African Catfish (Clarias Gariepinus) in Nigeria: Species Identification, Hatchery Practices, Population Genetics and Future Prospects for Genetic Improvement

Abstract

To understand the levels of inbreeding and genetic variation within and between farms, 282 fin samples were collected from broodstock of C. gariepinus in 35 locations (33 hatcheries, Rivers Niger and Benue). Next generation sequencing (DArTSeq) was used to develop SNP chips. From the results, 72,140 loci were identified from 280 samples (the remaining 2 samples failed). Bioinformatics analysis was carried out by Dr Trong T. of the WorldFish. Following quality control, 6,797 loci and 276 individuals were called from a total of 280 samples successfully sequenced. An average observed heterozygosity of 0.08 and an expected heterozygosity of 0.09 were recorded. The very low heterozygosity values could be due to very low and uneven sample sizes per farm; however, it also suggests that most of the farmed populations sampled are inbred.