Epistasis and the sensitivity of phenotypic screens for beta thalassaemia

Genetic disorders of haemoglobin, particularly the sickle cell diseases and the alpha and beta thalassaemias, are the commonest inherited disorders worldwide. The majority of affected births occur in low-income and lower-middle income countries. Screening programmes are a vital tool to counter these haemoglobinopathies by: (i) identifying individual carriers and allowing them to make informed reproductive choices, and (ii) generating population level gene-frequency estimates, to help ensure the optimal allocation of public health resources. For both of these functions it is vital that the screen performed is suitably sensitive. One popular first-stage screening option to detect carriers of beta thalassaemia in low-income countries is the One Tube Osmotic Fragility Test (OTOFT). Here we introduce a population genetic framework within which to quantify the likely sensitivity and specificity of the OTOFT in different epidemiological contexts. We demonstrate that interactions between the carrier states for beta thalassaemia and alpha thalassaemia, glucose-6-phosphate dehydrogenase deficiency and Southeast Asian Ovalocytosis have the potential to reduce the sensitivity of OTOFTs for beta thalassaemia heterozygosity to below 70%. Our results therefore caution against the widespread application of OTOFTs in regions where these erythrocyte variants co-occur

Communal or separate rearing of families in selective breeding of common carp (Cyprinus carpio L.)

This study reports on investigation of ways of improving the breeding programme for growth-related traits in common carp in Vietnam. The base population was synthesized following a single pair mating scheme from six carp stocks: (1) 2nd generation of family selection; (2) Hungarian 6th generation of mass selection; (3) Hungarian scaled carp; (4) Indonesian yellow 6th generation of mass selection; (5) Indonesian yellow carp; and (6) Vietnamese 6th generation of mass selection. The next two selected generations were produced using a partial factorial mating scheme, with each family being split and reared using communal early rearing (CER) or separate early rearing (SER) methods. The second generation (G2) was produced from selected fish from the CER G1 group. The total number of selection, control and reference families was 135 in the G1 and 101 in the G2 respectively. The control and reference (Hungarian P33 line) families were produced by single pair mating (reference families with the G2 only). Seven microsatellite loci were used for parentage assignment in the CER groups: 96.8% of the offspring (1284 individuals) and 96.2% offspring (1341 individuals) were unambiguously assigned to 113 families (selection, control) in the G1 and 99 families (selection, control and reference) in the G2 generations, respectively. Restricted maximum likelihood in the individual model was used to estimate phenotypic and genetic parameters. In CER, the estimated heritability values of common carp were from 0.20 ± 0.04 to 0.29 ± 0.05 for both weight and length at final harvest, indicating substantial additive genetic variation for selection on growth-related traits. The overall obtained maternal and common environmental effects were consistently close to zero. The average of direct response to selection for body weight was 15.0% per generation. In SER, the number of families in the G1 and G2 were 135 (selection and control) and 101 (selection, control and reference), respectively. The heritability estimates were from 0.20 ± 0.07 to 0.31 ± 0.08 at final measurement. Common environmental (full-sib family) effect were all lower at tagging and slightly higher at last measurement, ranging from 0.05 to 0.22. The response in each generation of selection as the difference between the selection and control lines was 8.1% on average for weight at final harvest, lower than under CER. The high genetic correlations of growth-related traits between the third (one year old, mature) and second (7 months old) measurements could allow selection to be based on the earlier assessment, reducing handling stress close to spawning. The benefits of using microsatellite markers to ascertain parentage, achieve greater growth rate (close to farming systems), shorten time to maturity and selection, and the overall relative merits of using CER v’s SER in this genetic improvement programme are discussed.EThOS - Electronic Theses Online ServiceVietnamese Oversea Scholarship ProgrammeGBUnited Kingdo

Marker-assisted selection in enhancing genetically male Nile tilapia (Oreochromis niloticus L.) production

All-male fry are preferred to prevent uncontrolled reproduction before harvest in intensive Nile tilapia (Oreochromis niloticus) aquaculture. Males also grow faster than females. An alternative approach to direct hormonal masculinisation of tilapia fry is to produce fry that are genetically male. However, sex determination system in tilapia is fairly complex. Recent developments have resulted in a linkage map and genetic markers that can be used to analyse the sex determination system. To analyse the genetic sex determination mechanism and to develop marker-assisted selection in the Stirling Nile tilapia population, a fully inbred line of clonal females (XX) was verified using test crosses and DNA markers (mostly microsatellites) to use as a standard reference line in sex determination studies. A series of crosses were performed involving this line of females and a range of males. Three groups of crosses were selected (each group consisted of three families) from progeny sex ratio distributions, and designated as type ‘A’ (normal XY males x clonal XX females), type ‘B’ (putative YY males x clonal XX females) and type ‘C’ (unknown groups of males x clonal XX females), for sex linkage study. For type ‘A’, inheritance of DNA markers and phenotypic sex was investigated using screened markers from tilapia linkage group 1 (LG1) to confirm the LG1-associated pattern of inheritance of phenotypic sex and the structure of LG1. Screened markers from LG1, LG3 and LG23 were used to investigate the association of markers with sex in families of type ‘B’ and ‘C’. In addition, a genome-wide scan of markers from the other 21 LGs was performed to investigate any association between markers and sex, in only families of cross type ‘B’. LG1 associated pattern of inheritance of phenotypic sex was confirmed by genotype and QTL analyses in families of cross type ‘A’. Analyses of genotypes in families of type ‘B’ and ‘C’ showed strong association with LG1 markers but no association with LG3 and LG23 markers. Genome wide scan of markers from all other LGs did not show any significant association between any markers and the sex. The allelic inheritance of two tightly linked LG1 markers (UNH995 and UNH104) in families of type ‘B’ and ‘C’ identified polymorphism in the sex determining locus: one of the alleles was associated mostly with male offspring whereas another allele was associated with both progeny (mostly males in type ‘B’ families, and approximately equal numbers in type ‘C’ families). This knowledge was used to identify and separate supermales (‘YY’ males) that should sire higher proportions of male progeny, reared to become sexually mature for use as broodstock. Two of them were crossed with XX females (one clonal and one outbred) to observe the phenotypic expression of the strongest male-associated allele in progeny sex. The observations of 98% male (99 males out of 101 progeny) and 100% male (N=75) from these two crosses respectively, suggest that a marker-assisted selection (MAS) programme for genetically male Nile tilapia production could be practical. This study also suggests that the departures from the sex ratios predicted using a “simple” XX/XY model (i.e., YY x XX should give all-male progeny) were strongly associated with the XX/XY system, due to multiple alleles, rather than being associated with loci in other LGs (e.g., LG3, LG23). This study also tentatively names the allele(s) giving intermediate sex ratios as “ambivalent” and emphasizes that the presence and actions of such allele(s) at the same sex-determining locus could explain departures from predicted sex ratios observed in some earlier studies in Nile tilapia.EThOS - Electronic Theses Online ServiceCommonwealth Scholarship CommissionGBUnited Kingdo

Selective improvement of rainbow trout : assessment of potential in UK strains

The research assessed the potential of developing a selective breeding programme for the UK rainbow trout industry. Levels of genetic variation at 12 microsatellite loci were first compared in seven different commercial strains. The Observed heterozygosity ranged from Ho = 48.1% in a gold rainbow trout strain (GTR) to Ho = 66.4% in a newly derived broodstock population constructed from a number of different sources (GIT). The Expected Heterozygosity (He) was highest in GIM1 (He= 79.5%) and lowest in the GTR strain (He = 56.9%). The Effective number of alleles (Mae) showed that the GIM1, GIM2, GIM3, and GIT strain (5.4; 5.2; 4.8; 4.2) were significantly more variable than the other strains and that GTR strain had the lowest value (2.5). There appears to be substantial genetic variability within the commercial United Kingdom rainbow trout strains surveyed in this study. This appears to be the case despite very different management histories and levels of record keeping. The strains appear to be genetically distinct (based on population genetic analyses), though the reasons for this remain unclear (and possibly unanswerable given the poor records kept by the different companies). The Glenwyllin farm strains (GIM) were chosen to form the base population for the project because of their high genetic variability, disease free status and because the farm produced around 20 million ova per year, so any genetic gains would have a widespread impact. The farm has an early (Strain A) and a late spawning (Strain B) and these were mated in a partial factorial design, 20 females and 20 neomales per strain (A ;B) were chosen on the basis of maturity and gamete quality in November 2002 so that each male was crossed to 4 females (2 in the same strain and 2 in the other), a total of 160 families were created. All broodstock were biopsied to enable them to be genotyped. The families were reared separately up to the eyed stage at which point the eggs from each family were divided into three to generate three communal replicate populations. One of these was sent to a fingerling producer (Iwerne Spring) for ongrowing to fingerling size and formed the basis of a commercial production trial at Test Valley Trout farm (TVT) in Hampshire. When the fish reached an average weight of 5 g they were transferred from Iwerne Spring to TVT and 1500 were randomly selected, PIT tagged and biopsied to enable them to be assigned to their family using 11 multiplexed microsatellite loci. Parental assignment was based on exclusion (FAP) but the results were compared with another parental assignment based on likelihood (PAPA). Of the 1500 offspring (OIM) PIT tagged 1242 82.8% could be assigned to a single family utilizing different combinations of more than 6 loci (6 to 11). The growth of the 1500 OIM fish was tracked throughout the grow out period before they were finally harvested and fully processed. The results of OIM strain at the end of the trial period were mean weight of 415.5 g, and a mean length of 314.5 mm. The visual measurement of colour gave a mean flesh colour values of 26.01 on the 20-34 scale (SalmoFan™), and 11.0 with the colotimetry evaluation of colour (a*). The heritability results for the IOM strain were 43 ± 9% for weight, 42 ± 9% for gutted, and 28 ± 8% for length. The heritability estimates for the visual colour variables were 19 ± 7% and when using the colorimeter, the red chromaticity (a*) heritability was 14 ± 6%. Therefore, the heritability results of the IOM strain indicate that there are opportunities of substantial and rapid improvement of the growth rate and flesh colour traits. Also no line effects were observed or indications of non-additive genetic variation. In contrast to these last results, the overall survival of the GIM strain from the time of the physical tagging with PIT until harvest was 52.8%, and survival heritability was extremely low, 3 ± 2%, hardly significant.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

The Impact of Escaped Farmed Atlantic Salmon (Salmo salar L.) on Catch Statistics in Scotland

In Scotland and elsewhere, there are concerns that escaped farmed Atlantic salmon (Salmo salar L.) may impact on wild salmon stocks. Potential detrimental effects could arise through disease spread, competition, or inter-breeding. We investigated whether there is evidence of a direct effect of recorded salmon escape events on wild stocks in Scotland using anglers' counts of caught salmon (classified as wild or farmed) and sea trout (Salmo trutta L.). This tests specifically whether documented escape events can be associated with reduced or elevated escapes detected in the catch over a five-year time window, after accounting for overall variation between areas and years. Alternate model frameworks were somewhat inconsistent, however no robust association was found between documented escape events and higher proportion of farm-origin salmon in anglers' catch, nor with overall catch size. A weak positive correlation was found between local escapes and subsequent sea trout catch. This is in the opposite direction to what would be expected if salmon escapes negatively affected wild fish numbers. Our approach specifically investigated documented escape events, contrasting with earlier studies examining potentially wider effects of salmon farming on wild catch size. This approach is more conservative, but alleviates some potential sources of confounding, which are always of concern in observational studies. Successful analysis of anglers' reports of escaped farmed salmon requires high data quality, particularly since reports of farmed salmon are a relatively rare event in the Scottish data. Therefore, as part of our analysis, we reviewed studies of potential sensitivity and specificity of determination of farmed origin. Specificity estimates are generally high in the literature, making an analysis of the form we have performed feasible

A Polyphasic Approach for Phenotypic and Genetic Characterization of the Fastidious Aquatic Pathogen Francisella noatunensis subsp. orientalis

Francisella noatunensis subsp. orientalis (Fno) is the causative agent of piscine francisellosis, an emerging infectious disease in Asia and Latin America. In this study two outbreaks of francisellosis were diagnosed in the UK on the basis of histopathology, electron microscopy, PCR, bacterial isolation and fulfilment of Koch’s postulates. Furthermore, a phenotypic fingerprint based on biochemical analyses, metabolic activity, chemotaxonomic composition and antimicrobial assays was generated for the novel isolates, the Fno type strain Ehime-1 from Asia and other Fno from Latin America. The genetic relatedness between the novel Fno and other Francisellaceae species was investigated by sequencing and comparing 8 housekeeping genes and the 16S rRNA-ITS-23S rRNA sequence. The phenotypic profiling indicated a high degree of similarity between the Fno taxon as all were able to metabolise dextrin, N-acetyl-D glucosamine, D-fructose, α-D-glucose, D-mannose, methyl pyruvate, acetic acid, α-keto butyric acid, L-alaninamide, L-alanine, L-alanylglycine, L-asparagine, L-glutamic acid, L-proline, L-serine, L-threonine, inosine, uridine, glycerol, D L-α-glycerol phosphate, glucose-1-phosphate and glucose-6-phosphate. The chemotaxonomic analyses indicated that 24:1 (20.3%), 18:1n-9 (16.9%), 24:0 (13.1%) 14:0 (10.9%), 22:0 (7.8%), 16:0 (7.6%) and 18:0 (5.5%) were the predominant structural fatty acids in Fno. The antimicrobial assays showed little variation between the isolates and high susceptibility to enrofloxacin, gentamicin, neomycin, streptomycin, amikacin, ciprofloxacin, gatifloxacin, nitrofurantoin, tobramycin, kanamycin, tetracycline, oxytetracycline, florfenicol, oxolinic acid and streptomycin in all the Fno analysed. In all the phylogenetic trees the Fno strains clustered together in independent branches confirming a high degree of homogeneity. Interestingly in five of the individual trees i.e mutS, putA, rpoB, the concatenated sequence and 16S rRNA-ITS-23S rRNA genes the two Francisella noatunensis ssp. diverged more from each other than from the closely related human pathogen Francisella philomiragia (Fp). The phenotypic and genetic characterisation confirmed the Fno isolates represent a solid phylo-phenetic taxon that in the current context of the genus seems to be misplaced within the species Fn. We propose the use of the present polyphasic approach in future studies to characterise strains of Fnn and Fp and verify their current taxonomic rank of Fno

Production and verification of the first Atlantic salmon (Salmo salar L.) clonal lines

In several fish species homozygous and heterozygous clonal lines have been produced using gynogenetic and androgenetic techniques. These lines are standardized and can be reproduced over generations. In rainbow trout such lines have existed for decades and has become important research tools in genome studies as well as in studies of commercially important traits. The Atlantic salmon is one of the best studied fish species globally, but all experiments are done on fish of wild or domesticated origin and access to standardized immortal fish lines would be of great benefit. Here, we describe the protocols developed to produce mitotic gynogenes, and from these the first clonal lines in Atlantic salmon.publishedVersio

A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus)

Background: Fish species often exhibit significant sexual dimorphism for commercially important traits. Accordingly, the control of phenotypic sex, and in particular the production of monosex cultures, is of particular interest to the aquaculture industry. Sex determination in the widely farmed Nile tilapia (Oreochromis niloticus) is complex, involving genomic regions on at least three chromosomes (chromosomes 1, 3 and 23) and interacting in certain cases with elevated early rearing temperature as well. Thus, sex ratios may vary substantially from 50%. Results: This study focused on mapping sex-determining quantitative trait loci (QTL) in families with skewed sex ratios. These included four families that showed an excess of males (male ratio varied between 64% and 93%) when reared at standard temperature (28°C) and a fifth family in which an excess of males (96%) was observed when fry were reared at 36°C for ten days from first feeding. All the samples used in the current study were genotyped for two single-nucleotide polymorphisms (rs397507167 and rs397507165) located in the expected major sex-determining region in linkage group 1 (LG 1). The only misassigned individuals were phenotypic males with the expected female genotype, suggesting that those offspring had undergone sex-reversal with respect to the major sex-determining locus. We mapped SNPs identified from double digest Restriction-site Associated DNA (ddRAD) sequencing in these five families. Three genetic maps were constructed consisting of 641, 175 and 1,155 SNPs from the three largest families. QTL analyses provided evidence for a novel genome-wide significant QTL in LG 20. Evidence was also found for another sex-determining QTL in the fifth family, in the proximal region of LG 1. Conclusions: Overall, the results from this study suggest that these previously undetected QTLs are involved in sex determination in the Nile tilapia, causing sex reversal (masculinisation) with respect to the XX genotype at the major sex-determining locus in LG 1

Species-Specific Marker Discovery in Tilapia

Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations

Genetic Approaches To The Analysis of Body Colouration in Nile Tilapia (Oreochromis niloticus)

Body colouration in tilapia is an important trait affecting consumer preference. In the Nile tilapia (Oreochromis niloticus), there are three colour variants which are normal (wild type), red and blond. In some countries, the red variant is important and reaches higher prices in the market. However, one major problem regarding red tilapia culture is their body colouration which is often associated with blotching (mainly black but also red) which is undesirable for the consumer. The overall aim of this work was to expand knowledge on various aspects of body colouration in Nile tilapia using genetic approaches. The results of this research are presented as four different manuscripts. The manuscripts (here referred as Papers) have either been published (Paper IV) or are to be submitted (Paper I, II and III) in relevant peer reviewed journals. Paper I and II investigated the inheritance of black blotching and other body colour components of the red body colour. Specifically, Paper I consisted of two preliminary trials (Trial 1 and 2), to look at the ontogeny of black blotching and body colour components over a period of six months. Trial 1 investigated the effect of tank background colour (light vs dark) on black blotching and other body colour components and was carried out using a fully inbred (all female) clonal red line. Trial 2 was carried out using mixed sex fish and was aimed to investigate the association of black blotching with the sex of the fish. The results from this study were used to guide the experiment described in Paper II. Sixteen red sires with various levels of black and red blotching were crossed to clonal females and the inheritance of blotching and other body colour components were investigated using parent-offspring regressions. The results showed no significant heritability for black blotching and body redness, but a significant correlation for body redness and black blotching was found in female offspring at one sampling point suggesting that attempts to increase body redness may increase black blotching, as had been hypothesized. Paper III was divided into two parts. The first objective was to map the blond locus onto the tilapia linkage map and the second was to investigate the interaction of the blond and red genes on black blotching using the blond-linked markers to distinguish different blond genotypes in heterozygous red fish (i.e. RrBlbl or Rrblbl). In the blond fish, the formation of melanin is almost blocked via much reduced melanophores and this feature may be able to help reducing the black blotching in red tilapia. Two intraspecific families (O. niloticus) and one interspecific family (O. aureus and O. niloticus) were used as mapping families and the blond locus was located in LG5. Four out of eight markers were successfully used to assess the interaction of blond on red blotched fish. The blond gene did not significantly reduce the area of blotching but did reduce the saturation (paler blotching) and enhanced the redness of body colour in the Rrblbl fish compared to the RrBlbl group. Finally, Paper IV aimed to find out the effect of male colouration on reproductive success in Nile tilapia. A choice of one wild type male and one red male was presented to red or wild type females and these fish were allowed to spawn under semi-natural spawning conditions. Eggs were collected from the female’s mouth after spawning and paternity was assessed using microsatellite genotyping and phenotype scoring. No significant departures from equal mating success were observed between the red and wild type males, however there was a significant difference between the red and wild type females in the frequency of secondary paternal contribution to egg batches. The results suggest that mating success of wild type and red tilapia is approximately equal. The results from this research help to broaden our knowledge and understanding on the aspects of body colouration in Nile tilapia and provide fundamental information for further research