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An important area of crop development is the introduction of new vegetable plants, one of which is the sweet potato Ipomoea batatas (L.) Lam. The aim of our research was genetic, biological and economic assessment of sweet potato accessions held in the collection of the Plant Introduction and Acclimatization Dept., Udmurt Federal Research Center, Ural Branch of the RAS (UdmFRC UB RAS).Within this experiment, DNA polymorphism of 16 accessions of I. batatas was tested using ISSR markers. All accessions were found to represent different genotypes; the VM 17 accession obtained as a result of a bud mutation differed significantly from the original accession in its genotype.Evaluation of 16 accessions of sweet potato cultivars was carried out in a small-plot field experiment. The results of biological and economic assessment witnessed to the prospects of sweet potato cultivation within the territory of the Udmurt Republic for marketable tuber production. The productivity of the accessions was 140–2700 g of tubers per plant. According to their productivity, the accessions were divided into clusters: the low-productivity group (up to 500 g), with ‘Betty’, Fioletovy, ‘Beauregard’, ‘Covington’ and Bezhevy; medium-productivity group (500–1000 g), with ‘Jewel’, Fioletovy Sochi, Brazilsky, Afgansky, Vinnitsky rozovy, Lyubitelsky and ‘Bayou Bell’; and high-productivity group (more than 1000 g), with Pobeda 100, ВM 17, Druzhkovsky and Bely NBS. On the basis of the evaluation, 11 sweet potato accessions were recommended for cultivation in the Middle Urals: Afgansky, ‘Bayou Bell’, Bely NBS, ВM 17, Brazilsky, Druzhkovsky, Fioletovy Sochi, ‘Jewel’, Lyubitelsky, Pobeda 100, and Vinnitsky rozovy.

Background. Identification of crop varieties is presently one of the most important aspects due a significant annual increase in the number of newly developed cultivars. Application of molecular markers makes it possible to identify cultivars and secure protection of plant breeders’ rights. Marker techniques based on SSR loci and PawS markers were evaluated for their efficiency in revealing the DNA polymorphism in Russian red clover cultivars, and the research results are presented in this publication.Materials and Methods. The total genome DNA was extracted by a modified SDS method from 30 seedlings per each cultivar. Nine simple sequence repeats (SSR) and 4 PawS markers were used for genotyping. The basic genetic diversity parameters were measured and analyzed using the software resources GelAnalyzer 2010а, MStools v.3, and Statistica 7.0.Results and conclusion. The mean level of intervarietal DNA polymorphism in red clover was 38.6%. Cultivar-specific amplicons were obtained for 4 accessions (cvs. ‘Trifon’, ‘Topaz’, ‘Trio’ and ‘Mars’) with SSR loci RCS1307 and RCS3095. These loci were found appropriate for identification and certification of such cultivars. The tested PawS markers (individually and in combinations) proved non-informative for the analysis of intervarietal DNA polymorphism in red clover. The only primer pair PawS5+PawS16 generated reproducible PCR products, but unique amplicons were absent in the DNA profiles. The data obtained in this study may be helpful for further identification and certification of Russian red clover cultivars and promising breeding materials.

Funder: International Max Planck Research School of Organismal Biology, Funder: Universities of the State of Baden-Württemberg, Animal species differ considerably in their ability to fight off infections. Finding the genetic basis of these differences is not easy, as the immune response is comprised of a complex network of proteins that interact with one another to defend the body against infection. Here, we used population- and comparative genomics to study the evolutionary forces acting on the innate immune system in natural hosts of the avian influenza virus (AIV). For this purpose, we used a combination of hybrid capture, next- generation sequencing and published genomes to examine genetic diversity, divergence, and signatures of selection in 127 innate immune genes at a micro- and macroevolutionary time scale in 26 species of waterfowl. We show across multiple immune pathways (AIV-, toll-like-, and RIG-I -like receptors signalling pathways) that genes involved genes in pathogen detection (i.e., toll-like receptors) and direct pathogen inhibition (i.e., antimicrobial peptides and interferon-stimulated genes), as well as host proteins targeted by viral antagonist proteins (i.e., mitochondrial antiviral-signaling protein, [MAVS]) are more likely to be polymorphic, genetically divergent, and under positive selection than other innate immune genes. Our results demonstrate that selective forces vary across innate immune signaling signalling pathways in waterfowl, and we present candidate genes that may contribute to differences in susceptibility and resistance to infectious diseases in wild birds, and that may be manipulated by viruses. Our findings improve our understanding of the interplay between host genetics and pathogens, and offer the opportunity for new insights into pathogenesis and potential drug targets.

Objective: In the present study, we investigated the effects of promoter polymorphism and an exon-1 mutation (G71R) in the UGT1A1 gene in neonates with unexplained hyperbilirubinemia and direct Coombs-negative [DC(-)] ABO incompatibility. Methods: Two-hundred term neonates in their first week of life and without additional icterogenic factors were included in the study. Neonates with a serum total bilirubin (STB) level ≥17 mg/dL constituted the hyperbilirubinemia group (n = 100), while the control group comprised healthy neonates with a STB level 0.05). Conclusions: UGT1A1 gene promoter polymorphism and G71R mutation are possible risk factors for Turkish neonates with DC(-) ABO incompatibility and unexplained hyperbilirubinemia. © 2017 Informa UK Limited, trading as Taylor & Francis Group.

This paper reviews how mammalian genomes are utilized in modern genetics for the detection of genes and polymorphisms (mutations) within domesticated animal (mostly livestock) genomes that are related to traits of economic importance to humans. Examples are given of how genetic analysis allows to determine key genes associated with the quality and quantity of milk in cattle and key genes for meat production. Various questions are reviewed, such as how contemporary methods of genome sequencing allow to maximise the effective detection of coding and regulatory DNA polymorphisms within the genomes of major domesticated mammals (cattle, sheep and pigs) and the history of their formation from the standpoint of genetics.

Although rice genome was sequenced in the year 2002, efforts in resequencing the large number of available accessions, landraces, traditional cultivars, and improved varieties of this important food crop are limited. We have initiated resequencing of the traditional cultivars from India. Kavuni is an important traditional rice cultivar from South India that attracts premium price for its nutritional and therapeutic properties. Whole-genome sequencing of Kavuni using Illumina platform and SNPs analysis using Nipponbare reference genome identified 1 150 711 SNPs of which 377 381 SNPs were located in the genic regions. Non-synonymous SNPs (62 708) were distributed in 19 251 genes, and their number varied between 1 and 115 per gene. Large-effect DNA polymorphisms (7769) were present in 3475 genes. Pathway mapping of these polymorphisms revealed the involvement of genes related to carbohydrate metabolism, translation, protein-folding, and cell death. Analysis of the starch biosynthesis related genes revealed that the granule-bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a two-nucleotide combination, which were reported to favour high amylose content and low glycemic index. The present study provided a valuable genomics resource to study the rice varieties with nutritional and medicinal properties.

European chestnut orchards are multifunctional agroforestry systems with a key role in environmental management. Their biodiversity is at risk of erosion and farmers do not have enough tools to protect and valorize traditional ecotypes. In particular, cost effective and reliable molecular markers for cultivar identification are lacking. The aim of this research was to develop a new molecular tool for varietal identification in European chestnuts. A set of cultivars was preliminarily characterized to evaluate the range of genetic diversity using random amplified polymorphic DNA (RAPD) markers. The genetic distances indicated a sufficiently wide variability range among tested genotypes and confirmed they were suitable for our goal. A single nucleotide polymorphism (SNP) mining within 64 expressed sequence tags (EST), covering all the linkage groups, was performed by high-resolution melting (HRM) and validated by target resequencing. Fifty-six SNPs were retrieved by monitoring the variability present on the whole set of considered cultivars in loci uniformly distributed on the genome. A subset of 37 SNPs was finally transformed into kompetitive allele-specific PCR (KASP) markers that were successfully evaluated for varietal discrimination. Three assays (C1083, G0115 and A5096) were identified as necessary and sufficient for distinguishing among the tested cultivars. The developed tools can be effectively exploited by stakeholders for improving the management of the European chestnut genetic resources.

Among various human tissue identity testing platforms, short tandem repeat (STR) genotyping has emerged as the most powerful and cost-effective method. Beyond forensic applications, tissue identity testing has become increasingly important in modern medical practice, in areas such as diagnostic pathology. Areas covered: A brief overview of various molecular/genetic techniques for identity testing is provided. This includes restriction fragment length polymorphism, single nucleotide polymorphism array and STR genotyping by multiplex PCR. Diagnostic applications of STR genotyping are covered in greater details: genotyping diagnosis of gestational trophoblastic disease, resolving tissue specimen mislabeling or histologic contaminant or 'floaters', bone marrow engraftment/chimerism analysis and interrogation of the primary source of malignancy in patients receiving organ donation. Four clinical cases are then presented to further illustrate these important clinical applications along with discussion of the interpretation, limitations, and pitfalls of STR genotyping. Expert commentary: STR genotyping is currently the most applicable method of identity testing and has extended its role well into the practice of diagnostic pathology with novel and powerful applications beyond forensics.

Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass., Author summary Individual fungi rely on particular host organisms or substrates for their nutrition. Therefore, the genomes of fungi feeding on plant biomass necessarily contain genes encoding plant cell wall-degrading enzymes, while animal parasites may depend on proteolytic activity. Molds in the genus Trichoderma (Ascomycota) display a unique nutritional versatility. They can feed on other fungi, attack animals, and degrade plant debris. The later property is so efficient that one species (T. reesei) is commercially used for the production of cellulolytic enzymes required for making biofuels and other industry. In this work, we have investigated the evolution of proteins required for plant cell wall degradation in nine Trichoderma genomes and found an unprecedented number of lateral gene transfer (LGT) events for genes encoding these enzymes. Interestingly, the transfers specifically occurred from Ascomycota molds that feed on plants. We detected no cases of LGT from other fungi (e.g., mushrooms or wood-rotting fungi from Basidiomycota) that are frequent hosts of Trichoderma. Therefore, we propose that LGT may be linked to the ability of Trichoderma to parasitize on related organisms. This is a characteristic ecological trait that distinguishes Trichoderma from other mycoparasitic fungi. In this report, we demonstrate that the lateral transfer of genes may result in a profound nutritional expansion and contribute to the emergence of a generalist capable of feeding on organic matter of any origin.

Background Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl (http://bioperl.org) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users. Results Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of the most popular BioPerl modules readily accessible on the command line to novice as well as to experienced bioinformatics practitioners. The initial release of BpWrapper includes four utilities with concise command-line user interfaces, bioseq, bioaln, biotree, and biopop, specialized for manipulation of molecular sequences, sequence alignments, phylogenetic trees, and DNA polymorphisms, respectively. Over a hundred methods are currently available as command-line options and new methods are easily incorporated. Performance of BpWrapper utilities lags that of precompiled utilities while equivalent to that of other utilities based on BioPerl. BpWrapper has been tested on BioPerl Release 1.6, Perl versions 5.10.1 to 5.25.10, and operating systems including Apple macOS, Microsoft Windows, and GNU/Linux. Release code is available from the Comprehensive Perl Archive Network (CPAN) at https://metacpan.org/pod/Bio::BPWrapper. Source code is available on GitHub at https://github.com/bioperl/p5-bpwrapper. Conclusions BpWrapper improves on existing sequence utilities by following the design principles of Unix text utilities such including a concise user interface, extensive command-line options, and standard input/output for serialized operations. Further, dozens of novel methods for manipulation of sequences, alignments, and phylogenetic trees, unavailable in existing utilities (e.g., EMBOSS, Newick Utilities, and FAST), are provided. Bioinformaticians should find BpWrapper useful for rapid prototyping of workflows on the command-line without creating custom scripts for comparative genomics and other bioinformatics applications. Electronic supplementary material The online version of this article (10.1186/s12859-018-2074-9) contains supplementary material, which is available to authorized users.

Population size is one of the main factors that determine the amount of DNA polymorphism. We examined a model under which the population size changed linearly. Because of the simplicity of this model, we could analytically obtain the expectation of nucleotide diversity, E(π), and the expectation of the amount of DNA polymorphism, E(θ), based on the number of segregating sites. The results suggest that E(π) is larger than E(θ) when the population size decreased and that E(π) is smaller than E(θ) when the population size increased. The expected time to the most recent common ancestor could also be obtained under this model.

Increased levels of fetal hemoglobin (HbF, α2γ2) may reduce sickle cell anemia severity due to its ability to inhibit HbS polymerization and also reduce the mean corpuscular HbS concentration. We have investigated the influence of three known major loci on the HbF trait (HBG2, rs748214; BCL11A, rs4671393; and HBS1L-MYB, rs28384513, rs489544 and rs9399137) and HbF levels in SCA patients from the State of Pará, Northern Brazil. Our results showed that high levels of HbF were primarily influenced by alleles of BCL11A (rs4671393) and HMIP (rs4895441) loci, and to a lesser extent by rs748214 Gγ-globin (HBG2) gene promoter. The SNPs rs4671393 and rs4895441 explained 10% and 9.2%, respectively, of the variation in HbF levels, while 4.1% of trait variation was explained by rs748214. The results can be considered as in accordance with the pattern of ancestry displayed by the SCA patients: 39.6% European, 29.6% African and 30.8% Native American, and reinforce the suggestion that studies of association between genetic modifiers and clinical and laboratory manifestations in Brazil must be controlled by ancestry.

Genetic diversity and interrelationships among 31 lentil genotypes were evaluated using 10 Inter-Simple Sequence Repeat (ISSR) and 10 directed amplification of minisatellite DNA region (DAMD) primers. A total of 43 and 48 polymorphic bands were amplified by ISSR and DAMD markers, respectively. Average polymorphism information content (PIC) for ISSR and DAMD markers were 0.37 and 0.41, respectively. All 31 lentil genotypes could be distinguished by ISSR markers into three groups and by DAMD markers into two groups. Various molecular markers show a different efficiency for evaluating DNA polymorphism in lentil and indicate that the patterns of variation are clearly influenced by the genetic marker used. Comparatively, the genetic diversity of examined lentil genotypes by two different marker techniques (ISSR and DAMD) was high and indicated that ISSR and DAMD are effective and promising marker systems for fingerprinting in lentil and give useful information on its genetic relationships.

Manioc, Manihot esculenta, is economically important in many tropical and subtropical countries. The genetic variability of the species has not been fully explored, and new information may help expand its use. Molecular markers based on retrotransposons have good potential for analysis of genetic diversity given their abundance in the genome. Eight long terminal repeat retrotransposons were selected for the development of inter-retrotransposon-amplified polymorphism markers. To test these primers, we analyzed 32 varieties from Anori, 30 from Manicoré and 10 Mandiocabas from the Manioc Germplasm Bank at Embrapa Western Amazonia. The six informative primer pairs yielded 20- 60 polymorphic bands, averaging 92% polymorphism (51.7-98.4) and 0.37 heterozygosity (0.17 to 0.40), with a Shannon information index of 0.54 (0.26-0.59). These markers can be used to explore the genetic diversity of manioc. © FUNPEC-RP.

In plant breeding programs with vegetatively propagated plants, induced mutations with low physiological effects and strong genetic effects are important approaches for broadening the genetic variation. In the present study, intersimple sequence repeat (ISSR) assays were used to identify DNA polymorphism among the mutant varieties of Curcuma alismatifolia (Chiang Mai Red, Sweet Pink, Kimono Pink) and one hybrid (Doi Tung 554) exposed to 0-, 10-, and 20-Gy optimum doses of acute gamma irradiation. To identify DNA polymorphism among the mutants (10 and 20 Gy) and non-treated (0 Gy) samples through ISSR assay, a total of 25 random primers were screened and 14 gave reproducible polymorphic bands. The number of presumed alleles revealed by the ISSR analysis ranged from three to 19 alleles with mean values of 6.5, 7.8, and 9.2 alleles per locus for doses of 0 (control), 10, and 20 Gy, respectively. The average effective number of alleles, Nei’s gene diversity, Shannon’s information index, and polymorphic information content (PIC) were 1.41 to 1.48, 0.24 to 0.33, 0.35 to 0.45, and 0.21 to 0.25 for the three doses, respectively. Percentages of polymorphic loci for non-irradiated (0 Gy), 10 Gy, and 20 Gy individual plants were 76.4%, 83.7%, and 85.8%, respectively, with an average of 81.9%. Jaccard’s genetic similarity coefficient varied from 0.19 to 1.0 indicating the level of genetic variation among the mutants studied. In terms of variety, the range of genetic variation (0.27 to 0.4) among individuals of the Doi Tung population was more than that observed in the other three varieties. In a dendrogram constructed based on genetic similarity coefficients, the 44 C. alismatifolia individual plants fell into seven major clusters at a coefficient level of 0.35. The study revealed that DNA polymorphism detected by ISSR analysis offered a useful molecular marker for the identification of mutants in gamma radiation-treated plants. Additionally, this research demonstrated that the DNA of the hybrid (Doi Tung 554) showed a greater response in induced mutation compared with the other varieties.

00000 ăWOS:000384167300004; International audience; Morphological and molecular tools were combined to resolve the misidentification between Glycymeris glycymeris and Glycymeris pilosa from Atlantic and Mediterranean populations. The ambiguous literature on the taxonomic status of these species requires this confirmation as a baseline to studies on their ecology and sclerochronology. We used classical and landmark-based morphometric approaches and performed bivariate and multivariate analyses to test for shell character interactions at the individual and population level. Both approaches generated complementary information. The former showed the shell width to length ratio and the valve asymmetry to be the main discriminant characters between Atlantic and Mediterranean populations. Additionally, the external microsculpture of additional and finer secondary ribs in G. glycymeris discriminates it from G. pilosa. Likewise, landmark-based geometric morphometrics revealed a stronger opisthogyrate beak and prosodetic ligament in G. pilosa than G. glycymeris. Our Bayesian and maximum likelihood phylogenetic analyses based on COI and ITS2 genes identified that G. glycymeris and G. pilosa form two separate monophyletic clades with mean interspecific divergence of 11% and 0.9% for COI and ITS2, respectively. The congruent patterns of morphometric analysis together with mitochondrial and nuclear phylogenetic reconstructions indicated the separation of the two coexisting species. The intraspecific divergence occurred during the Eocene and accelerated during the late Pliocene and Pleistocene. Glycymeris pilosa showed a high level of genetic diversity, appearing as a more robust species whose tolerance of environmental conditions allowed its expansion throughout the Mediterranean.

Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. Availability: http://vcftools.sourceforge.net Contact: rd@sanger.ac.uk

Diversity Arrays Technology (DArT) provides whole genome profiling for hundreds to thousands of polymorphic markers in a single assay using a high-throughput microarray platform. The presented work aimed to establish DArT genotyping for the genetically challenging genome of sugarcane. Due to the genome complexity of this sugar-producing crop of high economic importance, an application of DArT genotyping to this species required extensive testing and optimization. As the method of genome complexity reduction determines the efficiency of polymorphism identification in DArT, various approaches and several methods were tested, in order to establish the most optimal. The sugarcane DArT markers generated with these established methods identified high genetic differentiation of sugarcane ancestral species from modern cultivars, in agreement with the data available for other types of molecular markers for this crop. The majority of sugarcane DArT markers segregated in a Mendelian fashion and were readily incorporated into the framework genetic map. As the DArT markers are sequence-ready genomic clones, we sequenced 384 clones and found that one-third of sequenced markers came from the transcribed portion of the sugarcane genome. The presented results further validate the potential of DArT technology in providing cost-effective genetic profiles for plants, irrespective of their genome complexity, for effective applications in molecular-assisted breeding, diversity analysis or genetic identity testing.

The aim of this study is to ascertain the possible application of Random Amplification of Polymorphic DNA (RAPD) analysis as a genetic test to investigate DNA polymorphisms and detection of genomic markers in various types of leukemia. The results showed unique profiles of amplified DNA fragments produced in genomic DNA of three types of leukemia by an arbitrary primer of decamer oligonucleotides OPA-09. The primer produced four types of amplified DNA fragments (980, 1659, 2187 and 3162 bp). The smallest amplified DNA fragment (980 bp) appeared in 14.3 and 13.3% of tested acute myeloid leukemia and chronic myeloid leukemia patients, respectively; but was absent in genomic DNA of chronic lymphoid leukemia and normal individuals. Whereas the largest amplified fragment (3162 bp) was present in 12.5, 20 and 75% of chronic lymphoid leukemia, chronic myeloid leukemia and normal individuals, respectively and was absent in acute myeloid leukemia. On the other hand, the two amplified fragments (1659 and 2187 bp) were present in normal and leukemia patients. Cluster analysis of amplified DNA fragments grouped the leukemia patients in two main groups. The detected DNA polymorphisms by the arbitrary primer OPA-09 might find application in developing efficient RAPD primer for diagnosis of leukemia.

DNA polymorphism of the cellular lines of wheat resistant to the culture filtrate of G. graminis var. tritici and the plant-regenerants that were induced from them has been studied with the use of the method of ISSR-analysis. Specific changes in DNA sequences were detected in resistant calluses. It was found that all resistant cell lines were different from the initial callus and from the callus, which was not exposed to the selective factor. This difference was based on the presence of the specific 2347 bp (5′-TCTCTCTCTCTCTCTCG-3′ primer) and 1745 bp (5′-AGAGAGAGAGAGAGAGTC-3′ primer) amplicons and on the absence of the 1108 bp amplicon (5′-ACACACACACACACACC-3′ primer). These changes were also found in the plant-regenerants and in the R1 plants.

Summary Many inherited diseases occur in pure-bred dogs, but diagnosis at the level of DNA is impossible because the canine genome is largely unknown. Random amplification of polymorphic DNA (RAPD) provides many polymorphisms, but the reproducibility and Mendelian inheritance are not beyond doubt. An optimized polymerase chain reaction (PCR) was developed for canine DNA with respect to the annealing temperature and the concentrations of MgCl2, template DNA and primers. RAPD amplification products were in the range of 100–1500 base pairs. With six primers, 21 different reactions with different electrophoretic patterns were obtained, yielding 9–29 products per reaction. In DNA from dogs of 16 different breeds, 14% of the products were polymorphic; when only beagles were included the rate of polymorphism was 10%. All of the reaction products were completely reproducible in 16 DNA samples. Mendelian transmission was analysed in six beagle families (42 dogs). The segregation of polymorphic amplification products in 21 reactions performed on DNA from all beagles was nearly complete; in only two of the 630 reactions was there a product that could not be traced back to either of the parents. The reproducibility and Mendelian behaviour of polymorphisms generated by RAPD in dogs makes this tool very suitable for development of DNA markers of canine inherited diseases.

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26¿27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima¿s D and Fu and Li¿s F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T > C. Two SNPs (689C > A and 757C > T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCN-resistant cultivars.

Gastrodia tuber and its component gastrodin have many pharmacological effects. The chemical fingerprints and gastrodin contents of eight Gastrodia populations were determined, and the genomic DNA polymorphism of the populations was investigated. Genetic distance coefficients among the populations were calculated using the DNA polymorphism data. A dendrogram of the genetic similarities between the populations was constructed using the genetic distance coefficients. The results indicated that the genomic DNA of Gastrodia tubers was highly polymorphic; the eight populations clustered into three major groups, and the gastrodin content varied greatly among these groups. There were obvious correlations among genetic makeup, gastrodin content, and place of origin. The ecological environments in Guizhou and Shanxi may be conducive to evolution and to gastrodin biosynthesis, and more suitable for cultivation of Gastrodia tubers. These findings may provide a scientific basis for overall genetic resource management and for the selection of locations for cultivating Gastrodia tubers.

DNA polymorphism of the porcine leukemia inhibitory factory (LIF) was investigated and used to study the effects on litter size in Large White pigs. A total of 2,167 litter records from 420 sows genotyped at two SNP loci (LIF1 and LIF2) within LIF gene were analyzed to determine whether LIF influenced total number born (TNB) and number born alive (NBA). The results indicated that B allele at LIF1 locus and A allele at LIF2 locus seem to have advantageous effects on litter size. However, the combined analyzed results demonstrated that genotype AAAA, ABBB, and BBBB are better than genotype AAAB, AABB, and ABAB for TNB and NBA in either third to eighth parity or all parities. In all parities, the sows with AAAA genotype had an advantage of 1.76 piglets (P < 0.001) for TNB and 1.44 piglets (P < 0.01) for NBA per litter over the AAAB sows, respectively. The results in this study demonstrated that LIF gene was significantly associated with litter size in pigs.

A total of 124 chromosomes of 64 unrelated Indian β- thalassemia and β-thalassemia patients along with their family members were studied for their haplotype pattern and mutations. These included, 35 with β- thalassemia major, 4 with thalassemia trait, and 25 with β-thalassemia. Fourteen mutations were detected by PCR and Sequencing. The most common mutation IVS1-5 (G-C) was linked with 8 different haplotypes. Nineteen haplotypes were found on β-thalassemia mutations, with haplotype (+ - - - - + -) being the most widespread and was found associated with 39 chromosomes of IVS1-5 (G-C), 2 of HPFH and 1 each of CD41/42(-CTTT) and CD16 (-C).

WOS: 000377055800028, 27118180, The Potomida genus (Bivalvia, Unionida) has a Circum-Mediterranean distribution and like other freshwater mussel species, its populations have suffered dramatic declines. Although this genus is currently considered as monotypic, it has a long history of taxonomic revisions and presently many aspects of its systematics and evolutionary history are unclear. We sampled a total of 323 individuals from 39 different sites across the Potomida genus distribution, and sequenced two mitochondrial (16S rDNA and Cytochrome c Oxidase Subunit I) and one nuclear (28S rDNA) genes to clarify its phylogeny and phylogeographic history. Our results show that the genus includes two well-supported clades, one comprising solely the western Mediterranean species Potomida littoralis, and the other including two eastern Mediterranean species, the Greek endemic P. acarnanica and the Anatolian and Middle Eastern P. semirugata. We suggest that Potomida started radiating during the upper Miocene, and that both vicariance and dispersal events shaped the diversification and distribution of the genus along the Mediterranean region. P. littoralis is further divided in two mitochondrial lineages, one restricted to Europe and the other occurring mostly in North Africa. Moreover, some European basins present both lineages in sympatry. The conservation status of the three recognized species should be reevaluated, particularly P. acarnanica, since it is restricted to two Greek river basins presenting a high risk of extinction. Overall, our results clarify some important gaps in knowledge concerning the phylogeny, phylogeography and evolution of the Potomida genus in the Mediterranean region with important taxonomical, ecological and conservational implications. (C) 2016 Elsevier Inc. All rights reserved., Portuguese Foundation for Science and Technology (FCT) [SFRH/BPD/108445/2015, SFRH/BD/78402/2011, PTDC/AAC-AMB/117688/2010]; Biotope, Conchological Society of Great Britain and Ireland; Mohamed bin Zayed Species Conservation Fund [15256799], The authors wish to thank the two anonymous reviewers for helpful remarks and suggestions that improved the quality of the manuscript. Financial support was provided by Portuguese Foundation for Science and Technology (FCT) Grant to EF (SFRH/BPD/108445/2015), to DVG (SFRH/BD/78402/2011) and Project (PTDC/AAC-AMB/117688/2010) as well as by Biotope, Conchological Society of Great Britain and Ireland, and the Mohamed bin Zayed Species Conservation Fund (Reference 15256799). We thank Jose Maria Irurita, Jose Miguel Barea Azcon, Keiko Nakamura, Pablo Redin and Esther Penin for all their help during the Spanish field campaigns, Benjamin Adam, Panier Cucherat, Quentin Molina and Laurent Philippe for their help in sampling French specimens, and Dan Graf for providing us with the exact locations of previously sequenced animals. Official capture and sampling licenses were issued by the following agencies: (1) Junta de Castilla y Leon (Consejeria de Fomento y Medio Ambiente EP/CYL/331/2012, de 17 de Abril de 2012); (2) Junta de Andalucia (Consejeria de Medio Ambiente-SGYB/FOA/AFR/SFS, de 17 de Julio de 2012); (3) Gobierno de Aragon (Direccion General de Conservacion del Medio Natural - 136.071/2012 de 12 de julio de 2012); (4) Universite Cadi Ayyad (Faculte des Sciences, Semlalia, Marrakech, Maroc); (5) Hellenic Ministry of Agriculture and Institute of Marine Biological Resources and Inland Waters, Hellenic Centre for Marine Research (Greece).

Kumar, R., Kumar, S., Singh, D.P. and Gaur, P. 2007. DNA polymorphism at IL-2Rγ and IL-15Rα genes in Aseel native chicken. J. Appl. Anim. Res., 32: 107–110. DNA polymorphism at Interleukin-2R γ-chain (IL-2Rγ) and Interleukin-15R α-chain (IL-15Rα) genes was studied by PCR-RFLP technique in 60 random bred Aseel native chicken, selected out of 251 birds, on the basis of their response to sheep erythrocytes and categorized into high, medium and low groups. Amplification of these regions yielded products of 600 and 246 bp, respectively. Hph I digestion ofIL-2Rγ PCR product generated fragments of 465, 454 bp sizes. Only one type of homozygotes (with 465 bp fragment) and heterozygotes (with both 465 and 454 bp fragments) were observed. The gene and genotypie frequencies of A and B alleles and AA and AB genotypes were 0.82 and 0.18 and 0.64 and 0.36, respectively. Alu I PCR-RFLP analysis ofIL-15Rα revealed fragments of 123 and 80 bp in all the samples; a pattern of heterozygotes. Heterozygotes at IL-2Rγ ...

Using nitrogen-fixing Sinorhizobium species that interact with Medicago plants as a model system, we aimed at clarifying how sex has shaped the diversity of bacteria associated with the genus Medicago on the interspecific and intraspecific scales. To gain insights into the diversification of these symbionts, we inferred a topology that includes the different specificity groups which interact with Medicago species, based on sequences of the nodulation gene cluster. Furthermore, 126 bacterial isolates were obtained from two soil samples, using Medicago truncatula and Medicago laciniata as host plants, to study the differentiation between populations of Sinorhizobium medicae , Sinorhizobium meliloti bv. meliloti, and S. meliloti bv. medicaginis. The former two can be associated with M. truncatula (among other species of Medicago ), whereas the last organism is the specific symbiont of M. laciniata . These bacteria were characterized using a multilocus sequence analysis of four loci, located on the chromosome and on the two megaplasmids of S. meliloti. The phylogenetic results reveal that several interspecific horizontal gene transfers occurred during the diversification of Medicago symbionts. Within S. meliloti , the analyses show that nod genes specific to different host plants have spread to different genetic backgrounds through homologous recombination, preventing further divergence of the different ecotypes. Thus, specialization to different host plant species does not prevent the occurrence of gene flow among host-specific biovars of S. meliloti , whereas reproductive isolation between S. meliloti bv. meliloti and S. medicae is maintained even though these bacteria can cooccur in sympatry on the same individual host plants.

Several genes encoding for different cytokines may play crucial roles in host susceptibility to Brucellosis, since the cytokine production capacity varies among individuals and depends on the cytokine gene polymorphism. The association of the cytokine gene polymorphisms with the development of Brucellosis was investigated in this study. DNA samples were obtained from a Turkish population of 40 patients with Brucellosis, and 50 healthy control subjects. All genotyping (IL-6, IL10, IFN-gamma, TGF-beta and TNF-alpha) experiments were performed using sequence-specific primers PCR (PCR-SSP). When compared to the healthy controls, the frequencies of high/intermediate producing genotypes of IL-10 and high producing genotype of IL-6 were significantly more common in the patient group. These results suggest that IL-10 and IL-6 gene polymorphisms may affect susceptibility to Brucellosis and increase risk of developing the disease. In order to confirm the biological significance of our results, further studies should be performed in larger population groups. (c) 2007 Published by Elsevier Ltd.

WOS: 000251002300010 PubMed ID: 16981218 The highly polymorphic minisatellites contain a variable number of tandemly repeated (VNTR) DNA sequences. They are extremely useful and informative markers to study genetic variation among human populations. We have analysed the allele frequency distribution at the highly polymorphic apolipoprotein B (Apo B) VNTR locus in order to obtain the population data for the Cukurova region in Turkey by using the polymerase chain reaction and polyacrylamide gel electrophoresis. We observed 10 different alleles and 21 genotypes in a sample of 100 unrelated individuals. The allele frequencies ranged from 0.01 to 0.4, with an expected heterozygosity of 0.69 for the Apo B locus. Alleles 37 (frequency = 0.4) and 35 (frequency = 0.17) were the most common in the Cukurova population. There was a significant deviation from the Hardy-Weinberg equilibrium (HWE) for genotype frequencies (chi(2) = 29.12; df = 1; p = 0.000). This study possesses novelty as it is the first DNA polymorphism study conducted at the Cukurova population using an Apo B minisatellite locus. Copyright (C) 2006 John Wiley & Sons, Ltd.

Accumulating evidence provides support for the idea that determination of UGT1A1 polymorphisms before irinotecan (CPT-11) treatment is clinically useful and important for predicting and avoiding related toxicities. In 2005, the irinotecan label was updated in the USA in order to provide pharmacogenetic information. A dose reduction of irinotecan should be considered for patients known to be homozygous for the UGT1A1*28 allele when administered in combination with other agents or as a single agent. The feasibility of genotyping for DNA polymorphisms prior to treatment depends on the availability of rapid, accurate and efficient genotyping methods. Genotyping of UGT1A1*28, *6 and *27 by the newly developed Invader UGT1A1 Molecular Assay agreed completely with the genotyping results obtained with established methods, and this molecular assay provides rapid detection of polymorphisms. This newly developed method for detecting UGT1A1 polymorphisms is feasible and has the potential to be widely used for rapid and accurate screening before irinotecan treatment.

Early X-ray diffraction patterns from oriented fibres indicated that DNA must have a simple, repetitious structure and encouraged some researchers, who were already convinced that DNA was the genetic material, to undertake more detailed diffraction analyses and speculative modelling. The pioneering experimental work by Wilkins in the Wheatstone Laboratory at King's College London in the late 1940s first inspired, and then was overtaken by, the conjectural modelling of Watson and Crick in the Cavendish Laboratory at Cambridge. Why this was allowed to happen is still something of a puzzle. Here, I explore the puzzle and expose a peculiar flaw in the details of the original Watson-Crick model that was left for Wilkins to resolve.

Advances in molecular biology are being made in the fields of science, medicine, and pharmacy. The majority of students graduating from pharmaceutical university departments will be required to have knowledge of molecular biology techniques. Although it is not difficult to perform DNA experiments in a laboratory, they involve a series of operations. Therefore it is difficult to include such experiments in the curriculum for students at our university because of safety concerns and the experimental equipment and time required. This paper introduces a convenient experiment on plant DNA polymorphism using a polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) method that we developed. This experiment enables each student to handle DNA safely. Total DNA is extracted from a piece of leaf derived from Aconitum carmichaeli or Aquilegia flabellate, the nuclear 5.8S rRNA region is amplified by PCR, and the PCR product is digested by restriction enzymes. Different polymorphisms in the plants can be visualized on electrophoregrams. The total time required for the experiments is 2 days (about 4 h per day). In the field of pharmacognosy, authentication of herbal medicine using genetic analysis is increasingly important. Plant DNA polymorphisms required the same knowledge and techniques as genetic analysis and are part of the course content in medicinal plant science. The PCR-RFLP experiment proposed here is a suitable method to acquire molecular biological knowledge and techniques.

RAPD technique was used in this study to detect DNA band variations between both normal and abnormal male of broiler chicken based on RAPD marker. DNA polymorphisms between normal and mutant birds were detected using fifteen oligonucleiotide primers. Using these primers, DNA band loss ranged from 25 to 75%. Data demonstrated that RAPD marker could detect DNA alterations. (African Journal of Biotechnology: 2003 2(6): 153-156)

To evaluate germplasm variability and to discriminate between accessions of 'Ladolia', an ancient olive variety of Cyprus, different accessions from a germplasm collection were screened with 11 selected oligonucleotide primers in RAPD-PCRs. A total of 49 polymorphic markers were scored, the combination of which resulted in 70 distinct electrophoretic patterns. Based on either unique or combined patterns, all accessions were identified. Seven genotype-specific markers were detected. One RAPD marker could distinguish accessions according to fruit size. Genetic similarities between accessions, estimated using the Dice similarity coefficient, indicated a high degree of genetic diversity among 'Ladolia' accessions. Genetic relationships were estimated by the unweighted pair-group method with arithmetic averaging (UPGMA) and principal components analysis (PCA). Three main groups of accessions were detected. The first group was generally composed of accessions with small-sized fruits and could be further divided into two subgroups. According to PCA, most accessions with medium- or large-sized fruits were clustered together. Our results support previous observations suggesting that 'Ladolia' is actually a highly variable mixture of genetically distinct landraces.Key words: DNA polymorphism, germplasm variability, RAPD markers, Olea europaea.

Cet article presente une etude du polymorphisme genetique des populations de la musaraigne commune, Sorex araneus, par IS-PCR, autrement dit par amplification de sequences flanquees de SINEs (short interspersed elements). Les SINEs sont des retroposons courts, separes par 100 a 1000 paires de bases. Deux SINEs ont ete utilise, l'element MIR, apparement present chez tous les mammiferes, et l'element SOR, recemment decrit chez les musaraignes du genre Sorex. Huit populations de Sorex araneus, appartenant au moins a 7 races chromosomiques, ont ete comparees entre elles et a des individus de deux especes apparentees, S. tundrensis et S. satunini. Tant les analyses NJ qu'UPGMA ont revele une differenciation entre les races chromosomiques Neroosa, Moscou et Seliger (Russie d'Europe), ainsi qu'entre deux populations non caryotypees de Siberie occidentale. Si les valeurs de bootstrap ne supportent que faiblement les groupements correspondant aux races chromosomiques de Russie d'Europe, il convient de noter qu'aucune musaraigne n'est mal classee par nos analyses, y compris celles qui proviennent de la zone de contact Moscou-Seliger. Le groupement des musaraignes de Siberie est en revanche fortement supporte. Au niveau interspecifique, nos analyses regroupent S. tundrensis avec S. araneus.

Detecting natural selection signals in Plasmodium parasites antigens might be used for identifying potential new vaccine candidates. Fifty-nine Plasmodium vivax-Sal-I genes encoding proteins having a potential role in invasion were used as query for identifying them in recent P. vivax strain genome sequences and two closely-related Plasmodium species. Several measures of DNA sequence variation were then calculated and selection signatures were detected by using different approaches. Our results may be used for determining which genes expressed during P. vivax merozoite stage could be prioritised for further population genetics or functional studies for designing a P. vivax vaccine which would avoid allele-specific immune responses. © 2015 Elsevier B.V.

Net blotch, caused by the phytopathogen Drechslera teres, is a common disease of barley (Hordeum vulgare L) and is responsible for large economic losses in some barley growing areas. In this study the morphology and genetic variability of eight D. teres isolates from different regions of the Brazilian state of Rio Grande do Sul were investigated. Colony morphology was studied on potato-dextrose-agar (PDA) and genetic variability investigated using the random amplified polymorphic-DNA (RAPD) technique. 27 commercially available primers were tested of which 16 were selected for use in polymorphic analysis due to their good resolution and reproducibility. Similarity coefficients were used to construct dendrograms based on colony morphology and RAPD data showing the relationship between the eight isolates studied. Colony morphology showed variability between the isolates while RAPD assays showed high similarity coefficients, but grouping of the isolates according to the geographic origins of the seeds from which they were isolated was not possible.

The phytopathogenic fungus Drechslera tritici-repentis causes tan spot, an important disease of wheat in the southern Brazilian state of Rio Grande do Sul. Twelve D. tritici-repentis isolates were obtained from wheat seeds from different locations in the state. Their colony morphology on potato dextrose agar and polymorphisms in genomic DNA by the random amplified polymorphic DNA (RAPD) method were investigated. For the RAPD method, 23 primers were tested of which nine were selected for use in the study of D. tritici-repentis polymorphisms. The degree of similarity between isolates was calculated using a simple matching coefficient and dendrograms constructed by the unweighted pair-group method with arithmetical averages (UPGMA). The morphological and RAPD analyses showed intraspecific polymorphisms within the isolates, but it was not possible to establish a relationship between these polymorphisms and the geographical regions from where the host seeds were collected.

Hemp (Cannabis sativa) is an important fiber crop, and native cultivars exist widely throughout China. In the present study, we analyzed the genetic diversity of 27 important Chinese native hemp cultivars, by using inter-simple sequence repeats (ISSR) and chromosome markers. We determined the following chromosome formulas: 2n = 20 = 14m + 6sm; 2n = 20 = 20m; 2n = 20 = 18m + 2sm; 2n = 20 = 16m + 4sm; and 2n = 20 = 12m + 8sm. The results of our ISSR analysis revealed the genetic relationships among the 27 cultivars; these relationships were analyzed by using the unweighted pair-group method based on DNA polymorphism. Our results revealed that all of the native cultivars showed considerable genetic diversity. At a genetic distance of 0.324, the 27 varieties could be classified into five categories; this grouping corresponded well with the chromosome formulas. All of the investigated hemp cultivars represent relatively primitive types; moreover, the genetic distances show a geographical distribution, with a small amount of regional hybridity.

Brazil is a major producer and exporter of beef, with a herd of approximately 210 million animals. For the meat industry, a reliable animal traceback from its origin to the consumer market is paramount. Of all available identification systems, DNA is the only one that survives the slaughterhouse and reaches the dish of the consumer. DNA polymorphisms are already used for cattle traceback, but primarily for the subspecies Bos taurus taurus. However, in Brazil, another subspecies, B. taurus indicus predominates. We describe here the development of a DNA traceback method designed primarily for B. taurus indicus (Zebu), without leaving B. taurus taurus aside. We used insertion/deletion (indel) polymorphisms, which have the advantage of being simple and easily automatable, since in most cases, the variable loci are biallelic. We studied 94 indels, with a difference of two or more base pairs, in DNA pools of 60 Zebu and 60 taurine animals. A set of 22 indels with heterozygosity greater than 0.3 were selected and used to construct two multiplex PCRs. On the basis of the allelic frequency of these indels, the probability of random match was calculated to be 1.12 x 10(-8) for B. taurus indicus and 1.60 x 10(-6) for B. taurus taurus. Moreover, we estimated that an analysis would cost less than US$15.00 per animal. Thus, this system (MULTINDELS-BOV) is perfectly suited for building large genetic databases and offering viable prospects of a national system for cattle traceback DNA in Brazil.

Twenty Pisolithus tinctorius isolates from different geographic locations and different hosts were characterized by the random amplified polymorphic DNA technique. Thirteen arbitrary primers generated 87 DNA fragments, all of them polymorphic. These data were used to calculate genetic distances among the isolates. The pairwise genetic distances ranged from 1 to 100%, with an average of 58.7%. Cluster analysis based on the amplified fragments grouped the isolates according to their host and geographical origins. Group I contained isolates collected in Brazil and group II those collected in the Northern Hemisphere. In addition to the diversity seen at the molecular level, the isolates also showed host specificity. Greenhouse experiments demonstrated that isolates from the Northern Hemisphere colonized mainly Pinus whereas isolates from Brazil colonized only Eucalyptus. The molecular data suggest that the Pisolithus tinctorius isolates analyzed belong to two distinct groups. The data also suggest new guidelines for future investigations on the taxonomy and systematic of this important fungus species. Furthermore, these results support future experiments aimed at the selection and development of improved isolates of P. tinctorius.

A total of 70 isolates of Escherichia coli O157:H7 isolated from beef samples were examined with respect to plasmid profiles and random amplified polymorphic DNA (RAPD) patterns. All isolates carried the 90 kb pO157 plasmid alone or in combination with other smaller plasmids. Using Gen1-50-02 (5`-CAATGCGTCT-3`), Gen1-50-09 (5`-AGAGGCGATG-3`) and Gen1-50-10 (5`-CCATTTACGC-3`) as primers, respectively, we obtained DNA polymorphisms which allowed us to discriminate the E. coli O157:H7 isolates into one, six and five RAPD patterns; providing bands ranging in size from 0.25 to 4.0 kb. Our results demonstrate that both plasmid profiling and RAPD-PCR fingerprinting methods are suitable tools for a fast and reliable molecular typing of E. coli O157:H7. The RAPD-PCR method is more sensitive with respect to the individualization of isolates and that RAPD-PCR assay could be a valuable technique for epidemiological studies.

We describe a novel gross deletion of the factor VIII gene in 5 related patients with severe hemophilia A. The deletion extends from intron 15 to at least 8.5 kb beyond the 3′ end of the gene (at least 95 kb of extension), and is associated with variable levels of FVIII inhibitor in 4 of the patients. The carrier detection in the family was based on the abnormal restriction pattern of the partially deleted gene.

Resume Les recherches de paternite reposent sur des analyses biologiques qui ont beaucoup evolue dans les vingt dernieres annees. Selon les periodes, les recherches de paternite ont ete fondees sur l'etude des groupes sanguins du globule rouge, l'analyse du polymorphisme des enzymes du globule rouge et des proteines seriques, la determination des antigenes HLA-A et -B, et le polymorphisme moleculaire de l'ADN sous ses differentes formes. Cette etude vise a comparer les differents types d'analyses; chacune sert de reference aux autres pour determiner: 1) le niveau du seuil acceptable pour les calculs de probabilite de paternite; 2) les regles d'exclusion en fonction des nouvelles technologies. Avec l'etude de 877 cas, les auteurs analysent la performance relative des differentes combinaisons de tests. Desormais les etudes basees sur l'amplification genique des micro-satellites demontrent l'efficacite de cette technique: il importe neanmoins d'identifier les limites de ces tests et de traiter les cas complexes dans lesquels des analyses complementaires sont necessaires, en particulier l'etude des VNTR. En effet, au-dela des analyses biologiques les plus performantes, il faut concevoir la recherche de paternite comme un ensemble au sein duquel l'etude biologique n'est qu'une etape d'un processus. © 1999 Elsevier, Paris

To detect DNA polymorphism among isolates of the rice blast fungus Magnaporthe grisea, the AFLP (amplified fragment length polymorphism) technique was adopted. When each primer combination of EcoRl-AC/MseI-CA, EcoRI-AA/MseI-CA or EcoRI-AT/MseI-CA was used, every M. grisea isolate produced more than 30 fragments. The number was approximately 10 to 20 times higher than that for the RAPD technique using 10-nucleotide random primers. Moreover, in every primer set, 5 isolates from independent clonal lineages were distinguishable from each other by fragments showing polymorphism. On the other hand, 5 isolates including an original isolate and its pathogenic mutants produced the same number and size of amplified fragments in all 6 primer sets (the above plus EcoRI-AC/MseI-CC, EcoRI-AA/MseI-CC and EcoRI-AT/MseI-CC). These results show the higher utility and reproducibility of the AFLP technique in elucidating the ecology of rice blast fungus.

Almost 10% of the human genome consists of DNA sequences that share homology with retroviruses. These sequences, which represent a stable component of the human genome (although some may retain the ability to transpose), remain poorly understood. We used degenerate primers specific to the two conserved regions (boxes 4 and 5) of the retroviral pol gene, common to all retroviruses, and PCR-amplified related sequences from individuals representing two distinct populations: Caucasians and Dogrib Indians. The large number of sequences that are reproducibly amplified represent numerous sites of retroviral integration in the human genome. In both populations studied, one of the two primers yielded a polymorphic band, present in ~30% of the samples, that has probably been present in the human genome since before the divergence of the two populations ~10 000 years ago. It was established that this polymorphism was due to priming-site differences and not to deletions. Further, this priming site is duplicated at two genomic sites (representing 341- and 343-bp fragments) with at least two alleles each. Such novel polymorphisms should provide useful markers and permit assessment of evolutionary mechanisms associated with retroviral-related genomic evolution.Key words: Dogrib Indian, evolution, human genome, polymorphism, retrovirus.