Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits.
Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits.
复制标题
DOI：
10.1038/s41598-018-30655-8
复制
发表时间：
2018-08-14
影响因子：
4.6
通讯作者：
Salem M
中科院分区：
文献类型：
--
作者：
Ali A;Al-Tobasei R;Kenney B;Leeds TD;Salem M
肌肉产量和质量性状对于水产养殖业和消费者都很重要。这些性状的遗传选择是困难的，因为它们是多基因的，是多因素相互作用的结果。为了研究这些性状的遗传结构，在来自生长选择系的98个家族的约500条鱼中测量了全身重量（WBW）、肌肉产量、脂肪含量、剪切力和白度的表型表征。使用RNA-Seq对每个性状表现出不同表型的不同家族的肌肉转录组进行测序。我们在表现出截然不同表型的鱼类家族中分别鉴定了240个和1，280个差异表达（DE）蛋白质编码基因和长链非编码RNA（lncRNA）。许多DE lncRNA（n = 229）的表达与重叠，相邻或距离较远的蛋白质编码基因（n = 1，030）呈正相关，导致3，392种相互作用。三种DE反义lncRNA与已知影响肌肉品质性状的正义基因共表达。44个DE lncRNA对影响肌肉品质性状的miRNAs具有潜在的海绵功能。这项研究（1）定义了肌肉质量相关的蛋白质编码和非编码基因，（2）提供了深入了解非编码RNA参与调节虹鳟鱼的生长和鱼片质量性状。
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.
登录
查看更多内容
影响因子：
16.6
作者：
Berthelot, Camille;Brunet, Frederic;Chalopin, Domitille;Juanchich, Amelie;Bernard, Maria;Noel, Benjamin;Bento, Pascal;Da Silva, Corinne;Labadie, Karine;Alberti, Adriana;Aury, Jean-Marc;Louis, Alexandra;Dehais, Patrice;Bardou, Philippe;Montfort, Jerome;Klopp, Christophe;Cabau, Cedric;Gaspin, Christine;Thorgaard, Gary H.;Boussaha, Mekki;Quillet, Edwige;Guyomard, Rene;Galiana, Delphine;Bobe, Julien;Volff, Jean-Nicolas;Genet, Carine;Wincker, Patrick;Jaillon, Olivier;Roest Crollius, Hugues;Guiguen, Yann
通讯作者：
Guiguen, Yann
影响因子：
4.4
作者：
Danzmann RG;Kocmarek AL;Norman JD;Rexroad CE 3rd;Palti Y
通讯作者：
Palti Y
影响因子：
3.7
作者：
Al-Tobasei R;Paneru B;Salem M
通讯作者：
Salem M
影响因子：
4.6
作者：
Brockmann, Gudrun A.;Tsaih, Shirng-Wern;Li, Renhua
通讯作者：
Li, Renhua
影响因子：
4.5
作者：
Dufflocq, Pablo;Lhorente, Jean P.;Yanez, Jose M.
通讯作者：
Yanez, Jose M.