Development of Genetic Improvement in the African Catfish (Clarias gariepinus, Burchell, 1822)

Abstract

The African catfish, Clarias gariepinus, is the most important fish species for aquaculture in sub-Saharan Africa. Despite its long-standing history in aquaculture (since the 1950’s) and current rapid expansion, little work has been done on its genetics and the genetic management/improvement of different populations globally. The industry, currently worth over USD 720 million in Nigeria, and with so much more growth potential, is faced with numerous challenges. To understand the extent of these challenges and possible areas/types of intervention, the Nigerian catfish aquaculture industry was reviewed. Inadequate supply of good quality fingerlings/broodstock and feeds were notably the most significant challenges. As a step towards addressing the former, a survey of the current practise in catfish hatcheries was conducted, to identify problems and prospects therein. Over 90% of the hatcheries surveyed use shooters (fast growers) as broodstock, use only farmed broodstock and have no broodstock management/replacement programmes. Findings from these studies informed research on the development of genetic improvement for C. gariepinus. Just as in salmon, tilapia, carp, etc., the use of molecular markers as tools for genetic management and improvement of C. gariepinus was explored. Problem-solving markers, separating C. gariepinus from its closest relative, C. anguillaris, were developed. A total of 24 diagnostic SNP markers were identified from double-digest restriction-site associated DNA sequencing (ddRADseq). Following validation using KASP assay, 8 of the 24 SNPs were tested on a total of 291 Clarias catfishes and 7 Heterobranchus longifilis (out groups). The Clarias samples were separated into 259 putative C. gariepinus and 32 putative C. anguillaris. These are the first diagnostic markers for separating these species, for which morphological features perform poorly (effectively cryptic species). A set of eight new microsatellite markers was developed from the ddRADseq data and microsatellite enrichment. These microsatellite markers, together with four others sourced from the literature were optimised, multiplexed and used to genotype populations of C. gariepinus being evaluated for suitability for aquaculture. Although incomplete (due to problems with parental DNA quality), preliminary assessment of the assignment power by simulation shows that over 90% of the offspring could be assigned to a pair of parents. The high parentage assignment power and polymorphic information content (>0.5), suggest the usability and reliability of these markers in genetic management and improvement in the Clarias catfish industry, enabling parental assignment and kinship studies, and for evaluation of practices such as the use of “shooters” as broodstock in the industry.