scholarly journals Identification of eQTLs and sQTLs associated with meat quality in beef

2019 ◽  
Author(s):  
Joel David Leal Gutierrez ◽  
Mauricio A. Elzo ◽  
Raluca G. Mateescu
Keyword(s):  
Meat Quality ◽  
Fixed Effects ◽  
Differential Expression Analysis ◽  
Cytoskeletal Proteins ◽  
Longissimus Dorsi ◽  
Quality Traits ◽  
Master Regulators ◽  
Longissimus Dorsi Muscle ◽  
Meat Quality Traits ◽  
Dorsi Muscle

Abstract Background: Transcription has a substantial genetic control and genetic dissection of gene expression could help us understand the genetic architecture of complex phenotypes such as meat quality in cattle. The objectives of the present research were: 1) to perform eQTL and sQTL mapping analyses for meat quality traits in longissimus dorsi muscle; 2) to uncover genes whose expression is influenced by local or distant genetic variation; 3) to identify expression and splicing hot spots; and 4) to uncover genomic regions affecting the expression of multiple genes. Results: Eighty steers were selected for phenotyping, genotyping and RNA-seq evaluation. A panel of traits related to meat quality was recorded in longissimus dorsi muscle. Information on 112,042 SNPs and expression data on 8,588 autosomal genes and 87,770 exons from 8,467 genes were included in an expression and splicing quantitative trait loci (QTL) mapping (eQTL and sQTL, respectively). A gene, exon and isoform differential expression analysis previously carried out in this population identified 1,352 genes, referred to as DEG, as explaining part of the variability associated with meat quality traits. The eQTL and sQTL mapping was performed using a linear regression model in the R package Matrix eQTL. Genotype and year of birth were included as fixed effects, and population structure was accounted for by including as a covariate the first PC from a PCA analysis on genotypic data. The identified QTLs were classified as cis or trans using 1 Mb as the maximum distance between the associated SNP and the gene being analyzed. A total of 8,377 eQTLs were identified, including 75.6% trans, 10.4% cis, 12.5% DEG trans and 1.5% DEG cis; while 11,929 sQTLs were uncovered: 66.1% trans, 16.9% DEG trans, 14% cis and 3% DEG cis. Twenty-seven expression master regulators and 13 splicing master regulators were identified and were classified as membrane-associated or cytoskeletal proteins, transcription factors or DNA methylases. These genes could control the expression of other genes through cell signaling or by a direct transcriptional activation/repression mechanism. Conclusion: In the present analysis, we show that eQTL and sQTL mapping makes possible positional identification of gene and isoform expression regulators.

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

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.

scholarly journals Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Fernanda M. Rezende ◽  
Eduardo Rodriguez ◽  
Joel D. Leal-Gutiérrez ◽  
Mauricio A. Elzo ◽  
Dwain D. Johnson ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genomic Selection ◽  
Meat Quality ◽  
Additive Genetic Variance ◽  
Cytoskeletal Proteins ◽  
Pleiotropic Effects ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Meat Quality Traits ◽  
Genomic Regions

Carcass and meat quality are two important attributes for the beef industry because they drive profitability and consumer demand. These traits are of even greater importance in crossbred cattle used in subtropical and tropical regions for their superior adaptability because they tend to underperform compared to their purebred counterparts. Many of these traits are challenging and expensive to measure and unavailable until late in life or after the animal is harvested, hence unrealistic to improve through traditional phenotypic selection, but perfect candidates for genomic selection. Before genomic selection can be implemented in crossbred populations, it is important to explore if pleiotropic effects exist between carcass and meat quality traits. Therefore, the objective of this study was to identify genomic regions with pleiotropic effects on carcass and meat quality traits in a multibreed Angus–Brahman population that included purebred and crossbred animals. Data included phenotypes for 10 carcass and meat quality traits from 2,384 steers, of which 1,038 were genotyped with the GGP Bovine F-250. Single-trait genome-wide association studies were first used to investigate the relevance of direct additive genetic effects on each carcass, sensory and visual meat quality traits. A second analysis for each trait included all other phenotypes as covariates to correct for direct causal effects from identified genomic regions with pure direct effects on the trait under analysis. Five genomic windows on chromosomes BTA5, BTA7, BTA18, and BTA29 explained more than 1% of additive genetic variance of two or more traits. Moreover, three suggestive pleiotropic regions were identified on BTA10 and BTA19. The 317 genes uncovered in pleiotropic regions included anchoring and cytoskeletal proteins, key players in cell growth, muscle development, lipid metabolism and fat deposition, and important factors in muscle proteolysis. A functional analysis of these genes revealed GO terms directly related to carcass quality, meat quality, and tenderness in beef cattle, including calcium-related processes, cell signaling, and modulation of cell–cell adhesion. These results contribute with novel information about the complex genetic architecture and pleiotropic effects of carcass and meat quality traits in crossbred beef cattle.

scholarly journals Analysis of FTO and PLIN2 Polymorphisms in Relation to Carcass and Meat Quality Traits in Pigs

2019 ◽  
Vol 19 (1) ◽  
pp. 71-83 ◽  
Author(s):  
Daniel Polasik ◽  
Eva-Maria Kamionka ◽  
Mirosław Tyra ◽  
Grzegorz Żak ◽  
Arkadiusz Terman
Keyword(s):  
Meat Quality ◽  
Fat Content ◽  
Longissimus Dorsi ◽  
Quality Traits ◽  
Large White ◽  
Meat Quality Traits ◽  
Pcr Rflp ◽  
Perilipin 2 ◽  
Water Holding ◽  
Intramuscular Fat Content

AbstractThe aim of this study was to analyze the association of polymorphisms in alpha-ketoglutarate-dependent dioxygenase (FTO) and perilipin 2 (PLIN2) genes with carcass and meat quality traits in pigs reared in Poland. The research covered 578 sows that belong to the following breeds: Duroc, Hampshire, Polish Landrace, Pietrain, Puławska and Polish Large White. FTO (FM244720:g.400C>G) and PLIN2 (GU461317:g.98G>A) genes variants were determined by means of PCR-RFLP and ACRS-PCR methods respectively. Association between individual genotypes and analyzed traits was calculated by means of GLM procedure for Polish Landrace, Polish Large White and Puławska breeds separately and for all six breeds together in case of FTO gene. The results showed that FTO variants were associated with weight of loin without backfat and skin (WL), loin eye area (AL) and meat percentage (MP) in Polish Large White (P≤0.05), mean backfat thickness from 5 measurements (BFT) and pH measured 45 min after slaughter in m. longissimus dorsi (pH24 ld) as well as with water holding-capacity (WHC) in Puławska breed (P≤0.01). PLIN2 genotypes, however were correlated with WL and height of the loin eye (HL) in Polish Large White and Puławska (P≤0.05), AL in Polish Large White (P≤0.01) as well as luminosity (L*) in Puławska (P≤0.05) pigs. We observed most consistent relationships of PLIN2 SNP with intramuscular fat content (IMF) and WHC. In 3 analyzed breeds GG genotype was connected with highest values of these traits (P≤0.05).

The effect of slaughter handling system on pig welfare and meat quality

1992 ◽  
Vol 1992 ◽  
pp. 59-59
Author(s):  
C.M Weeding ◽  
E.J. Hunter ◽  
H.J. Guise ◽  
R.H.C. Penny
Keyword(s):  
Meat Quality ◽  
Analysis Of Variance ◽  
Longissimus Dorsi ◽  
Post Mortem ◽  
Handling System ◽  
Longissimus Dorsi Muscle ◽  
Single File ◽  
Dorsi Muscle ◽  
Muscle Ph

Pigs from 4 farms were slaughtered at 2 abattoirs, each with 2 slaughter handling systems. Pigs at abattoir 1 were electrically stunned, either in a floor pen holding 5 pigs or a race restrainer. A straight race 1m wide led to the floor pen. A stepped collection pen and single file race led to the race restrainer. At abattoir 2 a single file curved race led to a floor pen with electrical stunning and a circular collection pen led to a double race and dip-lift C02 stunner. Each replicate involved 2 farms sending 50 pigs to each abattoir. There were 16 replicates (3200 pigs). Stun system had a significant effect on the development of early rigor, muscle pH, muscle colour and skin blemish (GLM Analysis of Variance). At abattoir 1, pigs slaughtered through the race restrainer had a greater tendency to develop early rigor and more skin blemish. Pigs slaughtered through the race restrainer also had lower pH in the m. longissimus dorsi at both initial and ultimate readings post mortem. In general, pH readings were higher than would be expected in the pig m. longissimus dorsi. Muscle reflectance was higher in the m. longissimus dorsi of pigs slaughtered through the race restrainer at both initial and ultimate readings. Significant differences between means at abattoir 1 (two-sample t-tests) are contained in Table 1. At abattoir 2, the floor pen produced carcases with a greater tendency to develop early rigor and more skin blemish. There were no significant differences in muscle pH or colour. Significant differences between means at abattoir 2 (two-sample t-tests) are contained in Table 2.

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