Jonathan M. Wright

Microsatellite DNA in fishes

For the last 30 years, attempts have been made to discriminate among fish populations by using molecular markers. Although some techniques have proved successful in certain circumstances, the consistent trend to newer markers among fishery geneticists highlights the general lack of resolving power observed with older technologies. The last decade has seen the increasing use of satellite DNA in investigations of genetic variability and divergence. Applications to fish and fisheries-related issues initially concentrated on minisatellite single-locus probes. Although minisatellites have successfully addressed a number of fishery-related questions, this class of satellite DNA has not been widely adopted by fishery geneticists. Most of the current research effort is concentrated on another class of satellite DNA called microsatellites. The large interest in microsatellite loci is largely due to the very high levels of variability that have been observed and the ability to investigate this variation using PCR technology. The isolation and application of microsatellites to research fields as diverse as population genetics, parentage analyses and genome mapping are reviewed. Despite the undisputed advantages that the marker possesses, there are a number of potential problems associated with investigating variation at microsatellite loci. Statistical considerations (e.g. appropriate sample sizes, number of loci and the mutation model assumptions on which the estimate is based) have not been considered in detail yet and the problems are often exacerbated in fish species, as some species show very large numbers of alleles at microsatellite loci. These issues and others, e.g. null alleles, are reviewed and possible solutions are proposed

Birth weight and neonatal survival of harbour seal pups are positively correlated with genetic variation measured by microsatellites

We examined the relations between fitness-related traits of wild harbour seal (Phoca vitulina) pups with microsatellite heterozygosity, and with a measure of genomic diversity based on the mean squared distance between microsatellite alleles within an individual, mean d2. Birth weight was positively influenced by maternal age, pup sex, and either mean d2 or individual heterozygosity in separate multiple regression models. The association of birth weight with mean d2 was stronger than that with heterozygosity, however. The factors maternal age, pup sex, and mean d2 combined to account for 36.8% of the variation in birth weight, with mean d2 accounting for the greatest explanatory power (52.3% of the variance explained). Pups which survived until weaning had significantly higher mean d2 than pups which died, independent of birth weight. These effects are consistent with heterosis resulting from recent population mixing, and/or inbreeding depression in this population. Mean d2 thus provides (i) a better measure of individual genetic variability than heterozygosity for microsatellite data; and (ii) a convenient tool for assessing the effects of inbreeding and outbreeding in natural populations.

Microsatellites - Genetic-Markers for the Future

In the four accompanying reviews of this issue (Carvalho and Hauser, 1994; Ferguson, 1994; Park and Moran, 1994; Ward and Grewe, 1994), the authors have provided a thorough assessment of the molecular basis and utility of various genetic markers currently available to researchers in aquaculture and fisheries research. These reviews emphasize the pre-eminent roles of isozymes and mitochondrial DNA (mtDNA) in fisheries genetic research, with a rather more limited discussion of nuclear DNA markers and technologies. This emphasis is understandable, given the large volume of data and the established technology that prevail for allozymes, and to a lesser, but still significant extent, mtDNA. In this article we look to the future, and in doing so, take a more radical view. Here we argue the merits of a particular class of nuclear markers, variable numbers of tandem repeats (VNTR) loci. VNTRs themselves comprise two (probably related) classes of loci, the minisatellites and microsatellites (Wright, 1993, 1994; Park and Moran, 1994). Our intent in this commentary is to highlight the general utility of microsatellite VNTRs to fisheries and aquaculture research. In expounding our view, we draw primarily on the experience we have gained with microsatellites in the Marine Gene Probe Laboratory (MGPL) at Dalhousie University.

DNA fingerprint based analysis of paternal and maternal effects on offspring growth and survival in communally reared rainbow trout

Abstract This study was initiated to assess the feasibility of establishing pedigrees in mixed aquaculture populations and of selection programs for commercial aquaculture operations based on genetic profiling data from microsatellite markers. Complete factorial crosses between ten sires and ten dams were performed in a small rainbow trout farm. The largest and smallest progenies were sampled after 1 year of communal rearing, and their parentage was established with four or five microsatellite markers. About 91% of the fish could be traced to one or two parental couples out of the 100 possible couples. There were significant differences among sires and dams for the growth and survival of their progeny. There were also indications that progeny of inbred crosses have depressed performances. Based on these results, a breed improvement program has been implemented in this small hatchery.

Population structure and impact of supportive breeding inferred from mitochondrial and microsatellite DNA analyses in land‐locked Atlantic salmon Salmo salar L.

Four tributaries of Lake St‐Jean (Québec, Canada) are used for spawning and juvenile habitat by land‐locked Atlantic salmon. Spawning runs have drastically declined since the mid‐1980s, and consequently, a supportive‐breeding programme was undertaken in 1990. In this study, we analysed seven microsatellite loci and mtDNA, and empirically estimated effective population sizes to test the hypotheses that (i) fish spawning in different tributaries form genetically distinct populations and (ii) the supportive breeding programme causes genetic perturbations on wild populations. Allele frequency distribution, molecular variance and genetic distance estimates all supported the hypothesis of genetic differentiation among salmon from different tributaries. Gene flow among some populations was much more restricted than previously reported for anadromous populations despite the small geographical scale (40 km) involved. Both mtDNA and microsatellites revealed a more pronounced differentiation between populations from two tributaries of a single river compared with their differentiation with a population from a neighbouring river. The comparison of wild and F1‐hatchery fish (produced from breeders originating from the same river) indicated significant changes in allele frequencies and losses of low‐frequency alleles but no reduction in heterozygosity. Estimates of variance and inbreeding population size indicated that susceptibility to genetic drift and inbreeding in one population increased by twofold after only one generation of supplementation.

Early growth performance of Atlantic salmon full-sib families reared in single family tanks versus in mixed family tanks

The present experiment was designed to assess the impact of the confounding of environmental tank effect with genetic family effect during early rearing periods. In November 1989, two sets of mixed family tanks were created in the Salmon Genetic Research Program (SGRP) hatchery by pooling equal numbers of eggs from four and eight families, respectively. In July 1990, tissue samples and length and weight measurements were collected on fish from both individual family tanks and mixed family tanks. Four polymorphic microsatellites were used to determine unambiguously the family of origin of 790 mixed group fish. There was a strong correlation of family survival rates measured in the mixed tanks and in the single family tanks. Differences among families for length and growth were observed in both the mixed tanks and the single family tanks. However, family growth performance in the single tank environment was poorly correlated with family growth performance in the mixed tank environment and appeared to reflect environmental differences among tanks rather than genetic differences among families. Neither family growth performance in the mixed tanks nor in the single family tanks appeared strongly correlated with subsequent family growth performance up to smolt stage.

Male mating success in an aquatically mating pinniped, the harbour seal (Phoca vitulina), assessed by microsatellite DNA markers

Similar to many other pinniped species, harbour seals (Phoca vitulina) mate exclusively at sea. Here we present the first attempt to measure male mating success in an aquatically mating pinniped. Male mating success was estimated by paternity analysis in two cohorts of pups born at Sable Island, Nova Scotia, Canada, using microsatellite DNA markers. The genotypes of 275 pups born in 1994 and 1995 were compared to those of 90 candidate males at six microsatellite loci using a likelihood approach to resolve paternity. Paternity could be assigned for two, 22, 40 and 85 pups at confidence levels of 95, 80, 65 and 50%, respectively. Most successful males were assigned the paternity of a single offspring, suggesting a low variance in male mating success relative to most pinniped species. The proportion of paternal half sibs within cohorts and between maternally related sibs estimated by maximum likelihood were not significantly different from zero. It is thus unlikely that most offspring were sired by a small number of highly successful unsampled males, and that female harbour seals do not usually exhibit fidelity to the same male in sequential breeding seasons. A low level of polygyny in Sable Island harbour seals is consistent with predictions based on their breeding ecology, as females are highly mobile and widely dispersed in the aquatic mating environment at Sable Island.

Isolation of salmonid microsatellite loci and their application to the population genetics of Canadian east coast stocks of Atlantic salmon

Abstract Genetic variation at four microsatellite loci, two isolated from Atlantic salmon and two from rainbow trout, was assayed in five populations of Alantic salmon from Nova Scotia, Canada and in samples from Norway and Ireland. Up to 38 allelles per locus and heterozygosities of 0.9 were observed at some loci. Genetic distances, calculated over the four loci for all population samples show a clear grouping of populations according to geographic location. These loci show potential as genetic markers in Atlantic salmon due to the range of polymorphisms observed among individual loci and to the ease and speed of sample assay. Highly variable loci will be of use in the ‘genetic tagging’ of cultured fish and in the assessment of levels of gene introgression from cultured to wild stocks. The clear differences in both allele frequencies and alleles observed between continents will be of value in the assessment of the relative sizes of the contributions of Canadian and North European salmon to the mixed fishery off Greenland.

PCR primers for harbour seal (Phoca vitulina concolour) microsatellites amplify polymorphic loci in other pinniped species

Keywords: harbour seal; microsatellite; PCR; Phoca vitulina concolour; phocidae; pinniped

Molecular cytogenetic analysis of heterochromatin in the chromosomes of tilapia, Oreochromis niloticus (Teleostei: Cichlidae)

The structure of the heterochromatic bands in mitotic chromosomes of the important tropical aquaculture species of tilapia, Oreochromis niloticus, was investigated by the combination of the C-banding technique, chromosomal digestion with two restriction endonucleases and fluorescence in situ hybridization (FISH) of two satellite DNAs (SATA and SATB). The tilapia chromosomes presented heterochromatic bands in the centromeres and in the short arms of almost all chromosomes that were differentially digested by the restriction endonucleases HaeIII and EcoRI. FISH of SATA showed that this satellite sequence is distributed in the centromeric region of all chromosomes of tilapia. FISH also revealed an intense hybridization signal for SATB in only one chromosome pair, but less intense signals were also present in several other pairs. The digestion of tilapia chromosomes by HaeIII and EcoRI was positively correlated with the position of SATA and SATB in chromosomes as revealed by FISH. The results obtained may be useful in future molecular and genetic studies of tilapias.