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1.
Five full-sib families of the Pacific oyster （Crassostrea gigas） larvae were used to study the mode of inheritance at eight microsatellite loci, and the feasibility of these markers for kinship estimate was also examined. All eight microsatellite loci were compatible with Mendelian inheritance. Neither evidence of sex-linked barriers to transmission nor evidence of major barriers to fertilization between gametes from the parents was shown. Three of the eight loci showed the presence of null alleles in four families, demonstrating the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. Although the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from five full-sib families were unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers may be capable of discriminating between related and unrelated oyster larvae in the absence of pedigree information, and is applicable to the investigation of the effective number of parents contributing to the hatchery population of the Pacific oyster.  相似文献   

2.
Korean freshwater snails of the genus Semisulcospira are widely distributed across East Asia.It has been a very popular nutritional food in Korea,and is an ecologically important water quality indicator because it lives only in clean water.However,no microsatellite markers have been generated to study the population genetic diversity of this genus.In the present study,we developed and characterized 18 novel microsatellite loci from Semisulcospira coreana genomic DNA.The microsatellites were isolated using 454 GS-FLX titanium sequencing and 18 markers were used for genotyping in S.coreana.In addition,we also tested the cross-species transferability of the microsatellite markers in four additional Semisulcospira spp.We identified 18 polymorphic loci and the number of alleles per loci,and their polymorphism information content values ranged from 2 to 17 and 0.203 to 0.902,respectively.The observed and expected heterozygosities of the loci ranged from 0.063 to 0.924 and 0.226 to 0.924,respectively.According to the analysis of the cross-species transferability of these markers,four species,S.forticosta,S.gottschei,S.tegulata,and S.libertina,showed a very high transferability(80%–85%).These results show that this set of nuclear markers could be useful for population genetics studies of this species and closely related species.  相似文献   

3.
Iwagaki oyster,Crassostrea nippona,widely distributes along the seashore of Eastern Asia,and has been considered to be a potential breeding species due to its delicious taste and high commercial value.In order to study its genetic background and population structure,we developed 46 novel polymorphic microsatellite markers using next-generation sequencing technique and characterized them in 30 individuals.The number of alleles ranged from 3 to 22,while the observed and expected heterozygosities varied from 0.133 to 1.000 and 0.455 to 0.949,respectively.Fifteen microsatellite markers were selected and grouped into five highly informative multiplex PCRs for C.nippona.We evaluated and validated these multiplex PCRs in a cultured population including 173 candidate parents and 486 offspring.In actual parentage analysis,80%of the offspring were correctly assigned to their parental pairs using three multiplex PCRs.Furthermore,the success rate of parentage assignment reached 96%when the other two multiplex PCRs were added.These 46 microsatellite loci with high variability and the five multiplex PCRs described here provide a powerful tool for pedigree reconstruction,resource conservation and selective breeding program of C.nippona.  相似文献   

4.
Four successive mass selection lines of the Pacific oyster, Crassostrea gigas, selected for faster growth in breeding programs in China were examined at ten polymorphic microsatellite loci to assess the level of allelic diversity and estimate the effective population size. These data were compared with those of their base population. The results showed that the genetic variation of the four generations were maintained at high levels with an average allelic richness of 18.8–20.6, and a mean expected heterozygosity of 0.902–0.921. They were not reduced compared with those of their base population. Estimated effective population sizes based on temporal variances in microsatellite frequencies were smaller to that of sex ratio-corrected broodstock count estimates. Using a relatively large number of broodstock and keeping an equal sex ratio in the broodstock each generation may have contributed to retaining the original genetic diversity and maintaining relatively large effective population size. The results obtained in this study showed that the genetic variation was not affected greatly by mass selection progress and high genetic variation still existed in the mass selection lines, suggesting that there is still potential for increasing the gains in future generations of C. gigas. The present study provided important information for future genetic improvement by selective breeding, and for the design of suitable management guidelines for genetic breeding of C. gigas.  相似文献   

5.
Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic microsatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data (F_st =0.048 7, P<0.001) and mitochondrial DNA data (F_st =0.128, P<0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese flounder in the China seas and adjacent regions.  相似文献   

6.
Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of cultured and wild populations of Trachidermus fasciatus, an endangered catadromous fish species in China. Six selected primers were used to amplify DNA samples from 85 individuals, and 353 loci were detected. Relatively low genetic diversity was detected in the cultured population (the percentage of polymorphic loci PPL = 73.80%, Nei’s gene diversity h = 0.178 2, Shannon information index ...  相似文献   

7.
In order to determine whether growth performance could be improved by hybridizing full-sib families of Manila clam(Ruditapes philippinarum), crosses between two full-sib families including self and reciprocal crosses were carried out. The effects of heterosis, combining ability and interaction on the growth of shell length were estimated. The results showed that the growth of hybrid larvae was intermediate between parents on days 6 and 9. Heterosis on shell length was observed, which varied at juvenile stage. The cross of ♂A×♀B(Hp varied between 10.41% and 68.27%) displayed larger heterosis than ♂B×♀A(Hp varied between 1.89% and 32.33%) did, suggesting that ♂A×♀B was an ideal hatchery method of improving the growth performance of Manila clam. The variances of general combining ability(GCA), special combining ability(SCA) and interaction(I) were significant in shell length(P 0.05), indicating that both additive and non-additive genetic factors were important contributors to the growth of larvae and juveniles. The GCA for shell length of ♂A×♀B was higher than that of ♂B×♀A at both larval and juvenile stages. This confirmed that the cross between ♂A and ♀B showed great growth in shell length. In summary, the growth of Manila clam seeds could be improved by hybridizing selected parents from large numbers of full-sib families.  相似文献   

8.
Zhikong scallop （Chlamys farreri） is an important maricultured species in China. Many researches on this species, such as population genetics and QTL fine-mapping, need a large number of molecular markers. In this study, based on the ex- pressed sequence tags （EST）, a total of 300 putative single nucleotide polymorphisms （SNPs） were selected and validated using high resolution melting （HRM） technology with unlabeled probe. Of them, 101 （33.7%） were found to be polymorphic in 48 indi- viduals from 4 populations. Further evaluation with 48 individuals from Qingdao population showed that all the polymorphic loci had two alleles with the minor allele frequency ranged from 0.046 to 0.500. The observed and expected heterozygosities ranged from 0.000 to 0.925 and from 0.089 to 0.505, respectively. Fifteen loci deviated significantly from Hardy-Weinberg equilibrium and significant linkage disequilibrate was detected in one pair of markers. BLASTx gave significant hits for 72 of the 101 poly- morphic SNP- containing ESTs. Thirty four polymorphic SNP loci were predicted to be non-synonymous substitutions as they caused either the change of codons （33 SNPs） or pretermination of translation （1 SNP）. The markers developed can be used for the population studies and genetic improvement on Zhikong scallop.  相似文献   

9.
Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the fi rst genome-wide investigation of microsatellites in the Pacifi c oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacifi c oyster genome is rich in microsatellites. A total of 604 653 repeats were identifi ed, in average of one locus per 815 base pairs(bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of(A)n and(C)n repeats and abundant long(C)n repeats(≥24 bp); 3) large average length of(AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-fl anking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identifi ed. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the fi eld of oyster genetics, particularly for molecular-based selection and breeding.  相似文献   

10.
Zhikong scallop(Chlamys farreri) is an important maricultured species in China.Many researches on this species,such as population genetics and QTL fine-mapping,need a large number of molecular markers.In this study,based on the expressed sequence tags(EST),a total of 300 putative single nucleotide polymorphisms(SNPs) were selected and validated using high resolution melting(HRM) technology with unlabeled probe.Of them,101(33.7%) were found to be polymorphic in 48 individuals from 4 populations.Further evaluation with 48 individuals from Qingdao population showed that all the polymorphic loci had two alleles with the minor allele frequency ranged from 0.046 to 0.500.The observed and expected heterozygosities ranged from 0.000 to 0.925 and from 0.089 to 0.505,respectively.Fifteen loci deviated significantly from Hardy-Weinberg equilibrium and significant linkage disequilibrate was detected in one pair of markers.BLASTx gave significant hits for 72 of the 101 polymorphic SNP-containing ESTs.Thirty four polymorphic SNP loci were predicted to be non-synonymous substitutions as they caused either the change of codons(33 SNPs) or pretermination of translation(1 SNP).The markers developed can be used for the population studies and genetic improvement on Zhikong scallop.  相似文献   

11.
The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four controlled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four families were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.  相似文献   

12.
The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four con-trolled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four fami-lies were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.  相似文献   

13.
The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four con-trolled crosses,and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families,suggesting the...  相似文献   

14.
There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.  相似文献   

15.
Gene-centromere mapping is an essential prerequisite for understanding the composition and structure of genomes. Half-tetrad analysis is a powerful tool for mapping genes and understanding chromosomal behavior during meiosis. The Japanese scallop(Patinopecten yessoensis), a cold-tolerant species inhabiting the northwestern Pacific coast, is a commercially important marine bivalve in Asian countries. In this study, inheritance of 32 informative microsatellite loci was examined in 70-h D-shaped larvae of three induced meiogynogenetic diploid families of P. yessoensis for centromere mapping using half-tetrad analysis. The ratio of gynogenetic diploids was proven to be 100%, 100% and 96% in the three families, respectively. Inheritance analysis in the control crosses showed that 51 of the 53 genotypic ratios observed were in accordance with Mendelian expectations at the 5% level after Bonferroni correction. Seven of the 32 microsatellite loci showed the existence of null alleles in control crosses. The second division segregation frequency(y) of the microsatellite loci ranged from 0.07 to 0.85 with a mean of 0.38, suggesting the existence of positive interference after a single chiasma formation in some chromosomes in the scallop. Microsatellite-centromere distances ranged from 4 c M to 42 c M under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards the assembly of genetic maps in the commercially important scallop species.  相似文献   

16.
Scapharca broughtonii is a commercially important and over-exploited species.In order to investigate its genetic diversity and population structure,43 novel polymorphic microsatellites were isolated and characterized.The number of alleles per locus ranged from 3 to 22 with an average of 6.93,and the observed and expected heterozygosities varied between 0.233 and 1.000,and 0.250 and 0.953,with an average of 0.614 and 0.707,respectively.Three highly informative multiplex PCRs were developed from nine of those microsatellites for S.broughtonii.We evaluated and validated these multiplex PCRs in 8 full-sib families.The average polymorphism information content(PIC) was 0.539.The frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation patterns.Parentage analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex sets.Those 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of S.broughtonii.The 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction,population genetic analysis and brood stock management.  相似文献   

17.
There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(?21) used as a tail on each locus-specific forward primer and a single universal primer M13(?21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.  相似文献   

18.
Scapharca broughtonii is a commercially important and over-exploited species. In order to investigate its genetic diversity and population structure, 43 novel polymorphic microsatellites were isolated and characterized. The number of alleles per locus ranged from 3 to 22 with an average of 6.93, and the observed and expected heterozygosities varied between 0.233 and 1.000, and 0.250 and 0.953, with an average of 0.614 and 0.707, respectively. Three highly informative multiplex PCRs were developed from nine of those microsatellites for S. broughtonii. We evaluated and validated these multiplex PCRs in 8 full-sib families. The average polymorphism information content (PIC) was 0.539. The frequency of null alleles was estimated as 3.13% of all the alleles segregation based on a within-family analysis of Mendelian segregation patterns. Parentage analysis of real offspring demonstrated that 100% of all offspring were unambiguously allocated to a pair of parents based on 3 multiplex sets. Those 43 microsatellite loci with high variability will be helpful for the analysis of population genetics and conservation of wild stock of S. broughtonii. The 3 sets of multiplex PCRs could be an important tool of pedigree reconstruction, population genetic analysis and brood stock management.  相似文献   

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