Replication data for: Domestication in Aquaculture Fishes- Elucidating the Genetic Consequences in Nile Tilapia (Oreochromis niloticus)

A growing human population combined with a higher per capita consumption of fish has resulted in a greater demand for finfish. Fisheries production has plateaued over the last 30 years; thus, improving productivity in aquaculture to meet future market demands is vital. In particular, demand has increased for tilapia, the second most important group of commercially farmed finfish globally, due to their hardiness, low feed requirements and environmental adaptability. Despite its success in terrestrial systems, uptake of genetic improvement techniques, like selective breeding, have only recently gained momentum in aquaculture. In 2002, the Abbassa Strain (AS) of Nile tilapia (Oreochromis niloticus) was established by the WorldFish Center in Egypt. The AS originated from a combination of both wild and hatchery population founders, with the objective to increase harvest weight using a combination of between and within family selection. To date, the AS has experienced 3.8-7.0% improvement in growth per generation, a modest increase compared to the 7.1-15.0% increase observed in similar Nile tilapia selective breeding programs. As little is known about the genetic state of the AS, this difference in genetic gain highlighted the need to examine the accuracy of AS management practices and whether sufficient genetic diversity has been maintained within the line for selection to act upon. This thesis is the first comprehensive genetic study of a non-salmonid tropical finfish with five overarching objectives. These are to determine: i) the accuracy of pedigree traceability and the management of the AS; ii) the current and ongoing genetic status of the AS; iii) the genetic architecture of commercially important traits; iv) whether signatures of selection can be detected in the current stock; v) the extent of wild population structuring in Nile tilapia in Egypt; and vi) the potential effects AS escapees may have within its currently farmed regions and across Egypt where it is intended to be disseminated. Traditionally, genealogical data has been utilized to monitor inbreeding rates, relatedness, and co-ancestry within selective breeding programs. Errors within genealogical records are common and have been shown to be as high as 15% in terrestrial selective breeding programs, with little information available on aquatic breeding programs. These genealogical errors can lead to inaccurate calculation of breeding values, a reduction in genetic gain, and inaccurate estimates of inbreeding. To date, the AS has been managed solely based on genealogical data. To assess the accuracy of these genealogical records, firstly, stringently filtered genome-wide SNPs (1,040) were used to test and correct parentage assignments; secondly, 6,163 SNPs were used to determine the level of genetic diversity, the pedigree genetic structure and the number of families present within this line. Inbreeding coefficients and founder contributions were calculated from two founding events for 11 generations of the AS using molecularly corrected pedigree records. On average, AS pedigree error rates were found to be 45.5% per generation and are considered to be one of the most likely contributing factors leading to the relatively low genetic gain observed within the program. Inbreeding levels remained below 1% per generation; however, over 84.3% of available genetic material within the AS can be attributed to only 34 founders. This indicates that founder contribution has been eroded within the AS, and that optimal founder contribution should be taken into consideration in future management strategies to conserve genetic diversity while attaining genetic gain. To better understand the genomic effects of selective breeding and the genetic architecture of weight and sex in O. niloticus, genomic resources for the AS were developed. This study produced the first line-specific linkage map for the commercially important AS. This linkage map is one of the first population-based genetic linkage maps using small families (16 families ranging from 5-17 offspring: 136 individuals) and phase unknown data, demonstrating the viability of this method for map construction. Due to the atypical construction of this linkage map, independent maps were created based on the sex average, female, and male lines. A total of 2,399 markers were successfully mapped to a sex average map, 2,197 to the female map, and 2,125 to the male map. All maps and map orders were validated by the reference genome assembly, Orenil 1.1 (GenBank Assembly Accession: GCA_00188235.2). Phenotypic data was then utilized to undertake quantitative trait locus (QTL) analysis and genome-wide association studies (GWAS) to determine regions of the genome associated with sex and weight. QTL analyses were conducted using the two largest phased and phenotyped mapping families (8 and 10 offspring) available. Putative QTLs, or those QTLs observed in both families at a LOD > 10, associated with sex were found in...