Title: Transcriptomics, SNP discovery, and relative gene expression of fast- and slow-growing hybrid striped bass families and their application in a selective breeding program Authors
Submitted to: Book of Abstracts Aquaculture America
Publication Type: Abstract Only
Publication Acceptance Date: September 19, 2011
Publication Date: February 29, 2012
Citation: Fuller, S.A., Beck, B.H., Farmer, B.D., Mcentire, M.E., Freeman, D.W. 2012. Transcriptomics, SNP discovery, and relative gene expression of fast- and slow-growing hybrid striped bass families and their application in a selective breeding program [abstract]. Book of Abstracts Aquaculture America 2012: Bringing all the Players to the Table. p.173. Technical Abstract: The objectives of this study were to determine the genetic basis of production traits for selective improvement, and RNA-sequence (RNA-seq) fast-growing and slow-growing representatives to identify global expression differences and develop predictive single nucleotide polymorphisms (SNP) markers as part of a multi-year improvement project. Domesticated white bass and striped bass were bred and reared until large enough to PIT tag. Twenty-seven fish from each of 47 half-sib families were measured and weighed before being assigned to one of four 0.04 hectare communal ponds, resulting in 5072 tagged fingerlings. After 115 days, final length and weight were taken, and liver and muscle samples were flash frozen for real-time PCR (rtPCR) and RNA-seq analyses. RNA-seq was performed on replicates of liver from fast- vs slow-growing fish using Illumina protocols. RT-PCR assays were run, with expression levels of fast-growing fish reported relative to slow-growing fish after being normalized to the control gene beta-actin. Hybrid striped bass averaged 235.3+/-17.8 (SD) mm and 192.1+/-48.7g across all families. Mean survival was 90.7+/-0.05%. Genetic correlation between weight and length based on the sire and dam components of variance were 0.95 and 0.92 respective; the phenotypic correlation was 0.88. Analyses of covariance demonstrated highly significant differences in length and weight of fish among different paternal and maternal half-sib families (P<0.0001). At harvest, hybrid striped bass exhibited a range of body morphology so we also calculated relative weight (Wr) to compare an estimate of body composition across families, which was significant (P<0.0001) among families and it was obvious in the appearance of the fish. Estimates of heritability were high for both traits, with values for weight and length, respective, ranging from 0.33-0.75 for dams and 1.05-0.56 for sires. Liver RNA-seq analysis yielded 39,395 putative genes. Significantly differentially expressed genes identified via RNA-seq include proteins putatively involved in metabolism, myoglobin, cell membrane transport, sterol metabolism, calcium ion regulation, proteins involved in muscle development, and several proteins involved in immune and inflammatory response. A total of 267,254 SNP markers were identified. Several candidate genes involved in various phases of metabolism were evaluated via rtPCR for expression levels in fast- and slow-growing families of fish in both liver and muscle. Intriguingly, in all genes tested, a > -1X fold downregulation was evident in fast-growing fish relative to slow-growing fish. This is the first transcriptome sequenced from differentially performing families of hybrid striped bass reared in a common garden pond production setting. This genomic information will help us discover the underlying mechanisms involved in many performance-related aspects of hybrid striped bass aquaculture, including growth, reproduction, disease resistance and immune response, as well as many other issues important in modern aquaculture. Once the SNP markers have been validated and assays developed, they will be integrated into a broodstock and fingerling screening program to identify markers for future marker assisted selection and can be added to the existing Striped Bass microsatellite linkage map. Incorporating crossbred offspring performance into a genetic improvement program could also be used to successfully produce more rapidly growing hybrid striped bass and improve the profitability of the industry.