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.

The brown trout, Salmo trutta L., displays one of the most variable and polymorphic life-history strategies of all the salmonids. In some populations, individuals spend their whole life-cycle in the river (freshwater-resident) whereas in others, a varying proportion migrates to sea for variable amounts of time to better feeding conditions before returning to spawn (anadromous). The ‘decision’ if an individual will migrate or not will be determined by the balance of the costs and benefits of following a particular life-history strategy. The balance of these, which do not affect males and females equally, will determine the future success (measured by fitness) of each strategy. This research addresses the influences of parental contribution, mainly maternal effect, of anadromous and freshwater-resident brown trout on offspring performance and subsequent life-history. A partial migratory population of brown trout was studied in the Tadnoll Brook, one of the seven major tributaries on the River Frome. The tributary is classified as a circum-neutral chalk stream, 9.9 km long with a catchment approximately 50 km2. Carbon and nitrogen stable isotope analysis (SIA) was used to quantify maternal reproductive contribution of anadromous and freshwater-resident brown trout to offspring and determine the future success (measured by fitness) in terms of size and time of emergence. A panel of 12 microsatellite loci was used to assign parentage to 0+ parr. Using field data collected over 1.5 years on individual fish, this study tested parental influence on offspring performance in terms of size and growth rate and calculate the reproductive contribution of maternal/paternal anadromous and freshwater-residents. Adult life-history strategy was identified using a combination of results from SIA, PIT tag data and ecological data (body size, temperature). Parr life-history strategy (1+) was inferred using PIT tag detection data. The results of the SIA indicated fry of anadromous females emerged earlier and at a larger size than fry of freshwater-resident females. Parentage assignment of parr was low (28 %), with 8 parr assigned to both parents and 43 assigned to only a single parent. There was no detectable effect of parental life-history on parr size and growth rate, however the raw data may suggest offspring of anadromous parents have an early size advantage but a slower growth compared to offspring of freshwater-resident parents during the first year of the parr stage. Twenty-four percent of the offspring were identified as putative smolts at 2+ and both forms interbred and could produce offspring of each life-history. Estimates of reproductive contribution (SIA and growth) show a higher proportion of anadromous females and males (growth only) contributed to offspring production. The results of this research indicate that the maternal anadromous contribution is higher in the Tadnoll Brook population, affording fitness benefits to their offspring during early ontogeny such as size advantages and emerging at a more profitable time to establish feeding territories. Adult life-history does not appear to influence juvenile (0+ parr) life-history but may have an effect on offspring performance. The presence of both forms in the population suggests the anadromous fitness benefits to offspring may only have an affect during ontogeny and early stages of growth. Then after juveniles reach a size threshold environmental factors influence offspring life-history, resulting in the largest parr with the fastest growth adopting an anadromous life-history.

Examination of variation at polymorphic microsatellite loci is a widely accepted method for determining parentage and examining genetic diversity within rainbow trout (Oncorhynchus mykiss) breeding programs. Genotyping costs are considerable; therefore, we developed a single-step method of co-amplifying twelve microsatellite loci in two hexaplex reactions. The protocol is explicitly described to ensure reproducible results. I applied the protocol to samples previously analyzed at the National Center for Cool and Coldwater Aquaculture (NCCCWA) with previously reported marker sets for a comparison of results. Each marker within the multiplex system was evaluated for duplication, null alleles, physical linkage, and probability of genotyping errors. Data from four of the 12 markers were excluded from parental analysis based on these criteria. Parental assignments were compared to those of a previous study that used five independently amplified microsatellites. Percentages of progeny assigned to parents were higher using the subset of eight markers from the multiplex system than with five markers used in the previous study (98% vs. 92%). Through multiplexing, use of additional markers improved parental allocation while also improving efficiency by reducing the number of PCR reactions and genotyping runs required. I evaluated the methods further through estimation of F-statistics, pairwise genetic distances, and cluster analysis among brood-years at the NCCCWA facility. These estimates were compared to those from nine independently amplified microsatellites used in a previous study. Fst metrics calculated between brood-years showed similar values of genetic differentiation using both marker sets. Estimates of individual pairwise genetic distances were used for constructing neighbor-joining trees. Both marker-sets yielded trees that showed similar subpopulation structuring and agreed with results from a model-based cluster analysis and available pedigree information. These approaches for detecting population substructure and admixture portions within individuals are particularly useful for new breeding programs where the founders' relatedness is unknown. The 2005 NCCCWA brood-year (75 full-sib families) was challenged with Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease (BCWD). The overall mortality rate was 70%, with large variation among families. Resistance to the disease was assessed by monitoring post-challenge days-to-death. Phenotypic variation and additive genetic variation were estimated using mixed models of survival analysis. The microsatellite markers used were previously isolated from BAC clones that harbor genes of interest and mapped onto the rainbow trout genetic linkage map. A general relationship between UBA gene sequence types and MH-IA-linked microsatellite alleles indicated that microsatellites mapped near or within specific major histocompatibility (MH) loci reliably mark sequence variation at MH genes. The parents and grandparents of the 2005 brood-year families were genotyped with markers linked to the four MH genomic regions (MH-IA, MH-IB, TAP1, and MH-II) to assess linkage disequilibrium (LD) between those genomic regions and resistance to BCWD. Family analysis suggested that MH-IB and MH-II markers are linked to BCWD survivability. Tests for disease association at the population level substantiated the involvement of MH-IB with disease resistance. The impact of MH sequence variation on selective breeding for disease resistance is discussed in the context of aquaculture production. / Master of Science