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Demir E, Moravčíková N, Kaya S, Kasarda R, Bilginer Ü, Doğru H, Balcıoğlu MS, Karslı T. Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye. Anim Genet 2023; 54:721-730. [PMID: 37789609 DOI: 10.1111/age.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 09/01/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST ) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP-EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP-EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3-1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.
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Affiliation(s)
- Eymen Demir
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Sarp Kaya
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
| | - Ümit Bilginer
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Huriye Doğru
- Department of Medical Services and Techniques, Vocational School of Burdur Health Services, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - Murat Soner Balcıoğlu
- Department of Animal Science, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Taki Karslı
- Department of Animal Science, Faculty of Agriculture, Eskisehir Osmangazi University, Eskisehir, Türkiye
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2
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Wang S, Zhao J, Wang L, Zhang T, Zeng W, Lu H. METTL21C mediates lysine trimethylation of IGF2BP1 to regulate chicken myoblast proliferation. Br Poult Sci 2023; 64:74-80. [PMID: 36069737 DOI: 10.1080/00071668.2022.2121639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Methyltransferase-like 21C (METTL21C) and insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) play important roles in the proliferation of chicken myoblasts. However, it remains unclear whether there is protein-protein interaction between METTL21C and IGF2BP1 to regulate proliferation of chicken myoblasts.2. In this study, the Igf2bp1 gene was amplified from cDNA of liver tissue of Lueyang black-bone chicken to construct the overexpression vector HA-Igf2bp1. The HA-Igf2bp1 and Flag-Mettl21c vectors were individually transfected and co-transfected into HEK293T, respectively. Co-immunoprecipitation (Co-IP) assay indicated a protein-protein interaction between METTL21C and IGF2BP1.3. Using the Western blotting and LC-MS/MS, it was found that METTL21C could mediate the lysine methylation modification of IGF2BP1. Furthermore, the His-tagged overexpression vector HA-Igf2bp1-His was constructed, transfected and co-transfected with Flag-Mettl21c into HEK293T. His-tagged IGF2BP1 was purified by nickel ion affinity chromatography. Western blotting revealed that IGF2BP1 was successfully purified, and the trimethylation modification level of co-transfection group was significantly elevated compared with the single-transfection Igf2bp1 group.4. Mettl21c and Igf2bp1 overexpression vectors were transfected and co-transfected into primary chicken myoblasts, respectively. The results of 5-ethynyl-2'-deoxyuridine assay and the expression level of Pax7 and MyoD indicated that overexpression of Igf2bp1 alone inhibited the chicken myoblast proliferation, whereas co-expression of Mettl21c and Igf2bp1 eliminated the inhibitory effects of Igf2bp1, thereby favouring cell proliferation and differentiation.5. The results, for the first time, revealed that METTL21C mediated the lysine trimethylation modification of IGF2BP1 to regulate the proliferation of chicken myoblasts, which provided a new insight into in-depth analysis of the molecular mechanism of METTL21C methylation involved in regulating the growth and development of skeletal muscle in Lueyang black-bone chicken.
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Affiliation(s)
- S Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - J Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - L Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - T Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Department of Biology, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, Shaanxi, China
| | - W Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Department of Biology, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Hanzhong, Shaanxi, China
| | - H Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong, Shaanxi, China
- Shaanxi Province Key Laboratory of Bio-resources, Shaanxi University of Technology, Hanzhong, Shaanxi, China
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3
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Zequan X, Yonggang S, Heng X, Yaodong W, Xin M, Dan L, Li Z, Tingting D, Zirong W. Transcriptome-based analysis of early post-mortem formation of pale, soft, and exudative (PSE) pork. Meat Sci 2022; 194:108962. [PMID: 36126390 DOI: 10.1016/j.meatsci.2022.108962] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 07/02/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Pale, soft, and exudative (PSE) meat can cause consumer dissatisfaction and economic losses. This study determined meat quality, glycolytic enzyme activity, and differential gene expression in the longissimus lumborum (LL) and semimembranosus (SM) of normal and PSE pork carcasses. The SM did not result in PSE meat. Hexokinase, lactate dehydrogenase, and pyruvate kinase activities were lower in the SM of PSE carcasses than in the normal carcasses. Functional enrichment analysis revealed that immune, inflammatory, and muscle fibre genes were significantly enriched in PSE pork. More specifically, PPP1R3G and MSS51 may be key genes regulating pork quality in the SM. Meanwhile, the differential expression of PLVAB, ADIPOQ, LEP, MYH4, MYH7, MYL3, MYL6B, FOS, ATF3, and HSPA6 may induce PSE formation in the LL. These results may provide insights into PSE pork formation mechanisms and reveal candidate genes for improving meat quality after validation.
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Affiliation(s)
- Xu Zequan
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China; Tecon Biology Ltd., Urumqi, Xinjiang, China
| | - Shao Yonggang
- College of Animal Science, Xinjiang Agricultural University, Xinjiang, China
| | - Xu Heng
- Tecon Biology Ltd., Urumqi, Xinjiang, China
| | | | - Ma Xin
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Liu Dan
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Zhang Li
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Du Tingting
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Wang Zirong
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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4
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Ding R, Zhuang Z, Qiu Y, Wang X, Wu J, Zhou S, Ruan D, Xu C, Hong L, Gu T, Zheng E, Cai G, Huang W, Wu Z, Yang J. A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population. BMC Genomics 2022; 23:590. [PMID: 35964005 PMCID: PMC9375371 DOI: 10.1186/s12864-022-08804-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs. RESULTS Firstly, we performed a genome-wide analysis for CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 pigs. A total of 11,100 CNVs were detected, which were aggregated by overlapping 695 CNV regions (CNVRs). Next, we investigated CNVs of pigs from the same population by whole-genome resequencing. A genome-wide analysis of 21 pigs revealed 23,856 CNVRs that were further divided into three categories (851 gain, 22,279 loss, and 726 mixed), which covered 190.8 Mb (~ 8.42%) of the pig autosomal genome. Further, the identified CNVRs were used to determine an overall validation rate of 68.5% for the CNV detection accuracy of chip data. CNVR association analyses identified one CNVR associated with LMA, one with LMD and eight with LMP after applying stringent Bonferroni correction. The wssGWAS identified eight, six and five regions explaining more than 1% of the additive genetic variance for LMA, LMD and LMP, respectively. The CNVR analyses and wssGWAS identified five common regions, of which three regions were associated with LMA and two with LMP. Four genes (DOK7, ARAP1, ELMO2 and SLC13A3) were highlighted as promising candidates according to their function. CONCLUSIONS We determined an overall validation rate for the CNV detection accuracy of low-density chip data and constructed a genomic CNV map for Duroc pigs using resequencing, thereby proving a value genetic variation resource for pig genome research. Furthermore, our study utilized a composite genetic strategy for complex traits in pigs, which will contribute to the study for elucidating the genetic architecture that may be influenced and regulated by multiple forms of variations.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Guangdong Wens Breeding Swine Technology Co., Ltd, Guangdong, 527439, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China. .,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, 510642, P.R. China. .,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642, China.
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5
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Zhao Y, Kong X, Yang X, Zhu L, Liang R, Luo X, Zhang L, Hopkins DL, Mao Y, Zhang Y. Effect of energy metabolism and proteolysis on the toughness of intermediate ultimate pH beef. Meat Sci 2022; 188:108798. [DOI: 10.1016/j.meatsci.2022.108798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 10/18/2022]
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6
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León-Llanos LM, Flórez-Díaz H, Duque-Muñoz LG, Villarroel M, Miranda-de la Lama GC. Influence of temperament on performance and carcass quality of commercial Brahman steers in a Colombian tropical grazing system. Meat Sci 2022; 191:108867. [DOI: 10.1016/j.meatsci.2022.108867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 02/17/2022] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
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7
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Gagaoua M, Warner RD, Purslow P, Ramanathan R, Mullen AM, López-Pedrouso M, Franco D, Lorenzo JM, Tomasevic I, Picard B, Troy D, Terlouw EMC. Dark-cutting beef: A brief review and an integromics meta-analysis at the proteome level to decipher the underlying pathways. Meat Sci 2021; 181:108611. [PMID: 34157500 DOI: 10.1016/j.meatsci.2021.108611] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/07/2021] [Accepted: 06/14/2021] [Indexed: 01/06/2023]
Abstract
Comprehensive characterization of the post-mortem muscle proteome defines a fundamental goal in meat proteomics. During the last decade, proteomics tools have been applied in the field of foodomics to help decipher factors underpinning meat quality variations and to enlighten us, through data-driven methods, on the underlying mechanisms leading to meat quality defects such as dark-cutting meat known also as dark, firm and dry (DFD) meat. In cattle, several proteomics studies have focused on the extent to which changes in the post-mortem muscle proteome relate to dark-cutting beef development. The present data-mining study firstly reviews proteomics studies which investigated dark-cutting beef, and secondly, gathers the protein biomarkers that differ between dark-cutting versus beef with normal-pH in a unique repertoire. A list of 130 proteins from eight eligible studies was curated and mined through bioinformatics for Gene Ontology annotations, molecular pathways enrichments, secretome analysis and biological pathways comparisons to normal beef color from a previous meta-analysis. The major biological pathways underpinning dark-cutting beef at the proteome level have been described and deeply discussed in this integromics study.
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Affiliation(s)
- Mohammed Gagaoua
- Food Quality and Sensory Science Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.
| | - Robyn D Warner
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter Purslow
- Centro de Investigacion Veterinaria de Tandil (CIVETAN), Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil B7001BBO, Argentina
| | - Ranjith Ramanathan
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anne Maria Mullen
- Food Quality and Sensory Science Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - Maria López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15872 Santiago de Compostela, Spain
| | - Daniel Franco
- Centro Tecnológico de la Carne de Galicia, rúa Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas 32900, Ourense, Spain
| | - José M Lorenzo
- Centro Tecnológico de la Carne de Galicia, rúa Galicia n° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas 32900, Ourense, Spain; Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, Universidad de Vigo, 32004 Ourense, Spain
| | - Igor Tomasevic
- University of Belgrade, Faculty of Agriculture, Nemanjina 6, 11080, Belgrade, Serbia
| | - Brigitte Picard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Declan Troy
- Food Quality and Sensory Science Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | - E M Claudia Terlouw
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
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8
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Bautista-Fernández M, Estévez-Moreno LX, Losada-Espinosa N, Villarroel M, María GA, De Blas I, Miranda-de la Lama GC. Claw disorders as iceberg indicators of cattle welfare: Evidence-based on production system, severity, and associations with final muscle pH. Meat Sci 2021; 177:108496. [PMID: 33751984 DOI: 10.1016/j.meatsci.2021.108496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/27/2021] [Accepted: 03/10/2021] [Indexed: 01/16/2023]
Abstract
This study presents a novel approach to use claw disorders in cattle as a retrospective welfare indicator characterized at the abattoir. A total of 1040 cattle (2080 front and back left claws) were analyzed from 143 batches, originating from feedlots, free-range, and dairy systems. Our results indicate that abnormal claw shapes (>55%) and fissures of the claw wall (>25%) had the highest prevalence, regardless of the system of origin. For the seven types of lesions monitored, numerous associations were found between lesions in the front and rear limbs typical of each production system. Ultimate meat pH was higher in animals with white line disease and skin wounds in feedlot and free-range cattle. We conclude that claw disorders can be used as an iceberg indicator to provide valuable information about animal fitness, and the ability to cope with the husbandry and pre-slaughter environment. These indicators can be used to improve the level of welfare of the animals.
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Affiliation(s)
- M Bautista-Fernández
- Faculty of Veterinary Medicine, National Autonomous University of Mexico, UNAM, Mexico
| | - L X Estévez-Moreno
- Department of Animal Production and Food Science, Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - N Losada-Espinosa
- Faculty of Veterinary Medicine, National Autonomous University of Mexico, UNAM, Mexico
| | - M Villarroel
- CEIGRAM, ETSIAAB, Technical University of Madrid (UPM), Madrid, Spain
| | - G A María
- Department of Animal Production and Food Science, Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - I De Blas
- Department of Animal Pathology, Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - G C Miranda-de la Lama
- Department of Animal Production and Food Science, Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain; Department of Food Science, Metropolitan Autonomous University, UAM, Lerma, State of Mexico, Mexico.
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9
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Strobel P, Galaz A, Villaroel-Espíndola F, Apaoblaza A, Slebe JC, Jerez-Timaure N, Gallo C, Ramírez-Reveco A. Temperature, but not excess of glycogen, regulates "in vitro" AMPK activity in muscle samples of steer carcasses. PLoS One 2021; 16:e0229480. [PMID: 33507943 PMCID: PMC7842895 DOI: 10.1371/journal.pone.0229480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 12/08/2020] [Indexed: 12/29/2022] Open
Abstract
Postmortem muscle temperature affects the rate of pH decline in a linear manner from 37.5°C to 0-2°C. The pH decline is correlated with the enzymatic degradation of glycogen to lactate and this process includes the metabolic coupling between glycogenolysis and glycolysis, and that are strongly upregulated by the AMPK. In this study, we used 12 samples previously characterized by have different muscle glycogen concentration, lactate and AMPK activity, selected from 38 steers that produced high final pH (>5.9) and normal final pH (<5.8) carcasses at 24 h postmortem. Moreover, we evaluated changes in the AMPK activity in samples from both categories incubated at 37, 25, 17 and 5°C and supplemented with exogenous glycogen. Finally, we analysed if there were structural differences between polymers from both categories. Our results showed that "in vitro" enzymatic AMPK activity evaluated at both 0.5 or 24 h was greater in samples from normal then high pH categories (p <0.01), and in all temperature of incubation analysed (17, 25 and 37°C). For other hand, a greater AMPK activity were obtained in samples incubated at 17 that 25 or 37°C, in normal carcasses at both 0.5 or 24 h (p < 0.01), as also in samples from carcasses categorized as high pH, but at 24 h (p < 0.05). Interestingly, AMPK activity was totally abolished at 5°C, independent of final pH category of carcasses, and was confirmed that the incubation temperature at which the maximum activity was obtained (p < 0.01), at least in carcasses with a normal pH is at 17°C. The enzymatic AMPK activity did not change in relation to excess glycogen (p > 0.05) and we did not detect structural differences in the polymers present in samples from both categories (p > 0.05), suggesting that postmortem AMPK activity may be highly sensitive to temperature and not to in vitro changes in glycogen concentration (p > 0.05). Our results allow concluding that normal concentrations of muscle glycogen immediately at the time of slaughter (0.5 h) and an adequate cooling managing of carcasses are relevant to let an efficient glycogenolytic/glycolytic flow required for lactate accumulation and pH decline, through the postmortem AMPK signalling pathway.
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Affiliation(s)
- Pablo Strobel
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Alex Galaz
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Franz Villaroel-Espíndola
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Laboratorio Medicina Traslacional, Fundación Arturo López Pérez Cancer Center, Santiago, Chile
| | - Ariel Apaoblaza
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Juan Carlos Slebe
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Nancy Jerez-Timaure
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Carmen Gallo
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Alfredo Ramírez-Reveco
- Instituto de Ciencia Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
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10
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Fernández-Barroso MÁ, Caraballo C, Silió L, Rodríguez C, Nuñez Y, Sánchez-Esquiliche F, Matos G, García-Casco JM, Muñoz M. Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile. Animals (Basel) 2020; 10:ani10091715. [PMID: 32971875 PMCID: PMC7552750 DOI: 10.3390/ani10091715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/10/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The Iberian pig is the most representative autochthonous breed of the Mediterranean region with unique genetic and phenotypic characteristics. The breed has been successfully preserved by its high-quality meat and high-priced products. Tenderness is one of the most relevant meat quality traits, and meat tenderization is influenced by genetic and environmental effects such as pre-slaughter handling and post-mortem conditions. Tenderness could be included in Iberian pig breeding programs, mainly focused on the improvement of premium-cuts percentage, in order to avoid the meat quality decline. A better biological understanding of this trait is needed. In the current study, we analyze the transcriptome of pigs divergent for Warner–Bratzler shear force through RNA-seq technique for the identification, characterization and quantification of candidate genes involved in biological pathways, networks and functions affecting meat tenderness. Abstract Tenderness is one of the most important meat quality traits and it can be measured through shear force with the Warner–Bratzler test. In the current study, we use the RNA-seq technique to analyze the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with quantitative PCR (qPCR). Functional analyses showed an enrichment of DE genes in biological processes related to proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.
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Affiliation(s)
- Miguel Ángel Fernández-Barroso
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
- Correspondence:
| | - Carmen Caraballo
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - Luis Silió
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - Carmen Rodríguez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - Yolanda Nuñez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | | | - Gema Matos
- Sánchez Romero Carvajal—Jabugo, SRC, 21290 Huelva, Spain; (F.S.-E.); (G.M.)
| | - Juan María García-Casco
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - María Muñoz
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
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Zoabi M, Zhang L, Li TM, Elias JE, Carlson SM, Gozani O. Methyltransferase-like 21C (METTL21C) methylates alanine tRNA synthetase at Lys-943 in muscle tissue. J Biol Chem 2020; 295:11822-11832. [PMID: 32611769 DOI: 10.1074/jbc.ra120.014505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/26/2020] [Indexed: 12/24/2022] Open
Abstract
Protein-lysine methylation is a common posttranslational modification (PTM) throughout the human proteome that plays important roles in diverse biological processes. In humans, there are >100 known and candidate protein lysine methyltransferases (PKMTs), many of which are linked to human diseases. Methyltransferase-like protein 21C (METTL21C) is a PKMT implicated in muscle biology that has been reported to methylate valosin-containing protein/p97 (VCP) and heat shock 70-kDa protein 8 (HSPA8). However, a clear in vitro methyltransferase activity for METTL21C remains yet to be demonstrated, and whether it is an active enzyme that directly methylates substrate(s) in vivo is unclear. Here, we used an unbiased biochemistry-based screening assay coupled to MS, which identified alanine tRNA synthetase 1 (AARS1) as a direct substrate of METTL21C. We found that METTL21C catalyzes methylation of Lys-943 of AARS1 (AARS1-K943me) both in vitro and in vivo In vitro METTL21C-mediated AARS1 methylation was independent of ATP or tRNA molecules. Unlike for AARS1, and in conflict with previous reports, we did not detect METTL21C methylation of VCP and HSPA8. AARS1-K943 methylation in HEK293T cells depends upon METTL21C levels. Finally, METTL2C was almost exclusively expressed in muscle tissue, and, accordingly, we detected METTL21C-catalyzed methylation of AARS1 in mouse skeletal muscle tissue. These results reveal that AARS1 is a bona fide in vitro substrate of METTL21C and suggest a role for the METTL21C-AARS1 axis in the regulation of protein synthesis in muscle tissue. Moreover, our study describes a straightforward protocol for elucidating the physiological substrates of poorly characterized or uncharacterized PKMTs.
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Affiliation(s)
- Muhammad Zoabi
- Department of Biology, Stanford University, Stanford, California, USA
| | - Lichao Zhang
- Chan Zuckerberg Biohub, Stanford University, Stanford, California, USA
| | - Tie-Mei Li
- Department of Biology, Stanford University, Stanford, California, USA
| | - Josh E Elias
- Chan Zuckerberg Biohub, Stanford University, Stanford, California, USA
| | - Scott M Carlson
- Department of Biology, Stanford University, Stanford, California, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, California, USA
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