Sequencing of a RRL for SNP marker detection in Tilapia

To generate a set of Single Nucleotide Polymorphisms (SNPs) for tilapia, we sequenced a reduced representation library (RRL) derived from a pooled DNA sample of 20 individuals from the 10th generation of the GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 33 million short sequence reads (36 nucleotides) were generated. A de-novo RRL assembly was performed of sequence reads filtered for quality. After filtering for quality, 9.1 million reads were retained for use in the assembly. This assembly resulted in 174,950 contigs with a N50 of 73 nucleotides (van Bers et al., Mol. Ecol. Resources (2012).