Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs

RNA editing is a co-transcriptional/post-transcriptional modification that is mediated by the ADAR enzyme family. Profiling of RNA editing is very limited in pigs. In this study, we collated 3813 RNA-seq data from the public repositories across 23 tissues and carried out comprehensive profiling of RNA editing in pigs. In total, 127,927 A-to-I RNA-editing sites were detected. Our analysis showed that 98.2% of RNA-editing sites were located within repeat regions, primarily within the pig-specific SINE retrotransposon PRE-1/Pre0_SS elements. Subsequently, we focused on analyzing specific RNA-editing sites (SESs) in skeletal muscle tissues. Functional enrichment analyses suggested that they were enriched in signaling pathways associated with muscle cell differentiation, including DMD, MYOD1, and CAV1 genes. Furthermore, we discovered that RNA editing event in the 3'UTR of CFLAR mRNA influenced miR-708-5p binding in this region. In this study, the panoramic RNA-editing landscape of different tissues of pigs was systematically mapped, and RNA-editing sites and genes involved in muscle cell differentiation were identified. In summary, we identified modifications to pig RNA-editing sites and provided candidate targets for further validation.

Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle

Genome association studies (GWAS) provides knowledge about the genetic architecture of beef-related traits that allow linking the target phenotype to genomic information aiding breeding decision. Thus, the present study aims to uncover the genetic mechanism involved in carcass (REA: rib eye area, BF: backfat thickness, and HCW: hot carcass weight) and meat quality traits (SF: shear-force, MARB: marbling score, and IMF: intramuscular fat content) in Nellore cattle. For this, 6910 young bulls with phenotypic information and 23,859 animals genotyped with 435 k markers were used to perform the weighted single-step GBLUP (WssGBLUP) approach, considering two iterations. The top 10 genomic regions explained 8.13, 11.81, and 9.58% of the additive genetic variance, harboring a total of 119, 143, and 95 positional candidate genes for REA, BF, and HCW, respectively. For meat quality traits, the top 10 windows explained a large proportion of the total genetic variance for SF (14.95%), MARB (17.56%), and IMF (21.41%) surrounding 92, 155, and 111 candidate genes, respectively. Relevant candidate genes (CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, and PLA2G16) are related to physiological aspects affecting growth, carcass, meat quality, feed intake, and reproductive traits by signaling pathways controlling muscle control, key signal metabolic molecules INS / IGF-1 pathway, lipid metabolism, and adipose tissue development. The GWAS results provided insights into the genetic control of the traits studied and the genes found are potential candidates to be used in the improvement of carcass and meat quality traits.

The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis

The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme-substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.

Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.

Comparative proteomics reveals genetic mechanisms of body weight in Hu sheep and Dorper sheep

Body weight (BW) is a critical economic trait for meat production in sheep, and it is a complex trait affected by numerous elements. The aim of this study was to investigate the genetic mechanisms of sheep BW by a label-free proteomics approach. The result showed, a total of 27, 14, 61, and 65 differentially abundant proteins (DAPs) were identified in the Hu_HBW vs. Hu_LBW, DP_HBW vs. DP_LBW, Hu_HBW vs. DP_HBW, and Hu_LBW vs. DP_LBW comparisons, respectively. Five proteins (including ILK, AHCYL2, MLIP, CYB5A, and SMTNL1) related to fat synthesis and muscle development were detected in the Hu sheep group. In the Dorper sheep group, the screened DAPs strictly related to muscle development and fat synthesis were significantly enriched in MAP kinase activity (MAPK12), Arachidonic acid metabolism, and Steroid hormone biosynthesis (PGFS, LOC101107119) pathways. Several DAPs related to immune responses (SERPINA1, FGG, SERPINC1, and LOC101108131), fat deposition (APOH, GC, AHSG, SKP1, ACSL1, ACAT1, and ACADS), and muscle development (LMOD3 and LRRC39) were detected in the Hu vs. Dorper sheep comparison. These analyses indicated that the BW of sheep is regulated via a variety of pathways, and these DAPs can be further investigated as candidate markers for predicting the BW of sheep. SIGNIFICANCE: Body weight is one of the key traits in sheep and involves multiple coordinated regulatory mechanisms, but the genetic mechanism of BW is still unclear in sheep. In the current study, the label-free method was used to identify the proteins and pathways related to BW using LT muscle of Hu sheep and Dorper sheep with different BW. These findings will provide new candidate proteins and vital pathways into the molecular mechanisms involved growth traits in sheep.

Effects of age on subcutaneous adipose tissue proteins in Chinese indigenous Ningxiang pig by TMT-labeled quantitative proteomics

Adipose tissue not only affects meat quality and animal productivity, but also participates in inflammation and immunity. Ningxiang pig is famous for their excellent meat quality, disease resistance and tolerance of roughage. It is not yet well known how proteins in adipose tissue is dynamically regulated during the growth of Ningxiang pig. This report studies the proteomic changes in subcutaneous adipose tissue in Ningxiang pigs to gain a better understanding of the molecular mechanism of fat development during the growth period. By TMT-labeled quantitative proteomic analysis of subcutaneous adipose tissue of 9 purebred Ningxiang pigs of different ages, we identified 2533 unique proteins and 716 differentially abundant proteins (DAPs), of which more than half of the DAPs were concentrated in the 90d-210d period. Retrograde endocannabinoid signaling was only significantly enriched in DAPs of N90d vs N30d, Alcoholism and Graft-versus-host disease were only significantly enriched in DAPs of N210d vs N90d. Proteins related to dilated cardiomyopathy was found to be an important pathway in fat development and lipid metabolism. A variety of novel DAPs involved in maintaining mitochondrial function and cell viability, such as NDUFS6, SDHB, COX5A, ATP5D and TNNT1, which play a role in controlling the prediction networks, may indirectly regulate the development and functional maintenance of adipocytes. SIGNIFICANCE: These age-dependent DAPs discovered in this study may help expand the understanding of the molecular mechanisms of the development, function maintenance and transformation of adipose tissue in Ningxiang pig for developing new strategies for improving meat quality and pig breeding in the future.

Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia

BACKGROUND

The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).

RESULTS

The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance.

CONCLUSIONS

Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.

Preliminary identification and analysis of differential RNA editing between higher and lower backfat thickness pigs using DNA-seq and RNA-seq data

RNA editing is an essential post-transcriptional regulatory mechanism. However, few studies have investigated the functional RNA edits in the economic traits of livestock on a genome-wide scale. Pigs are one of the most important livestock species and their fat is the principal organ involved in the regulation of adipose deposition. Here, we used three full-sibling pairs, with each pair comprising a pig with higher backfat (BF) thickness and lower backfat thickness, to identify RNA editing events based on whole-genome and transcriptome sequencing data. A total of 60,903 non-redundant RNA editing sites with 59,472 (97.7%) A-to-G edits were detected using a revised bioinformatics pipeline. A specific sequence context with G preference was found one base downstream of the edited site, and the editing level was associated with the distribution of nucleotides across nearly sites. Moreover, the A-to-G editing sites mostly occurred in the pig-special short interspersed nuclear elements, Pre0_SS. Comparing the difference between pigs with higher BF and lower BF, we found 211 differentially edited sites (DESites). Functional enrichment analyses revealed a significant enrichment of genes containing DESites in terms of adipose deposition. The DESites located in the six adipose-related genes (SKP1, GSK3B, COL5A3, MDM4, NT5C2, and DENND2A) were selected as candidate RNA editing sites associated with adipose deposition, and thus require further evaluation. This study mined the potentially functional RNA editing sites in pig adipose tissue and indicated that RNA editing may play an important role in adipose deposition, which provides a new insight into the post-transcriptionally mediated regulation mechanism of fat development.