ARS | Publication request: Unlocking genetic secrets of the fast/slow growth in rainbow trout with next-generation sequencing

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 19, 2010
Publication Date: January 15, 2011
Citation: Salem, M., Leeds, T.D., Rexroad III, C.E., Yao, J. 2011. Unlocking genetic secrets of the fast/slow growth in rainbow trout with next-generation sequencing. Plant and Animal Genome Conference. W041.

Technical Abstract: Background: Fast-growth is the most desired trait affecting the profitability of food animal production including aquaculture species. Traditional phenotype-based selection is typically used to select for growth traits, however, it does not allow for optimal control over all phenotypic characteristics of the growth traits. As an alternative, Marker-Assisted Selection (MAS) aims to expedite genetic improvement in livestock breeding programs. Single nucleotide polymorphisms (SNPs) explain 90% of the phenotypic differences between individuals, therefore, they are most suitable for MAS. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. Results: Whole Transcriptome Shotgun Sequence analysis, RNA-seq, of cDNA samples from fish selected for fast versus slow growing rainbow trout families identified 318 putative type-I SNPs markers associated with the growth-rate. The allelic imbalances (the ratio between the allele ratio of the fast sample and that of the slow sample) were considered at score >5.0 as an amplification and <0.2 as loss of heterozygosity. Genotyping individuals of the fish discovery panel using the Sequenom iPLEX Genotyping platform validated association of 104 markers with the growth trait (p<0.01). Many of these markers are clustered into genes of the aerobic respiration enzyme pathway. In addition, gene expression analysis using Whole Transcriptome Sequencing revealed orchestrated expression of growth-associated metabolic pathways in fish muscle. Conclusion: The study proves the utility of the Whole Transcriptome Shotgun Sequencing as fast and effective means of identifying genetic polymorphism suitable for developing markers for MAS in non-model aquaculture species; with unknown genome sequence. In addition, it provides accurate characterization of the gene expression. Currently, those SNPs are being evaluated on 2000 individuals of parents/offspring panel from the broodstock population at the National Center for Cool and Cold Water Aquaculture (NCCCWA) and will be incorporated into the rainbow trout linkage map.