The impact on meat quality of strategies to improve feed conversion efficiency in pigs and the functional networks underpinning the relationship

Feed efficiency (FE) is defined as a measure of efficiency in converting metabolizable energy acquired from macronutrients into body mass. The overall aims of this thesis were to identify genomic regions associated with FE in a commercial line of Maxgro boars, to evaluate the molecular and phenotypic relationship between FE and meat quality in Maxgro x (German Landrace x Large White) pigs and to investigate the molecular mechanisms contributing to differences in FE, in liver, fat and skeletal muscle tissue. Firstly, 952 boars having measures of FE traits were genotyped and used for a genome-wide association study. Most of the quantitative trait loci identified by this method were described for the first time, although some of them were located not far from previously associated genomic regions. Secondly, three metabolically important tissues, including muscle, adipose and liver were analysed. Significant differences in meat traits such as sensory profile, texture and cook loss suggest a minor impairment of meat quality from high-FE pigs. This group also exhibited leaner carcasses and greater muscle content. Ontology analysis predicted a more efficient immune defence in the muscle of high-FE pigs, which may indicate that these animals are also more efficient in conserving resources for growth. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the altered post-mortem muscle pH profiles between FE groups. Moreover, differences in amino acid metabolism may influence growth in FE-divergent muscle, whereas decreased degradation of fibroblasts could impact on collagen turnover and alter tenderness of meat. Transcriptomic profiling of adipose tissue of FE-divergent pigs suggested the establishment of a dense extracellular matrix and inhibition of capillary formation might be underlying mechanisms to achieve suppressed adipogenesis. Furthermore, gene expression patterns in the liver of high-FE pigs suggested improved hepatic absorption of carbohydrates and cholesterol, and enhanced reverse cholesterol transport. The liver of high-FE pigs may be characterised by higher protein turnover and increased epithelial cell differentiation, whilst enhanced quantity of invariant natural killer T-cells and viability of natural killer cells could induce a faster and more effective hepatic response to inflammatory stimuli.Strategien zur Verbesserung der Futterverwertung bei Schweinen und ihre Auswirkungen auf die Fleischqualität sowie Einblicke in die funktionellen Netzwerke, die dieser Beziehung zugrunde liegen Die Futterverwertung (FE) beschreibt die Effektivität der Umwandlung von metabolisierbarer Energie aus Makronährstoffen in Körpermasse. Die übergeordneten Ziele dieser Arbeit waren genomische Regionen zu bestimmen, die mit der Ausprägung von FE-Merkmalen in einer kommerziellen Linie von Maxgro Ebern in Zusammenhang stehen; molekulare und phänotypische Beziehung zwischen FE und Fleischqualität in einer Maxgro x (German Landrace x Large White) Population aufzuzeigen; und zugrundeliegende molekulare Mechanismen in drei FE-relevanten Geweben zu identifizieren. Im ersten Teil der Studie wurden 952 FE-getestete Eber genotypisiert und im Rahmen einer genomweiten Assoziationsstudie analysiert. Die meisten der mit dieser Methode identifizierten Quantitative Trait Loci wurden erstmals beschrieben, obwohl einige von ihnen in der Nähe von zuvor assoziierten genomischen Regionen lagen. Der zweite Teil dieser Dissertation betrachtet Muskel-, Fett- und Lebergewebe. Signifikante Unterschiede in den Fleischmerkmalen, wie zum Beispiel von sensorischen Profilen, Fleischtextur und Kochverlust, deuten auf eine geringfügige Verminderung der Fleischqualität bei Schweinen mit hoher FE hin. Andererseits wies diese Gruppe magerere Schlachtkörper und einen höheren Muskelanteil auf. Die Analyse der Genontologie prognostizierte eine erhöhte Effizienz der Immunabwehr im Muskel von Schweinen mit hoher FE, was darauf hindeuten könnte, dass diese Tiere auch effizienter in ihrer Ressourcennutzung für Wachstumsprozesse sind. Verschiebungen in der muskulären Umwandlung von Kohlenhydraten zu Glukose zwischen FE-divergenten Tieren wurden auch auf Ebene der post-mortalen pH-Profile zwischen den Gruppen abgebildet. Darüber hinaus könnten Unterschiede im Aminosäurestoffwechsel das Muskelwachstum beeinflussen, während ein verminderter Fibroblastenabbau den Kollagenumsatz und die Zartheit des Fleisches beeinflussen kann. Transkriptionelle Unterschiede im Fettgewebe FE-divergenter Schweine implizieren, dass die Bildung einer dichten extrazellulären Matrix und die Hemmung der Kapillarbildung grundlegende Mechanismen sein könnten, um die Adipogenese zu unterdrücken. Die Analyse der hepatischen Genontologie deutete auf eine verbesserte Aufnahme von Kohlenhydraten und Cholesterin sowie einen verbesserten Rücktransport von Cholesterin aus der Peripherie in Schweinen mit hoher FE hin. Zudem implizieren die Ergebnisse Unterschiede im Proteinumsatz und in der Reaktion auf Entzündungsreize

Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

This project has received funding from the European Union‘s Seventh Framework Programme for research, technological development and demonstration as part of the ECO-FCE project under grant agreement No. 311794.peer-reviewedFeed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.This project has received funding from the European Union‘s Seventh Framework Programme for research, technological development and demonstration as part of the ECO-FCE project under grant agreement No. 311794

RNA-Seq of Liver From Pigs Divergent in Feed Efficiency Highlights Shifts in Macronutrient Metabolism, Hepatic Growth and Immune Response

Liver is a metabolically complex organ that influences nutrient partitioning and potentially modulates the efficiency of converting energy acquired from macronutrients ingestion into a muscle and/or adipose tissue (referred to as feed efficiency, FE). The objective of this study was to sequence the hepatic tissue transcriptome of closely related but differently feed efficient pigs (n = 16) and identify relevant biological processes that underpin the differences in liver phenotype between FE groups. Liver weight did not significantly differ between the FE groups, however, blood parameters showed that total protein, glucose, cholesterol and percentage of lymphocytes were significantly greater in high-FE pigs. Ontology analysis revealed carbohydrate, lipid and protein metabolism to be significantly enriched with differentially expressed genes. In particular, high-FE pigs exhibited gene expression patterns suggesting improved absorption of carbohydrates and cholesterol as well as enhanced reverse cholesterol transport. Furthermore, the inferred decrease in bile acid synthesis in high-FE pigs may contribute to the observed greater levels of serum glucose, which can be then delivered to cells and utilized for growth and maintenance. Gene ontology analysis also suggested that livers of more efficient pigs may be characterized by higher protein turnover and increased epithelial cell differentiation, whereby an enhanced quantity of invariant natural killer T-cells and viability of natural killer cells could induce a quicker and more effective hepatic response to inflammatory stimuli. Our findings suggest that this prompt hepatic response to inflammation in high-FE group may contribute to the more efficient utilization of nutrients for growth in these animals

Analysis of meat quality traits and gene expression profiling of pigs divergent in residual feed intake

peer-reviewedResidual feed intake (RFI), the difference between actual feed intake and predicted feed requirements, is suggested to impact various aspects of meat quality. The objective of this study was to investigate the molecular mechanisms underpinning the relationship between RFI and meat quality. Technological, sensory and nutritional analysis as well as transcriptome profiling were carried out in Longissimus thoracis et lumborum muscle of pigs divergent in RFI (n = 20). Significant differences in sensory profile and texture suggest a minor impairment of meat quality in more efficient pigs. Low RFI animals had leaner carcasses, greater muscle content and altered fatty acid profiles compared to high RFI animals. Accordingly, differentially expressed genes were enriched in muscle growth and lipid & connective tissue metabolism. Differences in protein synthesis and degradation suggest a greater turnover of low RFI muscle, while divergence in connective tissue adhesion may impact tenderness. Fatty acid oxidation tending towards decrease could possibly contribute to reduced mitochondrial activity in low RFI muscle

RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

peer-reviewedBackground Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE. Results RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were ‘haematological system development & function’, ‘lymphoid tissue structure & development’, ‘tissue morphology’, ‘cellular movement’ and ‘immune cell trafficking’. Top significant canonical pathways represented among the differentially expressed genes included ‘IL-8 signalling’, ‘leukocyte extravasation signalling, ‘sphingosine-1-phosphate signalling’, ‘PKCθ signalling in T lymphocytes’ and ‘fMLP signalling in neutrophils’. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition. Conclusions Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.The ECO-FCE project was funded by the European Union Seventh Framework Programme (FP7 2007/2013) under grant agreement No. 311794

Analysis of meat quality traits and gene expression profiling of pigs divergent in residual feed intake

Residual feed intake (RFI), the difference between actual feed intake and predicted feed requirements, is suggested to impact various aspects of meat quality. The objective of this study was to investigate the molecular mechanisms underpinning the relationship between RFI and meat quality. Technological, sensory and nutritional analysis as well as transcriptome profiling were carried out in Longissimus thoracis et lumborum muscle of pigs divergent in RFI (n = 20). Significant differences in sensory profile and texture suggest a minor impairment of meat quality in more efficient pigs. Low RFI animals had leaner carcasses, greater muscle content and altered fatty acid profiles compared to high RFI animals. Accordingly, differentially expressed genes were enriched in muscle growth and lipid & connective tissue metabolism. Differences in protein synthesis and degradation suggest a greater turnover of low RFI muscle, while divergence in connective tissue adhesion may impact tenderness. Fatty acid oxidation tending towards decrease could possibly contribute to reduced mitochondrial activity in low RFI muscle

Impact of sociodemographic factors on the consumption of tubers in Brazil

Abstract Background Although tubers play a significant role in Brazilian agriculture, very little is known about the intake of tubers among the Brazilian population. The objective of this study was to characterize the intake of tubers across Brazil. The types of tubers consumed were quantified, and the impact of geographic and sociodemographic factors was assessed. Methods This cross-sectional study is based on dietary intake data of 33,504 subjects obtained from the Brazilian National Dietary Survey. All tuber containing foods were identified, and the contribution of different tubers to overall tuber consumption in Brazil was quantified. Descriptive analyses assessed the impact of macroregion and sociodemographic characteristics on tuber consumption, and differences in intake were assessed using statistical tests. Lastly, the dietary intakes of tuber consumers and non-consumers were compared after adjusting for energy and covariates to determine if there were any major differences in dietary intakes between the two groups. Results Fifty-five percent of the Brazilian population consumed tubers, which differed by macroregion. The intake of tubers among consumers also differed between macroregions. Overall, rural areas reported significantly higher mean daily intakes of tubers (122 g/day) among tuber consumers than urban areas (95 g/day). Mandioca and potato were the most commonly consumed tubers (59 and 43% prevalence, respectively, on any of the 2 days), while the highest daily intakes amongst tuber consumers across Brazil were noted for sweet potato (156 g/day) and potato (95 g/day). On a macroregion level, among tuber consumers, mandioca had the highest prevalence of consumption in the North (94%), Northeast (83%), and Central-West (68%), while consumption of potatoes was most prevalent in the Southeast (63%) and South (62%). Compared to women, small but significantly higher tuber intakes were noted for males (108 vs. 85 g/day). There were no significant differences in intakes among income quintiles. After adjusting for energy and other covariates, nutrient intakes between tuber and non-tuber consumers were not meaningfully different, with the exception of sodium (+ 6.0% comparing non-tuber to tuber consumers), iron (+ 6.1%), zinc (+ 5.7%), vitamin C (+ 8.3%), riboflavin (+ 9.0%), and folate (+ 7.9%). Conclusions Tuber consumption is influenced by regional and sociodemographic characteristics of the Brazilian population. When looking at energy-adjusted nutrient intakes, diets of tuber consumers have resulted in somewhat lower intakes of some micronutrients, namely riboflavin, folate, vitamin C, iron, sodium, and zinc

Manhattan plot of the genome-wide association analysis of EBV FCR.

<p>The red and blue lines indicate the suggestive (-log10[p-value] ≥ 4.7) and the Bonferroni-adjusted genome-wide significance threshold (-log10[p-value] ≥ 6), respectively.</p

Association of the five SNPs, located in selected functional genes mapped within 1Mb of the genome-wide significant markers, with breeding values for FCR and D110.

<p>Lower breeding values indicate higher feed efficiency.</p