DOI: 10.7910/dvn/xaa5tv
title: Replication data for: Domestication in Aquaculture Fishes- Elucidating the Genetic Consequences in Nile Tilapia (Oreochromis niloticus)

description: 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 &gt; 10, associated with sex were found in LGs 12 and 23 in the sex average map and LG 23 in the male map. Suggestive QTLs, or QTLs identified in only one family at a LOD &gt; 10, associated with sex were identified in LGs 8 and 14 in all three maps. Suggestive sex QTLs were also identified in LGs 3, 12, 19, and 23 in the female map as well as in LG 12 in the male map. GWAS identified LG 23 as being associated with sex in all three maps. Although karyotyping of O. niloticus identified a male heterogametic sex determining (XX|XY) system, to date, no study, including the present one, has clearly assigned a linkage group to the sex chromosomes as both genetics and environment can trigger the mechanisms underlying sex determination in Nile tilapia. Nile tilapia’s sex determining system is further complicated by its readiness to hybridize with other tilapia species; including, O. aureus which accounts for approximately 10% of the AS genome. Considering this, LGs 3, 14, 12, and 19 may be associated with sex determination either in O. aureus, or in the reproductive interaction between O. niloticus and O. aureus. However, to unravel these associations additional and more targeted analyses are required.
Weight was found to be a polygenic trait in the AS, with suggestive QTLs identified in LGs 2, 3, 8, 13, 14, and 18 in all three maps; LGs 6, 7, 11, 16, 17, 19, and 20 in the sex average map; LGs 4, 5, 6, 12, and 19 in the female map; and LGs 4, 5, 17, and 20 in the male map. However, these suggestive QTLs were not supported in GWAS analyses. Such results indicate that weight is indeed a complex trait governed by many genes of small effects; however, additional genotype by phenotype studies with a higher density of markers and more individuals are necessary to dissect growth in tilapia. 
Domestication in conjunction with targeted selective breeding has a greater potential for detrimental genetic consequences, including the loss of genetic diversity and changes in allele frequencies compared to wild populations. For the first time, genetic data (9,287 SNPs) was used to identify population structure and signatures of selection amongst the AS and eight wild populations of Nile tilapia along the Nile River, Egypt. Two major genetic clusters (captive and wild populations) were observed. Wild populations showed evidence of isolation-by-distance between brackish Nile Delta and upstream riverine populations. Despite this, only a few outliers were detected in pairwise comparisons of wild populations. Approximately 6.9% of SNPs were identified as outliers (1.9% balancing outliers; 5.0% diversifying outliers) between captive and wild populations, but a lack of localized clustering suggests that no genes of major effect were detected. Subsequently, individuals belonging to the AS were easily distinguishable from individuals originating from wild populations, with a putative first-generation escapee being detected in the wild. The AS was also found to have retained high levels of genetic diversity (Ho_All = 0.21 ±0.01; He_All = 0.23 ±0.01) when compared to wild populations (Ho_All = 0.18 ±0.01; He_All = 0.17±0.01) despite 11 years of selective breeding. Additionally, 565 private SNPs were identified within the AS line, which in addition to increasing AS heterozygosity, adds support to the finding that introgression with O. aureus has occurred. Wild populations all exhibited different subsets of polymorphic loci per sampling location, indicating that hybridization with O. aureus may have also occurred in the wild. 
As a body of work, this thesis has found that both pedigree errors and the incorporation of genetic material from the smaller growing O. aureus into the AS have likely contributed to the modest genetic gain observed with the program. Despite this, genetic diversity indices and inbreeding levels within the program indicate that the AS is salvageable. To enhance future selective breeding efforts, three line-specific linkage maps were constructed using small family data. Novel and previously identified QTLs associated with both sex and weight were detected within the study, suggesting that both traits are polygenic. However, given small sample sizes and evidence of hybridization, further studies are required to validate these QTLs and determine their relevance to the AS before genomic selection is pursued. The AS were genetically distinct from their wild Nile tilapia counterparts, with putative AS escapees easily detectable. Wild population structure indicated some structuring due to isolation-by-distance; however, few outlier loci were detected amongst wild populations indicating that there are either no strong selective forces acting throughout their environmental range or that there is sufficient gene flow among populations to counteract selection. Additionally, signals of potential hybridization with O. aureus were detected in wild O. niloticus populations. Therefore, it could be speculated that the disseminating the AS throughout Egypt should not have detrimental effects to natural populations or the performance of the AS itself.
description: Those dataset used for Pipette and Paper are from anything labelled as DTi-15 or DTi-16