Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

Abstract

BackgroundSingle nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies. In order to provide the best genome coverage for the analysis of performance and production traits, a large number of relatively evenly distributed SNPs are needed. Gene-associated SNPs may fulfill these requirements of large numbers and genome wide distribution. In addition, gene-associated SNPs could themselves be causative SNPs for traits. The objective of this project was to identify large numbers of gene-associated SNPs using high-throughput next generation sequencing.ResultsTranscriptome sequencing was conducted for channel catfish and blue catfish using Illumina next generation sequencing technology. Approximately 220 million reads (15.6 Gb) for channel catfish and 280 million reads (19.6 Gb) for blue catfish were obtained by sequencing gene transcripts derived from various tissues of multiple individuals from a diverse genetic background. A total of over 35 billion base pairs of expressed short read sequences were generated. Over two million putative SNPs were identified from channel catfish and almost 2.5 million putative SNPs were identified from blue catfish. Of these putative SNPs, a set of filtered SNPs were identified including 342,104 intra-specific SNPs for channel catfish, 366,269 intra-specific SNPs for blue catfish, and 420,727 inter-specific SNPs between channel catfish and blue catfish. These filtered SNPs are distributed within 16,562 unique genes in channel catfish and 17,423 unique genes in blue catfish.ConclusionsFor aquaculture species, transcriptome analysis of pooled RNA samples from multiple individuals using Illumina sequencing technology is both technically efficient and cost-effective for generating expressed sequences. Such an approach is most effective when coupled to existing EST resources generated using traditional sequencing approaches because the reference ESTs facilitate effective assembly of the expressed short reads. When multiple individuals with different genetic backgrounds are used, RNA-Seq is very effective for the identification of SNPs. The SNPs identified in this report will provide a much needed resource for genetic studies in catfish and will contribute to the development of a high-density SNP array. Validation and testing of these SNPs using SNP arrays will form the material basis for genome association studies and whole genome-based selection in catfish.

Genome-wide identification of Hsp70 genes in channel catfish and their regulated expression after bacterial infection

“…In this study, we identified a full set of 57 catfish Hsp40 genes in the catfish genome. This was achieved by thorough analysis of rich genomic and transcriptomic resources including several hundred thousands of ESTs [33][34][35], RNA-Seq transcriptome assemblies [37,38], and the draft genome sequences (unpublished). Phylogenetic and syntenic analyses allowed annotation of Hsp40 genes.…”

RNA-Seq Technology and Its Application in Fish Transcriptomics

“…Several SNP identificationdirected RNA-seq studies in fishes have already been reported. To developing SNP arrays in catfish, Liu and colleagues conducted RNA-seq in multiple individuals of both channel catfish and blue catfish (Ictalurus furcatus) (Liu et al, 2011). With the help of the SNP calling module in CLC Genomics Workbench (CLC bio, Aarhus, Denmark), as well as a SNP quality screening procedure, they identified 342,104 intra-specific SNPs for channel catfish, 366,269 intraspecific SNPs for blue catfish, and 420,727 inter-specific SNPs between channel catfish and blue catfish; these SNPs were found to be distributed within 16,562 unique genes in channel catfish and 17,423 unique genes in blue catfish.…”

Genetic Applications in the Conservation of Neotropical Freshwater Fish

“…This approach allows data to be obtained for a single nucleotide variation profile, as well as transcriptome characteristics and gene expression levels, in a cost-effective way [148]. Additionally, transcriptome sequencing allows gene-associated SNP studies, depending on the exact genomic location and functional role that are inserted [149].…”

“…This approach allows data to be obtained for a single nucleotide variation profile, as well as transcriptome characteristics and gene expression levels, in a cost-effective way [148]. Additionally, transcriptome sequencing allows gene-associated SNP studies, depending on the exact genomic location and functional role that are inserted [149].RAD-seq is an important method of genome reduction in non-model fish for identifying and genotyping SNPs, and unlike RNA-seq, uses genomic DNA as a template. The technique uses the principles of RFLP by reducing the complexity of the genome by subsampling at sites defined by restriction enzymes [150].…”