1
|
Reis HBD, Carvalho ME, Espigolan R, Poleti MD, Ambrizi DR, Berton MP, Ferraz JBS, de Mattos Oliveira EC, Eler JP. Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle. Metabolites 2023; 14:6. [PMID: 38276296 PMCID: PMC10818672 DOI: 10.3390/metabo14010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs). After quality control analysis, 468,321 SNPs provided information on the number of genotyped animals. Genome-wide association analyses (GWAS) were performed for the characteristics of the rib eye area (REA), subcutaneous fat thickness (SFT), shear force at 7 days' ageing (SF7), and intramuscular fat (IMF), with the aid of the single-step genomic best linear unbiased prediction (ssGBLUP) method, with the purpose of identifying possible genomic windows (~1 Mb) responsible for explaining at least 0.5% of the genetic variance of the traits under analysis (≥0.5%). These genomic regions were used in a gene search and enrichment analyses using MeSH terms. The distributed heritability coefficients were 0.14, 0.20, 0.18, and 0.21 for REA, SFT, SF7, and IMF, respectively. The GWAS results indicated significant genomic windows for the traits of interest in a total of 17 chromosomes. Enrichment analyses showed the following significant terms (FDR ≤ 0.05) associated with the characteristics under study: for the REA, heat stress disorders and life cycle stages; for SFT, insulin and nonesterified fatty acids; for SF7, apoptosis and heat shock proteins (HSP27); and for IMF, metalloproteinase 2. In addition, KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis allowed us to highlight important metabolic pathways related to the studied phenotypes, such as the growth hormone synthesis, insulin-signaling, fatty acid metabolism, and ABC transporter pathways. The results obtained provide a better understanding of the molecular processes involved in the expression of the studied characteristics and may contribute to the design of selection strategies and future studies aimed at improving the productivity of Nellore cattle.
Collapse
Affiliation(s)
- Hugo Borges Dos Reis
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Minos Esperândio Carvalho
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Rafael Espigolan
- Department of Animal Science and Biological Sciences, Federal University of Santa Maria (UFSM), Av. Independencia, 3751, Palmeira das Missões 98300-000, RS, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Dewison Ricardo Ambrizi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Mariana Piatto Berton
- School of Agricultural and Veterinary Studies (FCAV), São Paulo State University, Jaboticabal 14884-900, SP, Brazil;
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Elisângela Chicaroni de Mattos Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Joanir Pereira Eler
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| |
Collapse
|
2
|
Lee B, Kim JY, Choi YM. Associations of Apoptotic and Anti-Apoptotic Factors with Beef Quality, Histochemical Characteristics, and Palatability of Hanwoo Longissimus thoracis Muscle. Animals (Basel) 2022; 12:ani12040467. [PMID: 35203175 PMCID: PMC8868170 DOI: 10.3390/ani12040467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/04/2022] [Accepted: 02/12/2022] [Indexed: 01/27/2023] Open
Abstract
This study compared the meat quality, histochemical traits, palatability, and expression levels of apoptotic (cytochrome c and caspases) and anti-apoptotic (small heat shock proteins) factors at 45 min and 24 h post-mortem of Hanwoo Longissimus thoracis muscles in groups categorized by Warner-Bratzler shear force (WBS) values to investigate the association between beef tenderness variation and apoptosis-related molecules. There were no differences in marbling scores, meat quality traits, or histochemical characteristics among the WBS groups (p > 0.05) indicating no significant effect on the tenderness variation in the current study. On the other hand, the low group exhibited higher levels of apoptotic and anti-apoptotic factors (except for αβ-crystallin) at 45 min post-mortem compared to the high WBS group, resulting in higher scores of tenderness attributes (p < 0.05). However, the level of αβ-crystallin at 45 min post-mortem was lower in the low and medium WBS groups compared to the high WBS group (p < 0.0106). At 24 h post-mortem, no significant differences were observed in the expression levels of apoptosis-related factors among the WBS groups (p > 0.05) except for heat shock protein 27 (p < 0.05).
Collapse
|
3
|
Lee B, Choi YM. Research Note: Expression level of heat shock protein 27 in PSE-like and fast-glycolyzing conditions of chicken pectoralis major muscle. Poult Sci 2021; 100:101424. [PMID: 34534854 PMCID: PMC8449046 DOI: 10.1016/j.psj.2021.101424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/14/2021] [Accepted: 08/02/2021] [Indexed: 12/02/2022] Open
Abstract
This study compared the meat quality traits, histochemical characteristics, and heat shock protein (HSP) 27 expression levels of the broiler Pectoralis major (PM) muscles in groups classified by pale, soft, and exudative (PSE)-like and fast-glycolyzing conditions using the lightness and muscle pH change values. Chicken PM muscles showing higher pH change value and paler meat surface (as HP group) could be associated with the PSE-like condition, and exhibited a lower pH24 h value and higher cooking loss compared to PM muscles showing lower pH change value and normal color (as LN group) (P < 0.05). Greater PM muscle weight and fiber area were observed in the HP group compared to the other groups (P < 0.05); meanwhile, the PM muscles showing higher pH change value with normal color (as HN group) and the PM muscles showing lower pH change value with paler color (as LP group) did not differ in the water holding capacity, Warner-Bratzler shear force, and muscle fiber characteristics (P > 0.05). Muscle samples showing a higher pH change value exhibited a greater level of HSP27 compared to muscle samples showing a lower pH change value (P < 0.05). Therefore, the current findings suggested that the expression level of HSP27 can be a useful indicator for explaining variations in the glycolytic rate of chicken breast muscle.
Collapse
Affiliation(s)
- Boin Lee
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju 37224, South Korea
| | - Young Min Choi
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju 37224, South Korea.
| |
Collapse
|
4
|
Research Note: Comparison of histochemical characteristics, chicken meat quality, and heat shock protein expressions between PSE-like condition and white-stripping features of pectoralis major muscle. Poult Sci 2021; 100:101260. [PMID: 34198090 PMCID: PMC8253903 DOI: 10.1016/j.psj.2021.101260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
The present study compared the histochemical and meat quality characteristics of broiler pectoralis major (PM) muscle among the groups categorized according to muscle abnormalities, including pale, soft, and exudative (PSE)-like condition and white-striping (WS) feature. Additionally, this study investigated the associations between muscular abnormalities and expression levels of heat shock proteins (HSPs), including αβ-crystallin, HSP70, and HSP90, at the early postmortem period. The WS breasts with normal quality condition showed greater PM muscle weight and were more associated with fiber hypertrophy, compared to the no WS breasts with PSE-like condition (P < 0.05). The PSE-like group exhibited paler surface color and tougher meat, causing more fluid loss after cooking, compared to the normal quality group (P < 0.05). However, there were no significant differences in the quality traits between the WS groups (P > 0.05), except for lightness and cooking loss. Higher αβ-crystallin and HSP90 expression levels were observed in PSE-like breast compared to normal quality breast (P < 0.05), whereas WS pattern was not related with HSPs levels (P > 0.05). Therefore, HSP levels at the early postmortem period, especially those of αβ-crystallin and HSP90, were associated with the breast quality characteristics of PSE-like condition broilers.
Collapse
|
5
|
Ramalingam V, Hwang I. Identification of Meat Quality Determining Marker Genes in Fibroblasts of Bovine Muscle Using Transcriptomic Profiling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3776-3786. [PMID: 33730852 DOI: 10.1021/acs.jafc.0c06973] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In the present study, we comparatively analyzed the transcriptomic profiling of fibroblasts derived from two different muscles, biceps femoris and longissimus dorsi with significant difference in the meat quality and tenderness. EBSeq algorithm was applied to analyze the data, and genes were considered to be significantly differentially expressed if the false discovery rate value was <0.05, the P value was <0.01, and the fold change was >0.585. The results revealed that 253 genes were differentially expressed genes (DEGs) (170 genes were upregulated, and 83 were downregulated) and more than 100 DEGs were probably associated with intramuscular fat deposition, tenderness, and toughness, which are driving the meat quality and were involved in biological processes such as collagen synthesis, cell differentiation, and muscle tissue and fiber development; molecular functions such as chemokine activity and collagen activity; cellular components such as cytoplasm and myofibril; and pathways such as collagen signaling and metabolic pathways. A gene-act network and a co-expression network revealed the close relationship between intramuscular fat deposition and meat tenderness. The expressions of 20 DEGs were validated by real-time PCR, and the results suggested that the DEGs are correlated with RNA-seq data and play crucial roles in muscle growth, development processes, toughness, and tenderness of the meat. Together, the genome-wide transcriptome analysis revealed that various genes are responsible for toughness and tenderness variance in the difference muscles of beef.
Collapse
Affiliation(s)
- Vaikundamoorthy Ramalingam
- Centre for Natural Products & Traditional Knowledge, CSIR-Indian Institute of Chemica Technology, Hyderabad, Telangana 500007, India
- Department of Animal Science, Jeonbuk National University, Jeonju 561-756, Republic of Korea
| | - Inho Hwang
- Department of Animal Science, Jeonbuk National University, Jeonju 561-756, Republic of Korea
| |
Collapse
|
6
|
Cho DK, Lee B, Kim SK, Hyeonbin O, Kim YS, Choi YM. Comparison of Quality Characteristics and Palatability between Sous-Vide Cooked Pork Loin Patties with Different Searing Treatments. Food Sci Anim Resour 2021; 41:214-223. [PMID: 33987544 PMCID: PMC8114998 DOI: 10.5851/kosfa.2020.e90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022] Open
Abstract
This study compared the quality, cooking, textural, and palatability
characteristics between sous-vide (SV) cooked pork loin patties with different
searing treatments (ST). Before SV cooking, STs were conducted on each side of
the pork loin patties for 0 (control) to 120 s (ST120), and all patties were
then cooked using an SV cooker at 75°C for 120 min. Noticeable
differences were observed in quality properties between the groups. The seared
SV loin patties exhibited lower lightness and higher browning index values
compared to the unseared SV loin patties (p<0.001). Cooking loss
gradually increased with increasing ST times, and the control group had a lower
percentage compared to the ST60 group (19.5 vs. 25.7%, p<0.001).
Changes in cooking properties were associated with the extent of ST, and the ST
groups exhibited a higher hardness value compared to the control group
(p<0.001). Regarding palatability, loin patties from the control group
scored lower in appearance acceptability compared to patties from the ST groups
(p<0.05) due to extent of browning on the surface. Moreover, the ST
groups did exhibit a higher flavor intensity compared to the control group, but
no differences were observed in tenderness and juiciness scores between the
control and ST60 groups. Due to these results, the ST60 group exhibited a
greater score in overall acceptability compared to the other groups except for
the ST90 group. Therefore, an additional ST before SV cooking can achieve a more
appealing appearance and palatability as well as to enhance the availability of
pork loin.
Collapse
Affiliation(s)
- Dong Kook Cho
- Department of Integrated Biomedical and Life Sciences, Korea University, Seoul 02841, Korea.,Department of Culinary, Hotel Lotte, Seoul 04533, Korea
| | - Boin Lee
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju 37224, Korea
| | - Song Ki Kim
- Department of Culinary, Hotel Lotte, Seoul 04533, Korea
| | - O Hyeonbin
- Department of Integrated Biomedical and Life Sciences, Korea University, Seoul 02841, Korea
| | - Young Soon Kim
- Department of Integrated Biomedical and Life Sciences, Korea University, Seoul 02841, Korea
| | - Young Min Choi
- Department of Animal Sciences and Biotechnology, Kyungpook National University, Sangju 37224, Korea
| |
Collapse
|
7
|
Gagaoua M, Bonnet M, Picard B. Protein Array-Based Approach to Evaluate Biomarkers of Beef Tenderness and Marbling in Cows: Understanding of the Underlying Mechanisms and Prediction. Foods 2020; 9:foods9091180. [PMID: 32858893 PMCID: PMC7554754 DOI: 10.3390/foods9091180] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/14/2022] Open
Abstract
This study evaluated the potential of a panel of 20 protein biomarkers, quantified by Reverse Phase Protein Array (RPPA), to explain and predict two important meat quality traits, these being beef tenderness assessed by Warner-Bratzler shear force (WBSF) and the intramuscular fat (IMF) content (also termed marbling), in a large database of 188 Protected Designation of Origin (PDO) Maine-Anjou cows. Thus, the main objective was to move forward in the progression of biomarker-discovery for beef qualities by evaluating, at the same time for the two quality traits, a list of candidate proteins so far identified by proteomics and belonging to five interconnected biological pathways: (i) energy metabolic enzymes, (ii) heat shock proteins (HSPs), (iii) oxidative stress, (iv) structural proteins and (v) cell death and protein binding. Therefore, three statistical approaches were applied, these being Pearson correlations, unsupervised learning for the clustering of WBSF and IMF into quality classes, and Partial Least Squares regressions (PLS-R) to relate the phenotypes with the 20 biomarkers. Irrespective of the statistical method and quality trait, seven biomarkers were related with both WBSF and IMF, including three small HSPs (CRYAB, HSP20 and HSP27), two metabolic enzymes from the oxidative pathway (MDH1: Malate dehydrogenase and ALDH1A1: Retinal dehydrogenase 1), the structural protein MYH1 (Myosin heavy chain-IIx) and the multifunctional protein FHL1 (four and a half LIM domains 1). Further, three more proteins were retained for tenderness whatever the statistical method, among which two were structural proteins (MYL1: Myosin light chain 1/3 and TNNT1: Troponin T, slow skeletal muscle) and one was glycolytic enzyme (ENO3: β-enolase 3). For IMF, two proteins were, in this trial, specific for marbling whatever the statistical method: TRIM72 (Tripartite motif protein 72, negative) and PRDX6 (Peroxiredoxin 6, positive). From the 20 proteins, this trial allowed us to qualify 10 and 9 proteins respectively as strongly related with beef tenderness and marbling in PDO Maine-Anjou cows.
Collapse
|