Title: Phenotypic and genetic evaluation of farmed and wild Clarias gariepinus broodstocks in Nigeria.

Clarias gariepinus accounts for more than a half of all Nigerian aquaculture production. The industry growth is limited due to poor seed quality which is suspected to be due to inbreeding within the broodstocks used by the industry. This study was conducted to explore the phenotypic and genetic variation among farmed and wild broodstocks of C. gariepinus in Nigeria. Nigeria was stratified into two, based on aquaculture intensity: High Aquaculture Area (HAA) and Low Aquaculture Area (LAA). Samples were collected from 10 farms (five farms each from HAA and LAA) and three rivers (wild). A total of 220 live broodstock samples (n = 20 per location) were collected for this study. Phenotypic characters such as morphometric and meristic characteristics, egg diameter, and fecundity were evaluated using standard procedures. C. gariepinus genetic characteristics were analyzed using Restriction site associated DNA sequencing (RADseq) marker to investigate the genetic relatedness and possible signals of inbreeding. The results of the morphometric, meristic, egg diameter and fecundity data showed that the farmed fish samples were significantly different (one-way ANOVA, P<0.05) from each other and from the wild samples. The cluster analysis of morphometric and meristic parameters showed high divergence among the fish sampled. One of the farms sampled in HAA clustered with the wild sample. The result of the genetic data showed that the relatedness within the farms varied from 0.14±0.18 to 0.67±0.09 and genetic relatedness between the farms ranged from -0.12±0.04 to 0.01±0.05. it therefore suggested a high level of relatedness within farm samples but not between farm samples. The PCA analysis revealed strong genetic variabilities among samples. A total of 21.17% of the genetic variability was accounted for PC1, separating strongly Farm 8 sample from the rest of the samples. A total of 17.94% of the genetic variability was observed on PC2 which differentiated strongly Farm 7 from the rest of the samples. The inbreeding coefficients (FIS) was above the value of 1 in all farms, suggesting high inbreeding levels. Observed morphological differences could be due to genetic differences and environmental factors. The high level of inbreeding and relatedness within each farm sample could be due to poor broodstock management practices.