Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout
Author ORCID Identifier
Davis College of Agriculture, Natural Resources and Design
Division of Animal and Nutritional Sciences
Coding/functional SNPs change the biological function of a gene and, therefore, could serve as “large-effect” genetic markers. In this study, we used two bioinformatics pipelines, GATK and SAMtools, for discovering coding/functional SNPs with allelic-imbalances associated with total body weight, muscle yield, muscle fat content, shear force, and whiteness. Phenotypic data were collected for approximately 500 fish, representing 98 families (5 fish/family), from a growth-selected line, and the muscle transcriptome was sequenced from 22 families with divergent phenotypes (4 low- versus 4 high-ranked families per trait).
GATK detected 59,112 putative SNPs; of these SNPs, 4798 showed allelic imbalances (>2.0 as an amplification and
These results demonstrate utility of RNA-Seq in assessing phenotype-associated allelic imbalances in pooled RNA-Seq samples. The SNPs identified in this study were included in a new SNP-Chip design (available from Affymetrix) for genomic and genetic analyses in rainbow trout.
Digital Commons Citation
Al-Tobasei, Rafet; Ali, Ali; Leeds, Timothy D.; Liu, Sixin; Palti, Yniv; Kenney, Brett; and Salem, Mohamed, "Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout" (2017). Faculty & Staff Scholarship. 1550.
Al-Tobasei, R., Ali, A., Leeds, T.D. et al. Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout. BMC Genomics 18, 582 (2017). https://doi.org/10.1186/s12864-017-3992-z
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