Identification of single nucleotide polymorphisms in Siganus canaliculatus for the development of a SNP-array to support genetic improvements in Qatar aquaculture industry

Abstract

Aquaculture in the Middle East is in the early stages of development as an industry but is growing in order to meet an increasing demand for high quality seafood. Egypt currently produces the most food by aquaculture, followed by Saudi Arabia, with considerably lower levels of production currently in Qatar.

However, a thrive in Qatari aquaculture is expected in the near future driven by increasing efforts towards sustainable industry development aimed to meet population’s needs, achieve and ensure food security and reduce reliance on food imports. Aquaculture development in Qatar is currently focused on several species, such as whiteleg shrimp and tilapia, but also aims to develop farming of local species, such as barramundi and the favored spinefoot or Safi, Siganus canaliculatus.

In this study, the aim is to provide the data to build a Single Nucleotide Polymorphism (SNP) array for S. canaliculatus which will allow efficient genotyping of the species and form the basis of any future genetic management. The work consisted of two major steps. The first step was to produce a chromosome level reference genome using WGS methods. The total genome size produced was ~530M bp with 24 superscaffolds and a quality value of 44. The second step was to re-sequence wild and cultured samples of S. canaliculatus for SNP discovery. Samples from each of 4 different locations (a total of ~120 fish) were sampled for re-sequencing, Al Wakrah, Al Ruwais, Doha port, and Aquatic Research Center. The re-sequenced whole genome data is aligned to the reference genome, SNPs Identified, and then filtered for features such as monomorphic flanking regions, sequence coverage, and enrichment of SNPs in exonic regions. The final list of markers included 194K SNPs of which 48K are in exons.