Co-localization of growth QTL with differentially expressed candidate genes in rainbow trout

Genome ◽  
2015 ◽  
Vol 58 (9) ◽  
pp. 393-403 ◽  
Author(s):  
Andrea L. Kocmarek ◽  
Moira M. Ferguson ◽  
Roy G. Danzmann
Keyword(s):  
Rainbow Trout ◽  
Body Size ◽  
Candidate Genes ◽  
White Muscle ◽  
Muscle Growth ◽  
Differentially Expressed ◽  
Large Fish ◽  
Growth Metabolism ◽  
Stickleback Genome ◽  
Half Sibling

We tested whether genes differentially expressed between large and small rainbow trout co-localized with familial QTL regions for body size. Eleven chromosomes, known from previous work to house QTL for weight and length in rainbow trout, were examined for QTL in half-sibling families produced in September (1 XY male and 1 XX neomale) and December (1 XY male). In previous studies, we identified 108 candidate genes for growth expressed in the liver and white muscle in a subset of the fish used in this study. These gene sequences were BLASTN aligned against the rainbow trout and stickleback genomes to determine their location (rainbow trout) and inferred location based on synteny with the stickleback genome. Across the progeny of all three males used in the study, 63.9% of the genes with differential expression appear to co-localize with the QTL regions on 6 of the 11 chromosomes tested in these males. Genes that co-localized with QTL in the mixed-sex offspring of the two XY males primarily showed up-regulation in the muscle of large fish and were related to muscle growth, metabolism, and the stress response.

scholarly journals Dietary methionine availability affects the main factors involved in muscle protein turnover in rainbow trout (Oncorhynchus mykiss)

2014 ◽  
Vol 112 (4) ◽  
pp. 493-503 ◽  
Author(s):  
Ikram Belghit ◽  
Sandrine Skiba-Cassy ◽  
Inge Geurden ◽  
Karine Dias ◽  
Anne Surget ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
White Muscle ◽  
Muscle Protein ◽  
Muscle Growth ◽  
Mrna Translation ◽  
Fish Feed ◽  
Mrna Levels ◽  
Methionine Deficiency ◽  
Main Factors

Methionine is a limiting essential amino acid in most plant-based ingredients of fish feed. In the present study, we aimed to determine the effect of dietary methionine concentrations on several main factors involved in the regulation of mRNA translation and the two major proteolytic pathways (ubiquitin–proteasome and autophagy-lysosomal) in the white muscle of rainbow trout (Oncorhynchus mykiss). The fish were fed for 6 weeks one of the three isonitrogenous diets providing three different methionine concentrations (deficient (DEF), adequate (ADQ) and excess (EXC)). At the end of the experiment, the fish fed the DEF diet had a significantly lower body weight and feed efficiency compared with those fed the EXC and ADQ diets. This reduction in the growth of fish fed the DEF diet was accompanied by a decrease in the activation of the translation initiation factors ribosomal protein S6 and eIF2α. The levels of the main autophagy-related markers (LC3-II and beclin 1) as well as the expression of several autophagy genes (atg4b, atg12 l, Uvrag, SQSTM1, Mul1 and Bnip3) were higher in the white muscle of fish fed the DEF diet. Similarly, the mRNA levels of several proteasome-related genes (Fbx32, MuRF2, MuRF3, ZNF216 and Trim32) were significantly up-regulated by methionine limitation. Together, these results extend our understanding of mechanisms regulating the reduction of muscle growth induced by dietary methionine deficiency, providing valuable information on the biomarkers of the effects of low-fishmeal diets.

scholarly journals THE EFFECTS OF BODY SIZE ON THE ACID-BASE AND METABOLITE STATUS IN THE WHITE MUSCLE OF RAINBOW TROUT BEFORE AND AFTER EXHAUSTIVE EXERCISE

1993 ◽  
Vol 180 (1) ◽  
pp. 195-207 ◽  
Author(s):  
R. A. Ferguson ◽  
J. D. Kieffer ◽  
B. L. Tufts
Keyword(s):  
Rainbow Trout ◽  
Body Size ◽  
White Muscle ◽  
Lactate Concentration ◽  
Exhaustive Exercise ◽  
Fish Length ◽  
Acid Base ◽  
Muscle Lactate ◽  
Before And After ◽  
Change In Mean

The effect of body size on the white muscle acid-base and metabolite status was examined in rainbow trout (Oncorhynchus mykiss) ranging in length from 8 to 54 cm. Following 5 min of exhaustive exercise, white muscle lactate concentration was approximately doubled (approximately 32 micromole g-1) in larger fish than in smaller fish (approximately 16 micromole g-1). Associated with this post-exercise increase in lactate was a nearly parallel increase in the number of metabolic protons produced by larger fish. Larger fish did not possess a greater non-bicarbonate buffering capacity or soluble protein concentration, so their mean muscle intracellular pH (pHi) decreased by approximately 0.70 units compared with a change in mean pHi of about 0.40 units in the smallest fish. The relationship between resting pHi and length was independent of size (mean pHi 7.31). Concentrations of muscle energy metabolites were also determined in trout white muscle before and after exercise. Under resting conditions, larger fish possessed a twofold greater concentration of ATP (approximately 7 micromole g-1) than did smaller fish (approximately 3micromole g-1). Similarly, resting values of muscle glycogen range from about 6 micromole g-1 in the smallest fish to as high as 15 micromole g-1 in the largest fish. However, the smaller fish had higher levels (approximately 35 micromole g- 1) of phosphocreatine (PCr) than the larger fish (approximately 25 micromole g-1). Following exercise, however, both ATP and glycogen concentrations remained size-dependent and increased with increases in fish length. Levels of PCr were size-independent following exercise. These results demonstrate that body size has an important influence on the acid- base and metabolic status of fish before and after exercise.

Northern Squawfish, Ptychocheilus oregonensis, O2 Consumption Rate and Respiration Model: Effects of Temperature and Body Size

1994 ◽  
Vol 51 (1) ◽  
pp. 8-12 ◽  
Author(s):  
Joseph J. Cech Jr. ◽  
Daniel T. Castleberry ◽  
Todd E. Hopkins ◽  
James H. Petersen
Keyword(s):  
Rainbow Trout ◽  
Body Size ◽  
Cross Sections ◽  
White Muscle ◽  
Consumption Rate ◽  
Live Weight ◽  
Acclimation Temperature ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Flow Through ◽  
Controlled Flow

Northern squawfish, Ptychocheilus oregonensis (live weight range 0.361–1.973 kg), O2 consumption was measured with temperature-controlled, flow-through respirometers for >24 h. Mean standard O2 consumption rate of northern squawfish increased with acclimation temperature: 24.3, 49.1, 75.0, and 89.4 mg∙kg−0.67∙h−1 at 9, 15, 18, and 21 °C, respectively. Q10 analysis showed that O2 consumption rate temperature sensitivity was greatest at the intermediate acclimation temperatures (15–18 °C, Q10 = 4.10), moderate at the lower acclimation temperatures (9–15 °C, Q10 = 3.23), and lowest at the higher acclimation temperatures (18–21 °C, Q10 = 1.80). Overall Q10 was 2.96 (9–21 °C). Body size (W, grams) and temperature (T, degrees Celcius) were related to O2 consumption ([Formula: see text], grams per gram per day) by [Formula: see text]W−0.285∙e0.105T. Northern squawfish red to white muscle ratios significantly exceeded those of rainbow trout, Oncorhynchus mykiss, in cross sections at 50 and 75% of standard length. High metabolic rates and red to white muscle ratios argue for comparability of northern squawfish with active predators such as sympatric rainbow trout.

scholarly journals Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1423
Author(s):  
André Albuquerque ◽  
Cristina Óvilo ◽  
Yolanda Núñez ◽  
Rita Benítez ◽  
Adrián López-Garcia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Growth ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Pig Breeds ◽  
Nfkb Activation ◽  
Main Gene ◽  
Slow Type ◽  
Longissimus Lumborum ◽  
Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

scholarly journals Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gregory M. Weber ◽  
Jill Birkett ◽  
Kyle Martin ◽  
Doug Dixon ◽  
Guangtu Gao ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Egg Quality ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Analysis Group ◽  
Maternal Transcripts ◽  
Single Batch ◽  
Insight Into

Abstract Background Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by fish hatcheries. Although levels of specific transcripts have been shown to associate with measures of egg quality, these differentially expressed genes (DEGs) have not been consistent among studies. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among 2 year classes of the same line (A1, A2) and a population from a different hatchery (B). The study compared 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Results There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Conclusions Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same line. Greater similarity in dysregulated transcripts within year classes of the same line than among lines suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes.

scholarly journals Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 835
Author(s):  
Mohammadreza Mohammadabadi ◽  
Farhad Bordbar ◽  
Just Jensen ◽  
Min Du ◽  
Wei Guo
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Meat Quality ◽  
Muscle Development ◽  
Muscle Growth ◽  
Farm Animals ◽  
Meat Production ◽  
Skeletal Muscle Development ◽  
Extrinsic Factors ◽  
Myogenic Regulatory Factor

Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.

scholarly journals Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pablo Cáceres ◽  
Agustín Barría ◽  
Kris A. Christensen ◽  
Liane N. Bassini ◽  
Katharina Correa ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Candidate Genes ◽  
Protein Phosphatase ◽  
Sea Lice ◽  
Genome Wide Association Studies ◽  
Dual Specificity ◽  
Dual Specificity Protein Phosphatase ◽  
Genomic Regions ◽  
Specificity Protein

AbstractSea lice (Caligus rogercresseyi) is an ectoparasite which causes major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The objectives of this study were to: (1) identify genomic regions associated with resistance to Caligus rogercresseyi in Atlantic salmon and rainbow trout by performing single-step Genome-Wide Association studies (ssGWAS), and (2) identify candidate genes related to trait variation based on exploring orthologous genes within the associated regions across species. A total of 2626 Atlantic salmon and 2643 rainbow trout were challenged and genotyped with 50 K and 57 K SNP panels, respectively. We ran two independent ssGWAS for sea lice resistance on each species and identified 7 and 13 regions explaining more than 1% of the genetic variance for the trait, with the most important regions explaining 3% and 2.7% for Atlantic salmon and rainbow trout, respectively. We identified genes associated with immune response, cytoskeleton function, and cell migration when focusing on important genomic regions for each species. Moreover, we found 15 common orthogroups which were present in more than one associated genomic region, within- or between-species; however, only one orthogroup showed a clear potential biological relevance in the response against sea lice. For instance, dual-specificity protein phosphatase 10-like (dusp10) and dual-specificity protein phosphatase 8 (dusp8) were found in genomic regions associated with lice density in Atlantic salmon and rainbow trout, respectively. Dusp10 and dusp8 are modulators of the MAPK pathway and might be involved in the differences of the inflammation response between lice resistant and susceptible fish from both species. Our results provide further knowledge on candidate genes related to sea lice resistance and may help establish better control for sea lice in fish populations.

scholarly journals Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 823
Author(s):  
Xiayi Liu ◽  
Xiaochen Wang ◽  
Jing Liu ◽  
Xiangyu Wang ◽  
Haigang Bao
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Gallus Gallus ◽  
Differentially Expressed ◽  
Tibet Plateau ◽  
Embryonic Liver ◽  
Selection Signature ◽  
Chicken Embryos ◽  
Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

scholarly journals Morphological and morphometric analysis of skeletal muscle between male and female young adult Colossoma macropomum (Characiformes: Serrasalmidae)

2016 ◽  
Vol 14 (2) ◽  
Author(s):  
Fernanda De Mello ◽  
Daruzi Felippe ◽  
Leandro C. Godoy ◽  
Nívia Lothhammer ◽  
Luis R. J. Guerreiro ◽  
...  
Keyword(s):  
Body Weight ◽  
Fish Species ◽  
White Muscle ◽  
Fiber Diameter ◽  
Muscle Growth ◽  
Weak Correlation ◽  
Morphological Pattern ◽  
Large Size ◽  
Large Fiber ◽  
Different Diameters

ABSTRACT This study aimed to evaluate muscle organization in tambaqui in order to describe the muscle growth process. We analyzed the morphometric pattern of fibers from white muscle of young-adults (300 days) by smaller diameter. The organization of white muscle exhibited a typical morphological pattern found in other fish species. Heavier animals showed higher frequency of larger diameter fibers (>50 μm ) and smaller animals had higher frequency of smaller diameter fibers (<20 μm ) (P =0.005). However, both animals showed the same frequency of intermediate diameter fibers (20-50 μm ). Body weight showed a positive correlation with muscle diameter fiber (r=0.45), being 20-50 μm the diameters that contributed the most to animal weight (P <0.0001). A weak correlation between fiber diameter and animal sex was observed (r=0.2). Females showed higher frequency of large fiber diameters (>50 μm ) than males. However, there was no difference between body weight and sex (P =0.8). Our results suggest that muscle growth is by hypertrophy and hyperplasia due to a mosaic appearance from different diameters fibers, which is characteristic of large size fish species.

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