Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle

Muniz, Maria Malane Magalhães; Fonseca, Larissa Fernanda Simielli; Silva, Danielly Beraldo dos Santos; Oliveira, Hinayah Rojas de; Baldi, Fernando; Chardulo, Artur Loyola; Ferro, Jesus Aparecido; Cánovas, Ángela; Albuquerque, Lúcia Galvão de

doi:10.1016/j.meatsci.2020.108378

Cited by 22 publications

(31 citation statements)

References 71 publications

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“…ATP5F1E, a mitochondrial membrane ATP synthase, is mainly involved in metabolic pathways and oxidative phosphorylation pathways. The previous study has reported that expression of ATP5F1E was downregulated in tender beef animals (28). ATP5F1E was downregulated in NR suspended group and dynamic changed between post-mortem 1 and 7 days, implying NR suspension might improve the tenderness of beef.…”

Section: Proteomic Analysismentioning

confidence: 80%

Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging

Cai

Wen

Che³

et al. 2021

Front. Nutr.

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Beef quality is the first deciding factor for consumers to consider before purchasing. The aim of this study was to evaluate the effects of suspension and aging time on beef quality. We compared the differences in pH, drip loss, cooking loss, color, shear force, myofibril fragmentation index (MFI), and electron microscope of three muscle tissues between Achilles tendon (AT) and neck-arm restraint (NR) suspensions during seven aging periods (days 0, 1, 2, 3, 7, 14, and 21) after slaughter using the carcasses of six Xinjiang brown cattle. We found that NR suspension could significantly increase the water loss rate and MFI, as well as reduce the shear force compared to AT suspension. The muscle fiber structure with NR suspension was more severely damaged. The proteomics of longissimus dorsi was checked for the post-mortem days 1, 7, and 14. We detected 50, 26, and 29 differentially expressed proteins between NR and AT suspension at post-mortem days 1, 7, and 14, respectively. These proteins were involved in metabolic and muscle structure associated pathways and contributed to a comprehensive understanding of suspension-dependent meat quality regulation by proteins in beef cattle. To conclude, NR suspension can accelerate the aging time of beef carcasses, which will reduce the cost of carcass suspension and bring more benefits in the beef industry.

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Section: Proteomic Analysismentioning

confidence: 80%

Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging

Cai

Wen

Che³

et al. 2021

Front. Nutr.

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“…MyHCs appear to be the most appropriate markers for muscle fiber-type delineation [ 27 ]. Indeed, upregulation of myosin heavy chains 1 ( MYH1 ) and 15 ( MYH15 ) have been detected in tough meat in previous studies on beef cattle and chicken, respectively [ 11 , 28 ]. Although myosin-related genes were found to be downregulated in this study—i.e., VIIB ( MYO7B ) in the β-alanine supplementation group and myosin binding protein H like ( MYBPH ) in the L-histidine supplementation group—no differentially-expressed MyHC gene was identified in this study.…”

Section: Discussionmentioning

confidence: 99%

RNA Profiles of the Korat Chicken Breast Muscle with Increased Carnosine Content Produced through Dietary Supplementation with β-Alanine or L-Histidine

Kubota

Promkhun

Sinpru

et al. 2021

Animals

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Korat chicken (KRC) is a slow-growing chicken bred in Thailand, whose meat exhibits a unique toughness. A previous study produced KRC breast meat containing high carnosine content through dietary supplementation with β-alanine or L-histidine; however, the KRC that were fed an L-histidine-supplemented diet produced meat that was significantly more tender. Herein, we performed RNA-Seq to identify candidate genes involved in the regulation of carnosine content and meat toughness. Total RNA was isolated from five female KRC breast muscles in each treatment group that KRC fed diets without supplementation, supplemented with β-alanine or L-histidine. Compared to the non-supplemented group, we identified 118 and 198 differentially expressed genes (DEGs) in the β-alanine or L-histidine supplementation groups, respectively. Genes potentially related to meat tenderness—i.e., those regulating myosin, collagen, intramuscular fat, and calpain—were upregulated (LOC107051274, ACSBG1, and CAPNS2) and downregulated (MYO7B, MYBPH, SERPINH1, and PGAM1). However, carnosine synthase gene was not identified. Functional enrichment analysis identified pathways affected by dietary supplementation, including the insulin signaling pathway (β-alanine supplementation) and the insulin resistance and adipocytokine signaling pathways (L-histidine supplementation). The FoxO signaling pathway was identified as a regulatory network for both supplementation groups. The identified genes can be used as molecular markers of meat tenderness in slow-growing chickens.

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“…The trimmed sequences were aligned to the bovine reference genome (ARS_UCD1.2; ftp://ftp.ensembl.org/pub/release-100/ ) using CLC genomics workbench, with a Large Gap Read Mapping (LGRM) approach [ 58 , 59 ]. The LGRM tool can map sequence reads that span introns without requiring prior transcript annotation, thus allowing the best match for a given read to be identified.…”

Section: Methodsmentioning

confidence: 99%

Identification of novel alternative splicing associated with mastitis disease in Holstein dairy cows using large gap read mapping

2022

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Background Mastitis is a very common disease in the dairy industry that producers encounter daily. Transcriptomics, using RNA-Sequencing (RNA - Seq) technology, can be used to study the functional aspect of mastitis resistance to identify animals that have a better immune response to mastitis. When the cow has mastitis, not only genes but also specific mRNA isoforms generated via alternative splicing (AS) could be differentially expressed (DE), leading to the phenotypic variation observed. Therefore, the objective of this study was to use large gap read mapping to identify mRNA isoforms DE between healthy and mastitic milk somatic cell samples (N = 12). These mRNA isoforms were then categorized based on being 1) annotated mRNA isoforms for gene name and length, 2) annotated mRNA isoforms with different transcript length and 3) novel mRNA isoforms of non - annotated genes. Results Analysis identified 333 DE transcripts (with at least 2 mRNA isoforms annotated, with at least one being DE) between healthy and mastitic samples corresponding to 303 unique genes. Of these 333 DE transcripts between healthy and mastitic samples, 68 mRNA isoforms are annotated in the bovine genome reference (ARS.UCD.1.2), 249 mRNA isoforms had novel transcript lengths of known genes and 16 were novel transcript lengths of non - annotated genes in the bovine genome reference (ARS.UCD.1.2). Functional analysis including gene ontology, gene network and metabolic pathway analysis was performed on the list of 288 annotated and unique DE mRNA isoforms. In total, 67 significant metabolic pathways were identified including positive regulation of cytokine secretion and immune response. Additionally, numerous DE novel mRNA isoforms showed potential involvement with the immune system or mastitis. Lastly, QTL annotation analysis was performed on coding regions of the DE mRNA isoforms, identifying overlapping QTLs associated with clinical mastitis and somatic cell score. Conclusion This study identified novel mRNA isoforms generated via AS that could lead to differences in the immune response of Holstein dairy cows and be potentially implemented in future breeding programs.

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Identification of novel mRNA isoforms associated with meat tenderness using RNA sequencing data in beef cattle

Cited by 22 publications

References 71 publications

Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging

Effects of Neck-Arm Restraint Suspension of Beef Carcasses on Meat Quality and Proteome of Different Muscles During Post-mortem Aging

RNA Profiles of the Korat Chicken Breast Muscle with Increased Carnosine Content Produced through Dietary Supplementation with β-Alanine or L-Histidine

Identification of novel alternative splicing associated with mastitis disease in Holstein dairy cows using large gap read mapping

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