title: RNA-Seq identifies SNP markers for growth traits in rainbow trout.
abstract: 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 commercially important 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.
authors.affiliation: Laboratory of Animal Biotechnology and Genomics, Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, West Virginia, United States of America. mosalem@mail.wvu.edu
authors.forename: Mohamed
authors.initials: M
authors.lastname: Salem
authors.forename: Roger L
authors.initials: RL
authors.lastname: Vallejo
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Leeds
authors.forename: Yniv
authors.initials: Y
authors.lastname: Palti
authors.forename: Sixin
authors.initials: S
authors.lastname: Liu
authors.forename: Annas
authors.initials: A
authors.lastname: Sabbagh
authors.forename: Caird E
authors.initials: CE
authors.lastname: Rexroad
authors.forename: Jianbo
authors.initials: J
authors.lastname: Yao
mesh_terms: D000818:Animals; D017756:Aquaculture; D002467:Cell Nucleus / Q000235:genetics; D005260:Female; D005819:Genetic Markers / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D008928:Mitochondria / Q000235:genetics; D058977:Molecular Sequence Annotation; D017686:Oncorhynchus mykiss / Q000235:genetics* / Q000254:growth & development*; D010641:Phenotype; D011110:Polymorphism, Genetic / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D005819:Genetic Markers