Screening of candidate genes related to differences in growth and development between Chinese indigenous and Western pig breeds

Neijiang (NJ) and Yacha (YC) are two indigenous pig breeds in the Sichuan basin of China, displaying higher resistance to diseases, lower lean ratio, and slower growth rate than the commercial Western pig breed Yorkshire (YS). The molecular mechanisms underlying the differences in growth and development between these pig breeds are still unknown. In the present study, five pigs from NJ, YC, and YS breeds were subjected to the whole genome resequencing, and then the differential single-nucleotide polymorphisms (SNPs) were screened using a 10-kb window sliding in 1-kb step using the F_st method. Finally, 48,924, 48,543, and 46,228 nonsynonymous single-nucleotide polymorphism loci (nsSNPs) were identified between NJ and YS, NJ and YC, and YC and YS, which highly or moderately affected 2,490, 800, and 444 genes, respectively. Moreover, three nsSNPs were detected in the genes of acetyl-CoA acetyltransferase 1 (ACAT1) insulin-like growth factor 2 receptor (IGF2R), insulin-like growth factor 2 and mRNA-binding protein 3 (IGF2BP3), which potentially affected the transformation of acetyl-CoA to acetoacetyl-CoA and the normal functions of the insulin signaling pathways. Moreover, serous determinations revealed significantly lower acetyl-CoA content in YC than in YS, supporting that ACAT1 might be a reason explaining the differences in growth and development between YC and YS breeds. Contents of phosphatidylcholine (PC) and phosphatidic acid (PA) significantly differed between the pig breeds, suggesting that glycerophospholipid metabolism might be another reason for the differences between Chinese and Western pig breeds. Overall, these results might contribute basic information to understand the genetic differences determining the phenotypical traits in pigs.

Carcass Composition and Physicochemical Characteristics of Meat from Pork Chains Based on Native and Hybrid Pigs

The purpose of the research was to investigate the carcass composition, meat quality and chemical composition of pigs from two pork chains for the production of traditional dry/cured products in Croatia. The trial involved 24 Black Slavonian barrows reared outdoors (NAT chain) and 24 PIC hybrid barrows kept under industrial conditions (INT chain); all animals were raised to 160 kg of live weight. After slaughter, carcass and meat quality traits were measured and samples for chemical composition were taken. After that, a full dissection of the carcasses was performed. The pigs from the INT pork chain had leaner carcasses, higher bone percentages, and lower fatness levels than the NAT carcasses. Pigs from the NAT chain exhibited a more desirable meat quality. No differences were found in moisture, and samples from the INT chain exhibited higher collagen and protein percentage. Muscles from the NAT chain had higher IMF and MUFA levels, and the SFA content was lower than in INT pork. Despite the superior carcass traits of the pigs from the INT chain, pigs from the NAT chain demonstrated better suitability for the production of dry/cured products.

A Comparative Analysis of Metabolic Profiles of Embryonic Skeletal Muscle from Lantang and Landrace Pigs

Simple Summary

The pig is one of the most important domesticated meat animals. Some studies have revealed that pigs with low meat production show more intense myogenesis at the early stage of embryonic muscle development than pigs with high meat production. Here, by gas chromatography–mass spectrometry GC–MS based metabolomics, we concluded that the nucleotide metabolism and energy metabolism of the longissimuslumborum (LL) were increased in Lantang pigs compared with Landrace pigs, indicating rapid synthesis of nucleic acids and ATP to meet the material and energy requirements of rapid cell proliferation and differentiation in Lantang pigs.

Abstract

Elucidation of the complex regulation of porcine muscle development is key to increasing pork output and improving pork quality. However, the molecular mechanisms involved in early porcine embryonic muscle development in different pig breeds remain largely unknown. Here, GC–MS based metabolomics and metabolomic profiling was used to examine the longissimus lumborum (LL) of the Lantang (LT) and the Landrace (LR) pig at embryonic day 35 (E35). Metabolites showed clear separation between LT and LR, with 40 metabolites having higher abundances in LT and 14 metabolites having lower abundances in LT compared with LR. In addition, these metabolic changes were mainly associated with nucleotide metabolism and energy metabolism, such as purine metabolism, pyrimidine metabolism, the pentose phosphate pathway, and the TCA cycle. More interestingly, the contents of DNA, RNA, and ATP per unit mass of LL tissues were higher in LT, indicating rapid synthesis of nucleic acids and ATP, to meet both the material and energy requirements of rapid cell proliferation and differentiation. Furthermore, enzyme activity associated with the TCA cycle and pentose phosphate pathway, including α-ketoglutaric dehydrogenase (KGDH), malate dehydrogenase (MDH), pyruvate dehydrogenase (PDH), succinate dehydrogenase (SDH), and glucose-6-phosphate dehydrogenase (G6PDH), were higher in LT. Based on these results, we conclude that there are significant differences in nucleotide metabolism and energy metabolism of LL between LT and LR, and we speculate that the enhanced nucleic acid metabolism and energy metabolism in LT can meet the material and energy requirements of rapid cell proliferation and differentiation, making myogenesis more intense in LT compared to LR which might be the metabolic mechanism underlying the distinct skeletal muscle development in the two breeds.

Meat quality of Pulawska breed pigs and image of longissimus lumborum muscle microstructure compared to commercial DanBred and Naima hybrids

The objective of this article was the evaluation of selected properties of meat quality including the characteristics of longissimus lumborum (LL) muscle microstructure of Pulawska breed pigs and fatteners of the DanBred and Naima hybrids which are used in national meat production. Three genetic groups of fatteners were studied in the experiment: group I – DanBred hybrid; group II – Naima hybrid; and group III – the Pulawska breed. Pig fattening took place under the same environmental conditions from the starting weight of 30 kg ± 2 kg to 103–105 kg. For the analysis of muscle fibre characteristics and meat quality from each group, 30 animals were selected ( 1:1 ). Physico-chemical properties and ultrastructure were evaluated in samples collected from the LL muscle. A statistically significant impact (P<0.01) of a genetic group on pH45, content of water, protein and ash, as well as on the colour of meat, the number of STOs (slow-twitch oxidatives) and the diameter of FTG (fast-twitch glycolytic) muscle fibres, was found. Meat of the Pulawska breed, compared to DanBred and Naima, showed a statistically significant (P<0.01) higher (by 2.05 % and 2.49 %, respectively) nutritional value expressed as protein content and mineral components. Overall, these results imply better biological properties of Pulawska meat than DanBred and Naima hybrids. The higher STO and lower FTG found in muscles from Pulawska pigs might partially explain meat quality differences found between the breeds in the present study. The data of the current study indicated that meat quality characteristics and muscle microstructure of fatteners showed differences, and these differences may be used for alternative pork meat production for the consumer.

Identification of Differentially Expressed Genes in Different Types of Broiler Skeletal Muscle Fibers Using the RNA-seq Technique

The difference in muscle fiber types is very important to the muscle development and meat quality of broilers. At present, the molecular regulation mechanisms of skeletal muscle fiber-type transformation in broilers are still unclear. In this study, differentially expressed genes between breast and leg muscles in broilers were analyzed using RNA-seq. A total of 767 DEGs were identified. Compared with leg muscle, there were 429 upregulated genes and 338 downregulated genes in breast muscle. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in cellular processes, single organism processes, cells, and cellular components, as well as binding and catalytic activity. KEGG analysis shows that a total of 230 DEGs were mapped to 126 KEGG pathways and significantly enriched in the four pathways of glycolysis/gluconeogenesis, starch and sucrose metabolism, insulin signalling pathways, and the biosynthesis of amino acids. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of 7 selected DEGs, and the results were consistent with RNA-seq data. In addition, the expression profile of MyHC isoforms in chicken skeletal muscle cells showed that with the extension of differentiation time, the expression of fast fiber subunits (types IIA and IIB) gradually increased, while slow muscle fiber subunits (type I) showed a downward trend after 4 days of differentiation. The differential genes screened in this study will provide some new ideas for further understanding the molecular mechanism of skeletal muscle fiber transformation in broilers.

Data Mining and Validation of AMPK Pathway as a Novel Candidate Role Affecting Intramuscular Fat Content in Pigs

Simple Summary

Intramuscular fat (IMF) is increasingly being recognized as a key meat trait in the modern pork industry. The aims of this research were to identify potential signaling pathways associated with IMF content in the longissimus dorsi (LD) muscle of different pig breeds and investigate the gene expression levels in the screened signaling pathways. Our results indicated that the AMPK signaling pathway may be related to IMF deposition in the LD muscle of pigs. The results of qRT-PCR analysis showed that the expression of ten key hub genes (AMPK, ADIPOR1, ADIPOR2, LKB1, CAMKKβ, CPT1A, CPT1B, PGC-1α, CD36, and ACC1) differed between the LD muscle of Min and Large White pigs. The protein expression levels of AMPK, LKB1, CaMKK2, CPT1A, and ACC1 were similar to the genes expression patterns in the LD muscle of Large White pigs. The results of this study provide novel insights into the regulatory function of the AMPK signaling pathway in relation to the IMF content in the LD muscle of different pigs.

Abstract

Intramuscular fat (IMF) is an important economic trait for pork quality and a complex quantitative trait regulated by multiple genes. The objective of this work was to investigate the novel transcriptional effects of a multigene pathway on IMF deposition in the longissimus dorsi (LD) muscles of pigs. Potential signaling pathways were screened by mining data from three gene expression profiles in the Gene Expression Omnibus (GEO) database. We designed quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) arrays for the candidate signaling pathways to verify the results in the LD muscles of two pig breeds with different IMF contents (Large White and Min). Western blot analysis was used to detect the expression levels of several candidate proteins. Our results showed that the AMPK signaling pathway was screened via bioinformatics analysis. Ten key hub genes of this signaling pathway (AMPK, ADIPOR1, ADIPOR2, LKB1, CAMKKβ, CPT1A, CPT1B, PGC-1α, CD36, and ACC1) were differentially expressed between the Large White and Min pigs. Western blot analysis further confirmed that LKB1/CaMKK2-AMPK-ACC1-CPT1A axis dominates the activity of AMPK signaling pathway. Statistical analyses revealed that AMPK signaling pathway activity clearly varied among the two pig breeds. Based on these results, we concluded that the activation of the AMPK signaling pathway plays a positive role in reducing IMF deposition in pigs.