Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

Abstract

When compared to modern lean-type breeds, Portuguese local Alentejano (AL) and Bísaro (BI) pig breeds present a high potential for subcutaneous and intramuscular fat (IMF) deposition which contributes for better meat quality. The aim of this work was to explore the genome function to better understand the underlying physiological mechanisms associated with body fat accretion. Dorsal subcutaneous fat samples were collected at slaughter from adult animals (n = 4 for each breed) with~150 kg body weight. Total RNA was obtained and sequenced for transcriptome analysis using DESeq2. A total of 458 differentially expressed (DE) genes (q-value < 0.05) were identified, with 263 overexpressed in AL and 195 in BI. Key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were upregulated in AL such as ACLY, FASN, ME1, ELOVL6 and SCD. A functional enrichment analysis of the DE genes was performed using Ingenuity Pathway Analysis. Cholesterol synthesis is suggested to be higher in AL via SREBF2, SCAP and PPARG, while lipolytic activity may be more active in BI through GH and AMPK signalling. Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.Genes 2020, 11, 422 2 of 20 inherent genetic value for biodiversity, local breeds are used to produce high quality dry-cured meat products, representing an important role in local economies, culture and landscape as the basics of sustainable local pork chains [2,4].Alentejano (AL) and Bísaro (BI) are the two main Portuguese pig breeds. AL evolved from the primitive Sus scrofa mediterraneus, belongs to the Mediterranean group of breeds [5] and is genetically similar to the Iberian (IB) pig [6]. This breed is commonly raised in the south of Portugal and generally characterized by its light bone structure, black color, short and slim extremities and energetic nature [7]. A medium-sized pig, the AL grows at a low rate (except under the finishing phase "montanheira") and presents a low prolificacy [8]. On the other hand, its high and early adipogenic activity provides a meat and fat composition that is attractive for both fresh meat market and for processing high-grade sausage and dry cured products [9,10]. Traditionally, the AL pig is raised under extensive conditions in an integrated pastoral system ("montado") and during the fattening season is fed with acorns from the existing Quercus forests from October to February [5,7]. BI breed belongs to the Celtic group [5], sharing ancestors with highly productive breeds such as Large-White and Landrace. Production of BI is distributed throughout the north of Portugal, from the Tagus River to the northern border with Spain. It is characterized by its docile temperament, presenting a large body with large legs, head and shoulders. BI pig presents a higher prolificacy and productivity than AL, though lower than other genotypes with similar origins but raised under intensive ...

Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels

“…In Iberian pigs, the ACACA gene was proposed as a candidate gene responsible for intramuscular content of saturated fatty acids and monounsaturated fatty acids fatty acids [ 47 ]. Furthermore, the up-regulation of FASN and SCD genes were reported in Alentejano pigs and related to the higher fat deposition observed in this breed [ 20 ]. The research performed on Iberian × Landrace pig cross lines indicated a significant association of the ACACA gene and IMF palmitic fatty acid percentage [ 48 ].…”

“…To date, in pigs, transcriptomic research has been applied to identify the regulation processes determining feed efficiency [ 18 ] and to examine the body’s response to different nutritional treatments [ 19 ]. Processes based on adipocyte tissue gene expression profiling in two Portuguese local pig breeds to determine the fat deposition via controlling of de novo fatty acid synthesis have been proposed, [ 20 ]. Furthermore, gene expression profiling in combination with genome resequencing has allowed for the detection of genes potentially related to backfat thickness [ 21 ].…”

“…The present study aimed to perform comprehensive whole transcriptome and miRNAome analyses [ 20 ] of adipocyte tissue to identify the molecular networks strongly related to the most crucial production traits, namely, fatness and feed intake in pigs.…”

Blocking NHE1 stimulates glioma tumor immunity by restoring OXPHOS function of myeloid cells

“…Reads were mapped to a mouse genome (mm10) using the STAR aligner with default setting and differential gene analysis was conducted using DESeq2 in Partek Flow 8.0 software (Partek, USA). Gene expression levels were obtained through the count of total exon reads for statistical analysis 19 . Enrichment analysis of DEGs was performed using Ingenuity Pathway Analysis (IPA®, QIAGEN Redwood City, www.qiagen.com/ingenuity) as described previously 20 .…”

The Efffect of Gender Differences to Fat Deposition In Yaks Based on an Integrated Transcriptomic and Metabonomics Analysis

“…Fat plays an important part in the life activities of livestock [1], including confronting starvation, lactation and parturition [2,3]. Meanwhile, as the core of the nutritional value of meat, the type and amount of fat are among those key factors which in uence meat quality like appearance, avor and tenderness [4][5][6], and is also essential to protect the carcass during cooling, avoiding cold shortening, drip loss and dark cutting [7][8][9][10].…”