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首页> 外文期刊>PLoS One >RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef
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RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef

机译：RNA-SEQ分析鉴定了牛肉中肉质的细胞骨骼结构基因和途径

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RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.
机译：RNA测序（RNA-SEQ）允许通过鉴定差异表达（DE）基因和途径来转录生物系统的转录分析。佛罗里达大学多宝葡萄球队牧群中选择了80个具有极端表型的阉牛。平均屠宰年龄为12.91±8.69个月。在Longissimus Dorsi肌肉中测量了感官面板评估的柔软，脂肪和结缔组织，以及大理石，华纳 - 布拉茨勒剪力（WBSF）和烹饪损失。从肌肉中提取总RNA，并且基于Illumina Hiseq-3000平台的协议构建，多路复用和测序一个RNA-SEQ库，以产生2×101bp配对端读数。使用Btau_4.6.1参考基因组的整体读取映射率为63％。使用两种不同的方法，表达协会和DE分析分析总共8,799个基因。在所有80个样品上使用肉质指数进行基因和外显子表达关联分析作为连续反应变量。来自1,565个基因的208个基因和3,280个外显子的表达与肉质指数（p值≤0.05）相关。进行基因和同种型De评估，分析两组，具有极端的WBSF，压痛和大理石。总共676（调节的P值≤0.05），70（调节的P值≤0.1）和198（调节的P值≤0.1）基因分别为WBSF，柔软和大理石。对于WBSF的98个基因的总共106种同种型，13个同种型来自13个基因的柔软，43个同种型来自来自42种的马蜂（FDR≤0.1）是de。在表达协会，DE和基因富集分析中鉴定了细胞骨骼和跨膜锚定基因和途径;这些蛋白质可以对肉质直接影响。细胞骨架蛋白和跨膜锚定分子可以通过允许与肌细胞和细胞器膜的细胞骨架相互作用来影响肉质，有助于细胞骨架结构和建筑维护后期。

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