small intestinal tissue proteomes of high-FE and low-FE pigs by the isobaric tag for relative and absolute quantification (iTRAQ) method. In this study, a total of 225 Duroc × (Landrace × Yorkshire) (DLY) commercial pigs were ranked according to feed efficiency, which ranged from 30 kg to 100 kg, and six pigs with extreme phenotypes were selected, three in each of the high and low groups. A total of 1219 differentially expressed proteins (DEPs) were identified between the high-FE and low-FE groups (fold change ≥1.2 or ≤0.84; p ≤ 0.05), of which 785 were upregulated, and 484 were downregulated. Enrichment analysis indicated that the DEPs were mainly enriched in actin filament formation, microvilli formation, and small intestinal movement pathways. Protein functional analysis and protein interaction networks indicated that RHOA, HCLS1, EZR, CDC42, and RAC1 were important proteins that regulate FE in pigs. This study provided new insights into the important pathways and proteins involved in feed efficiency in pigs. [ABSTRACT FROM AUTHOR]

Simple Summary: Cloning is the most promising technique for passing the excellent phenotypes of the best individuals in the population. Here we studied the effects of cloning on Duroc pig, which is the most popular sire used in pig production due to its good growth and meat quality. Understanding the changes of cloned Duroc pigs and their progenies is of great importance for animal breeding and public acceptance. The results of this study suggested that there were no difference in blood parameters between the cloned Duroc and the conventionally bred Duroc and their progenies. To increase public understanding in cloned animals produced by somatic cell nuclear transfer technology, our previous study investigated the carcass trait and meat quality of the clones (paper accepted), and this study we further evaluate differences by investigating the blood parameters in cloned pigs and their progeny. We collected blood samples from the clones and conventionally bred non-clones and their progeny, and investigated their hematological and blood biochemical characters. Our results supported the hypothesis that there was no significant difference between clones and non-clones, or their progeny. Taken together, the data demonstrated that the clones or their progeny were similar with their controls in terms of blood parameters, although there were still other kinds of disorders, such as abnormal DNA methylation or histone modifications that needs further investigation. The data in this study agreed that cloning technique could be used to preserve and enlarge the genetics of the superior boars in pig breeding industry, especially in facing of the deadly threat of African Swine fever happened in China. [ABSTRACT FROM AUTHOR]