Transcript variants of a region on SSC15 rich in QTLs associated with meat quality in pigs

Abstract A high meat percentage in the porcine carcass has been achieved as a result of selection, but it has contributed to a deterioration of pork quality. The level of intramuscular fat has significantly declined, the pork has lost its tenderness and drip loss in meat has substantially increased, which has led to a deterioration of meat flavour and its technological suitability. The recovery of good pork quality could be supported by the development of genetic markers enabling faster breeding progress. This study presents a method by using RNA-seq data that identifies new variants for a chromosome region rich in QTLs for pork quality and selects gene candidates for these traits. This work included two pig breeds: the Polish Landrace (PL) and Puławska (PUL), which differ in meat quality and fat content. The transcriptome profile was estimated for semimembranosus and longissimus dorsi muscles. Into variant calling analysis, transcripts of both muscles encoded by genes located in a region between microsatellites SW964 and SW906 (43-135.9 Mbp) in SSC15 were included. In total, 439 transcripts were searched, 2,800 gene variants were identified and 6 mutations with a high effect belonging to the frameshift variants were found (ENSSSCG00000015976, ENSSSCG00000027516, WRN and XIRP2). Moreover, several interesting significant missense variants in PDLIM3, PLCD4 and SARAF genes were detected. These genes are recommended as candidates for meat quality; however they require further investigation in an association study.

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Effects of pre-slaughter short-term factors on pork quality

Animal Production Science ◽

10.1071/an17665 ◽

2019 ◽

Vol 59 (12) ◽

pp. 2273

Author(s):

Fotios Mantis ◽

Iosif Bizelis ◽

George K. Symeon ◽

Emmanuel Rogdakis

Keyword(s):

Meat Quality ◽

Sarcomere Length ◽

Quality Parameters ◽

Climatic Conditions ◽

Longissimus Dorsi ◽

Pork Quality ◽

Drip Loss ◽

Short Term ◽

Blood Samples ◽

Meat Samples

We examined the effects of pre-slaughter short-term factors including season of the year, duration of transportation and lairage time, as well as sex of pigs, on pork quality. Meat samples were collected from 590 pigs (females, entire and castrated males) that were slaughtered in a commercial abattoir in Greece over a 15-month period. Meat quality parameters pH, colour, drip loss, cooking loss, Warner–Bratzler shear values and sarcomere length were measured on the longissimus dorsi. DNA was isolated from blood samples and the frequency of the recessive halothane gene mutation HALn was determined. The results demonstrated that pork quality with respect to pH and L* values was normal in 93.9% of the samples, with 5.1% of samples classified as PSE (pale, soft and exudative) and 1.0% as DFD (dark, firm and dry). Duration of transportation was critical: brief and long transfers had the ability to impair meat quality. A lairage time of 2–4 h before slaughter was adequate when the pigs were free of HALn and the climatic conditions were not extreme. Season of the year was a very important factor, with significant variations recorded in meat-quality parameters between winter and summer months. Finally, the sex of the animals was responsible for differences in meat quality, but these differences were small and unlikely to be identified by the consumers.

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PSII-22 Comparison of the meat quality traits of crossbred pigs and the Large Black pigs

Journal of Animal Science ◽

10.1093/jas/skz258.490 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 241-242

Author(s):

Yongjie Wang ◽

Keshari Thakali ◽

Sarah Shelby ◽

Jason Apple ◽

Yan Huang

Keyword(s):

Meat Quality ◽

Genomic Diversity ◽

Longissimus Dorsi ◽

Rna Seq ◽

Longissimus Dorsi Muscle ◽

A Value ◽

Dorsi Muscle ◽

Body Weights ◽

C Value ◽

Crossbred Pigs

Abstract The purpose of this study was to compare the meat quality and genomic differences between cross-bred commercial pig (CP) and domestic Large Black pig (BP). Seven cross-bred commercial pigs and eight British Large Black pigs were assigned to CP group and BP group, with initial mean body weights of 18.82±1.412 kg for CP group and 23.31±1.935 kg for BP group, P = 0.061, and fed ad libitum. The final BW of the CP at d101 was similar to the BP (130.0±8.16 kg vs. 121.1±2.80 kg, P = 0.132). However, the BP group took 108 days to reach the final BW. The ADG in the CP was higher than BP (1.102±0.0599 kg vs. 0.905±0.0138 kg, P = 0.003). The hot carcass weight of CP was higher (P < 0.01) than BP, but the backfat of BP was higher (P < 0.01) than CP. The a* value of CP was higher (P < 0.05) than BP, and the c* value of CP was tended to be higher (P < 0.10) than BP. However, the h value of BP was higher (P < 0.05) than CP. The longissimus dorsi muscle fat content of BP was higher (P < 0.05) than CP. For the fatty acid composition, the SFA and MUFA of BP were higher (P < 0.05) than CP, but the PUFA of CP was higher (P < 0.05) than BP. The metmyoglobin content of CP was tended to be higher (P < 0.10) than BP. For the meat metabolism, the oxygen consumption of longissimus dorsi muscle of BP was higher (P < 0.01) than CP. The RNA-Seq data showed that the expression of the genes related to lipid metabolism is higher in BP (fold change > 3, P < 0.05). To conclude, BP has higher meat quality, while CP has its advantages in growth performance. And the differences between these two breeds may due to the genomic diversity.

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Increased Inclusion of Dietary Methionine Sources Improves Pork Quality in Association with the Regulation of Energy and Protein Metabolism and Muscle’s Fiber Profile

10.21203/rs.3.rs-41425/v1 ◽

2020 ◽

Author(s):

Peiqiang Yuan ◽

Sen Lin ◽

Jiyong Peng ◽

Yunxia Li ◽

Yunhan Liu ◽

...

Keyword(s):

Meat Quality ◽

Protein Metabolism ◽

Shear Force ◽

Lipid Synthesis ◽

Short Chain Fatty Acids ◽

Pork Quality ◽

Fiber Types ◽

Drip Loss ◽

Lower Shear ◽

Nutritional Strategies

Abstract Background Intensive selection for faster growth rate and higher lean percentage led to increase in protein deposition but deterioration in meat quality of pigs, thus there is growing interest in exploring the nutritional strategies to improve meat quality. Methionine has been shown to activate mechanistic target of rapamycin complex 1 protein kinase that plays pivotal roles in the regulation of protein and lipid synthesis. However, few study reports are available regarding the effects of dietary methionine supplementation at levels beyond growth requirements on lipid and protein metabolism and thus on pork quality. The objective of this study was to assess whether pork quality was improved by increasing dietary digestible sulfur amino acids (SAA) levels, with pigs fed the control (100% SAA), DL-Methionine (125% SAA)- or OH-Methionine (125% SAA)-supplemented diets during 11–110 kg period. Results Increasing SAA above requirements did not significantly affect growth performance, whereas improved pork quality as indicated by the decreased drip loss and a tendency towards decrease in shear force of longissimus lumborum muscle. Moreover, fresh muscle from barrows fed OH-Methionine showed a higher lightness value compared with the control and DL-Methionine treatments. The relatively lower shear force might be explained by the decrease in crude protein and increase in glycolytic potential, while the decreased drip loss was associated with down-regulation of genes (like fast glycolytic IIx) regulating fiber types. The increased lightness value of fresh muscle from barrows fed OH-Met diets appeared to be associated with the increased lactate level, which can be further explained by the increased plasma short-chain fatty acids concentrations, up-regulated G-protein coupled receptor 43 activation and enhanced glucagon-like peptide 1 secretion. Conclusion Increased SAA consumption appeared to improve pork water-holding capacity and tenderness likely through regulation of energy and protein metabolism and muscle’s fiber profile, which provides new insights into the nutritional strategies to improve meat quality.

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The effect of transport density and gender on stress indicators and carcass and meat quality in pigs

Spanish Journal of Agricultural Research ◽

10.5424/sjar/2015133-6638 ◽

2015 ◽

Vol 13 (3) ◽

pp. e0606 ◽

Cited By ~ 6

Author(s):

Thuanny L. Pereira ◽

Anderson Corassa ◽

Cláudia M. Komiyama ◽

Cláudio V. Araújo ◽

Alessandra Kataoka

Keyword(s):

Lactate Dehydrogenase ◽

Meat Quality ◽

Pork Quality ◽

Drip Loss ◽

Finishing Pigs ◽

Blood Components ◽

Stress Indicators ◽

Ph Values ◽

And Gender

A total of 168 finishing pigs were used to investigate the effects of gender (barrows and gilts) and transport densities for slaughter (236, 251, and 275 kg/m²) on stress indicators and carcass and pork quality. The animals transported at 251 kg/m² (T251) presented cortisol values below those at 236 kg/m2 (T236), but no different from those at 275 kg/m2 (T275). The lactate dehydrogenase (LDH) values in pigs transported at T236 were the lowest. The blood components did not differ between T236 and T275. The pH values at 45 min (pH45) and at 24 h (pH24) postmortem were higher for pigs subjected to T236. However, the pH45 was higher at T251 than at T275, but pH24 was lower at T251 than at T275. The lightness values in the muscles of the pigs transported at T236 and T251 were higher than those at T275. Lower drip loss values were observed in the muscle of animals at T251. Carcasses of pigs at T236 contained more 1–5 cm lesions while those at T275 contained more 5–10 cmlesions in sections of loin. No significant effects of gender were found on the stress indicators, blood components, pH45, pH24, color, drip loss or carcass lesions in general. These results indicate that the pre-slaughter transport of pigs at densities of 251 kg/m² generates less physiological damage and smaller losses on carcass and pork quality irrespective of gender.

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Comparative Transcriptome Profile Analysis of Longissimus dorsi Muscle Tissues From Two Goat Breeds With Different Meat Production Performance Using RNA-Seq

Frontiers in Genetics ◽

10.3389/fgene.2020.619399 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jiyuan Shen ◽

Zhiyun Hao ◽

Jiqing Wang ◽

Jiang Hu ◽

Xiu Liu ◽

...

Keyword(s):

Signaling Pathway ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Collagen Fibers ◽

Production Performance ◽

Carcass Weight ◽

Longissimus Dorsi ◽

Meat Production ◽

Rna Seq ◽

Muscle Tissues

Carcass weight, meat quality and muscle components are important traits economically and they underpin most of the commercial return to goat producers. In this study, the Longissimus dorsi muscle tissues were collected from five Liaoning cashmere (LC) goats and five Ziwuling black (ZB) goats with phenotypic difference in carcass weight, some meat quality traits and muscle components. The histological quantitative of collagen fibers and the transcriptome profiles in the Longissimus dorsi muscle tissues were investigated using Masson-trichrome staining and RNA-Seq, respectively. The percentage of total collagen fibers in the Longissimus dorsi muscle tissues from ZB goats was less than those from LC goats, suggesting that these ZB goats had more tender meat. An average of 15,919 and 15,582 genes were found to be expressed in Longissimus dorsi muscle tissues from LC and ZB goats, respectively. Compared to LC goats, the expression levels of 78 genes were up-regulated in ZB goats, while 133 genes were down-regulated. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) were significantly enriched in GO terms related to the muscle growth and development and the deposition of intramuscular fat and lipid metabolism, hippo signaling pathway and Jak-STAT signaling pathway. The results provide an improved understanding of the genetic mechanisms regulating meat production performance in goats, and will help us improve the accuracy of selection for meat traits in goats using marker-assisted selection based on these differentially expressed genes obtained.

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The Meat Quality and Sensory Characteristics of Turkish Native Sheep Genotypes

Turkish Journal of Agriculture - Food Science and Technology ◽

10.24925/turjaf.v9i6.961-967.3497 ◽

2021 ◽

Vol 9 (6) ◽

pp. 961-967

Author(s):

Engin Yaralı

Keyword(s):

Fatty Acids ◽

Meat Quality ◽

Shear Force ◽

Saturated Fatty Acids ◽

Monounsaturated Fatty Acids ◽

Cooking Loss ◽

Sensory Characteristics ◽

Longissimus Dorsi ◽

Drip Loss ◽

Muscle Types

Some meat quality and sensory characteristics were determined of Kıvırcık (n=10), Eşme Kıvırcık (n=10), Karya (n=8) and Çine Çaparı (n=9) lambs in this research. Carcass divided into two parts along the spine and the three different type of muscle samples were taken from the between 8th and 9th vertebrae, 12th and 13th vertebrae and leg part of the left side of the carcasses. Drip loss, cooking loss and shear force values of these muscles were identified. Additionally, pH0, pH24, color, fatty acid composition and sensory properties were determined in M. Longissimus dorsi samples. When muscle types are evaluated separately were a statistically significant factor in terms of dripping and cooking loss and shear force. While the highest dripping loss were reported in M. Longissimus dorsi (3.72%), the highest cooking loss were reported in M. Longissimus thoracis (22.67%) and the highest shear force were reported in M. semitendinosus (4.38 kg). Genotype and muscle interaction were found to be highly significant for only cooking loss. The analysis results for fatty acids indicated that there was an important difference between Kıvırcık, Eşme Kıvırcık, Karya and Çine Çaparı on C10:0, C12:0, C14:0, C15:0, C16:0, tC18:1, CLA, tC18:3, C20:1, C22:0 fatty acids in the study. Genotypes showed no effect to SFA (Saturated fatty acids), MUFA (Monounsaturated fatty acids), PUFA (Polyunsaturated fatty acids) and P/S ratio parameters. Karya lambs performed higher for odor and tenderness, and Kıvırcık lambs showed a higher score for juiciness, flavor and total acceptability in sensory evaluation.

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Proteomic analysis of goat Longissimus dorsi muscles with different drip loss values related to meat quality traits

Food Science and Biotechnology ◽

10.1007/s10068-016-0058-y ◽

2016 ◽

Vol 25 (2) ◽

pp. 425-431 ◽

Cited By ~ 9

Author(s):

Zhenyu Wang ◽

Fan He ◽

Weili Rao ◽

Na Ni ◽

Qingwu Shen ◽

...

Keyword(s):

Meat Quality ◽

Proteomic Analysis ◽

Longissimus Dorsi ◽

Drip Loss ◽

Quality Traits ◽

Meat Quality Traits

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Variant analysis of RNA sequences in severe equine asthma

10.7287/peerj.preprints.3491v1 ◽

2017 ◽

Author(s):

Laurence Tessier ◽

Olivier Côté ◽

Dorothee Bienzle

Keyword(s):

Amino Acid ◽

Sanger Sequencing ◽

Protein Structures ◽

3D Structure ◽

Variant Calling ◽

Correct Identification ◽

Gene Variants ◽

Rna Seq ◽

Equine Asthma ◽

The Impact

Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. The disease in horses has complex inheritance including both dominant and recessive patterns that are ill defined. This study aimed to determine the utility of RNA-Seq to call gene variants and identify mutations potentially linked to disease. Methods. RNA-Seq data were generated from endobronchial biopsies collected from 6 asthmatic and 7 non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Coverage was visualized using Integrative Genomic Viewer software and variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools. Novel variant selection by VEP was based on score of <0.01 predicted with Sorting Intolerant From Tolerant (SIFT) software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For selected mutations, the effect of predicted variants on protein function was assessed with Polymorphism Phenotyping (PolyPhen) 2 and Screening for Non-Acceptable Polymorphism (SNAP) 2 softwares. RNA-Seq predicted variants were confirmed in all horses, and investigated in an additional 4 asthmatic and 7 non-asthmatic individuals with PCR and Sanger sequencing. Gene alignment and 3D protein structures were predicted with Geneious software. Results. Level of expression across the genome was similar in all individuals. RNA-Seq variant calling and filtering identified with highest confidence mutations in PACRG and RTTN. Sanger sequencing confirmed that the PACRG variant was appropriately identified in all 26 samples while the RTTN variant was identified correctly by RNA-Seq in 24 of 26 samples. SIFT and PolyPhen2 indicated both mutations would result in loss of function, and SNAP2 that they would be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, a change in both for RTTN; and a slight change in 3D structure for PACRG and RTTN. For PACRG, samples from additional individuals confirmed higher frequency of the heterozygous genotype in asthmatics, while the RTTN homozygous mutant phenotype was more prevalent in the asthmatic compared to non-asthmatic group. Discussion. RNA-Seq was sensitive and specific for calling gene variants in this disease model. Even moderate coverage (<10-20 cpm) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins are unknown at this point, but their role in structure and function of cilia may warrant further investigation.

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Effect of creatine monohydrate supplementation on carcass traits, meat quality and postmortem energy metabolism of finishing pigs

Animal Production Science ◽

10.1071/an14017 ◽

2016 ◽

Vol 56 (1) ◽

pp. 48 ◽

Cited By ~ 9

Author(s):

J. L. Li ◽

Z. Y. Guo ◽

Y. J. Li ◽

L. Zhang ◽

F. Gao ◽

...

Keyword(s):

Energy Metabolism ◽

Meat Quality ◽

Basal Diet ◽

Creatine Monohydrate ◽

Longissimus Dorsi ◽

Drip Loss ◽

Finishing Pigs ◽

Large White ◽

Longissimus Dorsi Muscle ◽

Dorsi Muscle

The objective of this study was to evaluate the effects of creatine monohydrate (CMH) supplementation on meat quality and postmortem energy metabolism of finishing pigs. In total, 48 healthy Duroc–Large White cross castrated male pigs were randomly allocated into two treatments, and fed either a CHM-free basal diet or a basal diet with CMH supplementation (0.8%) for 14 days. At the end of the experiment, six pigs from each treatment were weighed individually and slaughtered. The muscle from longissimus dorsi was collected to evaluate the meat quality and energy metabolism-related parameters. The results showed that CMH supplementation did not affect the loin eye area, back fat depth or dressing percentage (P > 0.05). The muscle pH45 min was higher, whereas drip loss and cooking loss were lower in the CMH supplementation group (P < 0.05). CMH supplementation increased the concentrations of creatine (P < 0.05), adenosine triphosphate (P < 0.05), adenosine diphosphate (P < 0.01) and creatine kinase activity (P < 0.05), and decreased the concentration of lactic acid (P < 0.05), and the activities of lactate dehydrogenase (P < 0.05) and pyruvate kinase (P < 0.05) in muscle postmortem. However, no differences were observed between groups for chemical composition, textural characteristics and glycolytic potential of longissimus dorsi muscle (P > 0.05). These findings suggest that dietary supplementation with CMH during the finishing period in pigs could delay early pH decline and decrease the rate of glycolysis in postmortem longissimus dorsi muscle resulting in a decreased drip loss.

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Welfare and carcass and meat quality of pigs being transported for two hours using two vehicle types during two seasons of the year

Canadian Journal of Animal Science ◽

10.4141/cjas2012-088 ◽

2013 ◽

Vol 93 (1) ◽

pp. 43-55 ◽

Cited By ~ 39

Author(s):

J. A. Correa ◽

H. W. Gonyou ◽

S. Torrey ◽

T. Widowski ◽

R. Bergeron ◽

...

Keyword(s):

Heart Rate ◽

Animal Welfare ◽

Meat Quality ◽

Longissimus Dorsi ◽

Vehicle Design ◽

Pork Quality ◽

Skin Damage ◽

L Value ◽

Quality Variation

Correa, J. A., Gonyou, H. W., Torrey, S., Widowski, T., Bergeron, R., Crowe, T. G., Laforest, J. P. and Faucitano, L. 2013. Welfare and carcass and meat quality of pigs being transported for two hours using two vehicle types during two seasons of the year. Can. J. Anim. Sci. 93: 43–55. A total of 3756 pigs were transported for 2 h in summer and winter using a “pot-belly” trailer (PB) and a hydraulic double-decked truck (DD) in order to assess the effect of vehicle design on animal welfare and carcass and meat quality. Animal welfare was assessed in randomly selected barrows by measuring heart rate of pigs and lactate and creatine phospho-kinase (CPK) concentrations in exsanguination blood. Skin damage was scored and meat quality was evaluated in the longissimus dorsi (LD), semimembranosus (SM) and adductor (AD) muscles. Heart rates in winter were higher (P< 0.01) during transport, at unloading and in lairage. Blood CPK and lactate concentrations at slaughter were higher (P<0.05 and P<0.01, respectively) in pigs transported on the PB trailer. Bruises increased in winter (P<0.001) and in pigs from the DD truck (P<0.05). The pHu was higher (P< 0.01) in all muscles and L* value was lower (P<0.05) in the LD muscle from pigs transported in the PB trailer. Overall, the results of this study indicate that the type of vehicle, animal location in the truck and the season affect the welfare of pigs during transport with clear consequences on skin bruises and pork quality variation.

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