Development of genomic resources for African Catfish aquaculture towards improved breeding and genetic management in Nigeria

Aquaculture has been prioritised as a major sector for development by the Nigerian government to combat poverty, improve food and nutrition security, and empower marginalised groups, particularly women. African catfish (Clarias gariepinus) is the most important aquaculture species in Nigeria. Even though Nigeria ranks second in Africa for aquaculture production, the sector is still technologically immature and suffers from numerous challenges including poor productivity, shortage of good quality fish seed, high cost of aquafeed, and many emerging issues from climate change (e.g., water quality deterioration, new disease, and environmental stress). Genetics and genomics can play crucial roles in combatting many of these issues.

Despite its popularity, catfish farming industry in Nigeria is still at infancy compared to its large market potential. This is mainly due to unavailability of good quality fish fingerlings. Existing catfish hatcheries in the country often lack any scientific protocol for genetic management or improvement of their broodstock. Indeed, various ill practices are prevalent among the hatcheries, e.g., use of a few broodfish for generating fingerlings and broodtsock for the next generation (leading to genetic bottleneck and inbreeding depression), indiscriminate hybridization among different catfish species, and recruitment of ‘shooter fish’ (cannibalistic fish that grow very fast) as broodfish. All these practices drastically erode the genetic quality of farmed stocks leading to many negative consequences (e.g., poor product quality, poor growth, greater cannibalism, loss of selection potential for genetic improvement).

Under the GCRF AgriFood Africa Innovation Award Round 5 (African Aquaculture Genetics), we would like to apply for a collaborative project with a Nigerian Commercial Hatchery (Spring Continental Harvest Ltd) and Worldfish to develop genomic resources for African catfish (C. gariepinus) that can be utilised towards genetic management and improvement of culture stock. The project will have the following main objectives:

•Performing low coverage sequencing of samples from six different catfish populations (three wild populations from Nigerian river systems and three farmed populations; 30 samples per population). •Identifying genome-wide SNP variants from the sequence data. •Genetic characterisation of the sequenced populations to create a baseline information for establishing hatchery broodstocks with broad genetic base. •Shortlisting of SNPs for building genotyping arrays that can be used for breeding improvement, genetic management, and/or characterisation of new populations. •Finding a set of minimum number of SNPs that can be routinely used for parentage assignment in aquaculture scenario towards genetic management and informed breeding.