Determination Of Genetic Relationships Research Articles

Development and Characterization of Microsatellites, Clone Identification, and Determination of Genetic Relationships among Rhus succedanea L. Individuals

To assist in the breeding and identification of Rhus succedanea L., which is cultivated in Japan to produce wax from its fruit, 12 microsatellite markers were developed from 96 clones sequenced from a genomic library generated from the traditional cultivar ‘Ikichi’. Using these markers, 50 genotypes were identified in 82 individuals (designated “the western group”) representing traditional cultivars and associated materials that have been selected from populations in western Japan and conserved for use in a breeding program. In a further analysis, of the 82 previously mentioned individuals and others from Chiba and Okinawa populations, 88 different genotypes were detected, with numbers of alleles per locus ranging from 3 to 19 and expected heterozygosity ranging from 0.22 to 0.85. Each traditional cultivar and old individual in the western group was closely genetically related to other trees in the group. In addition, according to Principal Coordinate Analysis, using Dice similarity coefficients based on the 88 genotypes, and pairwise FST values, the western group and the Chiba populations were considerably more closely related to each other than to the Okinawa populations. The implications of the findings for the future breeding of R. succedanea in Japan are discussed.

Development of a microsatellite multiplex genotyping tool for the fish Gilthead seabream (Sparus aurata): applicability in population genetics and pedigree analysis

In spite of the numerous studies performed in the aquacultured fish gilthead seabream, the overall structure of wild and cultivated stocks is rather confusing. In this study, we developed a 10 microsatellite genotyping tool SaGT(6+4), conformed by two polymerase chain reaction-multiplex reactions (SaGT6 and SaGT4), which can be simultaneously combined in automatic sequencers. The utility of this tool was proven through the following applications: (i) characterization and differentiation of wild and cultivated populations; (ii) pedigree reconstruction and estimation of the effective size in a cultivated stock; (iii) ability for pedigree reconstruction under different simulated situations; and (iv) determination of genetic relationships in the absence of data from parents. Based on our results, some recommendations have been provided on the management of the screened stocks. Our results also support the use of this tool in a standardized way, to understand the actual status of gilthead seabream from both wild and cultivated populations.

Genetic characterization of the Balkan endemic species, Merodon desuturinus (Diptera: Syrphidae)

Variation of 15 nuclear allozyme genes and a 708 bp fragment of DNA sequence of the mitochondrial cytochrome c oxi- dase subunit I (COI) gene were surveyed in a population of a hoverfly species, Merodon desuturinus Vuji¸ , Simi¸ & Radenkovi¸ , 1995 (Diptera, Syrphidae), endemic to the Balkan Peninsula. Based on phylogeography and taxonomy, Merodon desuturinus is of special interest from a biogeographical and conservation perspective. Characterization and determination of genetic relationships between M. desuturinus and taxa of the M. aureus, M. avidus, and M. ruficornis groups on the Balkan Peninsula were estimated based on molecular markers (allozymes and COI sequences). We observed that the mean number of alleles per allozyme locus was 1.1, frequency of polymorphic loci 0.067, and heterozygotes were absent. Our results showed an extremely low genetic variability in the M. desuturinus population sampled. We suggest that this taxon calls for a conservation management plan, as it is likely a vulner- able and threatened taxon, an endemic, spatially divided species and represents a unique genetic unit on the Balkan Peninsula.

Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders' rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat (Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

Assessment of the Utility of ISSR Markers for Evaluating Genetic Relationships Among Members of Asimina and Annona

The genus Asimina has the only temperate representatives of the tropical Annonaceae, or Custard Apple family, and includes eight species that are indigenous to North America. The North American pawpaw Asimina triloba (L.) Dunal has the largest edible fruit native to the United States and is the best-known of these species. The USDA National Clonal Germplasm Repository for Asimina species is located at Kentucky State Univ. (KSU); therefore, assessment of genetic diversity is an important research priority for KSU. The inter-simple sequence repeat PCR (ISSR-PCR) methodology has been used successfully to characterize genetic diversity within and among populations of many plant species. The objective of this study was to assess the utility of ISSR markers in evaluating genetic relationships in members of the Asimina genus, as well as closely related tropical relatives in the Annona genus. Leaf samples were collected from three plants each of Asimina longifolia, A. obovata, A. parviflora, A. reticulata, A. tetramera and A. triloba. Leaf samples were also collected from three plants each of Annona cherimola, A. squamosa, A. reticulata, A. muricata, A. glabra, A. diversifolia, and A. montana. DNA was extracted from leaf samples and subjected to ISSR-PCR using the REDExtract-N-Amp™ Plant PCR Kit. DNA samples were screened with ISSR primers using the Univ. of British Columbia microsatellite primer set #9. Three primers, UBC812, UBC841, and UBC873 were found to produce 84 scorable ISSR markers and allowed the determination of genetic relationships among Asimina and Annona members examined.

Inter and intra-species Inter Simple Sequence Repeat (ISSR) variations in the genus Cicer

Intra and inter-species ISSR variation and use of ISSR markers in determination of genetic relationship were investigated in an accession collection representing twoperennial and six annual Cicerspecies. Screening of Ciceraccessions with SSR primers revealed highly reproducible amplicon profiles with relatively high multiplex ratios. Many of the primers generated amplicon profiles with which not only the differences among species can readily be identified, but also polymorphisms within species could be detected more efficiently. PCR products at 150 gel positions detected using six SSR primers in Cicer accessions were treated as dominant DNA markers and utilized to compute the distances among accessions and species. Cluster analysis of accessions and species revealed groupings that corroborate our previous studies of relationships based on allozyme and AFLP analysis. Consistent with the AFLP analysis carried out in the same accession collection, ISSR-based groupings indicated that perennial C. incisumis genetically close to the annuals of the second crossability group (C. pinnatifidum,C. bijugum, C. judaicum) while C. reticulatum is the closest wild species to the cultivated chickpea. ISSR-based variation estimates were relatively higher when compared to previous estimates computed from RAPD and AFLP data. Technically, ISSR analysis combines the PCR-based targeting of microsatellite-associated polymorphisms with no prior sequence requirement and stringent PCR conditions. Similarly, when compared to AFLP analysis, it is less technically demanding allowing to survey polymorphic loci in the genome. Thus, ISSR-PCR technology is a reliable, fast, and cost-effective marker system that can be used to study genetic variation and genetic relationships in the genusCicer.

Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana.

Genetic markers such as single nucleotide polymorphisms (SNPs) are essential tools for positional cloning, association, or quantitative trait locus mapping and the determination of genetic relationships between individuals. We identified and characterized a genome-wide set of SNP markers by generating 10,706 expressed sequence tags (ESTs) from cDNA libraries derived from 6 different accessions, and by analysis of 606 sequence tagged sites (STS) from up to 12 accessions of the model flowering plant Arabidopsis thaliana. The cDNA libraries for EST sequencing were made from individuals that were stressed by various means to enrich for transcripts from genes expressed under such conditions. SNPs discovered in these sequences may be useful markers for mapping genes involved in interactions with the biotic and abiotic environment. The STS loci are distributed randomly over the genome. By comparison with the Col-0 genome sequence, we identified a total of 8051 SNPs and 637 insertion/deletion polymorphisms (InDel). Analysis of STS-derived SNPs shows that most SNPs are rare, but that it is possible to identify intermediate frequency framework markers that can be used for genetic mapping in many different combinations of accessions. A substantial proportion of SNPs located in ORFs caused a change of the encoded amino acid. A comparison of the density of our SNP markers among accessions in both the EST and STS datasets, revealed that Cvi-0 is the most divergent accession from Col-0 among the 12 accessions studied. All of these markers are freely available via the internet.

Cultivar identification and genetic relationship among selected breeding lines and cultivars in chickpea ( Cicer arietinum L.)

Twenty two RAPD and 22 ISSR markers were evaluated for their potential use in determination of genetic relationships in chickpea (Cicer arietinum L.) cultivars and breeding lines. We were able to identify six chickpea cultivars/breeding lines by cultivar-specific markers. All of the cultivars tested displayed a different phenotype generated either by the RAPD or ISSR primers. Though ISSR primers generated less markers than RAPD primers, the ISSR primers produced higher levels of polymorphism (% of polymorphic markers per primer) than RAPD primers. A high level of within cultivar homogeneity was observed in chickpea. Cultivars/breeding lines originating from a common genetic background showed closer genetic relationship. Chickpea lines with similar seed type(kabuli or desi) had a tendency to cluster together.

Strain characterization of Candida parapsilosis fungemia by molecular typing methods.

The present study used two molecular typing methods to investigate a cluster of eight cases of Candida parapsilosis fungemia in a hospital in Rio de Janeiro, Brazil. Candida parapsilosis is an important opportunistic pathogen that is frequently involved in outbreaks of nosocomial fungemia. Identification of a common source of infection and determination of genetic relatedness among the strains involved in outbreaks are important for infection control. Candida parapsilosis strains were isolated from the bloodstream of patients housed in an intensive-care unit (n=5) and in individual rooms (n=3). An additional strain of Candida parapsilosis was isolated from a hyperalimentation infusion flask, which was implicated by molecular typing to be the source of infection. All strains were identified using morphological and biochemical methods. The genetic relationship between patients' strains and the hyperalimentation infusion strain was assessed by electrophoretic karyotype (EK) analysis and random amplification of polymorphic DNA (RAPD). Both methods resulted in patterns that allowed differentiation of the isolates. Candida parapsilosis fungemia, in three of the eight patients, resulted from a common source of infection, as demonstrated by molecular typing methods. Image analysis of EK patterns indicated that these strains were closest to Candida parapsilosis Group II, a grouping that is a less frequent clinical isolate than the major Group I strains.

Determination of genetic relationships among five indigenous Chinese goat breeds with six microsatellite markers.

Microsatellite variation was analyzed in five Chinese indigenous goat breeds, which include four Cashmere breeds (Tibetan, Neimonggol, Liaoning, Taihang) and one Hubei local breed (Matou) used for meat production. Five ovine and one bovine microsatellites, selected from eight ovine microsatellites and five bovine microsatellites were suitable for use in this study. With these six microsatellites, allele frequencies, heterozygosity, polymorphism information content (PIC) and effective allele number were calculated. A neighbor-joining tree was constructed using Nei's standard genetic distance (1978). In the tree, Neimonggol and Liaoning were grouped together, then with Taihang; while Tibetan and Matou individually had their own branch. The genetic relationship of five breeds corresponds to their history and geographic origins.

Determination of genetic relationships among shape Phaseolus vulgaris populations in a conical cross from RAPD marker analyses

Random-amplified polymorphic DNA (RAPD) markers were used to determine genetic relationships among Phaseolus vulgaris breeding populations. Genetic distances were calculated from the distribution of 317 RAPD markers among 8 parents, 10 individuals from 8 cycle-one populations, 10 individuals from 6 cycle-two populations and 10 individuals from 2 cycle-three populations of a conical cross. Genetic distances between populations and parents were consistent with their degree of relationship in the crossing scheme indicating that a RAPD analysis is a sensitive and useful method for categorizing breeding materials according to their genetic similarities. Genetic variation among individuals within populations increased from cycle one to cycle three and variation among populations within the cycles decreased from cycle one to cycle three in the conical cross. The results showed that this crossing scheme can be used to collect the genetic diversity in eight parents into a single plant breeding population. Abbreviations: CBB, common bacterial blight; GD, genetic distance; RAPD, random-amplified polymorphic DNA

Quantitative assessment of genomic similarity from restriction fragment patterns

A quantitative algorithm for comparing restriction fragment patterns (RFPs) was developed and used to estimate the genomic similarity of 18 isolates of pseudorabies virus of known origin. Variants of this algorithm using either untransformed or square-root-transformed differences between fragment sizes were investigated with regard to their ability to classify RFPs. Multidimensional scaling was used to represent spatially the genomic relatedness among samples, with 3 dimensions producing the most meaningful results. The square-root transformation provided more interpretable dimensions. The first dimension differentiated samples geographically, separating North American from European isolates. The second and third dimensions differentiated isolates with specific gene deletions (gE and gG, respectively) from those not having these deletions. Clusters of isolates were identified that were related either by collection from the same geographic area during a specific time period, or by laboratory intervention to create vaccines. These methods offer increased precision in the determination of genetic relatedness based on RFPs, and thus offer increased diagnostic accuracy for the determination of sources of infection.

The nature of genetic variation among viruses

Genetic variation among viruses may seem unimportant and academic--related only to pedagogical classification of things--but accurate determination of genetic relationships can have important implications, from characterizing the molecular basis of attenuation of viral vaccines to furthering knowledge about origins of viruses and even of life itself. It can even help to establish priority in the discovery of viruses when properly applied. The purpose of this brief review is to demonstrate how viruses change and what implications these changes can have on the delicate balance between the viral parasite and its host. Examples will be drawn from the hepatitis viruses when possible.