Background: Intramuscular fat (IMF) content and its fatty acid (FA) composition are typically controlled by several genes, each with a small effect. In the current study, to pinpoint candidate genes and putative regulators involved in FA composition, we performed a multivariate integrative analysis between intramuscular FA and transcriptome profiles of porcine longissimus dorsi (LD) muscle. We also carried out a combination of network, regulatory impact factor (RIF), in silico prediction of putative target genes, and functional analyses to better support the biological relevance of our findings. Results: For this purpose, we used LD RNA-Seq and intramuscular FA composition profiles of 129 Iberian × Duroc backcrossed pigs. We identified 378 correlated variables (13 FA and 365 genes), including six FA (C20:4 n -6, C18:2 n -6, C20:3 n -6, C18:1 n -9, C18:0, and C16:1 n -7) that were among the most interconnected variables in the predicted network. The detected FA-correlated genes include genes involved in lipid and/or carbohydrate metabolism or in regulation of IMF deposition (e.g., ADIPOQ , CHUK , CYCS , CYP4B1 , DLD , ELOVL6 , FBP1 , G0S2 , GCLC , HMGCR , IDH3A , LEP , LGALS12 , LPIN1 , PLIN1 , PNPLA8 , PPP1R1B , SDR16C5 , SFRP5 , SOD3 , SNW1 , and TFRC ), meat quality ( GALNT15 , GOT1 , MDH1 , NEU3 , PDHA1 , SDHD , and UNC93A ), and transport (e.g., EXOC7 and SLC44A2 ). Functional analysis highlighted 54 over-represented gene ontology terms, including well-known biological processes and pathways that regulate lipid and carbohydrate metabolism. RIF analysis suggested a pivotal role for six transcription factors (CARHSP1, LBX1, MAFA, PAX7, SIX5, and TADA2A) as putative regulators of gene expression and intramuscular FA composition. Based on in silico prediction, we identified putative target genes for these six regulators. Among these, TADA2A and CARHSP1 had extreme RIF scores and present novel regulators in pigs. In addition, the expression of TADA2A correlated (either positively or negatively) with C20:4 n -6, C18:2 n -6, C20:3 n -6, C18:1 n -9, and that of CARHSP1 correlated (positively) with the C16:1 n -7 lipokine. We also found that these two transcription factors share target genes that are involved in lipid metabolism (e.g., GOT1 , PLIN1 , and TFRC ). Conclusions: This integrative analysis of muscle transcriptome and intramuscular FA profile revealed valuable information about key candidate genes and potential regulators for FA and lipid metabolism in pigs, among which some transcription factors are proposed to control gene expression and modulate FA composition differences.

Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candidate genes, biological processes, and pathways involved in the modulation of intramuscular FA profile fromlongissimus dorsimuscle. FA profile by gas chromatography of methyl esters and gene expression by RNA-Seq were determined in 129 Iberian × Duroc backcrossed pigs. An association analysis between the muscle transcriptome and its FA profile was performed, followed by a concordance and functional analysis. Overall, a list of well-known (e.g.,PLIN1,LEP, ELOVL6, SC5D,NCOA2,ACSL1, MDH1, LPL,LGALS12, TFRC, GOT1,andFBP1) and novel (e.g.,TRARG1, TANK, ENSSSCG00000011196,andENSSSCG00000038429) candidate genes was identified, either in association with specific or several FA traits. Likewise, several of these genes belong to biological processes and pathways linked to energy, lipid, and carbohydrate metabolism, which seem determinants in the modulation of FA compositions. This study can contribute to elucidate the complex relationship between gene expression and FA profile in pig muscle.

This paper studies parameters of a lactation curve such as peak yield (PY) and persistency (P), which do not conform to the usual selection criteria in the Murciano-Granadina (MG) breed, but are considered to be an alternative to benefit animal welfare without reducing production. Using 315,663 production records (of 122,883 animals) over a period of 24 years (1990–2014), genetic parameters were estimated with uni-, bi- and multivariate analysis using multiple trait derivative free restricted maximum likelihood (MTDFREML). The heritability (h²)/repeatability (r_e) of PY, yield (Y) and P was estimated as 0.13/0.19, 0.16/0.25 and 0.08/0.09 with the uni-trait and h² of bi- and multi-traits analysis ranging from 0.16 to 0.17 of Y, while that of PY and Y remained constant. Genetic correlations were high between PY–Y (0.94 ± 0.011) but low between PY–P (–0.16 ± 0.054 to –0.17 ± 0.054) and between Y–P (–0.06 ± 0.058 to –0.05 ± 0.058). Estimates of h²/r_e were low to intermediate. The selection for Y–PY or both can be implemented given the genetic correlation between these traits. PY–P and Y–P showed low to negligible correlation values indicating that if these traits are implemented in the early stages of evaluation, they would not be to the detriment of PY–Y. The combination of estimated breeding values (EBVs) for all traits would be a good criterion for selection.

The intramuscular fat (IMF) content is an important indicator of meat quality, affecting the sensory properties of meat. IMF is a complex trait with polygenic nature. This research aimed to identify differentially expressed (DE) genes and key transcription factors (TFs) associated with IMF deposition in the liver of two rabbit lines divergently selected for IMF (high-IMF: H and low-IMF: L). We used 48 rabbits (24 H and 24 L) belonging to the 9th generation of selection to determine their liver gene expression levels using 3′ RNA sequencing. We found 308 DE genes between H and L lines; 134 upregulated and 174 downregulated in the H line. Among them, ACBD4, ACOT1, ACOT4, AIFM2, CPT1A, CPT1B, CROT, CYP4B1, CYP4A6, HADHB, IGFBP1, IGFBP2, FABP4, GPAT3, MPZL2, MYLIP, MRPL15, NR4A2, PLIN2, PCTP, PRRG4, PAQR9, RAB34, SLC16A11, SLC18A1, SLC2A1, TPMT , and UBC , were related to lipid metabolism, energy metabolism, purine/thiopurine metabolism, and/or molecule transport that could influence the IMF deposition. Of the 308 DE genes, 210 target genes were predicted for 11 DE TFs through the gene regulatory networks. Notably, 3 TFs, namely ETV1 , NR4A1 , and IKZF3 appear to modulate gene expression of several putative targets (including common targets: CREM, NR4A2, and RRS1 ). Functional analysis of DE genes revealed an overrepresentation of 40 enriched terms, including the PPAR signalling pathway (associated genes: CPT1B, FABP4, and PLIN2 ) and other lipid metabolism bioprocesses. Collectively, our results enhance the understanding of the liver-muscle crosstalk that contributes to IMF deposition and improvement of rabbit meat quality.

In the ex situ conservation of chondrichthyan species, successful reproduction in aquaria is essential. However, these species often exhibit reduced reproductive success under human care. A key aspect is that conventional sperm analyses do not provide insights into the functional competence of sperm. However, proteomics analysis enables a better understanding of male physiology, gaining relevance as a powerful tool for discovering protein biomarkers related to fertility. The present work aims to build the first proteome database for shark semen and to investigate the proteomic profiles of seminal plasma and spermatozoa from small-spotted catsharks (Scyliorhinus canicula) related to the underlying adaptations to both natural and aquarium environments, thereby identifying the reproductive impact in aquarium specimens. A total of 305 seminal plasma and 535 spermatozoa proteins were identified. Among these, 89 proteins (29.2% of the seminal plasma set) were common to both spermatozoa and seminal plasma. In the seminal plasma, only adenosylhomocysteinase protein showed differential abundance (DAP) between wild and aquarium animals. With respect to the spermatozoa proteins, a total of 107 DAPs were found between groups. Gene Ontology enrichment analysis highlighted the primary functional roles of these DAPs involved in oxidoreductase activity. Additionally, KEGG analysis indicated that these DAPs were primarily associated with metabolic pathways and carbon metabolism. In conclusion, we have successfully generated an initial proteome database for S. canicula seminal plasma and spermatozoa. Furthermore, we have identified protein variations, predominantly within spermatozoa, between aquarium and wild populations of S. canicula. These findings provide a foundation for future biomarker discovery in shark reproduction studies. However, additional research is required to determine whether these protein variations correlate with reproductive declines in captive sharks.