Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Differential gene expression of candidate genes for growth in rainbow trout

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Growth in fishes is a complex trait, controlled by both genetic and environmental factors, that impacts many components of fitness. Gene expression studies may lead to the identification of candidate genes for growth and microarrays offer the opportunity to examine the expression of thousands of genes simultaneously. Gene expression differences in the liver and white muscle were examined in normally growing, 15 month-old, large and small size-selected rainbow trout (Oncorhynchus mykiss) derived from two different seasonal spawning groups (Sept. and Dec.). Examination of the gene expression differences in both liver and white muscle tissue allowed us to assess the seasonal influences upon gene expression patterns that occur in this species, and facilitated the identification of genes that may possess similar expression patterns regardless of seasonal effects. The analysis of global gene expression in large and small fish reared under standard conditions provides an understanding of typical growth patterns that may be observed in this species. The identification of candidate genes by this study may provide insight into the mechanisms of growth in fishes and may help to identify candidate genes for growth.

ORGANISM(S): Oncorhynchus mykiss

SUBMITTER: Andrea Kocmarek

PROVIDER: E-GEOD-42584 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:This study compared changes in gene expression in an oviparous female fish, the rainbow trout (Oncorhynchus mykiss), under two different photoperiod treatments, a natural photoperiod (NP) and a shortened photoperiod (SP; 60% of NP). Gene expression in the liver, ovary and pituitary were measured at one-four week intervals over the course of the reproductive cycle in each treatment. Total RNA was harvested from these tissues, cDNA prepared, and hybridized on the 16K GRASP cDNA microarray. Established indices of reproductive development (ovulation, gonadosomatic index, mean oocyte diameter, and plasma hormone levels) were also measured. The SP fish failed to ovulate and their reproductive trajectory was clearly different from the NP group, which ovulated as expected. A comparative examination of the reproductive indices in both groups shows that ovarian development initiated in the SP group and proceeded relatively normally for about two-thirds of the reproductive cycle. Plasma follicle-stimulating hormone levels were higher in the SP fish from the cycle onset. This may have dampened E2 synthesis, preventing the positive feedback signal on the pituitary for the normal, rapid increase in luteinizing hormone late in the cycle. Transcriptome analysis used an unsupervised k-means hierarchical clustering method to visualize changes in gene expression in the different organs from the NP fish that were assumed to represent the normal pattern leading to successful ovary development. In the NP, fish four, five, and six unique gene clusters were identified in the liver, ovary, and pituitary, respectively. These clusters ranged in size from 22 genes in one of the pituitary clusters to 302 genes in the liver. These clusters were then applied to the SP fish to determine if and how they were altered. The expression patterns of most genes in the SP fish were notably altered from the first time point. A SP in female rainbow trout initiated a rapid change in tr anscript levels within the liver, ovary, and pituitary, leading to ovarian failure and apparently disrupting normal endocrine signaling between the pituitary and ovary. Normal photoperiod: Two channel experiment; T=0 versus T= up to 330 days post spawn. 3 biological replicates for the later time points paired with a pooled laboratory standard t=0 control. One replicate per array Shortened photoperiod: Two channel experiment; T=0 versus T= up to 216 days post spawn. 3 biological replicates for the later time points paired with a pooled laboratory standard t=0 control. One replicate per array

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Differential gene expression of candidate genes for growth in rainbow trout

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