Genetic diversity and population structure of the African catfish, Clarias gariepinus (Burchell, 1822) in Kenya: implication for conservation and aquaculture

Abstract

ABSTRACT. African catfish, Clarias gariepinus, is an important species in aquaculture and fisheries in Kenya. Mitochondrial D-loop control region was used to determine genetic variation and population structure in samples of C. gariepinus from 10 sites including five natural populations (Lakes Victoria (LVG), Kanyaboli (LKG), Turkana (LTA), Baringo (LBA) and Jipe (LJP), and five farms (Sangoro Aquaculture Center (SAN), Sagana Aquaculture Centre (SAG), University of Eldoret Fish Farm (UoE), Kibos Fish Farm (KIB), and Wakhungu Fish Farm (WKU)) in Kenya. Similarly, samples from eight localities (four natural populations: LVG/LKG, LTA, LBA, and four farmed: SAN, SAG, KIB, UoE) were genotyped using six microsatellite DNA loci. For the D-loop control region, samples from natural sites exhibited higher numbers of haplotypes and haplotype diversities compared to farmed samples, and 88.2% of haplotypes were private. All except LJP and LTA shared haplotypes, and the highest number of shared haplotypes (8) was detected in KIB. The 68 haplotypes we found in 268 individuals grouped into five phylogenetic clades: LVG/LKG, LTA, LBA, LJP and SAG. Haplotypes of farmed C. gariepinus mostly have haplotypes typical of LVG/LKG, and some shared haplotypes of the LBA population. Microsatellite analysis showed farmed samples have higher numbers of alleles than natural samples, but higher observed and expected heterozygosity levels were found in samples of natural Belg. J. Zool. 147 (2): 105-127 (2017) 106 populations. Fifteen pair-wise comparisons had significantly different FST values. All samples were in Hardy-Weinberg equilibrium. Samples from the eight localities grouped into four genetic clusters (LVG/ LKG, LTA, LBA and SAG), indicating genetically distinct populations, which should be considered for aquaculture and conservation.

High genetic diversity and population differentiation in Clarias gariepinus of Yala Swamp: evidence from mitochondrial DNA sequences

“…This is supported by a negative D for all the populations, suggesting an increasing population size or a purifying selection at a locus (Tajima, ). The purifying selection that increases mutations at the locus could also be increasing genetic diversity at the locus, leading to the higher haplotype and nucleotide diversities in this study, compared with values reported by earlier studies in similar population (Barasa et al , ) and different populations (Roodt‐Wilding et al ., ; Barasa et al ., , ).…”

“…PCR conditions were as described by Nazia et al () and used by Barasa et al . (, ). Annealing temperature was 56° C. The success of the PCR reaction was confirmed by 2·0% agarose gel electrophoresis of PCR products.…”

“…PCR were done using AccuPower PCR PreMix (Bioneer; www.eng.bioneer.com), in 20 l containing 10 M each of forward and reverse primers and 50 ng DNA. PCR conditions were as described by Nazia et al (2010) and used by Barasa et al (2014Barasa et al ( , 2016. Annealing temperature was 56 ∘ C. The success of the PCR reaction was confirmed by 2·0% agarose gel electrophoresis of PCR products.…”

Development and characterization of 49 novel microsatellite markers in the African catfish, Clarias gariepinus (Burchell, 1822)

“…In the same time, the uncontrolled stocking and capture fishing have impacts on natural populations (e.g. fluctuating population size, decreasing genetic diversity, adaptability to changing environment and resistance to disease) [2,3].…”

“…These markers are also widely used to estimate the population genetic values (such as variability, heterozygosity, inbreeding or genetic structure) [3,4]. Due to the economic importance of the African catfish, more and more genetic studies analyze the genetic variability, yield deterioration and the conservation genetic background of farmed [5,19] and natural [2] productions. However, the availability of the species-specific microsatellite markers suitable for detailed analysis of genetic resources are limited in number.…”