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RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout

机译:RNA-Seq揭示了虹鳟鱼中与生长和肌肉品质性状相关的MicroRNA表达特征和遗传多态性

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摘要

The role of microRNA expression and genetic variation in microRNA-binding sites of target genes on growth and muscle quality traits is poorly characterized. We used RNA-Seq approach to investigate their importance on 5 growth and muscle quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, muscle shear force and whiteness. Phenotypic data were collected from 471 fish, representing 98 families (~5 fish/family) from a growth-selected line. Muscle microRNAs and mRNAs were sequenced from 22 families showing divergent phenotypes. Ninety microRNAs showed differential expression between families with divergent phenotypes, and their expression was strongly associated with variation in phenotypes. A total of 204 single nucleotide polymorphisms (SNPs) present in 3′ UTR of target genes either destroyed or created novel illegitimate microRNA target sites; of them, 78 SNPs explained significant variation in the aforementioned 5 muscle traits. Majority of the phenotype-associated SNPs were present in microRNA-binding sites of genes involved in energy metabolism and muscle structure. These findings suggest that variation in microRNA expression and/or sequence variation in microRNA binding sites in target genes play an important role in mediating differences in fish growth and muscle quality phenotypes.
机译:microRNA表达和遗传变异在目标基因的microRNA结合位点上对生长和肌肉质量性状的作用尚不清楚。我们使用RNA-Seq方法研究了它们在5种生长和肌肉质量特征上的重要性:体重(WBW),肌肉产量,肌肉粗脂肪含量,肌肉剪切力和白度。从代表生长选择的品系的98个科(约5个鱼/科)的471条鱼中收集了表型数据。对来自22个家族的肌肉microRNA和mRNA进行了测序,显示出不同的表型。九十个微RNA显示不同表型的家庭之间的差异表达,并且它们的表达与表型的变化密切相关。在靶基因的3'UTR中共有204个单核苷酸多态性(SNP)被破坏或创建了新的非法microRNA靶位点;其中的78个SNP解释了上述5种肌肉性状的显着变化。大多数与表型有关的SNP存在于与能量代谢和肌肉结构有关的基因的微小RNA结合位点中。这些发现表明,靶基因中微小RNA表达的变化和/或微小RNA结合位点的序列变化在介导鱼类生长和肌肉质量表型差异中起重要作用。

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