Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
Sci Rep. 2018 Aug 14;8(1):12111. doi: 10.1038/s41598-018-30655-8.
Muscle yield and quality traits are important for the aquaculture industry and consumers. Genetic selection for these traits is difficult because they are polygenic and result from multifactorial interactions. To study the genetic architecture of these traits, phenotypic characterization of whole body weight (WBW), muscle yield, fat content, shear force and whiteness were measured in ~500 fish representing 98 families from a growth-selected line. RNA-Seq was used to sequence the muscle transcriptome of different families exhibiting divergent phenotypes for each trait. We have identified 240 and 1,280 differentially expressed (DE) protein-coding genes and long noncoding RNAs (lncRNAs), respectively, in fish families exhibiting contrasting phenotypes. Expression of many DE lncRNAs (n = 229) was positively correlated with overlapping, neighboring or distantly located protein-coding genes (n = 1,030), resulting in 3,392 interactions. Three DE antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. Forty-four DE lncRNAs had potential sponge functions to miRNAs that affect muscle quality traits. This study (1) defines muscle quality associated protein-coding and noncoding genes and (2) provides insight into non-coding RNAs involvement in regulating growth and fillet quality traits in rainbow trout.
肌肉产量和品质特性对水产养殖业和消费者都很重要。由于这些特性是多基因的，并受到多因素相互作用的影响，因此对这些特性进行遗传选择很困难。为了研究这些特性的遗传结构，我们对代表生长选择系的 98 个家系中的约 500 条鱼进行了全身体重（WBW）、肌肉产量、脂肪含量、剪切力和白度的表型特征测定。我们对表现出每个性状不同表型的不同家系的肌肉转录组进行了 RNA-Seq 测序。我们分别鉴定了在表现出不同表型的鱼类家系中分别有 240 个和 1,280 个差异表达（DE）的蛋白编码基因和长非编码 RNA（lncRNA）。许多 DE lncRNA（n=229）的表达与重叠、相邻或远位的蛋白编码基因（n=1,030）呈正相关，导致产生 3,392 个相互作用。3 个 DE 反义 lncRNA 与已知影响肌肉品质性状的有义基因共表达。44 个 DE lncRNA 具有潜在的海绵功能，可作用于影响肌肉品质性状的 miRNAs。本研究（1）定义了与肌肉品质相关的蛋白编码和非编码基因，（2）深入了解非编码 RNA 参与调控虹鳟生长和鱼片品质性状的机制。
