Microsatellite variability in natural populations of the blackspot seabream Pagellus bogaraveo (Brunnick, 1768): a database to access parentage assignment in aquaculture (original) (raw)
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Aquaculture …, 2006
Andreia Lemos1, Ana Isabel Freitas2, Ana Teresa Fernandes2, Rita Gonc°alves2, Jose¤ Jesus1, Carlos Andrade3 & Anto¤nio Brehm2 1Department of Biology, University of Madeira, Funchal, Portugal 2Human Genetics Laboratory, University of Madeira, Funchal, ...
A microsatellite marker tool for parentage assessment in gilthead seabream ( Sparus aurata
Aquaculture, 2007
Eleven microsatellite loci previously described in Sparid species were evaluated for their suitability in paternity assignment of gilthead seabream (Sparus aurata). Nine hundred and ninety six offspring obtained by natural spawning from 159 potential breeders maintained in 8 different tanks were genotyped for this set of 11 loci. Given their high potential for parentage exclusion (Excl1 = 0.9999; Excl2 = 1) all offspring could be traced back to a single couple of parents. The families identified were used to analyze the performances of these loci for parentage analysis. Null alleles were the main source of false exclusions (70.1% of single mismatches) and were detected in five loci at frequencies between 4.9 × 10 − 3 and 0.084. The average mutation rate estimated over 21,912 gametes was 1.8 × 10 − 4 in the range reported within fish. All the loci analyzed conformed to Mendelian segregation. However, significant genotypic linkage disequilibrium was detected between SaGT1 and SaGT32, SaGT41a and SaGT41b, SaGT31 and PbMS6, and PbMS1 and PbMS16. A subset of five highly polymorphic and easily genotyped microsatellite loci, SaGT1, SaGT26, SaGT41a, PbMS2 and PbMS16, were selected for parentage assessment in S. aurata. In spite of their high combined exclusion potential (N 0.997), the actual exclusion power was 0.933, mostly due to the high relatedness between some parents in the broodstock. Exclusion and maximum likelihood-based strategies were compared for paternity inference using the data obtained. The former approach performed better in the context of this study, where a set of highly polymorphic microsatellites with the lowest genotyping error were selected.
Parentage analysis in aquaculture determines genealogical relationships between broodstock and progeny when the parents are unknown. Thus, parentage analysis is a useful tool to establish pedigree reports in molecular-assisted selection programs. Here, we evaluated 10 heterologous microsatellite markers for parentage assignment in abalone hybrids produced from 43 abalone broodstocks of red abalone (Haliotis rufescens) and Japanese abalone (H. discus hannai). The allele frequencies, exclusion probabilities and broodstock contributions were calculated using CERVUS, PAPA and GERUD software. The polymorphic information content (PIC) values showed that most of the microsatellite loci were highly informative (>0.7) and more than 90% of parentage assignment was possible with a minimum of 5-6 microsatellite markers. Parentage assignment for hybrid and pure-red progeny showed a better performance than pure-Japanese progeny. This result could be due to the high level of allele loss in the parental genotypes. In addition, results indicated that only two sires contributed over 80% and 90% of red and hybrid progenies, respectively. This study gives a new molecular tool to support marker-assisted selection in abalone hybrids produced in Chile.
Aquaculture, 2011
The European anchovy Engraulis encrasicolus L. is in high demand as a fish species, but most fishery stocks are currently at risk of collapsing. A pilot project for anchovy aquaculture was carried out in Spain to explore the potential of satisfying demand for fresh and canned fish and to establish a supportive breeding program that could enhance native populations. We have studied the spawning dynamics in this novel culture using microsatellite loci. Our main aims were to assess the effective breeding number (N e ) and the inbreeding coefficient that would result in use of these fish for an E. encrasicolus closed-cycle culture. A total of 183 wild breeders from the Bay of Biscay were adapted to culture and induced to spawn from November 2009 to January 2010. Two hundred and eighty-eight eggs were collected at four different times. Breeders and eggs were analyzed with two multiplex PCRs that included seven microsatellite loci. Breeders showed extremely high levels of genetic variation (mean number of alleles by locus = 35), but there was a significant reduction in genetic variation in progeny. Breeders were also found to be genetically different from all progeny. Parentage was successfully assigned at a rate of 93%. A total of 105 breeders (55 females and 50 males) took part in reproduction; however, there was significant unequal breeder contribution to progeny. Taking this into account, we found inbreeding coefficients and effective breeder numbers as follows: initial November ΔF = 6.5%, N e = 8; mid-November ΔF = 2.9%, N e = 17; December ΔF = 3.2%, N e =16; January ΔF = 3.5%, N e = 14 and overall ΔF = 1.8%, N e =27. We have concluded that the partial dominance of some breeders and the high family variance found in this study should be taken into account when establishing closed-cycle cultures of the European anchovy to help guarantee its sustainability. If one of the main goals is establishment of a supportive breeding program to enhance wild stocks, the inbreeding levels found here, which imply significant genetic differentiation between breeders and progeny, should also be taken into account to avoid genetic damage to wild populations over time.
Novel polymorphic microsatellite markers for the common pandora (Pagellus erythrinus)
Molecular Ecology Notes - MOL ECOL NOTES, 2003
Details of six highly polymorphic dinucleotide and one highly polymorphic tetranucleotide microsatellite markers are provided for Pagellus erythrinus. These markers are highly polymorphic, with an expected heterozygosity ranging from 0.713 to 0.959 and allele numbers ranging from seven to 36. These microsatellite markers should help determine population genetic structure and fisheries stocks for management purposes.
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 2006
Population substructure of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda), as investigated by genetic variation of microsatellite loci, has been reported to be significantly extensive around the Iberian Peninsula with F ST = 0.061 [Pérez-Losada, M., Guerra, A., Carvalho, G.R., Sanjuan, A., Shaw, P.W., 2002. Extensive population subdivision of the cuttlefish Sepia officinalis (Mollusca: Cephalopoda) around the Iberian Peninsula indicated by microsatellite DNA variation. Heredity 89, 417-424] and panmictic in the semi-enclosed Adriatic Sea with F ST = 0.011 [Garoia, F., Guarniero, I., Ramsak, A., Ungaro, N., Landi, M., Piccinetti, C., Mannini, P., Tinti, F., 2004. Microsatellite DNA variation reveals high gene flow and panmictic populations in the Adriatic shared stocks of the European squid and cuttlefish (Cephalopoda). Heredity 93, 166-174]. Yet, no verified genetic information on population substructure existed for the northern distribution range of this species in the English Channel and the Bay of Biscay.
Microsatellite-associated heterosis in hatchery-propagated stocks of the shrimp Penaeus stylirostris
2000
Correlation between DNA microsatellite heterozygosity and growth rate was investigated in two hatchery-propagated stocks of the shrimp Penaeus stylirostris, which had been genetically isolated from wild founders for 17 generations, and from each other for five more generations. Presumed demographic history of these populations suggested that they were maintained at small effective population sizes, and this was confirmed by significant changes in allelic frequencies between the two stocks. Despite a small sample size (n=60) and a small number of loci screened, a significant positive correlation was detected between microsatellite tri-locus heterozygosity and growth rate in one of the two stocks (r=0.3, P=0.02). In the other stock (n=48), the positive correlation was not significant, but the combined test of single locus heterozygote advantage over the three loci was significant (P=0.005). Use of DNA microsatellite markers, whose selectively neutral status is generally accepted, allowed us to reject the hypothesis of direct overdominance at marker loci as an explanation for an association of growth rate with heterozygosity. The average depression associated with one locus in our case is above or equivalent to the amount observed for a 10% increase of inbreeding in other species. These results suggest that heterozygosity at neutral marker loci is sufficiently well correlated with individual inbreeding coefficients to reveal a significant residual inbreeding load for growth rate in Tahitian P. stylirostris stocks. Inbreeding during hatchery propagation was, thus, insufficient to purge the ancestral load.
Parental assignment in farmed sea bream (Sparus aurata) using microsatellite genetics markers
Selective animal breeding is the main tool for a relative rapid improvement of economically important traits but one of the difficulties, especially in aquaculture, is obtaining and maintaining pedigree information. The approaches to determine parental assignment in aquacultural stocks are based on the use of different tanks in which each progeny is reared or on microsatellite genetics markers application. The genetic method offers different advantages in selective breeding program, avoiding that the environmental effects, common to full -sib groups, can be confused with the genetic effects. In this work we developed a protocol, using 9 microsatellite genetics markers, to perform the exact assignment between a cultured stock of 54 broodstock sea bream and a sample of 915 offspring. The protocol allowed to determine an high percentage (93%) of parental assignment. It is so possible to define families using natural reproduction and to develop superior fish broodstock or reduce inbreed...