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Circular RNA (circRNA) is a class of non-coding RNA (ncRNA) that plays an important regulatory role in various biological processes of the organisms and has a major function in muscle growth and development. However, its molecular mechanisms of how it regulates pork quality remain unclear at present. In this study, we compared the longissimus dorsi (LD) muscle expression profiles of Queshan Black (QS) and Large White (LW) pigs to explore the role of circRNAs in meat quality using transcriptome sequencing. A total of 62 differentially expressed circRNAs (DECs), including 46 up- and 16 down-regulated, 39 differentially expressed miRNAs (DEmiRNAs), including 21 up- and 18 down-regulated and 404 differentially expressed mRNAs (DEMs), including 174 up- and 230 down-regulated were identified, and most circRNAs were composed of exons. Our results indicated that the DEC parent genes and DEMs were enriched in the positive regulation of fast-twitch skeletal muscle fiber contraction, relaxation of skeletal muscle, regulation of myoblast proliferation, AMPK signaling pathway, Wnt and Jak-STAT signaling pathway. Furthermore, circSETBP1/ssc-miR-149/PIK3CD and circGUCY2C/ssc-miR-425-3p/CFL1 were selected by constructing the competitive endogenous RNA (ceRNA) regulatory network, circSETBP1, circGUCY2C, PIK3CD and CFL1 had low expression level in QS, while ssc-miR-149 and ssc-miR-425-3p had higher expression level than LW, our analysis revealed that circSETBP1, circGUCY2C, ssc-miR-149, ssc-miR-425-3p, PIK3CD and CFL1 were associated with lipid regulation, cell proliferation and differentiation, so the two ceRNAs regulatory networks may play an important role in regulating intramuscular fat (IMF) deposition, thereby affecting pork quality. In conclusion, we described the gene regulation by the circRNA-miRNA-mRNA ceRNA networks by comparing QS and LW pigs LD muscle transcriptome, and the two new circRNA-associated ceRNA regulatory networks that could help to elucidate the formation mechanism of pork quality. The results provide a theoretical basis for further understanding the genetic mechanism of meat quality formation., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Simple Summary: The analysis of pig saliva, which is easily available and rich in bioactive ingredients, has been widely studied, showing potential in disease diagnosis and treatment for pig production management. Studies have shown that porcine saliva analytes have important application potential in disease detection and can be used as disease biomarkers and therapeutic monitoring indicators, as well as for prognostic evaluation. Through the changes in specific proteins, metabolites, and microbial composition in porcine saliva, porcine saliva analytes can provide a new strategy for early diagnosis, prognosis assessment, and treatment of diseases. This review introduces the composition and function of analytes in porcine saliva. Different analytes in porcine saliva are widely employed in diseases. As an indicator of pig health, saliva can be used as a noninvasive sample for disease detection and monitoring. Saliva is an important exocrine fluid that is easy to collect and is a complex mixture of proteins and other molecules from multiple sources from which considerable biological information can be mined. Pig saliva, as an easily available biological liquid rich in bioactive ingredients, is rich in nucleic acid analytes, such as eggs, enzymes, amino acids, sugars, etc. The expression levels of these components in different diseases have received extensive attention, and the analysis of specific proteins, metabolites, and biological compositions in pig saliva has become a new direction for disease diagnosis and treatment. The study of the changes in analytes in pig saliva can provide a new strategy for early diagnosis, prognosis assessment, and treatment of diseases. In this paper, the detection methods and research progress of porcine salivary analytes are reviewed, the application and research progress of porcine salivary analytes in diseases are discussed, and the future application prospect is presented. [ABSTRACT FROM AUTHOR]

Background: China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of the Henan local pig breeds are still obscure. To understand the origin and the effects of selection on these breeds, we performed various analyses on lineage composition, genetic structure, and detection of selection sweeps and introgression in three of these breeds (Queshan, Nanyang and Huainan) using genotyping data on 125 Queshan, 75 Nanyang, 16 Huainan pigs and 878 individuals from 43 Eurasian pig breeds. Results: We found no clear evidence of ancestral domestic pig DNA lineage in the Henan local breeds, which have an extremely complicated genetic background. Not only do they share genes with some northern Chinese pig breeds, such as Erhualian, Hetaodaer, and Laiwu, but they also have a high admixture of genes from foreign pig breeds (33–40%). Two striking selection sweeps in small regions of chromosomes 2 and 14 common to the Queshan and Nanyang breeds were identified. The most significant enrichment was for lipid kinase activity (GO:0043550) with the genes FII, AMBRA1, and PIK3IP1. Another interesting 636.35-kb region on chromosome 14 contained a cluster of spermatogenesis genes (OSBP2, GAL3ST1, PLA2G3, LIMK2, and PATZ1), a bisexual sterility gene MORC2, and a fat deposition gene SELENOM. Reproduction and growth genes LRP4, FII, and ARHGAP1 were present in a 238.05-kb region on SSC2 under selection. We also identified five loci associated with body length (P = 0.004) on chromosomes 1 and 12 that were introgressed from foreign pig breeds into the Henan breeds. In addition, the Chinese indigenous pig breeds fell into four main types instead of the previously reported six, among which the Eastern type could be divided into two subgroups. Conclusions: Admixture of North China, East China and foreign pigs contributed to high genetic diversity of Henan local pigs. Ontology terms associated with lipid kinase activity and spermatogenesis and growth shaping by introgression of European genes in Henan pigs were identified through selective sweep analyses. [ABSTRACT FROM AUTHOR]

Simple Summary: With the improvement of living standards, people have higher requirements for pork quality. Intramuscular fat is among the important factors that determine the quality of pork, affecting the taste and flavor. Producing quality meat with high intramuscular fat content has been a major challenge for China's livestock industry. In addition, m6A modification is abundant in many circRNAs, and m6A-circRNAs play an important regulatory role in a variety of biological processes. In this study, a total of 12 putative m6A-circRNAs were identified, their potential molecular regulatory mechanisms on fat deposition and meat quality in Chinese and Western pigs were explored through a series of bioinformatics analyses, which laid a foundation for further elucidations of the functions of m6A-circRNAs in fat deposition and growth and development of pigs. It is well known that N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules, but many circRNA molecules have now been found to have a wide range of m6A modification sites as well. However, there are few relevant studies and information on the expression profile and functional regulatory properties of m6A-modified circRNAs (m6A-circRNAs) in longissimus dorsi. In this study, a total of 12 putative m6A-circRNAs were identified and characterized in the longissimus dorsi of Queshan Black and Large White pigs—8 of them were significantly more expressed in the longissimus dorsi of Queshan Black than in Large White pigs, while the other 4 were the opposite. These 12 putative m6A-circRNAs were also found to act as miRNA sponge molecules to regulate fat deposition by constructing the ceRNA regulatory network. Enrichment analysis also revealed that the 12 m6A-circRNAs parent genes and their adsorbed miRNA target genes were widely involved in fat deposition and cell proliferation and differentiation-related pathways, such as the HIF-1 signaling pathway, the pentose phosphate pathway, the MAPK signaling pathway, the glycosphingolipid biosynthesis-lacto and neolacto series, and the TNF signaling pathway, suggesting that the analyzed m6A-circRNAs may be largely involved in the formation of pork quality. These results provide new information to study the regulatory properties of m6A-circRNAs in the formation of pork quality. [ABSTRACT FROM AUTHOR]

As one of the important traits in pig production, meat quality has important research significance and value. Intramuscular fat (IMF) content is one of the most important factors affecting pork quality. Many experimental studies have shown that IMF content is closely related to the flavor, tenderness, and juiciness of pork. Therefore, it is of great significance to study the mechanism of porcine IMF deposition. Previous research indicated that miR-149-5p promoted the proliferation of porcine intramuscular (IM) preadipocytes and decreased their ability to differentiate, albeit the exact mechanism of action is unknown. In vitro, foreign pigs showed increased miR-149-5p expression and reduced fat deposition when compared to Queshan Black pigs. This study conducted metabolomics and transcriptomics analyses of porcine IM preadipocytes overexpressing miR-149-5p to verify their effects on lipid formation. According to metabolomics analysis, the overexpression of miR-149-5p has significantly altered the lipid, organic acid, and organic oxygen metabolites of porcine IM preadipocytes. Specially speaking, it has changed 115 metabolites, including 105 up-regulated and 10 down-regulated ones, as well as the composition of lipid, organic acid, and organic oxygen metabolism-related metabolites. RNA-seq analysis showed that overexpression of miR-149-5p significantly altered 857 genes, of which 442 were up-regulated, and 415 were down-regulated, with enrichment to MAPK, IL-17, PI3K-Akt, and ErbB signaling pathways. We found that overexpression of miR-149-5p inhibited adipogenic differentiation by changing cAMP signaling pathway in porcine IM preadipocytes. In addition, the overexpression of miR-149-5p may affect the transport of Cu2+ by targeting ATP7A and inhibiting adipogenic differentiation. These findings elucidate the regulatory function of miR-149-5p in porcine IM preadipocytes, which may be a key target for controlling pork quality. [ABSTRACT FROM AUTHOR]

Simple Summary: Whole-genome SNP data from 613 Chinese indigenous pigs were collected to comprehensively estimate the genetic diversity, genetic relationship, and population genetic structure of the indigenous pig meta-populations. These Chinese meta-populations were characterized by genetic distance, genetic difference index, and runs of homozygosity (ROH). The contribution of genetic diversity of each meta-population was scaled based on genetic and allelic diversity, which provides a basis for improving the conservation project. Further, a selective sweep analysis revealed that genes related to fat deposition and heat stress may contribute to the adaptability of the indigenous pigs to cold and heat. These findings provide a theoretical basis for the improvement of conservation strategies and insights into the environmental adaptability of Chinese indigenous pigs. The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs. [ABSTRACT FROM AUTHOR]

Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds. [ABSTRACT FROM AUTHOR]

Mitochondria follow non‐Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities. [ABSTRACT FROM AUTHOR]

Next, we predicted the target mRNAs of these miRNAs, with 103 target mRNAs for 13 upregulated miRNAs and 15 target mRNAs for four downregulated miRNAs in Queshan Black and Large White pigs. Thus, the present study enriched the differentially expressed miRNA target mRNAs to investigate miRNA functions, and the results showed that target mRNAs were mainly enriched in the AMPK signaling pathway [[26]], MAPK signaling pathway, PI3K-Akt signaling pathway, Jak-STAT signaling pathway, insulin signaling pathway, and sphingolipid signaling pathway. Keywords: Queshan Black pigs; Large White pigs; pork quality; RNA-seq; differentially expressed; miRNA EN Queshan Black pigs Large White pigs pork quality RNA-seq differentially expressed miRNA 1814 17 11/17/22 20221101 NES 221101 1. Red indicates upregulated differentially expressed miRNAs and mRNAs; blue indicates downregulated differentially expressed miRNAs and mRNAs; triangle represents miRNAs, and rounded rectangle represents mRNAs. [Extracted from the article]

Introgression of genetic features from European pigs into Chinese pigs was reported possibly contributing to improvements in productivity traits, such as feed conversion efficiency and body size. However, the genomic differences from European pigs and the potential role of introgression in Henan indigenous pigs remains unclear. In this study, we found significant introgression from European pigs into the genome of Chinese indigenous pigs, especially in Henan indigenous pigs. The introgression in Henan indigenous pigs, particularly in the Nanyang black pig, was mainly derived from Duroc pigs. Most importantly, we found that the NR6A1, GPD2 , and CSRNP3 genes were introgressed and reshaped by artificial selection, and these may have contributed to increases in pig body size and feed conversion efficiency. Our results suggest that human-mediated introgression and selection have reshaped the genome of Henan pigs and improved several of their desired traits. These findings contribute to our understanding of the history of Henan indigenous pigs and provide insights into the genetic mechanisms affecting economically important traits in pig populations. [ABSTRACT FROM AUTHOR]

Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5 , BMP6 , BMP7 , ACVR1 , INHBA , ZFYVE9 , TGFBR2 , DCN , ID4 , BAMBI , and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9 , SLC39A11 , SNCA , and UNC5D are candidate genes for reproduction traits. • A total of 13,955,609 SNPs and 2,666,366 indels were identified across the genome. • 3293 common differential SNPs and 439 common differential indels were fixed between groups. • Genes encoding components of the TGF-beta signaling pathway were identified to be associated with sow reproductive traits. • Fourteen candidate genes were identified to contribute to sow prolificacy and merit further investigations. [ABSTRACT FROM AUTHOR]

Simple Summary: Litter size is an important economic trait in pigs. Improving the number born alive is an important breeding goal of the pig husbandry. A shorter farrowing duration is welcome for facilitating the management and sows' health. Therefore, the aim of this study was to explore the effect of litter size and parity on farrowing duration, to determine whether a shorter length of farrowing duration could be considered as a breeding parameter in pig breeding. Our results showed the total number born had no significant relation with farrowing duration, but number of stillbirths increased with the prolongation of farrowing duration and decrease of live litter size if farrowing duration was longer than 240–300 min. Different parities sows had little difference in the same farrowing duration interval except for gilts. A shorter farrowing duration within 300 min might be considered in pig breeding without worrying about the decreasing of live litter size or the negative effect of parity. Litter size has increased and farrowing duration has also prolonged in recent years. The aim of this study was to analyze the effect of litter size and parity on farrowing duration (FAR) to estimate the possibility of selecting a short farrowing duration. We recorded 32,200 parturitions of 8420 Landrace × Yorkshire sows, determined farrowing duration, litter size, parity, gestation length. Results showed that total number of born (TNB) and parity obeyed a cubic (p = 0.0004, p = 0.004) relationship while number born alive (NBA) and number born dead (NBD) obeyed a linear (p = 0.0239, p = 0.0035) relationship with FAR. Gestation length obeyed a linear (p = 0.02) relationship with FAR. FAR of sows with stillbirth was longer than that of sows without stillbirth. Stillbirth rate increased rapidly from about 2% to 4%, especially when FAR was over 240 min. FAR gradually prolonged with the parities. FAR of 7th parity sows was longer than that of 1st~6th parity sows (p < 0.05), but different parity sows had little difference in the same FAR interval except for gilts. Results indicated it was possible and necessary to consider FAR into pig breeding without worrying about decreasing of live litter size or negative effect of parity if FAR was shorter than 300 min. [ABSTRACT FROM AUTHOR]