Comparison between the three porcine RN genotypes for growth,carcass composition and meat quality traits

A three-step experimental design has been carried out to add evidence about the existence of the RN gene, with two segregating alleles RN^- and rn⁺, having major effects on meat quality in pigs, to estimate its effects on production traits and to map the RN locus. In the present article, the experimental population and sampling procedures are described and discussed, and effects of the three RN genotypes on growth and carcass traits are presented. The RN genotype had no major effect on growth performance and killing out percentage. Variables pertaining to carcass tissue composition showed that the RN^- allele is associated with leaner carcasses (about 1 s.d. effect without dominance for back fat thickness, 0.5 s.d. effect with dominance for weights of joints). Muscle glycolytic potential (GP) was considerably higher in RN^- carriers, with a maximum of a 6.85 s.d. effect for the live longissimus muscle GP. Physico-chemical characteristics of meat were also influenced by the RN genotype in a dominant way, ultimate pH differing by about 2 s.d. between homozygous genotypes and meat colour by about 1 s.d. Technological quality was also affected, with a 1 s.d. decrease in technological yield for RN^- carriers. The RN genotype had a more limited effect on eating quality. On the whole, the identity between the acid meat condition and the RN^- allele effect is clearly demonstrated (higher muscle GP, lower ultimate pH, paler meat and lower protein content), and the unfavourable relationship between GP and carcass lean to fat ratio is confirmed.     

Expression profiling analysis for genes related to meat quality and carcass traits during postnatal development of backfat in two pig breeds

The competitive equilibrium of fatty acid biosynthesis and oxidation in vivo determines porcine sub-cutaneous fat thickness(SFT) and intramuscular fat(IMF) content.Obese and lean-type pig breeds show obvious differences in adipose deposition;however, the molecular mechanism underlying this phenotypic variation remains unclear.We used pathway-focused oligo microarray studies to examine the expression changes of 140 genes associated with meat quality and carcass traits in backfat at five growth stages(1―5 months) of Landrace(a leaner, Western breed) and Taihu pigs(a fatty, indigenous, Chinese breed).Variance analysis(ANOVA) revealed that differences in the expression of 25 genes in Landrace pigs were significant(FDR adjusted permutation, P<0.05) among 5 growth stages.Gene class test(GCT) indicated that a gene-group was very significant between 2 pig breeds across 5 growth stages(PErmineJ<0.01), which consisted of 23 genes encoding enzymes and regulatory proteins associ-ated with lipid and steroid metabolism.These findings suggest that the distinct differences in fat deposition ability between Landrace and Taihu pigs may closely correlate with the expression changes of these genes.Clustering analysis revealed a very high level of significance(FDR adjusted, P<0.01) for 2 gene expression patterns in Landrace pigs and a high level of significance(FDR adjusted, P<0.05) for 2 gene expression patterns in Taihu pigs.Also, expression patterns of genes were more diversified in Taihu pigs than those in Landrace pigs, which suggests that the regulatory mechanism of micro-effect polygenes in adipocytes may be more complex in Taihu pigs than in Landrace pigs.Based on a dy-namic Bayesian network(DBN) model, gene regulatory networks(GRNs) were reconstructed from time-series data for each pig breed.These two GRNs initially revealed the distinct differences in physiological and biochemical aspects of adipose metabolism between the two pig breeds;from these results, some potential key genes could be identified.Quantitative, real-time RT-PCR(QRT-PCR) was used to verify the microarray data for five modulated genes, and a good correlation between the two measures of expression was observed for both 2 pig breeds at different growth stages(R=0.874±0.071).These results highlight some possible candidate genes for porcine fat characteristics and provide some data on which to base further study of the molecular basis of adipose metabolism.     

Bayesian segregation analysis of milk flow in Swiss dairy cattle using Gibbs sampling

Segregation analyses with Gibbs sampling were applied to investigate the mode of inheritance and to estimate the genetic parameters of milk flow of Swiss dairy cattle. The data consisted of 204 397, 655 989 and 40 242 lactation records of milk flow in Brown Swiss, Simmental and Holstein cattle, respectively (4 to 22 years). Separate genetic analyses of first and multiple lactations were carried out for each breed. The results show that genetic parameters especially polygenic variance and heritability of milk flow in the first lactation were very similar under both mixed inheritance (polygenes + major gene) and polygenic models. Segregation analyses yielded very low major gene variances which favour the polygenic determinism of milk flow. Heritabilities and repeatabilities of milk flow in both Brown Swiss and Simmental were high (0.44 to 0.48 and 0.54 to 0.59, respectively). The heritability of milk flow based on scores of milking ability in Holstein was intermediate (0.25). Variance components and heritabilities in the first lactation were slightly larger than those estimates for multiple lactations. The results suggest that milk flow (the quantity of milk per minute of milking) is a relevant measurement to characterise the cows milking ability which is a good candidate trait to be evaluated for a possible inclusion in the selection objectives in dairy cattle.     

Developmental changes of carcass composition, meat quality and organs in the Jinhua pig and Landrace

The present study was aimed to compare the developmental changes of carcass composition, meat quality characteristics and organ weight in pigs of different breeds. Six pigs (sex balance) of each breed were slaughtered at 35, 80 and 125 days of age, respectively. The carcass was chilled and the left carcass side was dissected into bone, lean meat, fat and skin; additionally, organ weight and meat quality parameters were observed. Carcasses of the Jinhua pig were lighter (P < 0.001), contained less lean meat percentage (P < 0.01) and more carcass fat percentage (P < 0.05) than did carcasses of the Landrace. L*-values were lower in Jinhua pigs than in Landrace at 125 days of age (P < 0.05), but the Jinhua pig had higher a*-values compared with Landrace at the age of 80 days (P < 0.01) and 125 days (P < 0.01), respectively. In addition, Jinhua pigs showed lower colour scores (P < 0.05), higher intramuscular fat (IMF) percentage (P < 0.05), less marbling scores (P < 0.05) and lower drip loss (P < 0.05) than Landrace. For organ weight, Jinhua pigs had higher relative heart weight at the age of 80 days (P < 0.05) and 125 days (P < 0.001), and higher relative liver weight at 125 days of age (P < 0.01) than that of Landrace. In addition, the relative kidney weight was heavier (P < 0.001) in the Jinhua pig than in the Landrace during the whole experiment. These results indicated that developmental changes of carcass composition, meat quality parameters and organ weight displayed breed differences. Jinhua pigs were fatter than Landrace but the former had better quality characteristics in the meat.     

Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross

A whole-genome quantitative trait locus (QTL) scan for 31 phenotypes related to growth, carcass composition and meat quality was conducted using 1187 progeny of a commercial four-way cross. Animals were genotyped for 198 microsatellite markers that spanned the entire porcine genome. QTL analysis was conducted to extract information from paternal and maternal meioses separately using a rank-based nonparametric approach for half-sib designs. Nine QTL exceeded genome-wide significance: one QTL affecting growth (average daily gain on SSC1), two QTL influencing carcass composition (fatness on SSC3 and muscle mass on SSC15) and six QTL influencing meat quality (tenderness on SSC4 and SSC14; colour on SSC5, SSC6 and SSCX; and conductivity on SSC16). All but one of these coincided with previously reported QTL. In addition, we present evidence for 78 suggestive QTL with a combined false discovery rate of 40%.     

Effects of caponization on growth performance,carcass composition and meat quality of males of a layer line

The present experiment was conducted in order to evaluate the effects of caponization on growth, carcass composition and meat quality of males of a layer line reared until the 34th week of age. Two hundred and fifty males of a layer line were purchased and randomly divided in two equal groups: intact males and capons. Caponization was conducted at 45 days of age. Three slaughters were performed at the ages of 26, 30 and 34 weeks of age. Caponization did not affect feed intake and final live weight. Capons had a heavier breast and lighter leg than intact males. Lipid accumulation was enhanced by the caponization and fat was stored mainly at the fat pad and the skin of the commercial parts excluding the drumstick. The Pectoralis major muscle of capons had higher intramuscular fat content, lightness (L) and yellowness (b*) values and lower redness values (a*). In conclusion, caponization could be applied to a layer genotype in order to produce commercial chicken meat.     

Genome-wide identification of quantitative trait loci for carcass composition and meat quality in a large-scale White Duroc × Chinese Erhualian resource population

Carcass and meat quality traits are economically important in pigs. In this study, 17 carcass composition traits and 23 meat quality traits were recorded in 1028 F₂ animals from a White Duroc × Erhualian resource population. All pigs in this experimental population were genotyped for 194 informative markers covering the entire porcine genome. Seventy-seven genome-wide significant quantitative trait loci (QTL) for carcass traits and 68 for meat quality were mapped to 34 genomic regions. These results not only confirmed many previously reported QTL but also revealed novel regions associated with the measured traits. For carcass traits, the most prominent QTL was identified for carcass length and head weight at 57 cM on SSC7, which explained up to 50% of the phenotypic variance and had a 95% confidence interval of only 3 cM. Moreover, QTL for kidney and spleen weight and lengths of cervical vertebrae were reported for the first time in pigs. For meat quality traits, two significant QTL on SSC5 and X were identified for both intramuscular fat content and marbling score in the longissimus muscle, while three significant QTL on SSC1 and SSC9 were found exclusively for IMF. Both LM and the semimembranous muscle showed common QTL for colour score on SSC4, 5, 7, 8, 13 and X and discordant QTL on other chromosomes. White Duroc alleles at a majority of QTL detected were favourable for carcass composition, while favourable QTL alleles for meat quality originated from both White Duroc and Erhualian.     

Association analyses of porcine SERPINE1 reveal sex-specific effects on muscling, growth, fat accretion and meat quality

The serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 (SERPINE1) gene encodes plasminogen activator inhibitor type 1 (PAI), which is the major physiological inhibitor of tissue‐type and urokinase‐type plasminogen activators and plays a role in obesity and insulin resistance in women but not in men. We detected SNP FN396538:g.566G>A in intron 3 and a non‐synonymous substitution NM_213910:c.612A>G in exon 3 (p.Ile159Val) and mapped the gene to position 8.4 cM on the linkage map of chromosome 3. Association analyses were conducted on the 12th–15th generation of the Meishan × Large White (MLW) cross (n = 565), with records for weight at the end of test, lifetime daily gain, test time daily gain, loin depth and backfat depth, as well as on a European wild boar × Meishan (W × M) F₂ population (n = 333) with 47 traits recorded for carcass composition and meat quality. Analyses performed across the entire MLW population or in the male animals did not show any trait significantly associated with the loci studied. In female animals, both SNPs were associated with loin depth at nominal P < 0.05 with adjusted P values equal to 0.051 (g.566) and 0.057 (c.612). Differences between homozygotes were up to 0.65 SD. In the entire W × M population and female animals, SERPINE1 was significantly associated at adjusted P < 0.05 in descending order with muscling, growth and fat accretion and in male animals with meat quality (R‐value). In the studied populations, allele effects were in opposite directions, which implies that the SNPs are markers that are in linkage disequilibrium with a causative mutation.     

Bayesian species delimitation combining multiple genes and traits in a unified framework

Delimitation of species based exclusively on genetic data has been advocated despite a critical knowledge gap: how might such approaches fail because they rely on genetic data alone, and would their accuracy be improved by using multiple data types. We provide here the requisite framework for addressing these key questions. Because both phenotypic and molecular data can be analyzed in a common Bayesian framework with our program iBPP, we can compare the accuracy of delimited taxa based on genetic data alone versus when integrated with phenotypic data. We can also evaluate how the integration of phenotypic data might improve species delimitation when divergence occurs with gene flow and/or is selectively driven. These two realities of the speciation process are ignored by currently available genetic approaches. Our model accommodates phenotypic characters that exhibit different degrees of divergence, allowing for both neutral traits and traits under selection. We found a greater accuracy of estimated species boundaries with the integration of phenotypic and genetic data, with a strong beneficial influence of phenotypic data from traits under selection when the speciation process involves gene flow. Our results highlight the benefits of multiple data types, but also draws into question the rationale of species delimitation based exclusively on genetic data.     

Polymorphism of the pig acetyl-coenzyme A carboxylase α gene is associated with fatty acid composition in a Duroc commercial line

Acetyl-coenzyme A carboxylase α (ACACA) catalyses the first committed step in the biosynthesis of long-chain fatty acids (FA) by converting acetyl-CoA into malonyl-CoA. In pigs, the ACACA gene maps to a chromosome 12 QTL with important effects on FA composition. In the present study, we have sequenced the coding region of the pig ACACA gene in 15 pigs, identifying 21 polymorphic sites that were either synonymous or non-coding. Ten of these SNPs segregated in a Duroc commercial population ( n  = 350) for which lipid metabolism and meat and carcass quality trait records were available. Significant associations were found between two linked single nucleotide polymorphisms (c.4899G>A and c.5196T>C) and percentages of carcass lean, intramuscular fat, monounsaturated, saturated (myristic, palmitic and stearic) and polyunsaturated (linoleic) FAs in the longissimus thoracis et lumborum muscle, along with serum HDL-cholesterol concentration. The most important allele substitution effects were observed for the polyunsaturated/saturated FA ratio (13–21% of the phenotypic mean) as well as for the percentages of ω-6 and polyunsaturated FAs, especially linoleic acid (7–16% of the phenotypic mean). These results suggest the existence of a causal mutation, mapping to the chromosomal region containing the pig ACACA gene, with marked effects on FA composition of meat.     

Evaluation of the Chinese indigenous pig breed Dahe and crossbred Dawu for growth and carcass characteristics, organ weight, meat quality and intramuscular fatty acid and amino acid composition

The objectives of the experiment were to evaluate growth and carcass characteristics, organ weight, meat quality and intramuscular fatty acid (FA) and amino acid composition between the Chinese indigenous pig breed Dahe and the crossbred Dawu. The Dahe pigs had lower average daily gain (P < 0.001) and a higher feed conversion ratio (P < 0.001) compared with the Dawu pigs. The Dahe pigs contained less lean meat percentage (P < 0.001) and more carcass fat percentage (P < 0.001) compared with the Dawu pigs. For organ weight, the Dahe pigs had lower relative heart weight and small intestine weight, respectively, compared with that of the Dawu pigs (P < 0.001). In addition, the Dahe pigs showed higher pH values (at 45 min and 24 h, P < 0.001 and P < 0.001, respectively), higher Marbling score (P < 0.05), lower Minolta L values (at 45 min and 24 h, P < 0.001 and P < 0.05, respectively) and lower muscle fiber area (P < 0.05) than did the Dawu pigs. C18:1, C16:0, C18:0 and C18:2 were the main FAs and nine essential amino acids were found in the Longissimus dorsi of the two breeds.     

Effects of feeding and rearing systems on growth, carcass composition and meat quality in pigs

Animal growth performance and quality of pork depend on the interactive effects of pig genotype, rearing conditions, pre-slaughter handling, and carcass and meat processing. This paper focuses on the effects of feeding and rearing systems (feeding level and diet composition, housing, production system, etc.) on growth performance, carcass composition, and eating and technological qualities of pork. The feeding level and protein : energy ratio can be used to manipulate growth rate or composition of weight gain. Restricted feed allowance strongly reduces growth rate and carcass fatness and also intramuscular fat (IMF) level, resulting in decreased meat tenderness or juiciness. Expression of compensatory growth due to restricted followed by ad libitum feeding modifies the composition of weight gain at both carcass and muscle levels, and may improve meat tenderness due to higher in vivo protein turnover. Decreasing the protein : energy ratio of the diet actually increases IMF and improves eating quality, but gives fatter carcasses. In contrast, a progressive reduction in the protein : energy ratio leads to similar carcass composition at slaughter but with higher IMF. Technological meat traits (pH1, pHu, colour, drip loss) are generally not affected by the level or protein : energy in feed. Modification of fatty acid composition and antioxidant level in meat can be obtained through diet supplementations (e.g. vegetable sources with high n-3 fatty acids), thereby improving the nutritional quality of pork. Influences of pig rearing system on animal performance, carcass and meat traits result from interactive effects of housing (floor type, space allowance, ambient temperature, physical activity), feeding level and genotype in specific production systems. Indoor enrichment (more space, straw bedding) generally increases growth rate and carcass fatness, and may improve meat juiciness or flavour through higher IMF. Outdoor rearing and organic production system have various effects on growth rate and carcass fatness, depending on climatic conditions and feed allowance. Influence on meat quality is also controversial: higher drip and lower pHu and tenderness have been reported, whereas some studies show improved meat juiciness with outdoor rearing. Discrepancies are likely due to differences between studies in rearing conditions and physiological responses of pigs to pre-slaughter handling. Specific production systems of the Mediterranean area based on local breeds (low growth rate, high adiposity) and free-range finishing (pasture, forests), which allows pig to express their genetic potential for IMF deposition, clearly demonstrate the positive effects of genotype × rearing system interactions on the quality of pork and pork products.     

Effect of the inclusion of food waste in pig diets on growth performance, carcass and meat quality

Food waste from fish and fruit shops was used as an alternative to the grain in grower-finisher pig diets. Two diets were formulated on an iso-nutrient basis (14 MJ digestible energy per kg, 160 g crude protein per kg on a dry-matter basis) to contain 0 g of food waste per kg in the control diet and 50 g of fish-shop waste per kg and 120 g of fruit-shop waste per kg in the experimental diet. In the study, 28 pigs per diet (seven pigs per pen) were fed ad libitum from 20 kg to 100 kg, then, they were slaughtered and the carcass characteristics determined. The inclusion of food waste in the diet had no significant effect (P>0.05) on average daily feed intake (2.12 v. 2.20 kg/day), average daily gain (0.74 v. 0.78 kg/day), or gain/feed (0.35 v. 0.35 kg per kg). In the case of the experimental diet, backfat thickness was significantly lower (18.0 v. 21.3 mm, P < 0.01). The results of the taste test indicated that the meat from food waste-fed pigs had acceptable organoleptic quality although a very light aroma to fish was observed in the bacon (P < 0.01).It was concluded that food waste from the fish and fruit shops could be included in grower-finisher pig diets without any detrimental effect on growth performance and only minor effects on carcass characteristics and meat quality.     

Relationships among carcass weight, acid-base-balance of the blood, meat quality parameters and body composition of cultured rainbow trout (Oncorhynchus mykiss)

The relationshis among carcass weight, acid-base-balance of the blood as an indicator for metabolic load susceptibility, meat quality parameters, and body Composition were investigated in rainbow trout. Examinations were carried out in two replicates using a total of 300 trout from a Danish population. Within replicates, the trout were of aproximately the same age. In Replicate I trout, increasing carcass weight was accompanied by a more arkaline reaction of the blood. Carcass weight was significantly correlated with blood-pH and bicarbonate concentration (.19 and 26). Regression coefficients, however, confirmed only an increase of bicarbonate concentration with increasing carcass weight (b = .013 mmol/L per g, s_b= 0.005). In meat quality parameters, muscular pH₂₄ values decreased linearly in both replicates with increasing carcass weight, as shown by significant correlation estimates (-20 and -.27) and regression coefficients (b = -.0006, s_b=.0002, and b = -.001, s_b= .0003). Relationshis of other meat quality parameters to inmeasing carcass weight were evaluated differently by correlation and regression coefficients. No relationship was found between carcass weight and body composition. In general, correlation estimates describing interrelations between acid-base and meat quality parameters were on a very low level. Independent from carcass weight, there were clearly metabolically loaded and unloaded trout as well as trout with a mixed acid-base-status. Acid-base parameters were significantly correlated with each other. Generally, estimates for correlations between meat quality parameters were on a very low level. Body composition arameters, dry weight and crude fat content were highly significantly correlated (0.47) in Replicate II; in Replicate I there was no interrelation.     

Fungi Evolution Revisited: Application of the Penalized Likelihood Method to a Bayesian Fungal Phylogeny Provides a New Perspective on Phylogenetic Relationships and Divergence Dates of Ascomycota Groups

The depiction of evolutionary relationships within phylum Ascomycota is still controversial because of unresolved branching orders in the radiation of major taxa. Here we generated a dataset of 166 small subunit (18S) rDNA sequences, representative of all groups of Fungi and used as input in a Bayesian phylogenetic analysis. This phylogeny suggests that Discomycetes are a basal group of filamentous Ascomycetes and probably maintain ancestor characters since their representatives are intermingled among other filamentous fungi. Also, we show that the evolutionary rate heterogeneity within Ascomycota precludes the assumption of a global molecular clock. Accordingly, we used the penalized likelihood method, and for calibration we included a 400 million-year-old Pyrenomycete fossil considering two distinct scenarios found in the literature, one with an estimated date of 1576 Myr for the plant–animal–fungus split and the other with an estimated date of 965 Myr for the animal–fungus split. Our data show that the current classification of the fossil as a Pyrenomycete is not compatible with the second scenario. Estimates under the first scenario are older than dates proposed in previous studies based on small subunit rDNA sequences but support estimates based on multiprotein analysis, suggesting that the radiation of the major Ascomycota groups occurred into the Proterozoic era. Reviewing Editor: Dr. Nicolas Galtier     

Dried artichoke bracts in rabbits nutrition: effects on the carcass characteristics,meat quality and fatty-acid composition

In this study, the effects of the inclusion of artichoke bracts (AB) in rabbit diets on the carcass characteristics and rabbit meat quality were studied. A total of 120 rabbits aged 38 days were used and divided into three groups that were fed with different isonitrogenous and isocaloric diets supplemented with AB at 0%, 5% and 10%. The animals were single housed in wire cages at a temperature of 22±2°C and had free access to clean drinking water. At 96 days of age, 12 rabbits/group were slaughtered in an experimental slaughterhouse without fasting. The carcass was weighed and the weights of the skin and full gastrointestinal tract were recorded. Carcasses were chilled at +4°C for 24 h in a refrigerated room. The chilled carcass weight (CCW), dressing out percentage (CCW as percentage of slaughter weight), and the ratio of the head and liver were determined as a percentage of CCW. The reference carcass weight was also calculated. Carcasses were halved and the two longissimus dorsi (LD) muscles were excised. The left LD muscle was divided into two parts. The fore part was used to measure pH, colour and cooking losses. The hind part of the left LD was vacuum-packed, frozen at –20°C and then freeze-dried. Proximate composition, fatty-acid profile and thiobarbituric acid-reactive substances values were determined on freeze-dried samples. Results showed that carcass characteristics, LD muscle traits and its oxidative status were not affected by the AB supplementation, except for the meat ether extract content that increased from 0.68% to 0.94% on fresh matter basis with the increase of the AB supplementation (P<0.01). The α-linolenic acid proportion decreased with the increase of the AB supplementation from 3.58% to 2.59% in the LD muscle and from 4.74% to 3.62% in the perirenal fat, whereas the n-6/n-3 ratio increased significantly with increasing AB inclusion from 7.15 to 10.20 in the LD muscle and from 6.68 to 9.35 in the perirenal fat (P<0.01). Furthermore, no significant difference was found in preference among meat samples from each group. The enrichment of the rabbit’s diet with AB allows the production of rabbit meat with a good degree of unsaturation and low saturation, even if the n-6/n-3 ratio was slightly worse.     

Evidence for Multiple Determinants of the Body Mass Index: The National Heart,Lung, and Blood Institute Family Heart Study

The body mass index (BMI) is a complex phenotype representing the amount of fat mass, lean mass, body build and proportions, and it is likely to be affected by various metabolic processes, hormonal effects, energy intake and expenditure, and interactions within and among these broad categories of etiologic factors. Nonetheless, several previous studies have reported evidence for major gene segregation for the BMI in various populations. Data on a random sample of Caucasian families participating in the National Heart, Lung, and Blood Institute (NHLBI) Family Heart Study were analyzed to document the extent of familial resemblance and to investigate whether a similar monogenic inheritance pattern could be detected. Genetic analysis was carried out on age- and sex-adjusted BMI values. Familial correlations were significant implying a maximal heritability, including all genetic and environmentally inherited additive factors, of 41% to 59%. Segregation analysis revealed the presence of two maximum likelihood solutions, one characterized as a recessive Mendelian gene and the other as a major effect with an ambiguous transmission pattern. The presence of two such solutions is consistent with detection of two separate factors, each influencing the BMI distribution in a substantive manner. The evidence also supports a multifactorial background for BMI and suggests that the frequencies of these two factors, one of which appears to be a gene, may vary among diverse populations in the United States.