UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE
Location: Cool and Cold Water Aquaculture Research
Title: RNA-Seq identifies SNP markers for growth traits in rainbow trout
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 4, 2012
Publication Date: May 4, 2012
Citation: Salem, M., Vallejo, R.L., Leeds, T.D., Palti, Y., Liu, S., Sabbagh, A., Rexroad III, C.E., Yao, J. 2012. RNA-Seq identifies SNP markers for growth traits in rainbow trout. PLoS One. 7(5):e36264.
Interpretive Summary: Traits associated with fast and efficient growth have a major influence on the profitability of food animal production including aquaculture species. In addition, optimizing genetic and diet interactions to improve feed efficiency has the potential to reduce aquaculture effluents leading to more environmentally sustainable production. Successful selection for optimal growth rate or body weight is a key objective in aquaculture breeding programs. Traditional phenotype-based selection is typically used to select for growth traits, however, it requires several generations to optimize genetic improvement. In addition, insight into the genetic bases of growth can be used to make better selection decisions. We employed next-generation sequencing technology to identify genes and DNA sequence variation within genes which affect growth rate in rainbow trout. Our data show that this approach is a fast and effective method for identifying genes and genetic markers affecting traits in species whose genome has not yet been sequenced. The resulting genes and genetic markers are candidates for evaluating traits associated with growth in commercial populations.
Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. 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. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth.
RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n=54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences.