Genome‐wide proteomics analysis on longissimus muscles in Qinchuan beef cattle

He, Hongbin; Chen, Si; Liang, Wei; Liu, Xiaolin

doi:10.1111/age.12508

Cited by 14 publications

(9 citation statements)

References 35 publications

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“…In our study, we found several genes within ROH hotspots, which have been previously reported under selection in cattle 40–45 . Among them, we identified Heat Shock Protein Family A (Hsp70) Member 9 ( HSPA9 ) in seven Chinese local breed, this gene is immune-related genes, and also shows differentially expressed during bovine muscle development 46 . Previous studies suggested that HSPA9 abundance in muscle had positive correlation with beef tenderness 47,48 .…”

Section: Discussionmentioning

confidence: 99%

Genomic Patterns of Homozygosity in Chinese Local Cattle

Zhao

Liu

et al. 2019

Sci Rep

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Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5–1 Mb, Medium 1–5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.

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Section: Discussionmentioning

confidence: 99%

Genomic Patterns of Homozygosity in Chinese Local Cattle

Zhao

Liu

et al. 2019

Sci Rep

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“…In order to obtain high quality meat, researchers have conducted some studies to address these complex issues. The connections between beef quality and number and size of fiber have been examined by Mao et al (2016), the relation between the growth of cattle and beef quality is studied by He et al (2017). The impacts of manufacturing and storage means, as well as stock fodder on quality and a comparison between the quality of Angus beef and other variety of cattle have also been analyzed (Taye et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Quantitative proteomic comparison of protein differences in different parts of yak meat

Yan

et al. 2022

Food Sci. Technol

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Proteomics is a powerful tool to understand molecular connections between meat proteins and quality traits. In order to research the total proteome difference and molecular mechanisms related to quality traits in different parts of yak meat. This study was designed to investigate the differences in the proteomes of yak different muscles. In this paper, Tandem Mass Tags (TMT) coupled Liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the variations of proteome in different parts of yak after it is slaughtered. In total, 88 differentially expressed proteins (DEPs) were identified among striplon (WJR), slivsid (HGT) and chuck (JR). The quality analysis of DEPs showed heat shock proteins (HSPs) and structural proteins could be used as tenderness marker proteins for different parts of yak meat. Myosin and troponin-T may be flavour marker protein in yak meat. The bioinformatics analysis revealed that DEPs are involved in glycolysis, protein structure and phosphorylation. PPI analysis revealed thatmyosin, HSPs and metabolic enzymes may have the potential to be biological markers. This study highlights that the DEPs were responsible for meat quality different.

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“…Isobaric tagging for relative and absolute quantification (iTRAQ) is a recently developed method for the quantitative analysis of proteomes that can identify proteins and provide more accurate quantitative measurements of protein abundance than traditional two-dimensional electrophoresis analysis [8]. The iTRAQ method has been widely applied to investigate the proteomes of cattle [9], chicken [10], and pig [11]. Previous proteomics studies using iTRAQ have focused on muscle development [11], embryo development [12], meat tenderness [10], and lipid deposition [13] in livestock and poultry.…”

Section: Introductionmentioning

confidence: 99%

Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)

Lei

Zhang

et al. 2020

Animals

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Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.

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Genome‐wide proteomics analysis on longissimus muscles in Qinchuan beef cattle

Cited by 14 publications

References 35 publications

Genomic Patterns of Homozygosity in Chinese Local Cattle

Genomic Patterns of Homozygosity in Chinese Local Cattle

Quantitative proteomic comparison of protein differences in different parts of yak meat

Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)

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