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Sample records for molecular genetic markers

  1. DNA marker applications to molecular genetics and genomics in tomato

    PubMed Central

    Shirasawa, Kenta; Hirakawa, Hideki

    2013-01-01

    Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

  2. Intelligent DNA-based molecular diagnostics using linked genetic markers

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  3. Genetic diversity analysis of common beans based on molecular markers.

    PubMed

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  4. Genetic diversity analysis of common beans based on molecular markers

    PubMed Central

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  5. Fingerprinting and Genetic Stability of Rubus Using Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA markers were used to identify raspberries and blackberries and to evaluate genetic stability of four cryopreserved Rubus accessions following 12 years of storage in liquid nitrogen. In the first study, 12 genomic Simple Sequence Repeat (SSR) markers and one Expressed Sequence Tag- (EST)-SSR wer...

  6. Indel Group in Genomes (IGG) Molecular Genetic Markers.

    PubMed

    Toal, Ted W; Burkart-Waco, Diana; Howell, Tyson; Ron, Mily; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger; Brady, Siobhan M

    2016-09-01

    Genetic markers are essential when developing or working with genetically variable populations. Indel Group in Genomes (IGG) markers are primer pairs that amplify single-locus sequences that differ in size for two or more alleles. They are attractive for their ease of use for rapid genotyping and their codominant nature. Here, we describe a heuristic algorithm that uses a k-mer-based approach to search two or more genome sequences to locate polymorphic regions suitable for designing candidate IGG marker primers. As input to the IGG pipeline software, the user provides genome sequences and the desired amplicon sizes and size differences. Primer sequences flanking polymorphic insertions/deletions are produced as output. IGG marker files for three sets of genomes, Solanum lycopersicum/Solanum pennellii, Arabidopsis (Arabidopsis thaliana) Columbia-0/Landsberg erecta-0 accessions, and S. lycopersicum/S. pennellii/Solanum tuberosum (three-way polymorphic) are included. PMID:27436831

  7. Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers

    PubMed Central

    Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J.; Iqbal, Nayyer

    2015-01-01

    Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program. PMID:26697053

  8. Molecular genetic variation in cultivated peanut cultivars and breeding lines revealed by highly informative SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts e...

  9. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    PubMed

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-09-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  10. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    PubMed Central

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  11. Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects.

    PubMed

    Chenuil, Anne; Anne, Chenuil

    2006-05-01

    The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique. PMID:16850217

  12. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    PubMed Central

    Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

    2011-01-01

    A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm. PMID:21637550

  13. Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

  14. Gastrointestinal stromal tumors: molecular markers and genetic subtypes.

    PubMed

    Barnett, Christine M; Corless, Christopher L; Heinrich, Michael C

    2013-10-01

    Mutation-activated signaling from the KIT and PDGFRA kinases has been successfully targeted in gastrointestinal stromal tumors (GISTs), with subtle differences between the mutations serving to refine prognosis and more precisely tailor therapy. There is a growing understanding of the molecular drivers of GISTs lacking mutations in KIT or PDGFRA, so called wild-type GISTs, further aiding in management decisions. This article provides an overview of all the known molecular subtypes of GIST and provides information about clinical correlates, treatment, and prognosis depending on the subtype. PMID:24093165

  15. Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

    PubMed Central

    Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

    2014-01-01

    Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

  16. Molecular markers and cotton genetic improvement: current status and future prospects.

    PubMed

    Malik, Waqas; Ashraf, Javaria; Iqbal, Muhammad Zaffar; Khan, Asif Ali; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Ahmad, Muhammad Qadir; Abbasi, Ghulam Hasan

    2014-01-01

    Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

  17. Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum.

    PubMed

    Kim, Hyun Jung; Jung, Jungsu; Kim, Myung-Shin; Lee, Je Min; Choi, Doil; Yeam, Inhwa

    2015-10-01

    Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%-40%) followed by trinucleotide (25%-31%), tetranucleotide (1.5%-1.9%), and pentanucleotide (0.3%-1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus. PMID:26501479

  18. Molecular profiling for genetic variability in Capsicum species based on ISSR and RAPD markers.

    PubMed

    Thul, Sanjog T; Darokar, Mahendra P; Shasany, Ajit K; Khanuja, Suman P S

    2012-06-01

    The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic cluster analyses of 27 RAPD and eight ISSR primers, respectively, revealed genetic similarities in the ranges of 23-88% and 11-96%. Principal component analysis of the pooled RAPD and ISSR data further supports the genetic similarity and groupings. Different species showed variations in relation to corolla shade of flower. C. annuum accessions formed a single cluster in the molecular analysis as maintaining their flower characteristic. C. chinense accession shared flower features with the accessions of C. frutescens and were found to be closer at genotypic level. C. luteum was found to be rather closer to C. baccatum complex, both phenotypically and genetically. The only accession of C. eximium presenting purple flowers falls apart from the groupings. The floral characteristics and the molecular markers are found to be useful toward the delineation of the species specificity in Capsicum collection and identification of genetic stock. PMID:21861246

  19. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers.

    PubMed

    Ammar, Megahed H; Alghamdi, Salem S; Migdadi, Hussein M; Khan, Muhammad A; El-Harty, Ehab H; Al-Faifi, Sulieman A

    2015-05-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010-11 and 2011-12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  20. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers

    PubMed Central

    Ammar, Megahed H.; Alghamdi, Salem S.; Migdadi, Hussein M.; Khan, Muhammad A.; El-Harty, Ehab H.; Al-Faifi, Sulieman A.

    2015-01-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010–11 and 2011–12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  1. Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

    PubMed Central

    2011-01-01

    Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine

  2. Population genetic structure of rare and endangered plants using molecular markers

    USGS Publications Warehouse

    Raji, Jennifer; Atkinson, Carter T.

    2013-01-01

    This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

  3. [Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].

    PubMed

    Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

    2011-01-01

    Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic

  4. Genetic approaches for studying myiasis-causing flies: molecular markers and mitochondrial genomics.

    PubMed

    de Azeredo-Espin, Ana Maria Lima; Lessinger, Ana Cláudia

    2006-01-01

    "Myiasis-causing flies" is a generic term that includes species from numerous dipteran families, mainly Calliphoridae and Oestridae, of which blowflies, screwworm flies and botflies are among the most important. This group of flies is characterized by the ability of their larvae to develop in animal flesh. When the host is a live vertebrate, such parasitism by dipterous larvae is known as primary myiasis. Myiasis-causing flies can be classified as saprophagous (free-living species), facultative or obligate parasites. Many of these flies are of great medical and veterinary importance in Brazil because of their role as key livestock insect-pests and vectors of pathogens, in addition to being considered important legal evidence in forensic entomology. The characterization of myiasis-causing flies using molecular markers to study mtDNA (by RFLP) and nuclear DNA (by RAPD and microsatellite) has been used to identify the evolutionary mechanisms responsible for specific patterns of genetic variability. These approaches have been successfully used to analyze the population structures of the New World screwworm fly Cochliomyia hominivorax and the botfly Dermatobia hominis. In this review, various aspects of the organization, evolution and potential applications of the mitochondrial genome of myiasis-causing flies in Brazil, and the analysis of nuclear markers in genetic studies of populations, are discussed. PMID:16502089

  5. [Markers for non-invasive molecular genetic diagnosis of oncourological diseases].

    PubMed

    Mikhaĭlenko, D S; Perepechin, D V; Apolikhin, O I; Efremov, G D; Sivkov, A V

    2014-01-01

    Currently, there is accumulated mass of data on the molecular-genetic disorders in prostate cancer (PCa), bladder cancer (BC) and renal cancer (RC). Tumor cells in these diseases are present in the urine sediment; their number is sufficient for molecular genetic analysis that makes possible the development of noninvasive diagnosis of oncourological diseases. A characteristic feature of PCa includes the overexpression of the PCA3 gene; assay kit Progensa™ to quantify such overexpression has been developed; approximately 50% of tumors express a TMPRSS2-ERG chimeric oncogene. Combined analysis of PCA3 and TMPRSS2-ERG allows to detect PCa with a diagnostic accuracy of 84%, which is significantly higher than that of prostate specific antigen test. As a potential markers of BC, there are somatic mutations in FGFR3, PIK3CA, TERT genes in urine sediment, which are found in this disease with a frequency of about 60, 30 and 50%, respectively. The basis of the test system for DNA diagnosis of BC in urine sediment may include a definition of a combination of mutations in these genes with microsatellite instability. Aberrant methylation of the 5'-regulatory regions of tumor suppressor genes, integrated in the panel, also is considered as a tool in the diagnosis of RC (VHL, RASSF1, RARB2, CDH1), PCa (GSTP1, PTGS2, LGALS3) and BC (RASSF1, APC, SFRP2) after standardization of panels of loci investigated, sample preparation methods, bisulfite conversion, and the design of primers and probes. Thus, a test systems for molecular genetic diagnosis of oncourological diseases in urine sediment are currently available or may be developed in the near future. PMID:25807773

  6. Genetic diversity analysis of Croton antisyphiliticus Mart. using AFLP molecular markers.

    PubMed

    Oliveira, T G; Pereira, A M S; Coppede, J S; França, S C; Ming, L C; Bertoni, B W

    2016-01-01

    Croton antisyphiliticus Mart. is a medicinal plant native to Cerrado vegetation in Brazil, and it is popularly used to treat urogenital tract infections. The objective of the present study was to assess the genetic variability of natural C. antisyphiliticus populations using AFLP molecular markers. Accessions were collected in the states of Minas Gerais, São Paulo, and Goiás. The genotyping of individuals was performed using a LI-COR® DNA Analyzer 4300. The variability within populations was found to be greater than the variability between them. The F(ST) value was 0.3830, which indicated that the populations were highly structured. A higher percentage of polymorphic loci (92.16%) and greater genetic diversity were found in the population accessions from Pratinha-MG. Gene flow was considered restricted (N(m) = 1.18), and there was no correlation between genetic and geographic distances. The populations of C. antisyphiliticus exhibited an island-model structure, which demonstrates the vulnerability of the species. PMID:26909989

  7. Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

    PubMed

    Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

    2014-01-01

    Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. PMID:24977711

  8. Genetic Rearrangements of Six Wheat–Agropyron cristatum 6P Addition Lines Revealed by Molecular Markers

    PubMed Central

    Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

    2014-01-01

    Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat–A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat–A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

  9. Genetic variation in a wild population of the 'sleep' passion fruit (Passiflora setacea) based on molecular markers.

    PubMed

    Cerqueira-Silva, C B M; Santos, E S L; Conceição, L D H C S; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

    2012-01-01

    Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs. PMID:22576831

  10. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

    PubMed Central

    Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

  11. Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers.

    PubMed

    Sun, R X; Zhang, C H; Zheng, Y Q; Zong, Y C; Yu, X D; Huang, P

    2016-01-01

    Thirty-four Styphnolobium japonicum varieties were analyzed using sequence-related amplified polymorphism (SRAP) markers, to investigate genetic variation and test the effectiveness of SRAP markers in DNA fingerprint establishment. Twelve primer pairs were selected from 120 primer combinations for their reproducibility and high polymorphism. We found a total of 430 amplified fragments, of which 415 fragments were considered polymorphic with an average of 34.58 polymorphic fragments for each primer combination. The percentage of polymorphic fragments was 96.60%, and four primer pairs showed 100% polymorphism. Moreover, simple matched coefficients ranged between 0.68 and 0.89, with an average of 0.785, indicating that the genetic variation among varieties was relatively low. This could be because of the narrow genetic basis of the selected breeding material. Based on the similarity coefficient value of 0.76, the varieties were divided into four major groups. In addition, abundant and clear SRAP fingerprints were obtained and could be used to establish DNA fingerprints. In the DNA fingerprints, each variety had its unique pattern that could be easily distinguished from others. The results demonstrated that 34 varieties of S. japonicum had a relatively narrow genetic variation. Hence, a broadening of the genetic basis of breeding material is necessary. We conclude that establishment of DNA fingerprint is feasible by means of SRAP markers. PMID:27173318

  12. Analysis of genetic diversity of Persea bombycina "Som" using RAPD-based molecular markers.

    PubMed

    Bhau, Brijmohan Singh; Medhi, Kalyani; Das, Ambrish P; Saikia, Siddhartha P; Neog, Kartik; Choudhury, S N

    2009-08-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships in Persea bombycina, a major tree species for golden silk (muga) production, was investigated using 48 genotypes from northeast India. Thirteen RAPD primer combinations generated 93 bands. On average, seven RAPD fragments were amplified per reaction. In a UPGMA phenetic dendrogram based on Jaccard's coefficient, the P. bombycina accessions showed a high level of genetic variation, as indicated by genetic similarity. The grouping in the phenogram was highly consistent, as indicated by high values of cophenetic correlation and high bootstrap values at the key nodes. The accessions were scattered on a plot derived from principal correspondence analysis. The study concluded that the high level of genetic diversity in the P. bombycina accessions may be attributed to the species' outcrossing nature. This study may be useful in identifying diverse genetic stocks of P. bombycina, which may then be conserved on a priority basis. PMID:19424786

  13. Assessing Cheatgrass (Bromus tectorum) genetic diversity and population structure using RAPD and microsatellite molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two molecular marker systems, random amplified polymorphic DNA (RAPD) and microsatellites, were used to evaluate population diversity and differentiation in four northern Nevada Bromus tectorum populations. We found 16 RAPD primers that yielded 165 strong repeatable bands. Of those bands, 60 (35.8%...

  14. Acrocomia emensis (Arecaceae) genetic structure and diversity using SSR molecular markers.

    PubMed

    Neiva, D S; Melo Júnior, A F; Oliveira, D A; Royo, V A; Brandão, M M; Menezes, E V

    2016-01-01

    Acrocomia emensis, popularly known as the creeping tucum, belongs to the family Arecaceae, and is an oilseed specie of the Brazilian Savannah. The expansion of agricultural activity has rapidly destroyed its natural habitat, leading to a decrease in its population size. Genetic studies can be used to investigate the genetic variability, and may assist with the charting future conservation strategies. In this study the genetic diversity and structure of 150 individuals sampled in three locations in Minas Gerais were analysed, based on the transferability of six microsatellite markers, previously developed for A. aculeata. The results indicate that the populations studied have low levels of genetic variability (Ho = 0.148) and high, positive and significant inbreeding coefficient, indicating an excess of homozygotes. The average heterozygosity within the population (Hs = 0.700) accounted for 95.03% of the total genetic diversity, indicating that there is greater variability within population than between them, consistent with low genetic differentiation between population (GST = 0.046). Bayesian analysis identified three distinct groups; however, populations shared large numbers of alleles, which can be explained by the reduced distance between populations. These results reveal the need to implement genetic conservation programs for the maintenance of this species and to prioritize population from Bonito and Brasília, which showed the lowest values of genetic diversity. PMID:27050985

  15. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data

    PubMed Central

    Edwards, J. D.; Baldo, A. M.; Mueller, L. A.

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

  16. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.

    PubMed

    Edwards, J D; Baldo, A M; Mueller, L A

    2016-01-01

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining datasets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data and molecular marker fragment size data. Rice research has benefited from early adoption and extensive use of simple sequence repeat (SSR) markers; however, the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm and potentially user curated phenotypic interpretations as a community resource for genetic discovery and breeding in rice. PMID:27515824

  17. Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review.

    PubMed

    Chen, Chih-Ping; Chen, Ming; Su, Yi-Ning; Huang, Jian-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chang, Shun-Ping; Chen, Yu-Ting; Lee, Chen-Chi; Chen, Li-Feng; Pan, Chen-Wen; Wang, Wayseen

    2013-10-15

    We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case. PMID:23933412

  18. The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review.

    PubMed

    Damasceno, L S; Leitão, T M J S; Taylor, M L; Muniz, M M; Zancopé-Oliveira, R M

    2016-01-01

    Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations. PMID:26589702

  19. Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker

    NASA Astrophysics Data System (ADS)

    Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

    2008-01-01

    Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

  20. Genetic diversity of Capsicum chinensis (Solanaceae) accessions based on molecular markers and morphological and agronomic traits.

    PubMed

    Finger, F L; Lannes, S D; Schuelter, A R; Doege, J; Comerlato, A P; Gonçalves, L S A; Ferreira, F R A; Clovis, L R; Scapim, C A

    2010-01-01

    We estimated the genetic diversity of 49 accessions of the hot pepper species Capsicum chinensis through analyses of 12 physicochemical traits of the fruit, eight multi-categorical variables, and with 32 RAPD primers. Data from the physicochemical traits were submitted to analysis of variance to estimate the genetic parameters, and their means were clustered by the Scott-Knott test. The matrices from the individual and combined distance were estimated by multivariate analyses before applying Tocher's optimization method. All physicochemical traits were examined for genetic variability by analysis of variance. The responses of these traits showed more contribution from genetic than from environmental factors, except the percentage of dry biomass, content of soluble solids and vitamin C level. Total capsaicin had the greatest genetic divergence. Nine clusters were formed from the quantitative data based on the generalized distance of Mahalanobis, using Tocher's method; four were formed from the multi-categorical data using the Cole-Rodgers coefficient, and eight were formed from the molecular data using the Nei and Li coefficient. The accessions were distributed into 14 groups using Tocher's method, and no significant correlation between pungency and origin was detected. Uni- and multivariate analyses permitted the identification of marked genetic diversity and fruit attributes capable of being improved through breeding programs. PMID:20882481

  1. Genetic profiling of the Plasmodium falciparum population using antigenic molecular markers.

    PubMed

    Gupta, Purva; Singh, Ruchi; Khan, Haris; Raza, Adil; Yadavendu, Veena; Bhatt, R M; Singh, Vineeta

    2014-01-01

    About 50% of malaria infections in India are attributed to Plasmodium falciparum but relatively little is known about the genetic structure of the parasite populations. The molecular genotyping of the parasite populations by merozoite surface protein (msp1 and msp2) and glutamate-rich protein (glurp) genes identifies the existing parasite population in the regions which help in understanding the molecular mechanisms involved in the parasite's drive for survival. This study reveals the genetic profile of the parasite population in selected regions across the country with varying degree of endemicity among them. We also report the prevalence of Pfcrt mutations in this parasite population to evaluate the pattern of drug resistance development in them. PMID:25405214

  2. Soybean Molecular Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A history of the various DNA marker types used in the assessment of molecular genetic diversity in soybean [Glycine max (L.) Merr.] is followed by a description of a number of studies on the assessment of genetic diversity. These studies include a review of reports on 1) the quantification and comp...

  3. Genetic diversity in Tunisian populations of faba bean (Vicia faba L.) based on morphological traits and molecular markers.

    PubMed

    Backouchi, I Z; Aouida, M; Khemiri, N; Jebara, M

    2015-01-01

    Genetic diversity within Vicia faba L. is key to the genetic improvement of this important species. In this study, morphological traits and RAPD molecular markers were used to assess the levels of polymorphism across 12 Tunisian populations, three major and nine minor from different locations. Analysis of morphological traits indicated that the three major populations showed significant differences and the nine minor populations exhibited considerable variation for most traits. The grain yield of the Alia population could be increased by inoculation. Of the seven primers tested, it was clear that the Cs12 primer would be recommend for genetic diversity analysis of V. faba.Within population genetic diversity exhibited 94% of total diversity. Intra-population genetic diversity (HS) was 0.16, which was clearly higher than between population genetic diversity (DST = 0.06) UPG-MA showed a high level of genetic variation between major and minor populations of V. faba L. Particularly the minor populations showed a high level of diversity and was divided into two subclusters. Ltaifia was separated from the other populations. In addition to a high grain yield, these populations showed the lowest Nei and Shannon indices (H = 0.08 and I = 0.13) justifying their homogeneity. For these reasons, these cultivars can be considered a selected population. However, the Takelsa population showed the highest Nei and Shannon indices (H = 0.13 and I = 0.21), indicating that this population was the most heterogeneous, which is interesting for breeding programs. PMID:26214437

  4. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

    PubMed Central

    2013-01-01

    Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different

  5. Identification of Single-Copy Orthologous Genes between Physalis and Solanum lycopersicum and Analysis of Genetic Diversity in Physalis Using Molecular Markers

    PubMed Central

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei’s genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

  6. Identification of single-copy orthologous genes between Physalis and Solanum lycopersicum and analysis of genetic diversity in Physalis using molecular markers.

    PubMed

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei's genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

  7. Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the Genus Linum

    PubMed Central

    Melnikova, Nataliya V.; Kudryavtseva, Anna V.; Zelenin, Alexander V.; Lakunina, Valentina A.; Yurkevich, Olga Yu.; Speranskaya, Anna S.; Dmitriev, Alexey A.; Krinitsina, Anastasia A.; Belenikin, Maxim S.; Uroshlev, Leonid A.; Snezhkina, Anastasiya V.; Sadritdinova, Asiya F.; Koroban, Nadezda V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Guzenko, Elena V.; Lemesh, Valentina A.; Savilova, Anastasya M.; Rachinskaia, Olga A.; Kishlyan, Natalya V.; Rozhmina, Tatiana A.; Bolsheva, Nadezhda L.; Muravenko, Olga V.

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  8. Retrotransposon-based molecular markers for analysis of genetic diversity within the Genus Linum.

    PubMed

    Melnikova, Nataliya V; Kudryavtseva, Anna V; Zelenin, Alexander V; Lakunina, Valentina A; Yurkevich, Olga Yu; Speranskaya, Anna S; Dmitriev, Alexey A; Krinitsina, Anastasia A; Belenikin, Maxim S; Uroshlev, Leonid A; Snezhkina, Anastasiya V; Sadritdinova, Asiya F; Koroban, Nadezda V; Amosova, Alexandra V; Samatadze, Tatiana E; Guzenko, Elena V; Lemesh, Valentina A; Savilova, Anastasya M; Rachinskaia, Olga A; Kishlyan, Natalya V; Rozhmina, Tatiana A; Bolsheva, Nadezhda L; Muravenko, Olga V

    2014-01-01

    SSAP method was used to study the genetic diversity of 22 Linum species from sections Linum, Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposons FL9 and FL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism of Fl1a, Fl1b, and Cassandra insertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation of Linum species. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sections Dasylinum, Stellerolinum, Adenolinum, and Linum. All species of sect. Adenolinum clustered apart from species of sect. Linum. The data confirmed the accuracy of the separation in these sections. Members of section Linum are not as closely related as members of other sections, so taxonomic revision of this section is desirable. L. usitatissimum accessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization of Cassandra retrotransposon in Linum species was determined. PMID:25243121

  9. Molecular markers in colorectal cancer: genetic bases for a customised treatment.

    PubMed

    Casado, E; De Castro, J; Belda-Iniesta, C; Cejas, P; Feliu, J; Sereno, M; González-Barón, M

    2007-09-01

    Colorectal cancer (CRC) is the second leading cause of cancer death in Western countries. CRC treatment is based on the employment of three chemotherapeutic drugs, including 5-fluorouracil, oxaliplatin and irinotecan, and the use of recently incorporated targeted agents directed to vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR). The approval of these biologicals and of others to come holds great promise for the improvement of patient outcome. The molecular bases for this lethal disease have been extensively investigated, laying the foundations for a rational and customised treatment approach, expanding the therapeutic index of current drugs and easing the incorporation of new molecules. Individual markers have been mainly investigated based on drug targets and metabolism. Also, the increasing availability of highthroughput technologies has prompted the opportunity for blind studies capable of screening new markers and of identifying the specific oncogenic pathways responsible for drug resistance in a given patient. An updated review of the field is presented in this article. PMID:17921101

  10. Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers.

    PubMed

    Sharafi, Ata Allah; Abkenar, Asad Asadi; Sharafi, Ali; Masaeli, Mohammad

    2016-01-01

    Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime "witches' broom disease". PMID:27186022

  11. Molecular Assay for Detection of Genetic Markers Associated with Decreased Susceptibility to Cephalosporins in Neisseria gonorrhoeae

    PubMed Central

    Peterson, S. W.; Martin, I.; Demczuk, W.; Bharat, A.; Hoang, L.; Wylie, J.; Allen, V.; Lefebvre, B.; Tyrrell, G.; Horsman, G.; Haldane, D.; Garceau, R.; Wong, T.

    2015-01-01

    The incidence of antimicrobial-resistant Neisseria gonorrhoeae continues to rise in Canada; however, antimicrobial resistance data are lacking for approximately 70% of gonorrhea infections that are diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs). We developed a molecular assay for surveillance use to detect mutations in genes associated with decreased susceptibility to cephalosporins that can be applied to both culture isolates and clinical samples. Real-time PCR assays were developed to detect single nucleotide polymorphisms (SNPs) in ponA, mtrR, penA, porB, and one N. gonorrhoeae-specific marker (porA). We tested the real-time PCR assay with 252 gonococcal isolates, 50 nongonococcal isolates, 24 N. gonorrhoeae-negative NAAT specimens, and 34 N. gonorrhoeae-positive NAAT specimens. Twenty-four of the N. gonorrhoeae-positive NAAT specimens had matched culture isolates. Assay results were confirmed by comparison with whole-genome sequencing data. For 252 N. gonorrhoeae strains, the agreement between the DNA sequence and real-time PCR was 100% for porA, ponA, and penA, 99.6% for mtrR, and 95.2% for porB. The presence of ≥2 SNPs correlated with decreased susceptibility to ceftriaxone (sensitivities of >98%) and cefixime (sensitivities of >96%). Of 24 NAAT specimens with matched cultures, the agreement between the DNA sequence and real-time PCR was 100% for porB, 95.8% for ponA and mtrR, and 91.7% for penA. We demonstrated the utility of a real-time PCR assay for sensitive detection of known markers for the decreased susceptibility to cephalosporins in N. gonorrhoeae. Preliminary results with clinical NAAT specimens were also promising, as they correlated well with bacterial culture results. PMID:25878350

  12. Molecular Assay for Detection of Genetic Markers Associated with Decreased Susceptibility to Cephalosporins in Neisseria gonorrhoeae.

    PubMed

    Peterson, S W; Martin, I; Demczuk, W; Bharat, A; Hoang, L; Wylie, J; Allen, V; Lefebvre, B; Tyrrell, G; Horsman, G; Haldane, D; Garceau, R; Wong, T; Mulvey, M R

    2015-07-01

    The incidence of antimicrobial-resistant Neisseria gonorrhoeae continues to rise in Canada; however, antimicrobial resistance data are lacking for approximately 70% of gonorrhea infections that are diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs). We developed a molecular assay for surveillance use to detect mutations in genes associated with decreased susceptibility to cephalosporins that can be applied to both culture isolates and clinical samples. Real-time PCR assays were developed to detect single nucleotide polymorphisms (SNPs) in ponA, mtrR, penA, porB, and one N. gonorrhoeae-specific marker (porA). We tested the real-time PCR assay with 252 gonococcal isolates, 50 nongonococcal isolates, 24 N. gonorrhoeae-negative NAAT specimens, and 34 N. gonorrhoeae-positive NAAT specimens. Twenty-four of the N. gonorrhoeae-positive NAAT specimens had matched culture isolates. Assay results were confirmed by comparison with whole-genome sequencing data. For 252 N. gonorrhoeae strains, the agreement between the DNA sequence and real-time PCR was 100% for porA, ponA, and penA, 99.6% for mtrR, and 95.2% for porB. The presence of ≥2 SNPs correlated with decreased susceptibility to ceftriaxone (sensitivities of >98%) and cefixime (sensitivities of >96%). Of 24 NAAT specimens with matched cultures, the agreement between the DNA sequence and real-time PCR was 100% for porB, 95.8% for ponA and mtrR, and 91.7% for penA. We demonstrated the utility of a real-time PCR assay for sensitive detection of known markers for the decreased susceptibility to cephalosporins in N. gonorrhoeae. Preliminary results with clinical NAAT specimens were also promising, as they correlated well with bacterial culture results. PMID:25878350

  13. Genetic identification of bucktooth parrotfish Sparisoma radians (Valenciennes, 1840) (Labridae, Scarinae) by chromosomal and molecular markers

    PubMed Central

    Paim, Fabilene Gomes; Brandão, José Henrique Souza Galdino; Sampaio, Iracilda; de Mello Affonso, Paulo Roberto Antunes; Diniz, Débora

    2014-01-01

    Parrotfishes (Labridae, Scarinae) comprise a large marine fish group of difficult identification, particularly during juvenile phase when the typical morphology and coloration of adults are absent. Therefore, the goal of this study was to test cytogenetic markers and DNA barcoding in the identification of bucktooth parrtotfish Sparisoma radians from the northeastern coast of Brazil. Sequencing of cytochrome c oxidase subunit I (COI) confirmed all studied samples as S. radians, and all showed high similarity (99–100%) with Caribbean populations. The karyotype of this species was divergent from most marine Perciformes, being composed of 2n = 46 chromosomes. These consisted of a large number of metacentric and submetacentric pairs with small amounts of heterochromatin and GC-rich single nucleolar organizer regions (NORs) not syntenic to 5S rDNA clusters. These are the first data about DNA barcoding in parrotfish from the Brazilian province and the first refined chromosomal analysis in Scarinae, providing useful data to a reliable genetic identification of S. radians. PMID:25505839

  14. Development of molecular genetic markers from a cDNA subtraction library of Frosty Pod inoculated cacao

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have been employing a candidate gene approach to identify molecular markers associated with disease resistance in Theobroma cacao. Candidate genes can be turned into molecular markers using single strand conformation polymorphism (SSCP) analysis. As a novel approach to identifying genes associa...

  15. Assessment of genetic relationship in Persea spp by traditional molecular markers.

    PubMed

    Reyes-Alemán, J C; Valadez-Moctezuma, E; Barrientos-Priego, A F

    2016-01-01

    Currently, the reclassification of the genus Persea is under discussion with molecular techniques for DNA analysis representing an alternative for inter- and intra-specific differentiation. In the present study, the traditional random-amplified polymorphic DNA (RAPD) and the inter simple sequence repeat (ISSR) markers were used to determine the genomic relationship of different species and hybrids representative of the subgenera Eriodaphne and Persea in a population conserved in a germplasm bank. The data were analyzed statistically using multivariate methods. In the RAPD analysis, a total of 190 polymorphic bands were produced, with an average of 23.7 bands per primer, the percentage contribution of each primer was from 7.66 to 19.63; the polymorphic information content (PIC) ranged from 0.23 to 0.45, with an average of 0.35. In the ISSR analysis, a total of 111 polymorphic bands were considered, with an average of 18.5 bands per primer, the percentage contribution of each was from 11.83 to 19.57; the PIC ranged from 0.35 to 0.48, with an average of 0.42. The phenograms obtained in each technique showed the relationship among the accessions through the clusters formed. In general, both the techniques grouped representatives of the Persea americana races (P. americana var. drymifolia, P. americana var. guatemalensis, and P. americana var. americana). However, it was not possible to separate the species of Persea used as reference into independent clades. In addition, they tended to separate the representatives of subgenera Eriodaphne and Persea. PMID:27173181

  16. Genetic variability of oil palm parental genotypes and performance of its' progenies as revealed by molecular markers and quantitative traits.

    PubMed

    Abdullah, Norziha; Rafii Yusop, Mohd; Ithnin, Maizura; Saleh, Ghizan; Latif, M A

    2011-04-01

    Studies were conducted to assess the genetic relationships between the parental palms (dura and pisifera) and performance of their progenies based on nine microsatellite markers and 29 quantitative traits. Correlation analyses between genetic distances and hybrids performance were estimated. The coefficients of correlation values of genetic distances with hybrid performance were non-significant, except for mean nut weight and leaf number. However, the correlation coefficient of genetic distances with these characters was low to be used as predicted value. These results indicated that genetic distances based on the microsatellite markers may not be useful for predicting hybrid performance. The genetic distance analysis using UPGMA clustering system generated 5 genetic clusters with coefficient of 1.26 based on quantitative traits of progenies. The genotypes, DP16, DP14, DP4, DP13, DP12, DP15, DP8, DP1 and DP2 belonging to distant clusters and greater genetic distances could be selected for further breeding programs. PMID:21513898

  17. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An ultra-dense consensus (UDC) genetic map of tetraploid cotton was constructed using six high-density component maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cut...

  18. Molecular phylogeography of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae) and genetic relationships with congeners using cytochrome b gene marker.

    PubMed

    Yong, Hoi-Sen; Eamsobhana, Praphathip; Song, Sze-Looi; Prasartvit, Anchana; Lim, Phaik-Eem

    2015-08-01

    Angiostrongylus cantonensis is an important emerging zoonotic parasite causing human eosinophilic meningitis (or meningoencephalitis) in many parts of the world. To-date there is only a single study using mitochondrial cytochrome b (CYTB) gene to determine its genetic structure in eight geographical localities in Thailand. The present study examined the molecular phylogeography of this rat lungworm and its phylogenetic relationship with congeners using CYTB gene marker. A total of 15 CYTB haplotypes was found in 37 sequences from 14 geographical localities (covering north, west, east, central and south regions) in Thailand. These CYTB haplotypes were distinct from those of A. cantonensis for China and Hawaii. In Thailand, some CYTB haplotypes appeared to be confined to specific geographical localities. The partial CYTB DNA nucleotide sequences separated unequivocally the A. cantonensis isolates of Thailand, China and Hawaii as well as the congeners Angiostrongylus malaysiensis, A. costaricensis and Angiostrongylus vasorum, with A. malaysiensis grouped with A. cantonensis and A. costaricensis grouped with A. vasorum. Likewise the congeners of Metastrongylus and Onchocerca genera could also be clearly differentiated. The present study added two new definitive hosts (Bandicota savilei and Rattus losea) and three new localities (Mae Hong Son in the north, Tak in the west, and Phang Nga in the south) for A. malaysiensis in Thailand, indicating its wide occurrence in the country. Three CYTB haplotypes were found in the Thailand samples of A. malaysiensis. In addition to differentiation of congeners, CYTB gene marker could be used for determining the genetic diversity of a given population/taxon. PMID:25930187

  19. Using molecular markers to analyze genetic diversity in forage, turf, and biofuel crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ex situ conservation of plant genetic resources has received worldwide attention for many years. Agriculture in the USA, as well as in many other countries, is primarily based on crop plants native to other parts of the world. Improvement of major crops for yield, quality, and resistance to bio...

  20. Application of Molecular Genetics and Transformation to Barley Improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter of the new barley monograph summarizes current applications of molecular genetics and transformation to barley improvement. The chapter describes recent applications of molecular markers including association genetics, QTL mapping and marker assisted selection in barley programs, and in...

  1. Genetic markers as instrumental variables

    PubMed Central

    von Hinke, Stephanie; Davey Smith, George; Lawlor, Debbie A.; Propper, Carol; Windmeijer, Frank

    2016-01-01

    The use of genetic markers as instrumental variables (IV) is receiving increasing attention from economists, statisticians, epidemiologists and social scientists. Although IV is commonly used in economics, the appropriate conditions for the use of genetic variants as instruments have not been well defined. The increasing availability of biomedical data, however, makes understanding of these conditions crucial to the successful use of genotypes as instruments. We combine the econometric IV literature with that from genetic epidemiology, and discuss the biological conditions and IV assumptions within the statistical potential outcomes framework. We review this in the context of two illustrative applications. PMID:26614692

  2. Analysis of genetic stability through intersimple sequence repeats molecular markers in micropropagated plantlets of Anoectochilus formosanus Hayata, a medicinal plant.

    PubMed

    Zhang, Fusheng; Lv, Yali; Dong, Hailing; Guo, Shunxing

    2010-01-01

    Anoectochilus formosanus HAYATA, commonly known as "Jewel Orchids," which has been used as Chinese folk medicines, is being subjected to a huge crisis, whose wild resources have gradually become more and more scarce. Hence, micropropagation protocol by axillary branching established for A. formosanus was employed for large-scale commercial production. In this study, due to the somaclonal variation and on the basis of some virtue of intersimple sequence repeats (ISSR) analysis, we firstly utilized the ISSR primers to investigate the genetic stability of A. formosanus propagated in vitro for a period of more than 5 years. Among the total 100 bands amplified by 17 ISSR markers, 77 bands were distributed in size from 500 bp to 1.5 kbp, while only 5 bands were beyond 1.8 kbp in size. Meanwhile, according to the cluster analysis, genetic similarity was more than 94% and the polymorphism rate was only 2.76% among the total 1810 scorable bands. All results demonstrate A. formosanus, multiplied by axillary branching, maintained high genetic fidelity even after a period of more than 5 years under in vitro propagation with only a low risk of genetic instability. The results from this study provide an important basis for giving evidence of genetic stability of A. formosanus before micropropagation for large-scale commercial production. PMID:20190397

  3. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers.

    PubMed

    Medhi, K; Sarmah, D K; Deka, M; Bhau, B S

    2014-12-01

    The genetic diversity in Zanthoxylum species viz.  Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454

  4. Assessment of genetic diversity and variation of Robinia pseudoacacia seeds induced by short-term spaceflight based on two molecular marker systems and morphological traits.

    PubMed

    Yuan, C Q; Li, Y F; Sun, P; Sun, Y H; Zhang, G J; Yang, M S; Zhang, Y Y; Li, Y; Wang, L

    2012-01-01

    The black locust (Robinia pseudoacacia) is a forest legume that is highly valued as a honey plant and for its wood. We explored the effect of short-term spaceflight on development of R. pseudoacacia seedlings derived from seeds that endured a 15-day flight; the genetic diversity and variation of plants sampled from space-mutagenized seeds were compared to plants from parallel ground-based control seeds using molecular markers and morphological traits. In the morphology analysis, the space-mutagenized group had apparent variation compared with the control group in morphological traits, including plant height, basal diameter, number of branches, branch stipular thorn length, branch stipular thorn middle width, leaflet vertex angle, and tippy leaf vertex angle. Simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) molecular marker analyses showed a slightly higher levels of genetic diversity in the space-mutagenized group compared to the control group. In the SRAP analysis, the space-mutagenized group had 115 polymorphic bands vs 98 in the controls; 91.27% polymorphic loci vs 77.78% in the controls; 1.9127 ± 0.2834 alleles vs 1.7778 ± 0.4174 in the controls; Nei's genetic diversity (h) was 0.2930 ± 0.1631 vs 0.2688 ± 0.1862 in the controls, and the Shannon's information index (I) was 0.4452 ± 0.2177 vs 0.4031 ± 0.2596 in the controls. The number of alleles was significantly higher in the space-mutagenized group. In the SSR analysis, the space-mutagenized group also had more polymorphic bands (51 vs 46), a greater percentage of polymorphic loci (89.47% vs 80.70%); h was also higher (0.2534 ± 0.1533 vs 0.2240 ± 0.1743), as was I (0.3980 ± 0.2069 vs 0.3501 ± 0.2412). These results demonstrated that the range of genetic variation in the populations of R. pseudoacacia increased after spaceflight. It also suggested that the SSR and SRAP markers are effective markers for studying mutations and genetic diversity in R. pseudoacacia. The data

  5. Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers (2010) Fungal Genetics and Biology

    SciTech Connect

    Murat, Claude; Riccioni, C; Belfiori, B; Cichocki, N; Labbe, Jessy L; Morin, Emmanuelle; Tisserant, Emilie; Paolocci, F; Rubini, A; Martin, Francis

    2011-01-01

    The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexanucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system.

  6. Genetic markers on chromosome 7.

    PubMed Central

    Tsui, L C

    1988-01-01

    Chromosome 7 is frequently associated with chromosome aberrations, rearrangements, and deletions. It also contains many important genes, gene families, and disease loci. This brief review attempts to summarise these and other interesting aspects of chromosome 7. With the rapid accumulation of cloned genes and polymorphic DNA fragments, this chromosome has become an excellent substrate for molecular genetic studies. PMID:3290488

  7. Molecular Imaging in Genetic Medicine

    PubMed Central

    Jacob, Ayden; Van Gestel, Frederick; Yaghoubi, Shahriar

    2016-01-01

    The field of biomedical imaging has made significant advances in recent times. This includes extremely high-resolution anatomic imaging and functional imaging of physiologic and pathologic processes as well as novel modalities in optical imaging to evaluate molecular features within the cellular environment. The latter has made it possible to image phenotypic markers of various genotypes that are implicated in human development, behavior, and disease. This article discusses the role of molecular imaging in genetic and precision medicine.  PMID:27186447

  8. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    PubMed

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application. PMID:24354624

  9. A Preliminary Study of Genetic Variation in Populations of Monstera adansonii var. klotzschiana (Araceae) from North-East Brazil, Estimated with AFLP Molecular Markers

    PubMed Central

    Andrade, I. M.; Mayo, S. J.; van den Berg, C.; Fay, M. F.; Chester, M.; Lexer, C.; Kirkup, D.

    2007-01-01

    Background and Aims This study sought genetic evidence of long-term isolation in populations of Monstera adansonii var. klotzschiana (Araceae), a herbaceous, probably outbreeding, humid forest hemi-epiphyte, in the brejo forests of Ceará (north-east Brazil), and clarification of their relationships with populations in Amazonia and the Atlantic forest of Brazil. Methods Within-population genetic diversity and between-population dissimilarity were estimated using AFLP molecular markers in 75 individuals from eight populations located in Ceará, the Brazilian Atlantic Forest and Amazonia. Key Results The populations showed a clinal pattern of weak genetic differentiation over a large geographical region (FST = 0·1896). A strong correlation between genetic and geographical distance (Mantel test: r = 0·6903, P = 0·002) suggests a historical pattern of isolation by distance. Genetic structure analysis revealed at least two distinct gene pools in the data. The two isolated Ceará populations are significantly different from each other (pairwise ΦPT = 0·137, P = 0·003) and as diverse (Nei's gene diversity, average He = 0·1832, 0·1706) as those in the Atlantic and Amazon forest regions. The population in southern Brazil is less diverse (Nei's gene diversity, average He = 0·127) than the rest. The Ceará populations are related to those of the Atlantic forest rather than those from Amazonia (AMOVA, among-groups variation = 11·95 %, P = 0·037). Conclusions The gene pools detected within an overall pattern of clinal variation suggest distinct episodes of gene flow, possibly correlated with past humid forest expansions. The Ceará populations show no evidence of erosion of genetic diversity, although this was expected because of their isolation. Their genetic differentiation and relatively high diversity reinforce the importance of conserving the endangered brejo forests. PMID:17823112

  10. Introductory molecular genetics

    SciTech Connect

    Edwards-Moulds, J.

    1986-01-01

    This book begins with an overview of the current principles of genetics and molecular genetics. Over this foundation, it adds detailed and specialized information: a description of the translation, transcription, expression and regulation of DNA and RNA; a description of the manipulation of genetic material via promoters, enhancers, and gene splicing; and a description of cloning techniques, especially those for blood group genes. The last chapter looks to the impact of molecular genetics on transfusion medicine.

  11. Estimation of genetic diversity using SSR markers in sunflower

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sunflower is a major oilseed crop in central Asia, but little is known of the molecular diversity among collections of sunflower from Pakistan region. This paper described inherent genetic relationships among sunflower collections using Simple Sequence Repeat molecular markers. Results should help...

  12. Use of molecular markers to study the effects of environmental impacts on genetic diversity in brown bullhead (Ameirus nebulosus) populations.

    PubMed

    Silbiger, R N; Leonard, A C; Dimsoski, P; Foré, S; Guttman, S I; Roth, A C; Gordon, D A; Wessendarp, T; Toth, G P; Smith, M K

    2001-11-01

    Conservation biology needs sound biological information in order to maintain biological diversity in the face of the current rate of loss. An important component of the information needed is the level of genetic diversity within and between populations, especially for those species faced with exposure to environmental stressors. We applied multilocus DNA profile analysis (highly variable number tandem repeats [HVNTR] and randomly amplified polymorphic DNA [RAPD] techniques) and allozyme analysis to test whether individuals from historically degraded sites display levels of genetic diversity different from individuals taken from reference sites. Four Lake Erie tributaries, two impacted and two reference sites, were the sources of brown bullhead (Ameiurus nebulosus) samples. Pairwise comparison of the sampled populations demonstrated an association of decreased genetic diversity with exposure of brown bullhead to stressors using both RAPD and HVNTR analysis. PMID:11699785

  13. Genetic identity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Indonesia is the 3rd largest cocoa producing countries in the world and 71% of its production is from Sulawesi Island. Knowledge about the genetic background of farmer selections is highly important for effective identification and rational deployment of superior cacao clones in farmers’ fields. Mor...

  14. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining data sets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data, and mol...

  15. Molecular genetic evidence for the human settlement of the Pacific: analysis of mitochondrial DNA, Y chromosome and HLA markers.

    PubMed Central

    Hagelberg, E; Kayser, M; Nagy, M; Roewer, L; Zimdahl, H; Krawczak, M; Lió, P; Schiefenhövel, W

    1999-01-01

    Present-day Pacific islanders are thought to be the descendants of Neolithic agriculturalists who expanded from island South-east Asia several thousand years ago. They speak languages belonging to the Austronesian language family, spoken today in an area spanning half of the circumference of the world, from Madagascar to Easter Island, and from Taiwan to New Zealand. To investigate the genetic affinities of the Austronesian-speaking peoples, we analysed mitochondrial DNA, HLA and Y-chromosome polymorphisms in individuals from eight geographical locations in Asia and the Pacific (China, Taiwan, Java, New Guinea highlands, New Guinea coast, Trobriand Islands, New Britain and Western Samoa). Our results show that the demographic expansion of the Austronesians has left a genetic footprint. However, there is no simple correlation between languages and genes in the Pacific. PMID:10091254

  16. Analysis of genetic diversity in earthworms using DNA markers.

    PubMed

    Sharma, Anshul; Sonah, Humira; Deshmukh, Rupesh K; Gupta, Navneet K; Singh, Nagendra K; Sharma, Tilak R

    2011-01-01

    Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals. PMID:21186943

  17. Genetic Structure of Earthworm Populations at a Regional Scale: Inferences from Mitochondrial and Microsatellite Molecular Markers in Aporrectodea icterica (Savigny 1826)

    PubMed Central

    Torres-Leguizamon, Magally; Mathieu, Jérôme; Decaëns, Thibaud; Dupont, Lise

    2014-01-01

    Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci) and mitochondrial markers (COI). Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations. PMID:25003795

  18. Molecular Markers Reveal Limited Population Genetic Structure in a North American Corvid, Clark’s Nutcracker (Nucifraga columbiana)

    PubMed Central

    Dohms, Kimberly M.; Burg, Theresa M.

    2013-01-01

    The genetic impact of barriers and Pleistocene glaciations on high latitude resident species has not been widely investigated. The Clark’s nutcracker is an endemic North American corvid closely associated with Pinus-dominated forests. The nutcracker’s encompasses known barriers to dispersal for other species, and glaciated and unglaciated areas. Clark’s nutcrackers also irruptively disperse long distances in search of pine seed crops, creating the potential for gene flow among populations. Using the highly variable mitochondrial DNA control region, seven microsatellite loci, and species distribution modeling, we examined the effects of glaciations and dispersal barriers on population genetic patterns and population structure of nutcrackers. We sequenced 900 bp of mitochondrial control region for 169 individuals from 15 populations and analysed seven polymorphic microsatellite loci for 13 populations across the Clark’s nutcracker range. We used species distribution modeling and a range of phylogeographic analyses to examine evolutionary history. Clark’s nutcracker populations are not highly differentiated throughout their range, suggesting high levels of gene flow among populations, though we did find some evidence of isolation by distance and peripheral isolation. Our analyses suggested expansion from a single refugium after the last glacial maximum, but patterns of genetic diversity and paleodistribution modeling of suitable habitat were inconclusive as to the location of this refugium. Potential barriers to dispersal (e.g. mountain ranges) do not appear to restrict gene flow in Clark’s nutcracker, and postglacial expansion likely occurred quickly from a single refugium located south of the ice sheets. PMID:24223982

  19. Update on genetic markers for pork quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To determine the robustness of reported marker associations with pork quality traits, assay systems were developed for as many polymorphisms from the literature as possible. These assays were genotyped across pigs (n = 1,291) with pork quality data available from four populations. Genetic marker-phe...

  20. Molecular genetic analysis of Plasmodium vivax isolates from Eastern and Central Sudan using pvcsp and pvmsp-3α genes as molecular markers.

    PubMed

    Talha, Albadawi Abdelbagi; Pirahmadi, Sekineh; Mehrizi, Akram Abouie; Djadid, Navid Dinparast; Nour, Bakri Y M; Zakeri, Sedigheh

    2015-06-01

    In Sudan, Plasmodium vivax accounts for approximately 5-10% of malaria cases. This study was carried out to determine the genetic diversity of P. vivax population from Sudan by analyzing the polymorphism of P. vivax csp (pvcsp) and pvmsp-3α genes. Blood samples (n=76) were taken from suspected malaria cases from 2012-2013 in three health centers of Eastern and Central Sudan. Parasite detection was performed by microscopy and molecular techniques, and genotyping of both genes was performed by PCR-RFLP followed by DNA sequence for only pvcsp gene (n=30). Based on microscopy analysis, 76 (%100) patients were infected with P. vivax, whereas nested-PCR results showed that 86.8% (n=66), 3.9% (n=3), and 3.9% (n=3) of tested samples had P. vivax as well as Plasmodium falciparum mono- and mixed infections, respectively. Four out of 76 samples had no results in molecular diagnosis. All sequenced samples were found to be of VK210 (100%) genotype with six distinct amino acid haplotypes, and 210A (66.7%) was the most prevalent haplotype. The Sudanese isolates displayed variations in the peptide repeat motifs (PRMs) ranging from 17 to 19 with GDRADGQPA (PRM1), GDRAAGQPA (PRM2) and DDRAAGQPA (PRM3). Also, 54 polymorphic sites with 56 mutations were found in repeat and post-repeat regions of the pvcsp and the overall nucleotide diversity (π) was 0.02149±0.00539. A negative value of dN-dS (-0.0344) was found that suggested a significant purifying selection of Sudanese pvcsp, (Z test, P<0.05). Regarding pvmsp-3α, three types were detected: types A (94.6%, 52/55), type C (3.6%, 2/55), and type B (1.8%, 1/55). No multiclonal infections were detected, and RFLP analysis identified 13 (Hha I, A1-A11, B1, and C1) and 16 (Alu I, A1-A14, B1, and C1) distinct allelic forms. In conclusion, genetic investigation among Sudanese P. vivax isolates indicated that this antigen showed limited antigenic diversity. PMID:25721363

  1. Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster

    SciTech Connect

    Hoskins, Roger A.; Phan, Alexander C.; Naeemuddin, Mohammed; Mapa, Felipa A.; Ruddy, David A.; Ryan, Jessica J.; Young, Lynn M.; Wells, Trent; Kopczynski, Casey; Ellis, Michael C.

    2001-04-16

    For nearly a century, genetic analysis in Drosophila melanogaster has been a powerful tool for analyzing gene function, yet Drosophila lacks the molecular genetic mapping tools that have recently revolutionized human, mouse and plant genetics. Here, we describe the systematic characterization of a dense set of molecular markers in Drosophila using an STS-based physical map of the genome. We identify 474 biallelic markers in standard laboratory strains of Drosophila that the genome. The majority of these markers are single nucleotide polymorphisms (SNPs) and sequences for these variants are provided in an accessible format. The average density of the new markers is 1 marker per 225 kb on the autosomes and 1 marker per 1 Mb on the X chromosome. We include in this survey a set of P-element strains that provide additional utility for high-resolution mapping. We demonstrate one application of the new markers in a simple set of crosses to map a mutation in the hedgehog gene to an interval of <1 Mb. This new map resource significantly increases the efficiency and resolution of recombination mapping and will be of immediate value to the Drosophila research community.

  2. Primer on molecular genetics

    SciTech Connect

    Not Available

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  3. Estimates of Spatial Genetic Structure within and among Clones of Wild Lowbush Blueberry in Maine using EST-PCR Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using recently developed EST-PCR markers, several levels of spatial genetic structure of wild lowbush blueberry, Vaccinium angustifolium Ait., were investigated. Knowledge of this structure (or lack of it) is a prerequisite to testing hypotheses regarding the dramatic yield variation among individu...

  4. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide molecular markers are readily being applied to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorp...

  5. Molecular identification of blood meal sources of ticks (Acari, Ixodidae) using cytochrome b gene as a genetic marker

    PubMed Central

    Che Lah, Ernieenor Faraliana; Yaakop, Salmah; Ahamad, Mariana; Md Nor, Shukor

    2015-01-01

    Abstract Blood meal analysis (BMA) from ticks allows for the identification of natural hosts of ticks (Acari: Ixodidae). The aim of this study is to identify the blood meal sources of field collected on-host ticks using PCR analysis. DNA of four genera of ticks was isolated and their cytochrome b (Cyt b) gene was amplified to identify host blood meals. A phylogenetic tree was constructed based on data of Cyt b sequences using Neighbor Joining (NJ) and Maximum Parsimony (MP) analysis using MEGA 5.05 for the clustering of hosts of tick species. Twenty out of 27 samples showed maximum similarity (99%) with GenBank sequences through a Basic Local Alignment Search Tool (BLAST) while 7 samples only showed a similarity range of between 91–98%. The phylogenetic trees showed that the blood meal samples were derived from small rodents (Leopoldamys sabanus, Rattus tiomanicus and Sundamys muelleri), shrews (Tupaia glis) and mammals (Tapirus indicus and Prionailurus bengalensis), supported by 82–88% bootstrap values. In this study, Cyt b gene as a molecular target produced reliable results and was very significant for the effective identification of ticks’ blood meal. The assay can be used as a tool for identifying unknown blood meals of field collected on-host ticks. PMID:25685009

  6. Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers

    PubMed Central

    Heikrujam, Monika; Kumar, Jatin; Agrawal, Veena

    2015-01-01

    To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC) value and marker index (MI) of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h) and Shannon index (I) were calculated for each genotype and found that the genotype “MS F” (in both markers) was highly diverse and genotypes “Q104 F” (SCoT) and “82–18 F” (CBDP) were least diverse among the female genotype populations. Among male genotypes, “32 M” (CBDP) and “MS M” (SCoT) revealed highest h and I values while “58-5 M” (both markers) was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system) Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major groups

  7. Study of genetic variation of eggplant cultivars by using RAPD-PCR molecular markers and the relationship with Phomopsis blight disease reaction.

    PubMed

    Asad, H A; Meah, M B; Begum, S N; Khalil, M I; Rafii, M Y; Latif, M A

    2015-01-01

    Disease susceptibility and genetic variability in 10 eggplant genotypes were studied after inoculating Phomopsis vexans under confined field conditions. Random amplified polymorphic DNA (RAPD) markers were used to assess genetic variation and relationships among eggplant genotypes. The disease index of leaves ranged 0.208-13.79%, while fruit infection ranged 2.15-42.76%. Two varieties, Dohazari G and Laffa S, were found to be susceptible, 6 were moderately resistant, 1 was moderately susceptible, and BAU Begun-1 was resistant to P. vexans. Amplification of genomic DNA by using 3 RAPD primers produced 20 bands: 14 (70%) were polymorphic and 6 (30%) were monomorphic. The highest intra-variety similarity indices values were found in ISD 006, Ishurdi L, Jessore L, and BAU Begun-1 (100%), while the lowest was in Dohazari G (90%). The lowest genetic distance (0.0513) and the highest genetic identity (0.9500) were observed between the ISD 006 and Ishurdi L combinations. A comparatively higher genetic distance (0.3724) and the lowest genetic identity (0.6891) were observed between the ISD 006 and Dohazari G combinations. A dendogram was constructed based on Nei's genetic distance, which produced 2 main clusters of the genotypes - Cluster I: ISD 006, Ishurdi L, Marich begun L, BAU Begun-1, Marich begun S, and Chega and Cluster 2: Laffa S, Dohazari G, Jessore L, and Singhnath. Genetic variation and its relationship with disease susceptibility were assessed using RAPD markers, to develop disease-resistant varieties and improve eggplant crops. PMID:26681048

  8. Construction of a genetic linkage map for identification of molecular markers associated with resistance to Xanthomonas arboriciola pv. pruni in peach [Prunus persica (L.) Batsch

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacterial spot, caused by Xanthomonas campestris pv. pruni, is a serious disease that can affect peach fruit quality and production. The molecular basis of its tolerance and susceptibility is yet to be understood. To study the genetics of the peach in response to bacterial spot, an F2 population of ...

  9. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Characterization of safflower (Carthamus tinctorius L.) germplasm with molecular markers is needed to enhance germplasm management and utilization. Amplified Fragment Length Polymorphism (AFLP) analysis was completed in safflower using two selective primer pairs resulting in 102 unambiguous polymor...

  10. MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

    Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

  11. (ISEA) MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

    Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

  12. Confirmation of Clematis hybrids using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The hybrid origin of two progeny from reciprocal crosses of Clematis tubulosa and C. brevicaudata was investigated using molecular markers generated by randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and single nucleotide polymorphisms (SNPs). Morphologi...

  13. Genetic diversity in the fungus Fusarium solani f.sp. cucurbitae race 1, the casual agent of root and crown rot of cucurbits in Iran, using molecular markers.

    PubMed

    Alymanesh, M R; Falahatirastegar, M; Jafarpour, B; Mahdikhanimoghadam, E

    2009-06-01

    Fusarium solani f.sp. cucurbitae race 1 is a pathogen on cucurbit plants. In this study genetic diversity among 26 isolates of Fusarium solani f.sp. cucurbitae race 1 was studied using Restriction Fragment Length Polymorphism (RFLP) of ITS (Interal Transcribed Spacer) regions and Random Amplified Polymorphic DNAs (RAPD) markers. Outcome of digestion with six restriction enzymes including EcoR I, Rsa I, Bme 181, Msp I, Hae III and Hind III, together with the patterns of restriction fragment length polymorphism of ITS regions divided the isolates into two groups. Deoxy Ribonuckin Acid DNA pattern was obtained for the isolates using 12 random primers and genetic distance between them was calculated and relationships (by cluster analysis) determined. Among the primers used, seven primers showed polymorphism. Genetic distance between isolate pairs ranged from 0.03 to 0.48. Genetic diversity was high (e.g., the isolates were distributed into 10 genetic groups at a similarity percentage of 75). The lowest distance was observed between isolates 50 and 73 and the highest distance observed between isolates 50 and 73 with isolate 102. Restriction fragment length polymorphism results show diversity in ITS regions, without any correlation to geographic origin and RAPD. However, this genomic regions usually have high constancy in species, but in this study diversity was shown in ITS regions even for race 1. The data suggest that taxonomical situation of Foc race 1 probably needs revision. PMID:19803117

  14. Molecular genetics of ependymoma

    PubMed Central

    Yao, Yuan; Mack, Stephen C.; Taylor, Michael D.

    2011-01-01

    Brain tumors are the leading cause of cancer death in children, with ependymoma being the third most common and posing a significant clinical burden. Its mechanism of pathogenesis, reliable prognostic indicators, and effective treatments other than surgical resection have all remained elusive. Until recently, ependymoma research was hindered by the small number of tumors available for study, low resolution of cytogenetic techniques, and lack of cell lines and animal models. Ependymoma heterogeneity, which manifests as variations in tumor location, patient age, histological grade, and clinical behavior, together with the observation of a balanced genomic profile in up to 50% of cases, presents additional challenges in understanding the development and progression of this disease. Despite these difficulties, we have made significant headway in the past decade in identifying the genetic alterations and pathways involved in ependymoma tumorigenesis through collaborative efforts and the application of microarray-based genetic (copy number) and transcriptome profiling platforms. Genetic characterization of ependymoma unraveled distinct mRNA-defined subclasses and led to the identification of radial glial cells as its cell type of origin. This review summarizes our current knowledge in the molecular genetics of ependymoma and proposes future research directions necessary to further advance this field. PMID:21959044

  15. Molecular genetic analysis of some mutations in the cystic fibrosis gene in Moldova: Characterization of molecular markers and their linkage to various mutations

    SciTech Connect

    Gimbovskaya, S.D.; Kalinin, V.N.; Ivashchenko, T.E.; Baranov, V.S.

    1994-12-01

    Sixty-one patients with cystic fibrosis (CF) from Moldova were tested for mutations {Delta}F508, G551D, and R553X. Frequencies of various alleles of the repeated GATT sequence in intron 6B of the GFTR gene, their linkage to other polymorphic markers, and various mutations were determined. The frequency of occurrence of mutation {Delta}F508 was only 25%. An absolute majority of CF patients (80%) had pancreatic insufficiency. Mutations G551D and R553X were not found in our sample. Each of 31 chromosomes with mutation {Delta}F508 carry the 6-GATT allele. Most {open_quotes}non {Delta}F508{close_quotes} (78%) and normal (80%) chromosomes were marked by the 7-GATT allele. Twenty-seven {Delta}F508 chromosomes (96.4%) belong to haplotype B6, and only one to D6. Most chromosomes with {open_quotes}non {Delta}F508{close_quotes} mutations are associated with haplotypes D7 (26.3%) and C7 (21%). In addition, a significant portion of chromosomes from this subgroup were associated with haplotypes A7 (23.7%), A6 (10.5%), and C6 (2.7%), which are not yet described for mutant chromosomes. The results obtained demonstrate that CF in Moldova is mainly associated with mutations other than {Delta}F508, G551D, and R553X. Severe forms of the disease, with pancreatic insufficiency, are more frequently caused by these mutations; moreover, our data provides strong evidence for the presence of at least seven additional CF mutations in Moldova, apart from {Delta}F508, G551D, and R553X. Some of these are probably not described.

  16. Genetic markers: Potential candidates for cardiovascular disease.

    PubMed

    Rather, Riyaz Ahmad; Dhawan, Veena

    2016-10-01

    The effective prevention of cardiovascular disease depends upon the ability to recognize the high-risk individuals at an early stage of the disease or long before the development of adverse events. Evolving technologies in the fields of proteomics, metabolomics, and genomics have played a significant role in the discovery of cardiovascular biomarkers, but so far these methods have achieved the modest success. Hence, there is a crucial need for more reliable, suitable, and lasting diagnostic and therapeutic markers to screen the disease well in time to start the clinical aid to the patients. Gene polymorphisms associated with the cardiovascular disease play a decisive role in the disease onset. Therefore, the genetic marker evaluation to classify high-risk patients from low-risk patients trends an effective approach to patient management and care. Currently, there are no genetic markers available for extensive adoption as risk factors for coronary vascular disease, yet, there are numerous promising, biologically acceptable candidates. Many of these gene biomarkers, alone or in combination, can play an essential role in the prediction of cardiovascular risk. The present review highlights some putative emerging genetic biomarkers that could facilitate more authentic and fast diagnosis of CVD. This review also briefly describes few technological approaches employed in the biomarker search. PMID:27416153

  17. Fluctuating asymmetry and genetic variability in the roe deer (Capreolus capreolus): a test of the developmental stability hypothesis in mammals using neutral molecular markers.

    PubMed

    Zachos, F E; Hartl, G B; Suchentrunk, F

    2007-06-01

    Fluctuating asymmetry (FA), used as an indicator of developmental stability, has long been hypothesized to be negatively correlated with genetic variability as a consequence of more variable organisms being better suited to buffer developmental pathways against environmental stress. However, it is still a matter of debate if this is due to metabolic properties of enzymes encoded by certain key loci or rather to overall genomic heterozygosity. Previous analyses suggest that there might be a general difference between homeo- and poikilotherms in that only the latter tend to exhibit the negative correlation predicted by theory. In the present study, we addressed these questions by analysing roe deer (Capreolus capreolus) from five German populations with regard to FA in metric and non-metric skull and mandible traits as well as variability at eight microsatellite loci. Genetic variability was quantified by heterozygosity and mean d2 parameters, and although the latter did not show any relationship with FA, we found for the first time a statistically significant negative correlation of microsatellite heterozygosity and non-metric FA among populations. Because microsatellites are non-coding markers, this may be interpreted as evidence for the role of overall genomic heterozygosity in determining developmental stability. To test if the threshold character of non-metric traits is responsible for the metric vs non-metric difference we also carried out calculations where we treated our metric traits as threshold values. This, however, did not yield significant correlations between FA and genetic variability either. PMID:17375126

  18. Molecular genetics of alopecias.

    PubMed

    Ramot, Yuval; Zlotogorski, Abraham

    2015-01-01

    Recent developments in research methods and techniques, such as whole-exome and -genome sequencing, have substantially improved our understanding of genetic conditions. Special progress has been made in the field of genotrichoses, or hereditary hair diseases, a field that has been obscure for many years. The underlying genes for many of the monogenic hair diseases are now known. Additionally, complex analyses of large cohorts of patients have given us the first clues to the genes associated with polygenic hair disorders, such as androgenetic alopecia and alopecia areata. Thanks to these major findings, the sophisticated regulation of the morphogenesis, development and growth of hair follicles has begun to be revealed, and new players in this delicate molecular interplay have been exposed. PMID:26370647

  19. Genetic and biological markers in drug abuse and alcoholism

    SciTech Connect

    Braude, M.C.; Chao, H.M.

    1986-01-01

    This book contains 11 selections. Some of the titles are: Polymorphic Gene Marker Studies; Pharmacogenetic Approaches to the Prediction of Drug Response; Genetic Markers of Drug Abuse in Mouse Models; Genetics as a Tool for Identifying Biological Markers of Drug Abuse; and Studies of an Animal Model of Alcoholism.

  20. Molecular markers and conservation of plant species in Latin America: the case of Phaedranassa viridflora (Amaryllidaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites are molecular markers with great potential for investigating genetic structure of populations. This information is valuable for generating effective conservation plans. We studied the endemic and endangered Phaedranassa viridiflora (Amaryllidaceae) to show the utility of microsatelli...

  1. An improved micropropagation of Arnebia hispidissima (Lehm.) DC. and assessment of genetic fidelity of micropropagated plants using DNA-based molecular markers.

    PubMed

    Phulwaria, Mahendra; Rai, Manoj K; Shekhawat, N S

    2013-07-01

    An efficient and improved in vitro propagation method has been developed for Arnebia hispidissima, a medicinally and pharmaceutically important plant species of arid and semiarid regions. Nodal segments (3-4 cm) with two to three nodes obtained from field grown plants were used as explants for shoot proliferation. Murashige and Skoog's (MS) medium supplemented with cytokinins with or without indole-3-acetic acid (IAA) or naphthalene acetic acid was used for shoot multiplication. Out of different PGRs combinations, MS medium containing 0.5 mg l(-1) 6-benzylaminopurine and 0.1 mg l(-1) IAA was optimal for shoot multiplication. On this medium, explants produced the highest number of shoots (47.50 ± 0.38). About 90 % of shoots rooted ex vitro on sterile soilrite under the greenhouse condition when the base (2-4 mm) of shoots was treated with 300 mg l(-1) of indole-3-butyric acid for 5 min. The plantlets were hardened successfully in the greenhouse with 85-90 % survival rate. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic stability of in vitro-regenerated plants of A. hispidissima. Out of 40 (25 RAPD and 15 ISSR) primers screened, 15 RAPD and 7 ISSR primers produced a total number of 111 (77 RAPD and 34 ISSR) reproducible amplicons. The amplified products were monomorphic across all the micropropagated plants and were similar to the mother plant. To the best of our knowledge, it is the first report on the assessment of the genetic fidelity in micropropagated plants of A. hispidissima. PMID:23645417

  2. Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

  3. The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers.

    PubMed

    Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A; Latif, Mohammad Abdul; Aslani, Farzad

    2015-01-25

    MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars. PMID:25445269

  4. [Progress in InDel as a new generation of genetic marker].

    PubMed

    Sun, Kuan; Zhang, Su-Hua; Zhu, Ru-Xin; Zhao, Shu-Min; Li, Cheng-Tao

    2013-04-01

    As forensic DNA typing experienced three generations of genetic marker researching stage, short tandem repeat (STR) has been widely used in forensic identification as a mature tool. Further exploration of the human genome led to the discovery of polymorphism markers of single nucleotide polymorphism (SNP) and Insertion/Deletion (InDel). InDel, which combines the desirable characteristics of previous genetic markers as a new type of genetic marker, has got extensive concern in fields like medical molecular biology and forensic biology. This paper generally reviews the history of research and the corresponding results of InDel along the line of time axis as well as the different aims of these research focusing on the progress in the multiple amplification system with several InDel as the genetic marker (autosomal or X chromosome) in forensic biology and anthropology. Finally, the direction of research in this field and the problems to be solved have been put forward. PMID:23930511

  5. De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population Genetics

    PubMed Central

    Lin, Qiang; Luo, Wei; Wan, Shiming; Gao, Zexia

    2016-01-01

    Seahorse conservation has been performed utilizing various strategies for many decades, and the deeper understanding of genomic information is necessary to more efficiently protect the germplasm resources of seahorse species. However, little genetic information about seahorses currently exists in the public databases. In this study, high-throughput RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 unigenes for H. mohnikei. Among them, 17,338 (46.23%) unigenes for H. erectus and 17,900 (49.57%) for H. mohnikei were successfully annotated based on the information available from the public databases. Through comparing the unigenes of two seahorse species, 7,802 candidate orthologous genes were identified and 5,268 genes among them could be annotated. In addition, gene ontology analysis of two species was similarly performed on biological processes, cellular components, and molecular functions. Twenty-four and twenty-one unigenes in H. erectus and H. mohnikei were annotated in the biosynthesis of unsaturated fatty acids pathways, and both seahorses lacked the Δ12 and Δ15 desaturases. Total of 8,992 and 9,116 SSR loci were obtained from H. erectus and H. mohnikei unigenes, respectively. Dozens of SSR were developed and then applied to assess the population genetic diversity, as well as cross-amplified in a related species, H. trimaculatus. The HO and HE values of the tested populations for H. erectus, H. mohnikei, and H. trimaculatus were medium. These resources would facilitate the conservation of the species through a better understanding of the genomics and comparative genome analysis within the Hippocampus genus. PMID:27128031

  6. Molecular Genetics of Mycobacteriophages

    PubMed Central

    HATFULL, GRAHAM F.

    2014-01-01

    Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond. PMID:25328854

  7. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling of whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genom...

  8. Developing AFLP Markers to study genetic differentiation of the Cotton Fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic comparisons of fleahopper populations in cotton and weed hosts may be useful for identifying the weed sources contributing the majority of fleahoppers in cotton. Molecular markers such as amplified fragment length polymorphisms (AFLP) are useful to identify genetic similarities and differen...

  9. Molecular Genetics in Glaucoma

    PubMed Central

    Liu, Yutao

    2015-01-01

    Glaucoma is a family of diseases whose pathology is defined by the progressive loss of retinal ganglion cells. Clinically, glaucoma presents as a distinctive optic neuropathy with associated visual field loss. Primary open-angle glaucoma (POAG), chronic angle closure glaucoma (ACG), and exfoliation glaucoma (XFG) are the most prevalent forms of glaucoma globally and are the most common causes of glaucoma-related blindness worldwide. A host of genetic and environmental factors contribute to glaucoma phenotypes. This review examines the current status of genetic investigations of POAG, ACG, XFG, including the less common forms of glaucoma primary congenital glaucoma (PCG), the developmental glaucomas, and pigment dispersion glaucoma. PMID:21871452

  10. Functional molecular markers for crop improvement.

    PubMed

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered. PMID:26171816

  11. Development of new candidate gene and EST-based molecular markers for Gossypium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New source of molecular markers accelerates the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum expressed sequence tag (EST) sequences, and validated them through amplification, ge...

  12. The chloroplast psbK-psbI intergenic region, a potential genetic marker for broad sectional relationships in Anthurium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nuclear and chloroplast genetic markers have been extensively used for plant identification and molecular taxonomy studies. The efficacy of genetic markers to be used as DNA barcodes is under constant evaluation and improvement, with identification of new barcodes that provide greater resolution an...

  13. De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

    PubMed Central

    Liang, Mei; Yang, Xiaoming; Li, Hang; Su, Shiying; Yi, Hualin; Chai, Lijun; Deng, Xiuxin

    2015-01-01

    Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. PMID:25799271

  14. Genetic variability of watermelon accessions based on microsatellite markers.

    PubMed

    de S Gama, R N C; Santos, C A F; de C S Dias, R

    2013-01-01

    We analyzed the genetic variability of 40 watermelon accessions collected from 8 regions of Northeastern Brazil using microsatellite markers, in order to suggest strategies of conservation and utilization of genetic variability in this species. These accessions are not commercial cultivars. They were sampled in areas of traditional farmers that usually keep their own seeds for future plantings year after year. An UPGMA dendrogram was generated from a distance matrix of the Jaccard coefficient, based on 41 alleles of 13 microsatellite loci. Analysis of molecular variance was made by partitioning between and within geographical regions. The similarity coefficient between accessions ranged from 37 to 96%; the dendrogram gave a co-phenetic value of 0.80. The among population genetic variability was high ( (^)ϕST = 0.319). Specific clusters of accessions sampled in 3 regions of Maranhão were observed while the other 5 regions did not presented specific clusters by regions. We conclude that watermelon genetic variability is not uniformly dispersed in the regions analyzed, indicating that geographical barriers or edaphoclimatic conditions have limited open mating. We suggest sampling a greater number of populations, so regional species diversity will be better represented and preserved in the germplasm bank. PMID:23546958

  15. Genetic diversity in three natural populations of Pitcairnia flammea (l.) John (Bromeliaceae) estimated by ISSR markers.

    PubMed

    Souza-Sobreira, F B; Souza, G B; Rosado, C C G; Miranda, F D; Soares, T C B; Gontijo, A B P L

    2015-01-01

    Bromeliads are greatly represented in the Atlantic Forest, although many species are threatened with extinction owing to habitat fragmentation and intense extraction for ornamental purposes. Therefore, it is necessary to conduct studies generating knowledge about genetic diversity and the distribution of this diversity among and within natural populations to establish conservation strategies. These studies can be performed with the use of molecular markers. Molecular markers are advantageous for studies of natural populations, for conservation programs, and to aid in properly classifying plant species. This study aimed to evaluate the genetic diversity among and within natural populations of Pitcairnia flammea, occurring in three fragments of the Atlantic Forest in the southern State of Espírito Santo through the use of inter-simple sequence repeat (ISSR) markers. DNA samples from 55 individuals were amplified with 18 ISSR primers, generating 180 bands, 159 of which were polymorphic. The Shannon genetic diversity index ranged from 0.348 to 0.465, with an average of 0.412. The Bayesian approach for the molecular data indicated the existence of two genetic groups. Analysis of molecular variance indicated the existence of 90.3% diversity within the population and 9.74% among populations. The amount of genetic differentiation of populations was moderate (0.0974), indicating that gene flow rates may be enough to counteract the effects of genetic drift. Greater genetic variability found in population B indicates that this area is an important source of genetic variability. PMID:26634557

  16. The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera

    PubMed Central

    Coates, Brad Steven; Bayles, Darrell O.; Wanner, Kevin W.; Robertson, Hugh M.; Hellmich, Richard L.; Sappington, Thomas W.

    2011-01-01

    Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data. PMID:22303334

  17. Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis

    PubMed Central

    Desikan, Srinidhi; Narayanan, Sujatha

    2015-01-01

    Molecular epidemiology (ME) is one of the main areas in tuberculosis research which is widely used to study the transmission epidemics and outbreaks of tubercle bacilli. It exploits the presence of various polymorphisms in the genome of the bacteria that can be widely used as genetic markers. Many DNA typing methods apply these genetic markers to differentiate various strains and to study the evolutionary relationships between them. The three widely used genotyping tools to differentiate Mycobacterium tuberculosis strains are IS6110 restriction fragment length polymorphism (RFLP), spacer oligotyping (Spoligotyping), and mycobacterial interspersed repeat units - variable number of tandem repeats (MIRU-VNTR). A new prospect towards ME was introduced with the development of whole genome sequencing (WGS) and the next generation sequencing (NGS) methods, where the entire genome is sequenced that not only helps in pointing out minute differences between the various sequences but also saves time and the cost. NGS is also found to be useful in identifying single nucleotide polymorphisms (SNPs), comparative genomics and also various aspects about transmission dynamics. These techniques enable the identification of mycobacterial strains and also facilitate the study of their phylogenetic and evolutionary traits. PMID:26205019

  18. Developmnent of molecular markers for powdery mildew resistance in grapevines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers have been used as a tool for plant breeding for two decades. Markers linked to disease resistance can be used to pyramid resistance genes for improved durability and to improve the efficiency of evaluation. To develop molecular markers linked to resistance to grape powdery mildew ...

  19. Cancer Genetic Markers of Susceptibility | Office of Cancer Genomics

    Cancer.gov

    The Cancer Genetic Markers of Susceptibility (CGEMS) project began in 2005 as a 3-year pilot study to identify inherited genetic susceptibility to prostate and breast cancer. CGEMS has developed into a successful research program of genome-wide association studies (GWAS) to identify genetic variants that affect a person’s risk of developing cancer.

  20. Genetic analysis and molecular mapping of a new fertility restorer gene Rf8 for Triticum timopheevi cytoplasm in wheat (Triticum aestivum L.) using SSR markers.

    PubMed

    Sinha, Pallavi; Tomar, S M S; Vinod; Singh, Vikas K; Balyan, H S

    2013-12-01

    A study on mode of inheritance and mapping of fertility restorer (Rf) gene(s) using simple sequence repeat (SSR) markers was conducted in a cross of male sterile line 2041A having Triticum timopheevi cytoplasm and a restorer line PWR4099 of common wheat (Triticum aestivum L.). The F1 hybrid was completely fertile indicating that fertility restoration is a dominant trait. Based on the pollen fertility and seed set of bagged spikes in F2 generation, the individual plants were classified into fertile and sterile groups. Out of 120 F2 plants, 97 were fertile and 23 sterile (based on pollen fertility) while 98 plants set ≥ 5 seeds/spike and 22 produced ≤ 4 or no seed. The observed frequency fits well into Mendelian ratio of 3 fertile: 1 sterile with χ(2) value of 2.84 for pollen fertility and 2.17 for seed setting indicating that the fertility restoration is governed by a single dominant gene in PWR4099. The three linked SSR markers, Xwmc503, Xgwm296 and Xwmc112 located on the chromosome 2DS were placed at a distance of 3.3, 5.8 and 6.7 cM, respectively, from the Rf gene. Since, no known Rf gene is located on the chromosome arm 2DS, the Rf gene in PWR4099 is a new gene and proposed as Rf8. The closest SSR marker, Xwmc503, linked to the Rf8 was validated in a set of Rf, maintainer and cytoplasmic male sterile lines. The closely linked SSR marker Xwmc503 may be used in marker-assisted backcross breeding facilitating the transfer of fertility restoration gene Rf8 into elite backgrounds with ease. PMID:24129675

  1. Molecular genetics of colorectal cancer.

    PubMed

    Bogaert, Julie; Prenen, Hans

    2014-01-01

    Approximately 90% of colorectal cancer cases are sporadic without family history or genetic predisposition, while in less than 10% a causative genetic event has been identified. Historically, colorectal cancer classification was only based on clinical and pathological features. Many efforts have been made to discover the genetic and molecular features of colorectal cancer, and there is more and more evidence that these features determine the prognosis and response to (targeted) treatment. Colorectal cancer is a heterogeneous disease, with three known major molecular groups. The most common is the chromosomal instable group, characterized by an accumulation of mutations in specific oncogenes and tumor suppressor genes. The second is the microsatellite instable group, caused by dysfunction of DNA mismatch repair genes leading to genetic hypermutability. The CpG Island Methylation phenotype is the third group, distinguished by hypermethylation. Colorectal cancer subtyping has also been addressed using genome-wide gene expression profiling in large patient cohorts and recently several molecular classification systems have been proposed. In this review we would like to provide an up-to-date overview of the genetic aspects of colorectal cancer. PMID:24714764

  2. Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map.

    PubMed

    Wang, Wei; Chen, Bingzhi; Zhang, Lei; Yan, Junjie; Lu, Yuanping; Zhang, Xiaoyin; Jiang, Yuji; Wu, Taju; van Peer, Arend Frans; Li, Shaojie; Xie, Baogui

    2015-01-01

    Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi. PMID:26204838

  3. Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map

    PubMed Central

    Wang, Wei; Chen, Bingzhi; Zhang, Lei; Yan, Junjie; Lu, Yuanping; Zhang, Xiaoyin; Jiang, Yuji; Wu, Taju; van Peer, Arend Frans; Li, Shaojie; Xie, Baogui

    2015-01-01

    Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi. PMID:26204838

  4. Development and use of molecular markers to accelerate peanut cultivar development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Close cooperation between conventional plant breeders and molecular geneticists will be needed to efficiently and effectively utilize modern genetic tools in the development of peanut cultivars. We have used this approach at Tifton to develop molecular markers for resistance to the peanut root-knot...

  5. Genetic markers and the coregonid problem

    USGS Publications Warehouse

    Stott, W.; Todd, T.N.

    2007-01-01

    Coregonid fishes are the forage base in many ecosystems in the northern hemisphere and they have traditionally been part of commercial and native fisheries. Coregonids display extreme variability in morphology, life history, and behavior. Defining boundaries among coregonid taxa has been (and continues to be) the focus of many studies. Cytogenetic, biochemical, and molecular methods have been used to study the 'coregonid problem'. A survey of the literature reveals that questions of taxonomy, followed by phylogeography are most often studied. Sample collections have occurred throughout a representative portion of the coregonid range. The whitefish species Coregonus clupeaformis and C. lavaretus are most often studied. This was expected however because they are the most widely distributed, display the most variation, and are the most commercially important. However, species with restricted ranges such as the Irish pollan (C. pollan) or omul (C. migratorius) have also been studied intensively. Genetic methods have provided insights into several issues, including the placement of Stenodus and the status of C. clupeaformis and C. lavaretus. More recently, studies of sympatric forms over broad geographic scales shed light on processes involved in the evolution of the group and suggest different approaches for management and designation of taxa. ?? 2007 E. Schweizerbart'sche Verlagsbuchhandlung.

  6. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.; D'Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

    1991-12-15

    Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

  7. The molecular genetics of cultivated mushrooms.

    PubMed

    Whiteford, J R; Thurston, C F

    2000-01-01

    The types, economic significance and methods of production of the principal cultivated mushrooms are described in outline. These organisms are all less than ideal for conventional genetic analysis and breeding, so molecular methods afford a particular opportunity to advance our understanding of their biology and potentially give the prospect of improvement by gene manipulation. The sequences described are limited to those found in GenBank by August 1999. The gene sequences isolated from the white button mushroom Agaricus bisporus, the shiitake Lentinula edodes, the oyster mushrooms Pleurotus spp., the paddy straw mushroom Volvariella volvacea and the enotake Flammulina velutipes are described. The largest group are genes from A. bisporus, which includes 29 for intracellular proteins and 12 for secreted proteins. In comparison, only a total of 26 sequences can be reported for the other cultivated species. A. bisporus is also the only cultivated species for which molecular karyotyping is already supported by reliable markers for all 13 of its chromosomes. PMID:10907549

  8. Validation of genetic markers associated with chalkbrood resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chalkbrood is one of the major fungal diseases of honey bee brood. Systemic mycoses caused by the fungus, Ascosphaera apis, may significantly reduce brood population, and consequently, colony strength and productivity. Developing genetic marker(s) associated with the enhanced brood survival will be ...

  9. Molecular genetics of myocardial infarction

    PubMed Central

    Ichihara, Sahoko; Nishida, Tamotsu

    2008-01-01

    Abstract Myocardial infarction (MI) is an important clinical problem because of its large contribution to mortality. The main causal and treatable risk factors for MI include hypertension, hypercholesterolemia or dyslipidemia, diabetes mellitus, and smoking. In addition to these risk factors, recent studies have shown the importance of genetic factors and interactions between multiple genes and environmental factors. Disease prevention is an important strategy for reducing the overall burden of MI, with the identification of markers for disease risk being key both for risk prediction and for potential intervention to lower the chance of future events. Although genetic linkage analyses of families and sib-pairs as well as candidate gene and genome-wide association studies have implicated several loci and candidate genes in predisposition to coronary heart disease (CHD) or MI, the genes that contribute to genetic susceptibility to these conditions remain to be identified definitively. In this review, we summarize both candidate loci for CHD or MI identified by linkage analyses and candidate genes examined by association studies. We also review in more detail studies that have revealed the association with MI or CHD of polymorphisms in MTHFR, LPL, and APOE by the candidate gene approach and those in LTA and at chromosomal region 9p21.3 by genome-wide scans. Such studies may provide insight into the function of implicated genes as well as into the role of genetic factors in the development of CHD and MI. PMID:18704761

  10. Development of Public Immortal Mapping Populations, Molecular Markers, and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Past research efforts on genetic mapping in Brassica oleracea and Brassica rapa have been disconnected, utilizing separate mapping populations and different sets of molecular markers. Here we present public immortal mapping populations, molecular markers and linkage maps for rapid cycling B. rapa a...

  11. Novel Molecular Markers for Breast Cancer

    PubMed Central

    Inoue, Kazushi; Fry, Elizabeth A.

    2016-01-01

    The use of molecular biomarkers assures that breast cancer (BC) patients receive optimal treatment. Established biomarkers, such as estrogen receptor, progesterone receptor, HER2, and Ki67, have been playing significant roles in the subcategorization of BC to predict the prognosis and decide the specific therapy to each patient. Antihormonal therapy using 4-hydroxytamoxifen or aromatase inhibitors have been employed in patients whose tumor cells express hormone receptors, while monoclonal antibody to HER2 has been administered to HER2-positive BCs. Although new therapeutic agents have been developed in the past few decades, many patients still die of the disease due to relapse; thus, novel molecular markers that predict therapeutic failure and those that can be targets for specific therapy are expected. We have chosen four of such molecules by reviewing recent publications, which are cyclin E, B-Myb, Twist, and DMP1β. The oncogenicity of these molecules has been demonstrated in vivo and/or in vitro through studies using transgenic mice or siRNAs, and their expressions have been shown to be associated with shortened overall or disease-free survival of BC patients. The former three molecules have been shown to accelerate epithelial–mesenchymal transition that is often associated with cancer stem cell-ness and metastasis; all these four can be novel therapeutic targets as well. Thus, large prospective studies employing immunohistochemistry will be needed to establish the predictive values of these molecules in patients with BC. PMID:26997872

  12. Molecular genetics of retinitis pigmentosa.

    PubMed Central

    Farber, D. B.; Heckenlively, J. R.; Sparkes, R. S.; Bateman, J. B.

    1991-01-01

    Retinitis pigmentosa is a model for the study of genetic diseases. Its genetic heterogeneity is reflected in the different forms of inheritance (autosomal dominant, autosomal recessive, or X-linked) and, in a few families, in the presence of mutations in the visual pigment rhodopsin. Clinical and molecular genetic studies of these disorders are discussed. Animal models of retinal degeneration have been investigated for many years with the hope of gaining insight into the cause of photoreceptor cell death. Recently, the genes responsible for two of these animal disorders, the rds and rd mouse genes, have been isolated and characterized. The retinal degeneration of the rd mouse is presented in detail. The possible involvement of human analogues of these mouse genes in human retinal diseases is being investigated. Images PMID:1771877

  13. Genetic relationships among Heliconia (Heliconiaceae) species based on RAPD markers.

    PubMed

    Marouelli, L P; Inglis, P W; Ferreira, M A; Buso, G S C

    2010-01-01

    The family Heliconiaceae contains a single genus, Heliconia, with approximately 180 species of Neotropical origin. This genus was formerly allocated to the family Musaceae, but today forms its own family, in the order Zingiberales. The combination of inverted flowers, a single staminode and drupe fruits is an exclusive characteristic of Heliconia. Heliconias are cultivated as ornamental garden plants, and are of increasing importance as cut flowers. However, there are taxonomic confusions and uncertainties about the number of species and the relationships among them. Molecular studies are therefore necessary for better understanding of the species boundaries of these plants. We examined the genetic variability and the phylogenetic relationships of 124 accessions of the genus Heliconia based on RAPD markers. Phenetic and cladistic analyses, using 231 polymorphic RAPD markers, demonstrated that the genus Heliconia is monophyletic. Groupings corresponding to currently recognized species and some subgenera were found, and cultivars and hybrids were found to cluster with their parents. RAPD analysis generally agreed with morphological species classification, except for the position of the subgenus Stenochlamys, which was found to be polyphyletic. PMID:20645261

  14. New models and molecular markers in evaluation of developmental toxicity

    SciTech Connect

    Huuskonen, Hannele . E-mail: hannele.huuskonen@sttv.fi

    2005-09-01

    Mammalian and non-mammalian embryos and embryonic stem cells may be used as models in mechanistic studies and in testing embryotoxicity of compounds. In addition to conventional culture methods, genetic modifications and use of molecular markers offer significant advantages in mechanistic studies as well as in developing new test methods for embryotoxicity. Zebrafish model has been used for a long time and at present several applications are available. It is an easy vertebral non-mammalian model, whose genome is largely known and several genetic modifications are easily constructed to study gene expression or knocked down genes. Fluorescent marker proteins can be used also in zebrafish to indicate gene activation in transgenic models. Chemical genetics approach has been developed using zebrafish model. This is a new approach to screen small molecules that regulate signaling pathways. Embryonic stem cells have been used in mechanistic studies and mouse embryonic stem cell test has been validated to study embryotoxicity in vitro. This method has been improved using quantitative measurements of molecular endpoints by real-time RT-PCR or fluorescent activated cell sorting methods (FACS). Methods facilitating differentiation to several different cell types are available. We have studied preimplantation mouse embryos as a possible model for in vitro testing. In this method, superovulated and in vivo fertilized preimplantation embryos were collected at morula stage and cultured up to blastocysts. The mouse preimplantation culture test was improved by quantitative gene expression measurement using two-step real-time RT-PCR methods. New endpoints improve the tests of in vitro embryotoxicity because subjective assessments are replaced by objective measurements. In addition, automation is possible and less time is needed for analysis. Thus, high throughput screening will come possible to test large numbers of compounds.

  15. Evolving Molecular Genetics of Glioblastoma

    PubMed Central

    Li, Qiu-Ju; Cai, Jin-Quan; Liu, Cheng-Yin

    2016-01-01

    Objective: To summary the recent advances in molecular research of glioblastoma (GBM) and current trends in personalized therapy of this disease. Data Sources: Data cited in this review were obtained mainly from PubMed in English up to 2015, with keywords “molecular”, “genetics”, “GBM”, “isocitrate dehydrogenase”, “telomerase reverse transcriptase”, “epidermal growth factor receptor”, “PTPRZ1-MET”, and “clinical treatment”. Study Selection: Articles regarding the morphological pathology of GBM, the epidemiology of GBM, genetic alteration of GBM, and the development of treatment for GBM patients were identified, retrieved, and reviewed. Results: There is a large amount of data supporting the view that these recurrent genetic aberrations occur in a specific context of cellular origin, co-oncogenic hits and are present in distinct patient populations. Primary and secondary GBMs are distinct disease entities that affect different age groups of patients and develop through distinct genetic aberrations. These differences are important, especially because they may affect sensitivity to radio- and chemo-therapy and should thus be considered in the identification of targets for novel therapeutic approaches. Conclusion: This review highlights the molecular and genetic alterations of GBM, indicating that they are of potential value in the diagnosis and treatment for patients with GBM. PMID:26879021

  16. Genetic breeding and diversity of the genus Passiflora: progress and perspectives in molecular and genetic studies.

    PubMed

    Cerqueira-Silva, Carlos Bernard M; Jesus, Onildo N; Santos, Elisa S L; Corrêa, Ronan X; Souza, Anete P

    2014-01-01

    Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit. PMID:25196515

  17. Genetic Breeding and Diversity of the Genus Passiflora: Progress and Perspectives in Molecular and Genetic Studies

    PubMed Central

    Cerqueira-Silva, Carlos Bernard M.; Jesus, Onildo N.; Santos, Elisa S. L.; Corrêa, Ronan X.; Souza, Anete P.

    2014-01-01

    Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit. PMID:25196515

  18. Toward Diagnostic and Phenotype Markers for Genetically Transmitted Speech Delay

    ERIC Educational Resources Information Center

    Shriberg, Lawrence D.; Lewis, Barbara A.; Tomblin, J. Bruce; McSweeny, Jane L.; Karlsson, Heather B.; Scheer, Alison R.

    2005-01-01

    Converging evidence supports the hypothesis that the most common subtype of childhood speech sound disorder (SSD) of currently unknown origin is genetically transmitted. We report the first findings toward a set of diagnostic markers to differentiate this proposed etiological subtype (provisionally termed "speech delay-genetic") from other…

  19. Beyond STRs: The Role of Diallelic Markers in Forensic Genetics

    PubMed Central

    Schneider, Peter M.

    2012-01-01

    Short tandem repeat (STR) polymorphisms have been firmly established as standard DNA marker systems since more than 15 years both in forensic stain typing as well as in paternity and kinship testing. However, when analyzing genetic relationships in deficiency cases, STRs have a couple of disadvantages due to the sometimes poor biostatistical efficiency as well as the possibility to observe one or more genetic inconsistencies that could also be explained by mutational events. In such situations, additional robust markers with negligible mutations rates such as single nucleotide polymorphisms (SNPs) and insertion/deletion markers (indels) can be used as adjuncts to provide decisive genetic information in favor for or against the assumed relationship. Both SNPs and indels can now be typed more easily using multiplexes of up to 50 loci based on fragment length analysis on instruments available in all routine forensic and paternity testing laboratories, thus making it possible to extend the range of markers beyond the currently used STRs. PMID:22851932

  20. Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology

    PubMed Central

    Kirk, Heather; Freeland, Joanna R.

    2011-01-01

    The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. PMID:21747718

  1. Analysis of Variance Components for Genetic Markers with Unphased Genotypes

    PubMed Central

    Wang, Tao

    2016-01-01

    An ANOVA type general multi-allele (GMA) model was proposed in Wang (2014) on analysis of variance components for quantitative trait loci or genetic markers with phased or unphased genotypes. In this study, by applying the GMA model, we further examine estimation of the genetic variance components for genetic markers with unphased genotypes based on a random sample from a study population. In one locus and two loci cases, we first derive the least square estimates (LSE) of model parameters in fitting the GMA model. Then we construct estimators of the genetic variance components for one marker locus in a Hardy-Weinberg disequilibrium population and two marker loci in an equilibrium population. Meanwhile, we explore the difference between the classical general linear model (GLM) and GMA based approaches in association analysis of genetic markers with quantitative traits. We show that the GMA model can retain the same partition on the genetic variance components as the traditional Fisher's ANOVA model, while the GLM cannot. We clarify that the standard F-statistics based on the partial reductions in sums of squares from GLM for testing the fixed allelic effects could be inadequate for testing the existence of the variance component when allelic interactions are present. We point out that the GMA model can reduce the confounding between the allelic effects and allelic interactions at least for independent alleles. As a result, the GMA model could be more beneficial than GLM for detecting allelic interactions. PMID:27468297

  2. [Study of genetic markers of duodenal ulcer].

    PubMed

    Tsimmerman, Ia S; Onosova, E A; Tsimmerman, I Ia

    1989-05-01

    The results of determination of various hereditary predisposition markers in peptic ulcer are given: in the population, in patients with duodenal ulcer and in their siblings (risk group). Of importance for revealing subjects with hereditary predisposition to duodenal ulcer are the clinico-genealogical analysis, determination of the blood group, especially in simultaneous determination of a "secretory status" ("status of non-secretion" of the ABH blood system agglutinogen in the saliva), increase in the mass of parietal cells and, to some extent, of the distinguishing features of dermatoglyphics (in combination with the above markers). Determination of taste sensitivity to phenylthiocarbamide is non-informative. PMID:2770215

  3. Molecular genetics of Thiobacillus ferrooxidans.

    PubMed Central

    Rawlings, D E; Kusano, T

    1994-01-01

    Thiobacillus ferrooxidans is a gram-negative, highly acidophilic (pH 1.5 to 2.0), autotrophic bacterium that obtains its energy through the oxidation of ferrous iron or reduced inorganic sulfur compounds. It is usually dominant in the mixed bacterial populations that are used industrially for the extraction of metals such as copper and uranium from their ores. More recently, these bacterial consortia have been used for the biooxidation of refractory gold-bearing arsenopyrite ores prior to the recovery of gold by cyanidation. The commercial use of T. ferrooxidans has led to an increasing interest in the genetics and molecular biology of the bacterium. Initial investigations were aimed at determining whether the unique physiology and specialized habitat of T. ferrooxidans had been accompanied by a high degree of genetic drift from other gram-negative bacteria. Early genetic studies were comparative in nature and concerned the isolation of genes such as nifHDK, glnA, and recA, which are widespread among bacteria. From a molecular biology viewpoint, T. ferrooxidans appears to be a typical member of the proteobacteria. In most instances, cloned gene promoters and protein products have been functional in Escherichia coli. Although T. ferrooxidans has proved difficult to transform with DNA, research on indigenous plasmids and the isolation of the T. ferrooxidans merA gene have resulted in the development of a low-efficiency electroporation system for one strain of T. ferrooxidans. The most recent studies have focused on the molecular genetics of the pathways associated with nitrogen metabolism, carbon dioxide fixation, and components of the energy-producing mechanisms. PMID:8177170

  4. [Molecular epidemiology of imported malaria in Italy: the use of genetic markers and in vitro sensitivity test in a study of chloroquine resistance in Plasmodium falciparum].

    PubMed

    Menegon, Michela; Sannella, Anna Rosa; Severini, Carlo; Paglia, Maria Grazia; Matteelli, Alberto; Caramello, Pietro; Severini, Francesco; Taramelli, Donatella; Majori, Giancarlo

    2006-01-01

    The emergence of Plasmodium falciparum drug-resistance, especially chloroquine resistance, represents one of the main obstacles to the control of malaria. Several studies have shown that in P. falciparum the mechanism of chloroquine resistance is linked to specific point mutations in the pfcrt gene of the parasite. In the present study we have analyzed 120 Italian imported malaria cases to evaluate the prevalence of 76T and 220S mutantions in the pfcrt gene. Moreover, the correlation between the presence of pfcrt point mutations and in vitro chloroquine resistance has been evaluated on 25 plasmodial isolates. The results showed a high prevalence of the pfcrt point mutations in isolates analyzed and a significant association between point mutations and in vitro chloroquine resistance. Molecular screening on imported malaria cases can be a useful tool to be employed in surveillance activity and also in monitoring the development and spread of drug resistance in endemic areas. PMID:17033142

  5. Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

    PubMed

    Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

    2016-01-01

    Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content. PMID:27323023

  6. Molecular genetics in affective illness

    SciTech Connect

    Mendlewicz, J.; Sevy, S.; Mendelbaum, K. )

    1993-01-01

    Genetic transmission in manic depressive illness (MDI) has been explored in twins, adoption, association, and linkage studies. The X-linked transmission hypothesis has been tested by using several markers on chromosome X: Xg blood group, color blindness, glucose-6-phosphate dehydrogenase (G6PD), factor IX (hemophilia B), and DNA probes such as DXS15, DXS52, F8C, ST14. The hypothesis of autosomal transmission has been tested by association studies with the O blood group located on chromosome 9, as well as linkage studies on chromosome 6 with the Human Leucocyte Antigens (HLA) haplotypes and on Chromosome 11 with DNA markers for the following genes: D2 dopamine receptor, tyrosinase, C-Harvey-Ras-A (HRAS) oncogene, insuline (ins), and tyrosine hydroxylase (TH). Although linkage studies support the hypothesis of a major locus for the transmission of MDI in the Xq27-28 region, several factors are limiting the results, and are discussed in the present review. 105 refs., 1 fig., 2 tabs.

  7. Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus

    PubMed Central

    2013-01-01

    Background The Rlnn1 locus, which resides on chromosome 7A of bread wheat (Triticum aestivum L.) confers moderate resistance against the root lesion nematode Pratylenchus neglectus. Prior to this research, the exact linkage relationships of Rlnn1 with other loci on chromosome 7A were not clear and there were no simple codominant markers available for selection of Rlnn1 in wheat breeding. The objectives of the research reported here were to (1) develop an improved genetic map of the Rlnn1 region of chromosome 7A and (2) develop molecular markers that could be used in marker-assisted selection to improve resistance of wheat against P. neglectus. Results A large-effect quantitative trait locus (QTL) for resistance against P. neglectus was genetically mapped using a population of Excalibur/Kukri doubled haploid lines. This QTL coincides in position with the rust resistance gene(s) Lr20/Sr15, the phytoene synthase gene Psy-A1 and 10 molecular markers, including five new markers designed using wheat-rice comparative genomics and wheat expressed sequence tags. Two of the new markers are suitable for use as molecular diagnostic tools to distinguish plants that carry Rlnn1 and Lr20/Sr15 from those that do not carry these resistance genes. Conclusions The genomic location of Rlnn1 was confirmed to be in the terminal region of the long arm of chromosome 7A. Molecular markers were developed that provide simple alternatives to costly phenotypic assessment of resistance against P. neglectus in wheat breeding. In Excalibur, genetic recombination seems to be completely suppressed in the Rlnn1 region. PMID:24377498

  8. Genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) evaluated using ISSR markers.

    PubMed

    Vidal, Á M; Vieira, L J; Ferreira, C F; Souza, F V D; Souza, A S; Ledo, C A S

    2015-01-01

    Molecular markers are efficient for assessing the genetic fidelity of various species of plants after in vitro culture. In this study, we evaluated the genetic fidelity and variability of micropropagated cassava plants (Manihot esculenta Crantz) using inter-simple sequence repeat markers. Twenty-two cassava accessions from the Embrapa Cassava & Fruits Germplasm Bank were used. For each accession, DNA was extracted from a plant maintained in the field and from 3 plants grown in vitro. For DNA amplification, 27 inter-simple sequence repeat primers were used, of which 24 generated 175 bands; 100 of those bands were polymorphic and were used to study genetic variability among accessions of cassava plants maintained in the field. Based on the genetic distance matrix calculated using the arithmetic complement of the Jaccard's index, genotypes were clustered using the unweighted pair group method using arithmetic averages. The number of bands per primer was 2-13, with an average of 7.3. For most micropropagated accessions, the fidelity study showed no genetic variation between plants of the same accessions maintained in the field and those maintained in vitro, confirming the high genetic fidelity of the micropropagated plants. However, genetic variability was observed among different accessions grown in the field, and clustering based on the dissimilarity matrix revealed 7 groups. Inter-simple sequence repeat markers were efficient for detecting the genetic homogeneity of cassava plants derived from meristem culture, demonstrating the reliability of this propagation system. PMID:26214457

  9. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. Separation and scoring of 392 markers was completed using the Beckman CEQ8000 capillary electrophoresis system. Twelve plants from each of eight...

  10. Uniparental genetic markers in South Amerindians.

    PubMed

    Bisso-Machado, Rafael; Bortolini, Maria Cátira; Salzano, Francisco Mauro

    2012-04-01

    A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data. PMID:22888284

  11. Uniparental genetic markers in South Amerindians

    PubMed Central

    Bisso-Machado, Rafael; Bortolini, Maria Cátira; Salzano, Francisco Mauro

    2012-01-01

    A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data. PMID:22888284

  12. Marker reconstitution mutagenesis: a simple and efficient reverse genetic approach.

    PubMed

    Tang, Xie; Huang, Junqi; Padmanabhan, Anup; Bakka, Kavya; Bao, Yun; Tan, Brenda Yuelin; Cande, W Zacheus; Balasubramanian, Mohan K

    2011-03-01

    A novel reverse genetic approach termed 'marker reconstitution mutagenesis' was designed to generate mutational allelic series in genes of interest. This approach consists of two simple steps which utilize two selective markers. First, using one selective marker, a partial fragment of another selective marker gene is inserted adjacently to a gene of interest by homologous recombination. Second, random mutations are introduced precisely into the gene of interest, together with the reconstitution of the latter selective marker by homologous recombination. This approach was successfully tested for several genes in the fission yeast Schizosaccharomyces pombe. It circumvents the problems encountered with other methods and should be adaptable to any organism that incorporates exogenous DNA by homologous recombination. PMID:21360732

  13. Genetic markers cannot determine Jewish descent

    PubMed Central

    Falk, Raphael

    2015-01-01

    Humans differentiate, classify, and discriminate: social interaction is a basic property of human Darwinian evolution. Presumably inherent differential physical as well as behavioral properties have always been criteria for identifying friend or foe. Yet, biological determinism is a relatively modern term, and scientific racism is, oddly enough, largely a consequence or a product of the Age of Enlightenment and the establishment of the notion of human equality. In recent decades ever-increasing efforts and ingenuity were invested in identifying Biblical Israelite genotypic common denominators by analysing an assortment of phenotypes, like facial patterns, blood types, diseases, DNA-sequences, and more. It becomes overwhelmingly clear that although Jews maintained detectable vertical genetic continuity along generations of socio-religious-cultural relationship, also intensive horizontal genetic relations were maintained both between Jewish communities and with the gentile surrounding. Thus, in spite of considerable consanguinity, there is no Jewish genotype to identify. PMID:25653666

  14. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    PubMed

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  15. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

    PubMed Central

    Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  16. Molecular-Genetic Imaging of Cancer

    PubMed Central

    Minn, Il; Menezes, Mitchell E.; Sarkar, Siddik; Yarlagadda, Keerthi; Das, Swadesh K.; Emdad, Luni; Sarkar, Devanand; Fisher, Paul B.; Pomper, Martin G.

    2015-01-01

    Molecular-genetic imaging of cancer using nonviral delivery systems has great potential for clinical application as a safe, efficient, noninvasive tool for visualization of various cellular processes including detection of cancer, and its attendant metastases. In recent years, significant effort has been expended in overcoming technical hurdles to enable clinical adoption of molecular-genetic imaging. This chapter will provide an introduction to the components of molecular-genetic imaging and recent advances on each component leading to safe, efficient clinical applications for detecting cancer. Combination with therapy, namely, generating molecular-genetic theranostic constructs, will provide further impetus for clinical translation of this promising technology. PMID:25287688

  17. Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.)

    PubMed Central

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N.; Aslam, M.N.; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A.; Kilian, A.; Sharpe, Andrew G.; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  18. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).

    PubMed

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N; Aslam, M N; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A; Kilian, A; Sharpe, Andrew G; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  19. New high density genetic marker technology for use in breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in genetic marker technology have enhanced our ability to evaluate rice breeding materials more quickly and with greater coverage. In 2005, as a result of an international collaboration, the japonica rice variety, Nipponbare, was the first crop plant to be completely sequenced. Subse...

  20. Association of genetic markers in cattle receiving differing implant protocols

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The potential interaction of growth-promoting implants and genetic markers previously reported to be associated with growth, carcass traits, and tenderness was evaluated. Two implant protocols were applied to subsets of steers (n=383) and heifers (n=65) that were also genotyped for 47 SNP reported ...

  1. SSR Marker Analysis of Genetic Relationships within Hydrangea paniculata

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity studies using 26 simple-sequence repeat (SSR) markers were conducted with 36 taxa of Hydrangea paniculata Sieb. The SSR loci were highly variable among the taxa, producing a mean of 5.8 alleles per locus. Three cultivars (Boskoop, Compact Grandiflora and Webb) were either identic...

  2. SSR Marker Analysis of Genetic Relationships within Hydrangea Macrophylla

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity studies using 39 SSR markers were carried out with 114 taxa of H. macrophylla. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. Subspecies serrata contained nearly t...

  3. Evaluation of algorithms used to order markers on genetic maps.

    PubMed

    Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

    2009-12-01

    When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. PMID:19639011

  4. Molecular genetic medicine. Vol. 2

    SciTech Connect

    Friedmann, T.

    1992-01-01

    Theodore Friedmann has put together an interesting spectrum of articles for volume 2 of Molecular Genetic Medicine. Perhaps related to his own interest in the X chromosome, three articles deal with X-chromosomal topics, while two deal with autosomal disorders and two treat viral disorders. The fragile-X syndrome is thoroughly covered by Brown and Jenkins with an article that is heavily weighted to clinical aspects and now out-of-date RFLP approaches. The timeliness of the volume is insured by the coverage (albeit brief) that they give to the cloning of FMR-1. Gartler et al. present a balanced review of X inactivation - the oft-surveyed subject was comprehensively covered in a manner that provided new perspectives. Lambert et al. provide an exhaustive review of natural and induced mutation of hypoxanthine phosphoribosyltransferase. For autosomal disorders, an excellent review of the molecular genetics of hemoglobin syntheses and their alterations in disease is provided by Berg and Schecter. The level of detail presented seemed just right to this reviewer. A concise review of recent advances in the study of Down syndrome and its animal model, trisomy 16 mice, is provided by Holtzman and Epstein. With regard to viral topics, Chisari thoughtfully reviews hepatitis B virus structure and function and the possible pathogenic mechanisms involved in its induction of hepatocellular carcinoma. Wong-Staal and Haseltine's up-to-date review of the increasingly complex regulatory genes of HIV is marred by a mix-up in figure legends - an exception to an otherwise well-proofread book. In summary, this is a good volume of its type and is recommended for those who might benefit from reading such review articles.

  5. [Molecular genetics of Parkinson's disease].

    PubMed

    Toda, Tatsushi

    2007-08-01

    Parkinson's disease (PD) is the second most common neurodegenerative disorder in the world. The occurrence of PD is largely sporadic, while several families with Mendelian segregation of PD have been reported. PD is thought to be caused by mitochondrial dysfunction, oxidative stress and inflammation based on multiple genetic and environmental factors, resulting in the apoptosis of dopaminergic cells. Six causal genes for Mendelian inherited PD have been identified to date, which indicate the importance of the ubiquitin-proteasome pathway in the molecular pathogenesis of dopaminergic cell death. Recent studies have also indicated the involvement of genetic factors in the pathogenesis of sporadic PD. Many association studies on candidate genes have examined the relationship between PD and polymorphisms; We identified a-synuclein as a definite susceptibility gene for sporadic PD. Since 2001, significant linkage to several loci have been reported in samples of affected sibling pairs. With the recent advances in human genome analyses, genome-wide association studies by SNP chip are being performed to identify susceptibility genes and to establish tailor-made medicine for PD. PMID:17713117

  6. Genetic Authentication of Gardenia jasminoides Ellis var. grandiflora Nakai by Improved RAPD-Derived DNA Markers.

    PubMed

    Mei, Zhiqiang; Zhou, Boxu; Wei, Chunli; Cheng, Jingliang; Imani, Saber; Chen, Hanchun; Fu, Junjiang

    2015-01-01

    The evergreen shrub, Gardenia jasminoides Ellis var. grandiflora Nakai is one of the most popular garden-plants, with significant ornamental importance. Here, we have cloned improved random amplified polymorphic DNA (RAPD) derived fragments into T-vector, and developed sequence-characterized amplified region (SCAR) markers. These markers have been deposited in GenBank database with the accession numbers KP641310, KP641311, KP641312 and KP641313 respectively. The BLAST search of database confirmed the novelty of these markers. The four SCAR markers, namely ZZH11, ZZH31, ZZH41 and ZZH51 can specifically recognize the genetic materials of G. jasminoides from other plant species. Moreover, SCAR marker ZZH31 can be used to distinguish G. jasminoides Ellis var. grandiflora Nakai from other G. jasminoides on the market. Together, this study has developed four stably molecular SCAR markers by improved RAPD-derived DNA markers for the genetic identification and authentication, and for ecological conservation of medicinal and ornamental plant G. jasminoides. PMID:26569205

  7. Molecular Markers Predictive of Chemotherapy Response in Colorectal Cancer

    PubMed Central

    Shiovitz, Stacey; Grady, William M.

    2015-01-01

    Recognition of the molecular heterogeneity of colorectal cancer (CRC) has led to the classification of CRC based on a variety of clinical and molecular characteristics. Although the clinical significance of the majority of these molecular alterations is still being ascertained, it is widely anticipated that these characteristics will improve the accuracy of our ability to determine the prognosis and therapeutic response of CRC patients. A few of these markers, such as microsatellite instability and the CpG island methylator phenotype (CIMP), show promise as predictive markers for cytotoxic chemotherapy. KRAS is a validated biomarker for EGFR-targeted therapy, while NRAS and PI3KCA are evolving markers for targeted therapies. Multiple new actionable drug targets are being identified on a regular basis, but most are not ready for clinical use at this time. This review focuses on key molecular features of CRCs and the application of these molecular alterations as predictive biomarkers for CRC. PMID:25663616

  8. [Research progress on molecular genetics of forest musk deer].

    PubMed

    Jie, Hang; Zheng, Cheng-li; Wang, Jian-ming; Feng, Xiao-lan; Zeng, De-jun; Zhao, Gui-jun

    2015-11-01

    Forest musk deer is one of the large-scale farming musk deer animals with the largest population at the same time. The male musk deer can secrete valuable medicines, which has high medicinal and economic value. Due to the loss of habitat and indiscriminate hunting, the numbers of wild population specie and the distribution have been drastically reduced. Therefore, in-depth understanding of the molecular genetics progress of forest musk deer will pave a way for musk deer protection and breeding. In this review, the progress associated with the molecular marker, genetic classification, artificial breeding, musk secretion and disease in past decades were reviewed, in order to provide a theoretical basis for subsequent molecular genetic researches in forest musk deer. PMID:27097400

  9. Molecular marker database for efficient use in agricultural breeding programs

    PubMed Central

    Kim, Chang-Kug; Lee, Gang-Seob; Mo, Ji-Su; Bae, Seon-Hwa; Lee, Tae-Ho

    2015-01-01

    The National Agricultural Biotechnology Information Center (NABIC) constructed a web-based molecular marker database to provide information about 7,847 sequence-tagged site (STS) markers identified in the 11 species using a next generation sequencing (NGS) technologies. The database consists of three major functional categories: keyword search, detailed viewer and download function. The molecular marker annotation table provides detailed information such as ownership information, basic information, and STS-related characterization information. Availability The database is available for free at http://nabic.rda.go.kr/Molecularmarker PMID:26527854

  10. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment.

    PubMed

    Yıldız, M; Koçak, M; Baloch, F S

    2015-01-01

    Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra. PMID:26400290

  11. (-)-Menthol biosynthesis and molecular genetics.

    PubMed

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L; Wildung, Mark R

    2005-12-01

    (-)-Menthol is the most familiar of the monoterpenes as both a pure natural product and as the principal and characteristic constituent of the essential oil of peppermint (Mentha x piperita). In this paper, we review the biosynthesis and molecular genetics of (-)-menthol production in peppermint. In Mentha species, essential oil biosynthesis and storage is restricted to the peltate glandular trichomes (oil glands) on the aerial surfaces of the plant. A mechanical method for the isolation of metabolically functional oil glands, has provided a system for precursor feeding studies to elucidate pathway steps, as well as a highly enriched source of the relevant biosynthetic enzymes and of their corresponding transcripts with which cDNA libraries have been constructed to permit cloning and characterization of key structural genes. The biosynthesis of (-)-menthol from primary metabolism requires eight enzymatic steps, and involves the formation and subsequent cyclization of the universal monoterpene precursor geranyl diphosphate to the parent olefin (-)-(4S)-limonene as the first committed reaction of the sequence. Following hydroxylation at C3, a series of four redox transformations and an isomerization occur in a general "allylic oxidation-conjugate reduction" scheme that installs three chiral centers on the substituted cyclohexanoid ring to yield (-)-(1R, 3R, 4S)-menthol. The properties of each enzyme and gene of menthol biosynthesis are described, as are their probable evolutionary origins in primary metabolism. The organization of menthol biosynthesis is complex in involving four subcellular compartments, and regulation of the pathway appears to reside largely at the level of gene expression. Genetic engineering to up-regulate a flux-limiting step and down-regulate a side route reaction has led to improvement in the composition and yield of peppermint oil. PMID:16292524

  12. (-)-Menthol biosynthesis and molecular genetics

    NASA Astrophysics Data System (ADS)

    Croteau, Rodney B.; Davis, Edward M.; Ringer, Kerry L.; Wildung, Mark R.

    2005-12-01

    (-)-Menthol is the most familiar of the monoterpenes as both a pure natural product and as the principal and characteristic constituent of the essential oil of peppermint ( Mentha x piperita). In this paper, we review the biosynthesis and molecular genetics of (-)-menthol production in peppermint. In Mentha species, essential oil biosynthesis and storage is restricted to the peltate glandular trichomes (oil glands) on the aerial surfaces of the plant. A mechanical method for the isolation of metabolically functional oil glands, has provided a system for precursor feeding studies to elucidate pathway steps, as well as a highly enriched source of the relevant biosynthetic enzymes and of their corresponding transcripts with which cDNA libraries have been constructed to permit cloning and characterization of key structural genes. The biosynthesis of (-)-menthol from primary metabolism requires eight enzymatic steps, and involves the formation and subsequent cyclization of the universal monoterpene precursor geranyl diphosphate to the parent olefin (-)-(4 S)-limonene as the first committed reaction of the sequence. Following hydroxylation at C3, a series of four redox transformations and an isomerization occur in a general “allylic oxidation-conjugate reduction” scheme that installs three chiral centers on the substituted cyclohexanoid ring to yield (-)-(1 R, 3 R, 4 S)-menthol. The properties of each enzyme and gene of menthol biosynthesis are described, as are their probable evolutionary origins in primary metabolism. The organization of menthol biosynthesis is complex in involving four subcellular compartments, and regulation of the pathway appears to reside largely at the level of gene expression. Genetic engineering to up-regulate a flux-limiting step and down-regulate a side route reaction has led to improvement in the composition and yield of peppermint oil.

  13. Human Escherichia coli O157:H7 Genetic Marker in Isolates of Bovine Origin

    PubMed Central

    Abedon, Stephen T.; Takemura, Kaori; Christie, Nicholas P.; Sreevatsan, Srinand

    2004-01-01

    The antiterminator Q gene of bacteriophage 933W (Q933) was identified upstream of the stx2 gene in 90% of human disease–origin Escherichia coli O157:H7 isolates and in 44.5% of bovine isolates. Shiga toxin production was higher in Q933-positive isolates than Q933-negative isolates. This genetic marker may provide a useful molecular tool for epidemiologic studies. PMID:15496255

  14. Development of INDEL Markers for Genetic Mapping Based on Whole Genome Resequencing in Soybean

    PubMed Central

    Song, Xiaofeng; Wei, Haichao; Cheng, Wen; Yang, Suxin; Zhao, Yanxiu; Li, Xuan; Luo, Da; Zhang, Hui; Feng, Xianzhong

    2015-01-01

    Soybean [Glycine max (L.) Merrill] is an important crop worldwide. In this study, a Chinese local soybean cultivar, Hedou 12, was resequenced by next generation sequencing technology to develop INsertion/DELetion (INDEL) markers for genetic mapping. 49,276 INDEL polymorphisms and 242,059 single nucleotide polymorphisms were detected between Hedou 12 and the Williams 82 reference sequence. Of these, 243 candidate INDEL markers ranging from 5–50 bp in length were chosen for validation, and 165 (68%) of them revealed polymorphisms between Hedou 12 and Williams 82. The validated INDEL markers were also tested in 12 other soybean cultivars. The number of polymorphisms in the pairwise comparisons of 14 soybean cultivars varied from 27 to 165. To test the utility of these INDEL markers, they were used to perform genetic mapping of a crinkly leaf mutant, and the CRINKLY LEAF locus was successfully mapped to a 360 kb region on chromosome 7. This research shows that high-throughput sequencing technologies can facilitate the development of genome-wide molecular markers for genetic mapping in soybean. PMID:26483012

  15. Molecular Pathology: Predictive, Prognostic, and Diagnostic Markers in Lymphoid Neoplasms.

    PubMed

    Ho, Caleb; Kluk, Michael J

    2016-09-01

    Lymphoid neoplasms show great diversity in morphology, immunophenotypic profile, and postulated cells of origin, which also reflects the variety of genetic alterations within this group of tumors. This review discusses many of the currently known genetic alterations in selected mature B-cell and T-cell lymphoid neoplasms, and their significance as diagnostic, prognostic, and therapeutic markers. Given the rapidly increasing number of genetic alterations that have been described in this group of tumors, and that the clinical significance of many is still being studied, this is not an entirely exhaustive review of all of the genetic alterations that have been reported. PMID:27523974

  16. On marker-assisted prediction of genetic value: beyond the ridge.

    PubMed Central

    Gianola, Daniel; Perez-Enciso, Miguel; Toro, Miguel A

    2003-01-01

    Marked-assisted genetic improvement of agricultural species exploits statistical dependencies in the joint distribution of marker genotypes and quantitative traits. An issue is how molecular (e.g., dense marker maps) and phenotypic information (e.g., some measure of yield in plants) is to be used for predicting the genetic value of candidates for selection. Multiple regression, selection index techniques, best linear unbiased prediction, and ridge regression of phenotypes on marker genotypes have been suggested, as well as more elaborate methods. Here, phenotype-marker associations are modeled hierarchically via multilevel models including chromosomal effects, a spatial covariance of marked effects within chromosomes, background genetic variability, and family heterogeneity. Lorenz curves and Gini coefficients are suggested for assessing the inequality of the contribution of different marked effects to genetic variability. Classical and Bayesian methods are presented. The Bayesian approach includes a Markov chain Monte Carlo implementation. The generality and flexibility of the Bayesian method is illustrated when a Lorenz curve is to be inferred. PMID:12586721

  17. Elucidating genetic diversity among sour orange rootstocks: a comparative study of the efficiency of RAPD and SSR markers.

    PubMed

    Lamine, Myriam; Mliki, Ahmed

    2015-03-01

    In order to compare the effectiveness of two molecular marker systems, a set of six RAPD and nine SSR markers were used to study the genetic diversity in a population of 46 sour orange accessions, a common rootstock used in almost all citrus orchards in Tunisia. Genetic diversity parameters [average and effective number of alleles, percentage of polymorphism, polymorphic information content (PIC), effective marker index (EMI), and marker index (MI) parameters] for RAPD, SSR, and RAPD + SSR were determined in order to assess the efficiency of the two marker systems. The results revealed that these parameters were significantly higher when using RAPD markers. Similarly, cluster analysis using the results of RAPD was practically the same as that obtained when combining data from the two marker systems (RAPD + SSR) demonstrating the efficiency of RAPD in discriminating between sour orange accessions. Therefore, the use of SSR markers, known to be more efficient and discriminatory, does not bring significant supplementary information in this work. Indeed, results would have been obtained using only the RAPD markers. Accordingly, this work highlights the efficiency and advantages of RAPD, as an easy and efficient technique, in studying citrus rootstock's genetic diversity, and establishing genetic relationships among citrus accessions. PMID:25586488

  18. Molecular markers for leaf rust resistance genes in wheat.

    PubMed

    Chełkowski, J; Stepień, L

    2001-01-01

    Over 100 genes of resistance to rust fungi: Puccinia recondita f. sp. tritici, (47 Lr - leaf rust genes), P. striiformis (18 Yr - yellow rust genes) and P. graminis f. sp. tritici (41 Sr - stripe rust genes) have been identified in wheat (Triticum aestivum L.) and its wild relatives according to recent papers. Sixteen Lr resistance genes have been mapped using restriction fragments length polymorphism (RFLP) markers on wheat chromosomes. More than ten Lr genes can be identified in breeding materials by sequence tagged site (STS) specific markers. Gene Lrk 10, closely linked to gene Lr 10, has been cloned and its function recognized. Available markers are presented in this review. The STS, cleaved amplified polymorphic sequence (CAPS) and sequence characterized amplified regions (SCAR) markers found in the literature should be verified using Triticum spp. with different genetic background. Simple sequence repeats (SSR) markers for Lr resistance genes are now also available. PMID:14564046

  19. Development of microsatellite markers from an enriched genomic library for genetic analysis of melon (Cucumis melo L.)

    PubMed Central

    Ritschel, Patricia Silva; Lins, Tulio Cesar de Lima; Tristan, Rodrigo Lourenço; Buso, Gláucia Salles Cortopassi; Buso, José Amauri; Ferreira, Márcio Elias

    2004-01-01

    Background Despite the great advances in genomic technology observed in several crop species, the availability of molecular tools such as microsatellite markers has been limited in melon (Cucumis melo L.) and cucurbit species. The development of microsatellite markers will have a major impact on genetic analysis and breeding of melon, especially on the generation of marker saturated genetic maps and implementation of marker assisted breeding programs. Genomic microsatellite enriched libraries can be an efficient alternative for marker development in such species. Results Seven hundred clones containing microsatellite sequences from a Tsp-AG/TC microsatellite enriched library were identified and one-hundred and forty-four primer pairs designed and synthesized. When 67 microsatellite markers were tested on a panel of melon and other cucurbit accessions, 65 revealed DNA polymorphisms among the melon accessions. For some cucurbit species, such as Cucumis sativus, up to 50% of the melon microsatellite markers could be readily used for DNA polymophism assessment, representing a significant reduction of marker development costs. A random sample of 25 microsatellite markers was extracted from the new microsatellite marker set and characterized on 40 accessions of melon, generating an allelic frequency database for the species. The average expected heterozygosity was 0.52, varying from 0.45 to 0.70, indicating that a small set of selected markers should be sufficient to solve questions regarding genotype identity and variety protection. Genetic distances based on microsatellite polymorphism were congruent with data obtained from RAPD marker analysis. Mapping analysis was initiated with 55 newly developed markers and most primers showed segregation according to Mendelian expectations. Linkage analysis detected linkage between 56% of the markers, distributed in nine linkage groups. Conclusions Genomic library microsatellite enrichment is an efficient procedure for marker

  20. Myeloproliferative neoplasms: Current molecular biology and genetics.

    PubMed

    Saeidi, Kolsoum

    2016-02-01

    Myeloproliferative neoplasms (MPNs) are clonal disorders characterized by increased production of mature blood cells. Philadelphia chromosome-negative MPNs (Ph-MPNs) consist of polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). A number of stem cell derived mutations have been identified in the past 10 years. These findings showed that JAK2V617F, as a diagnostic marker involving JAK2 exon 14 with a high frequency, is the best molecular characterization of Ph-MPNs. Somatic mutations in an endoplasmic reticulum chaperone, named calreticulin (CALR), is the second most common mutation in patients with ET and PMF after JAK2 V617F mutation. Discovery of CALR mutations led to the increased molecular diagnostic of ET and PMF up to 90%. It has been shown that JAK2V617F is not the unique event in disease pathogenesis. Some other genes' location such as TET oncogene family member 2 (TET2), additional sex combs-like 1 (ASXL1), casitas B-lineage lymphoma proto-oncogene (CBL), isocitrate dehydrogenase 1/2 (IDH1/IDH2), IKAROS family zinc finger 1 (IKZF1), DNA methyltransferase 3A (DNMT3A), suppressor of cytokine signaling (SOCS), enhancer of zeste homolog 2 (EZH2), tumor protein p53 (TP53), runt-related transcription factor 1 (RUNX1) and high mobility group AT-hook 2 (HMGA2) have also identified to be involved in MPNs phenotypes. Here, current molecular biology and genetic mechanisms involved in MNPs with a focus on the aforementioned factors is presented. PMID:26697989

  1. Finding Markers That Make a Difference: DNA Pooling and SNP-Arrays Identify Population Informative Markers for Genetic Stock Identification

    PubMed Central

    Ozerov, Mikhail; Vasemägi, Anti; Wennevik, Vidar; Diaz-Fernandez, Rogelio; Kent, Matthew; Gilbey, John; Prusov, Sergey; Niemelä, Eero; Vähä, Juha-Pekka

    2013-01-01

    Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global FST, pairwise FST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise FST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species. PMID:24358184

  2. Finding markers that make a difference: DNA pooling and SNP-arrays identify population informative markers for genetic stock identification.

    PubMed

    Ozerov, Mikhail; Vasemägi, Anti; Wennevik, Vidar; Diaz-Fernandez, Rogelio; Kent, Matthew; Gilbey, John; Prusov, Sergey; Niemelä, Eero; Vähä, Juha-Pekka

    2013-01-01

    Genetic stock identification (GSI) using molecular markers is an important tool for management of migratory species. Here, we tested a cost-effective alternative to individual genotyping, known as allelotyping, for identification of highly informative SNPs for accurate genetic stock identification. We estimated allele frequencies of 2880 SNPs from DNA pools of 23 Atlantic salmon populations using Illumina SNP-chip. We evaluated the performance of four common strategies (global F ST, pairwise F ST, Delta and outlier approach) for selection of the most informative set of SNPs and tested their effectiveness for GSI compared to random sets of SNP and microsatellite markers. For the majority of cases, SNPs selected using the outlier approach performed best followed by pairwise F ST and Delta methods. Overall, the selection procedure reduced the number of SNPs required for accurate GSI by up to 53% compared with randomly chosen SNPs. However, GSI accuracy was more affected by populations in the ascertainment group rather than the ranking method itself. We demonstrated for the first time the compatibility of different large-scale SNP datasets by compiling the largest population genetic dataset for Atlantic salmon to date. Finally, we showed an excellent performance of our top SNPs on an independent set of populations covering the main European distribution range of Atlantic salmon. Taken together, we demonstrate how combination of DNA pooling and SNP arrays can be applied for conservation and management of salmonids as well as other species. PMID:24358184

  3. Genetic Kinship Investigation from Blood Groups to DNA Markers

    PubMed Central

    Geserick, Gunther; Wirth, Ingo

    2012-01-01

    The forensic application of hereditary characteristics became possible after the discovery of human blood groups by Karl Landsteiner in 1901. The foundation for their use in kinship investigation was laid by Emil von Dungern and Ludwig Hirschfeld in 1910 by clarification of the inheritance of the ABO groups. Up to the middle of the 20th century further red cell membrane systems were discovered. From the 1920s Fritz Schiff and Georg Strassmann fought for the introduction of blood groups into forensic kinship investigation. A new era of hemogenetics was opened from 1955 as genetic polymorphisms were described in serum proteins. Starting in 1958 there followed the complex HLA system of white blood cells, which from 1963 was joined by polymophisms in erythrocyte enzymes. Therefore, from the 1980s, it was possible to clarify the majority of kinship cases with a combination of conventional markers. From 1990 to 2000 the conventional markers were gradually replaced by the more effective DNA markers. Simultaneously typing shifted from the phenotype level to the genotype level. The genomic structure of conventional genetic markers could also now be explained. As a reflection of scientific progress the legal situation also changed, particularly in the form of the official guidelines for kinship investigation. PMID:22851931

  4. Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers.

    PubMed

    Alikhani, Leila; Rahmani, Mohammad-Shafie; Shabanian, Naghi; Badakhshan, Hedieh; Khadivi-Khub, Abdollah

    2014-11-15

    Persian oak (Quercus brantii Lindl.) is one of the most important woody species of the Zagros forests in Iran. Three molecular marker techniques: start codon targeted (SCoT), inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) markers were compared for fingerprinting of 125 individuals of this species collected from different geographical locations of north-west of Iran. A total of 233 bands were amplified by 18 ISSR primers, of which 224 (96.10%) were polymorphic, and 126 polymorphic bands (97.65%) were observed in 129 bands amplified by 10 IRAP primers. Besides, 118 bands were observed for all 10 SCoT primers, of which 113 were polymorphic (95.71%). Average polymorphism information content (PIC) for ISSR, IRAP and SCoT markers was 0.30, 0.32 and 0.38, respectively, and this revealed that SCoT markers were more informative than IRAP and ISSR for the assessment of diversity among individuals. Based on the three different molecular types, cluster analysis revealed that 125 individuals taken for the analysis can be divided into three distinct clusters. The Jaccard's genetic similarity based on the combined data ranged from 0.23 to 0.76. These results suggest that efficiency of SCoT, IRAP and ISSR markers was relatively the same in fingerprinting of individuals. All molecular marker types revealed a low genetic differentiation among populations, indicating the possibility of gene flow between the studied populations. These results have an important implication for Persian oak (Q. brantii) germplasm characterization, improvement, and conservation. PMID:25241382

  5. Electrophysiological markers of genetic risk for attention deficit hyperactivity disorder

    PubMed Central

    Tye, Charlotte; McLoughlin, Gráinne; Kuntsi, Jonna; Asherson, Philip

    2014-01-01

    Electroencephalography (EEG) is an ideal neuroscientific approach, providing a direct measurement of neural activity that demonstrates reliability, developmental stability and high heritability. This systematic review of a subset of domains evaluates the utility of electrophysiological measures as potential intermediate phenotypes for ADHD in the domains of quantitative EEG indices of arousal and intra-individual variability, and functional investigations of inhibitory and error processing using the event-related potential (ERP) technique. Each domain demonstrates consistent and meaningful associations with ADHD, a degree of genetic overlap with ADHD and potential links to specific genetic variants. Investigations of the genetic and environmental contributions to EEG/ERP and shared genetic overlap with ADHD may enhance molecular genetic studies and provide novel insights into aetiology. Such research will aid in the precise characterisation of the clinical deficits seen in ADHD and guide the development of novel intervention and prevention strategies for those at risk. PMID:21426626

  6. Assessment of genetic diversity in Brazilian barley using SSR markers

    PubMed Central

    Ferreira, Jéssica Rosset; Pereira, Jorge Fernando; Turchetto, Caroline; Minella, Euclydes; Consoli, Luciano; Delatorre, Carla Andréa

    2016-01-01

    Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs. PMID:27007902

  7. Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean

    PubMed Central

    2012-01-01

    Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron

  8. Genetic markers for western corn rootworm resistance to Bt toxin.

    PubMed

    Flagel, Lex E; Swarup, Shilpa; Chen, Mao; Bauer, Christopher; Wanjugi, Humphrey; Carroll, Matthew; Hill, Patrick; Tuscan, Meghan; Bansal, Raman; Flannagan, Ronald; Clark, Thomas L; Michel, Andrew P; Head, Graham P; Goldman, Barry S

    2015-03-01

    Western corn rootworm (WCR) is a major maize (Zea mays L.) pest leading to annual economic losses of more than 1 billion dollars in the United States. Transgenic maize expressing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely used for the management of WCR. However, cultivation of Bt-expressing maize places intense selection pressure on pest populations to evolve resistance. Instances of resistance to Bt toxins have been reported in WCR. Developing genetic markers for resistance will help in characterizing the extent of existing issues, predicting where future field failures may occur, improving insect resistance management strategies, and in designing and sustainably implementing forthcoming WCR control products. Here, we discover and validate genetic markers in WCR that are associated with resistance to the Cry3Bb1 Bt toxin. A field-derived WCR population known to be resistant to the Cry3Bb1 Bt toxin was used to generate a genetic map and to identify a genomic region associated with Cry3Bb1 resistance. Our results indicate that resistance is inherited in a nearly recessive manner and associated with a single autosomal linkage group. Markers tightly linked with resistance were validated using WCR populations collected from Cry3Bb1 maize fields showing significant WCR damage from across the US Corn Belt. Two markers were found to be correlated with both diet (R2 = 0.14) and plant (R2 = 0.23) bioassays for resistance. These results will assist in assessing resistance risk for different WCR populations, and can be used to improve insect resistance management strategies. PMID:25566794

  9. Genetic Markers for Western Corn Rootworm Resistance to Bt Toxin

    PubMed Central

    Flagel, Lex E.; Swarup, Shilpa; Chen, Mao; Bauer, Christopher; Wanjugi, Humphrey; Carroll, Matthew; Hill, Patrick; Tuscan, Meghan; Bansal, Raman; Flannagan, Ronald; Clark, Thomas L.; Michel, Andrew P.; Head, Graham P.; Goldman, Barry S.

    2015-01-01

    Western corn rootworm (WCR) is a major maize (Zea mays L.) pest leading to annual economic losses of more than 1 billion dollars in the United States. Transgenic maize expressing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely used for the management of WCR. However, cultivation of Bt-expressing maize places intense selection pressure on pest populations to evolve resistance. Instances of resistance to Bt toxins have been reported in WCR. Developing genetic markers for resistance will help in characterizing the extent of existing issues, predicting where future field failures may occur, improving insect resistance management strategies, and in designing and sustainably implementing forthcoming WCR control products. Here, we discover and validate genetic markers in WCR that are associated with resistance to the Cry3Bb1 Bt toxin. A field-derived WCR population known to be resistant to the Cry3Bb1 Bt toxin was used to generate a genetic map and to identify a genomic region associated with Cry3Bb1 resistance. Our results indicate that resistance is inherited in a nearly recessive manner and associated with a single autosomal linkage group. Markers tightly linked with resistance were validated using WCR populations collected from Cry3Bb1 maize fields showing significant WCR damage from across the US Corn Belt. Two markers were found to be correlated with both diet (R2 = 0.14) and plant (R2 = 0.23) bioassays for resistance. These results will assist in assessing resistance risk for different WCR populations, and can be used to improve insect resistance management strategies. PMID:25566794

  10. Genetic characterization of the gypsy moth from China (Lepidoptera, Lymantriidae) using inter simple sequence repeats markers.

    PubMed

    Chen, Fang; Shi, Juan; Luo, You-Qing; Sun, Shuang-Yan; Pu, Min

    2013-01-01

    This study provides the first genetic characterization of the gypsy moth from China (Lymantriadispar), one of the most recognized pests of forests and ornamental trees in the world. We assessed genetic diversity and structure in eight geographic populations of gypsy moths from China using five polymorphic Inter simple sequence repeat markers, which produced reproducible banding patterns. We observed 102 polymorphic loci across the 176 individuals sampled. Overall genetic diversity (Nei's, H) was 0.2357, while the mean genetic diversity within geographic populations was 0.1845 ± 0.0150. The observed genetic distance among the eight populations ranged from 0.0432 to 0.1034. Clustering analysis (using an unweighted pair-group method with arithmetic mean and multidimensional scaling), revealed strong concordance between the strength of genetic relationships among populations and their geographic proximity. Analysis of molecular variance demonstrated that 25.43% of the total variability (F ST = 0.2543, P < 0.001) was attributable to variation among geographic populations. The results of our analyses investigating the degree of polymorphism, genetic diversity (Nei's and Shannon) and genetic structure, suggest that individuals from Hebei may be better able to adapt to different environments and to disperse to new habitats. This study provides crucial genetic information needed to assess the distribution and population dynamics of this important pest species of global concern. PMID:23951339

  11. Genetics and molecular biology of breast cancer

    SciTech Connect

    King, M.C.; Lippman, M.

    1992-12-31

    This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.

  12. Genetic traceability of black pig meats using microsatellite markers.

    PubMed

    Oh, Jae-Don; Song, Ki-Duk; Seo, Joo-Hee; Kim, Duk-Kyung; Kim, Sung-Hoon; Seo, Kang-Seok; Lim, Hyun-Tae; Lee, Jae-Bong; Park, Hwa-Chun; Ryu, Youn-Chul; Kang, Min-Soo; Cho, Seoae; Kim, Eui-Soo; Choe, Ho-Sung; Kong, Hong-Sik; Lee, Hak-Kyo

    2014-07-01

    Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and -0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10(-14) in population J, 3.17×10(-9) in population B, and 1.03×10(-12) in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers. PMID:25050032

  13. Association of Wegener's granulomatosis with HLA antigens and other genetic markers.

    PubMed Central

    Papiha, S S; Murty, G E; Ad'Hia, A; Mains, B T; Venning, M

    1992-01-01

    The frequencies of the HLA-A, B, C, DR, DQ antigens and of several other genetic markers in biopsy proved and well characterised patients with Wegener's granulomatosis were compared with control frequencies of the region. A highly significant increase in HLA-DR1 was found. The percentage combined frequency of DR1-DQw1 was significantly higher in patients than in the controls. Interestingly, association with the red cell enzyme GLOI and complement locus C4B was also seen. As both of these markers are either linked or within the major histocompatibility complex region (MHC) this is further evidence for the involvement of chromosome 6 in the pathogenesis of Wegener's granulomatosis. To understand the pathology of the disease fully molecular genetic studies of the MHC region are warranted. PMID:1550412

  14. Identification and validation of a core set of microsatellite markers for genetic diversity analysis in watermelon, Citrullus lanatus Thunb. Matsum. & Nakai

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Watermelon is an important vegetable crop worldwide. Watermelon has a narrow genetic base, which makes it difficult in detection and utilization of the genetic variations, cultivar identification and increasing genetic diversity that are some important tasks for watermelon breeders. Molecular marker...

  15. First genetic linkage map for the mud crab (Scylla paramamosain) constructed using microsatellite and AFLP markers.

    PubMed

    Ma, H Y; Li, S J; Feng, N N; Ma, C Y; Wang, W; Chen, W; Ma, L B

    2016-01-01

    The mud crab (Scylla paramamosain) is of economic importance for the fisheries and aquaculture industry in China. In this study, we constructed the first genetic linkage map for this species using microsatellite and amplified fragment length polymorphism (AFLP) markers. The map consisted of 65 linkage groups, including 34 triplets and 9 doublets. A total of 212 molecular markers were mapped, including 60 microsatellites and 152 AFLP markers. The linkage groups ranged from 7 to 102.5 cM and covered 2746.4 cM in length. The mean length was 42.3 cM per linkage group, and the mean spacing was 18.68 cM. The genome size was estimated to be 5539.62 cM, with 50% coverage by the present map. Moreover, we reported 5 transcriptome-derived polymorphic microsatellite markers and characterized their polymorphism in a first-generation family. This study will facilitate studies on high-density maps and molecular marker-assisted selection in S. paramamosain and related crustacean species. PMID:27323059

  16. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources. PMID:26782500

  17. Pilocytic astrocytoma: pathology, molecular mechanisms and markers.

    PubMed

    Collins, V Peter; Jones, David T W; Giannini, Caterina

    2015-06-01

    Pilocytic astrocytomas (PAs) were recognized as a discrete clinical entity over 70 years ago. They are relatively benign (WHO grade I) and have, as a group, a 10-year survival of over 90%. Many require merely surgical removal and only very infrequently do they progress to more malignant gliomas. While most show classical morphology, they may present a spectrum of morphological patterns, and there are difficult cases that show similarities to other gliomas, some of which are malignant and require aggressive treatment. Until recently, almost nothing was known about the molecular mechanisms involved in their development. The use of high-throughput sequencing techniques interrogating the whole genome has shown that single abnormalities of the mitogen-activating protein kinase (MAPK) pathway are exclusively found in almost all cases, indicating that PA represents a one-pathway disease. The most common mechanism is a tandem duplication of a ≈2 Mb-fragment of #7q, giving rise to a fusion between two genes, resulting in a transforming fusion protein, consisting of the N-terminus of KIAA1549 and the kinase domain of BRAF. Additional infrequent fusion partners have been identified, along with other abnormalities of the MAP-K pathway, affecting tyrosine kinase growth factor receptors at the cell surface (e.g., FGFR1) as well as BRAF V600E, KRAS, and NF1 mutations among others. However, while the KIAA1549-BRAF fusion occurs in all areas, the incidence of the various other mutations identified differs in PAs that develop in different regions of the brain. Unfortunately, from a diagnostic standpoint, almost all mutations found have been reported in other brain tumor types, although some retain considerable utility. These molecular abnormalities will be reviewed, and the difficulties in their potential use in supporting a diagnosis of PA, when the histopathological findings are equivocal or in the choice of individualized therapy, will be discussed. PMID:25792358

  18. Role of emerging molecular markers in pancreatic cyst fluid.

    PubMed

    Al-Haddad, Mohammad

    2015-01-01

    Cystic lesions of the pancreas (CLPs) are increasingly diagnosed due to the growing utilization of cross-sectional imaging modalities. The differentiation between true cysts (epithelial tumors) and nonepithelial lesions (such as pseudocysts) relies on clinical and imaging characteristics, but more reliably obtained by endoscopic ultrasound (EUS) fine-needle aspiration. Due to their malignant potential, some of the true pancreatic cysts require further assessment and periodic follow-up. Therefore, it is important to establish a solid diagnosis at the time of detection of the various types of pancreatic cysts. Due to the limitations of cytology and biochemical markers in accurately classifying cyst pathology, the search for specific molecular markers associated with each type of cyst is ongoing. In this chapter, we will review some of the emerging molecular markers in pancreatic cystic fluid and their potential impact on endosonography and pancreatic cyst management. PMID:26643693

  19. Acceleration of peanut breeding programs by molecular marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut breeding has played a significant role in yield increases and disease control. Conventional breeding focuses on field selection and phenotypic analysis and it typically takes 12-15 years before a new cultivar can be released. Molecular markers developed from sequencing data can be of great ...

  20. Clinical Relevance of Prognostic and Predictive Molecular Markers in Gliomas.

    PubMed

    Siegal, Tali

    2016-01-01

    Sorting and grading of glial tumors by the WHO classification provide clinicians with guidance as to the predicted course of the disease and choice of treatment. Nonetheless, histologically identical tumors may have very different outcome and response to treatment. Molecular markers that carry both diagnostic and prognostic information add useful tools to traditional classification by redefining tumor subtypes within each WHO category. Therefore, molecular markers have become an integral part of tumor assessment in modern neuro-oncology and biomarker status now guides clinical decisions in some subtypes of gliomas. The routine assessment of IDH status improves histological diagnostic accuracy by differentiating diffuse glioma from reactive gliosis. It carries a favorable prognostic implication for all glial tumors and it is predictive for chemotherapeutic response in anaplastic oligodendrogliomas with codeletion of 1p/19q chromosomes. Glial tumors that contain chromosomal codeletion of 1p/19q are defined as tumors of oligodendroglial lineage and have favorable prognosis. MGMT promoter methylation is a favorable prognostic marker in astrocytic high-grade gliomas and it is predictive for chemotherapeutic response in anaplastic gliomas with wild-type IDH1/2 and in glioblastoma of the elderly. The clinical implication of other molecular markers of gliomas like mutations of EGFR and ATRX genes and BRAF fusion or point mutation is highlighted. The potential of molecular biomarker-based classification to guide future therapeutic approach is discussed and accentuated. PMID:26508407

  1. Confirmation of hybrid origin in Arisaema (Araceae) using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A population of hybrids between Arisaema triphyllum subsp. stewardsonii and A. dracontium was investigated using molecular markers to document the hybrid origin. Total genomic DNA was extracted from A. triphyllum, A. dracontium, and the hybrids, and subjected to sequence analysis of various regions...

  2. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.

    1990-10-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.

  3. Molecular genetic variation in cultivated peanuts germplasm of Henan and detection of their elite allelic variations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts i...

  4. Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane propagates asexually through vegetative cuttings. To validate the genetic identity of sugarcane clones during shipping and handling, we produced molecular fingerprints based on 21 microsatellite (SSR) DNA markers for 116 Louisiana parental clones that were included in the crossing program...

  5. Analysis of genetic diversity identified by amplified fragment length polymorphism marker in hybrid wheat.

    PubMed

    Ejaz, M; Qidi, Z; Gaisheng, Z; Na, N; Huiyan, Z; Qunzhu, W

    2015-01-01

    Amplified fragment length polymorphism markers were used to assess genetic diversity in 10 male sterile wheat crop lines (hetero-cytoplasm with the same nucleus) in relation to a restorer wheat line. These male sterile lines were evaluated using 64 amplified fragment length polymorphism primer combinations, and 13 primers produced polymorphic bands, generating a total 682 fragments. Of the 682 fragments, 113 were polymorphic. The polymorphic information content and marker index values demonstrated the utility of the primer combinations used in the present study. Unweighted pair group method with arithmetic mean and principal coordinate analysis of the genotypic data revealed clustering of accessions based on genetic relationships, and accessions were separated into 2 groups with their restorer line. Jaccard's similarity coefficient values suggested good variability among the male sterile lines, indicating their utility in breeding programs. The fallouts of analysis of molecular variance showed large within-group population variation, accounting for 77% of variation, while among-group comparison accounted for 23% of the total molecular variation, which was statistically significant. The molecular diversity observed in this study will be useful for selecting appropriate accessions for plant improvement and hybridization through molecular-breeding approaches and for developing suitable conservation strategies. PMID:26345825

  6. Genetic diversity of popcorn genotypes using molecular analysis.

    PubMed

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

    2015-01-01

    In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients. PMID:26345916

  7. The genomic Echinococcus microsatellite EmsB sequences: from a molecular marker to the epidemiological tool.

    PubMed

    Knapp, J; Bart, J M; Maillard, S; Gottstein, B; Piarroux, R

    2010-03-01

    In the field of molecular and epidemiological parasitology, characterization of fast evolving genetic markers appears as an important challenge to consider the diversity and genetic structure of parasites. The study of respective populations can help us to understand their adaptive strategies to survive and perpetuate the species within different host populations, all trying to resist infection. In the past, the relative monomorphic features of Echinococcus multilocularis, the causative agent of alveolar echinococcosis and a severe human parasitic disease, did not stimulate studies dealing with the genetic variability of Echinococcus species or respective populations. A recently developed, characterized and validated original multilocus microsatellite, named EmsB, tandemly repeated in the genome, offered an additional opportunity for this line of investigation. We have compiled in this review new insights brought by this molecular tracker on the transmission activity of Echinococcus among different hosts and at different geographical scales. PMID:20025824

  8. Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

    PubMed Central

    Liu, Yaling; Zhang, Pengfei; Song, Meiling; Hou, Junling; Qing, Mei; Wang, Wenquan; Liu, Chunsheng

    2015-01-01

    Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR). Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice. PMID:26571372

  9. Analysis of plant diversity with retrotransposon-based molecular markers

    PubMed Central

    Kalendar, R; Flavell, A J; Ellis, T H N; Sjakste, T; Moisy, C; Schulman, A H

    2011-01-01

    Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants. PMID:20683483

  10. Molecular Genetics of Mitochondrial Disorders

    ERIC Educational Resources Information Center

    Wong, Lee-Jun C.

    2010-01-01

    Mitochondrial respiratory chain (RC) disorders (RCDs) are a group of genetically and clinically heterogeneous diseases because of the fact that protein components of the RC are encoded by both mitochondrial and nuclear genomes and are essential in all cells. In addition, the biogenesis, structure, and function of mitochondria, including DNA…

  11. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges.

    PubMed

    Kanthaswamy, S

    2015-10-01

    This review highlights the importance of domestic animal genetic evidence sources, genetic testing, markers and analytical approaches as well as the challenges this field is facing in view of the de facto 'gold standard' human DNA identification. Because of the genetic similarity between humans and domestic animals, genetic analysis of domestic animal hair, saliva, urine, blood and other biological material has generated vital investigative leads that have been admitted into a variety of court proceedings, including criminal and civil litigation. Information on validated short tandem repeat, single nucleotide polymorphism and mitochondrial DNA markers and public access to genetic databases for forensic DNA analysis is becoming readily available. Although the fundamental aspects of animal forensic genetic testing may be reliable and acceptable, animal forensic testing still lacks the standardized testing protocols that human genetic profiling requires, probably because of the absence of monetary support from government agencies and the difficulty in promoting cooperation among competing laboratories. Moreover, there is a lack in consensus about how to best present the results and expert opinion to comply with court standards and bear judicial scrutiny. This has been the single most persistent challenge ever since the earliest use of domestic animal forensic genetic testing in a criminal case in the mid-1990s. Crime laboratory accreditation ensures that genetic test results have the courts' confidence. Because accreditation requires significant commitments of effort, time and resources, the vast majority of animal forensic genetic laboratories are not accredited nor are their analysts certified forensic examiners. The relevance of domestic animal forensic genetics in the criminal justice system is undeniable. However, further improvements are needed in a wide range of supporting resources, including standardized quality assurance and control protocols for sample

  12. Reviewing and Updating the Major Molecular Markers for Stem Cells

    PubMed Central

    Calloni, Raquel; Cordero, Elvira Alicia Aparicio; Henriques, João Antonio Pêgas

    2013-01-01

    Stem cells (SC) are able to self-renew and to differentiate into many types of committed cells, making SCs interesting for cellular therapy. However, the pool of SCs in vivo and in vitro consists of a mix of cells at several stages of differentiation, making it difficult to obtain a homogeneous population of SCs for research. Therefore, it is important to isolate and characterize unambiguous molecular markers that can be applied to SCs. Here, we review classical and new candidate molecular markers that have been established to show a molecular profile for human embryonic stem cells (hESCs), mesenchymal stem cells (MSCs), and hematopoietic stem cells (HSCs). The commonly cited markers for embryonic ESCs are Nanog, Oct-4, Sox-2, Rex-1, Dnmt3b, Lin-28, Tdgf1, FoxD3, Tert, Utf-1, Gal, Cx43, Gdf3, Gtcm1, Terf1, Terf2, Lefty A, and Lefty B. MSCs are primarily identified by the expression of CD13, CD29, CD44, CD49e, CD54, CD71, CD73, CD90, CD105, CD106, CD166, and HLA-ABC and lack CD14, CD31, CD34, CD45, CD62E, CD62L, CD62P, and HLA-DR expression. HSCs are mainly isolated based on the expression of CD34, but the combination of this marker with CD133 and CD90, together with a lack of CD38 and other lineage markers, provides the most homogeneous pool of SCs. Here, we present new and alternative markers for SCs, along with microRNA profiles, for these cells. PMID:23336433

  13. Genetic and Molecular Ecotoxicology: A Research Framework

    PubMed Central

    Anderson, Susan; Sadinski, Walter; Shugart, Lee; Brussard, Peter; Depledge, Michael; Ford, Tim; Hose, JoEllen; Stegeman, John; Suk, William; Wirgin, Isaac; Wogan, Gerald

    1994-01-01

    Participants at the Napa Conference on Genetic and Molecular Ecotoxicology assessed the status of this field in light of heightened concerns about the genetic effects of exposure to hazardous substances and recent advancements in our capabilities to measure those effects. We present here a synthesis of the ideas discussed throughout the conference, including definitions of important concepts in the field and critical research needs and opportunities. While there were many opinions expressed on these topics, there was general agreement that there are substantive new opportunities to improve the impact of genetic and molecular ecotoxicology on prediction of sublethal effects of exposure to hazardous substances. Future studies should emphasize integration of genetic ecotoxicology, ecological genetics, and molecular biology and should be directed toward improving our understanding of the ecological implications of genotoxic responses. Ecological implications may be assessed at either the population or ecosystem level; however, a population-level focus may be most pragmatic. Recent technical advancements in measuring genetic and molecular responses to toxicant exposure will spur rapid progress. These new techniques have considerable promise for increasing our understanding of both mechanisms of toxicity on genes or gene products and the relevance of detrimental effects to individual fitness. — Environ Health Perspect 102(Suppl 12):3–8 (1994) PMID:7713030

  14. Quantitative PCR for genetic markers of human fecal pollution.

    PubMed

    Shanks, Orin C; Kelty, Catherine A; Sivaganesan, Mano; Varma, Manju; Haugland, Richard A

    2009-09-01

    Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 x 10(6) copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters. PMID:19592537

  15. The molecular genetics of holoprosencephaly.

    PubMed

    Roessler, Erich; Muenke, Maximilian

    2010-02-15

    Holoprosencephaly (HPE) has captivated the imagination of Man for millennia because its most extreme manifestation, the single-eyed cyclopic newborn infant, brings to mind the fantastical creature Cyclops from Greek mythology. Attempting to understand this common malformation of the forebrain in modern medical terms requires a systematic synthesis of genetic, cytogenetic, and environmental information typical for studies of a complex disorder. However, even with the advances in our understanding of HPE in recent years, there are significant obstacles remaining to fully understand its heterogeneity and extensive variability in phenotype. General lessons learned from HPE will likely be applicable to other malformation syndromes. Here we outline the common, and rare, genetic and environmental influences on this conserved developmental program of forebrain development and illustrate the similarities and differences between these malformations in humans and those of animal models. PMID:20104595

  16. Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar

    PubMed Central

    2012-01-01

    present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection. PMID:23170872

  17. [THE SOMATIC MUTATIONS AND ABERRANT METHYLATION AS POTENTIAL GENETIC MARKERS OF URINARY BLADDER CANCER].

    PubMed

    Mikhailenko, D S; Kushlinskii, N E

    2016-02-01

    All around the world, more than 330 thousands cases of bladder cancer are registered annually hence representing actual problem of modern oncology. Still in demand are search and characteristic of new molecular markers of bladder cancer detecting in tumor cells from urinary sediment and having high diagnostic accuracy. The studies of last decade, especially using methods of genome-wide sequencing, permitted to receive a large amount of experimental data concerning development and progression of bladder cancer The review presents systematic analysis of publications available in PubMed data base mainly of last five years. The original studies of molecular genetic disorders under bladder cancer and meta-analyzes were considered This approach permitted to detected the most common local alterations of DNA under bladder cancer which can be detected using routine genetic methods indifferent clinical material and present prospective interest for development of test-systems. The molecular genetic markers of disease can be activating missense mutations in 7 and 10 exons of gene of receptor of growth factor of fibroblasts 3 (FGFR3), 9 and 20 exons of gene of Phosphatidylinositol-4,5-bi-phosphate-3-kinase (PIK3CA) and mutation in -124 and -146 nucleotides in promoter of gene of catalytic subunit telomerase (TERT). The development of test-systems on the basis of aberrant methylation of CpG-islets of genes-suppressors still is seemed as a difficult task because of differences in pattern of methylation of different primary tumors at various stages of clonal evolution of bladder cancer though they can be considered as potential markers. PMID:27455559

  18. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers

    PubMed Central

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei’s genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance

  19. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    PubMed

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  20. Molecular Genetic Analysis of Chlamydia Species.

    PubMed

    Sixt, Barbara S; Valdivia, Raphael H

    2016-09-01

    Species of Chlamydia are the etiologic agent of endemic blinding trachoma, the leading cause of bacterial sexually transmitted diseases, significant respiratory pathogens, and a zoonotic threat. Their dependence on an intracellular growth niche and their peculiar developmental cycle are major challenges to elucidating their biology and virulence traits. The last decade has seen tremendous advances in our ability to perform a molecular genetic analysis of Chlamydia species. Major achievements include the generation of large collections of mutant strains, now available for forward- and reverse-genetic applications, and the introduction of a system for plasmid-based transformation enabling complementation of mutations; expression of foreign, modified, or reporter genes; and even targeted gene disruptions. This review summarizes the current status of the molecular genetic toolbox for Chlamydia species and highlights new insights into their biology and new challenges in the nascent field of Chlamydia genetics. PMID:27607551

  1. STRENGTHS AND WEAKNESSES OF MOLECULAR MARKERS FOR STUDIES OF DIVERSITY IN GENEBANK HOLDINGS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers have many potential advantages over morphological or other marker types to characterize within- and between-species diversity, useful for management of genebank holdings. These include greater number (potentially unlimited) of markers, freedom from pleiotropic effects, greater ease...

  2. A global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan.

    PubMed

    Chang, C S; Chen, C F; Berthouly-Salazar, C; Chazara, O; Lee, Y P; Chang, C M; Chang, K H; Bed'Hom, B; Tixier-Boichard, M

    2012-04-01

    Molecular and phenotypic data have been combined to characterize the genetic diversity of six local chicken breeds maintained with a long-term conservation programme. Hua-Tung, Hsin-Yi, Ju-Chi and Quemoy originated from Taiwan, Shek-Ki is from South China, and Nagoya is from Japan. Molecular tools included 24 microsatellite markers, melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) (MC1R), the LEI0258 marker located within the major histocompatibility complex (MHC), and mitochondrial DNA. Performance was recorded on the same individuals for body weight, panting rate in summer and antibody response (antigens: Newcastle disease virus and sheep red blood cells). A multivariate method previously proposed for taxonomy was used to combine the different data sets. Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) and the MCW330 marker contributed the most to the first axis of the multiple coinertia analysis of molecular markers. Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) showed evidence of selection, probably related to its effect on feather colour. The MHC exhibited a large diversity, with 16 alleles of the LEI0258 marker. Immune response traits contributed the most to the principal component analysis of phenotypic data. Eight mitochondrial DNA haplotypes related to clades A, B, C and E were distributed across breeds and revealed an important contribution of Indian and European breeds to Ju-Chi, Quemoy and Hsin-Yi. Phenotypic data contributed less than molecular data to the combined analysis, and two markers, LEI0258 and LEI0228, contributed the most. The combined analysis could clearly discriminate all breeds, except Ju-Chi, which was similar to Quemoy for many criteria, except immune response. PMID:22404353

  3. Molecular tumor markers for asbestos-related mesothelioma: serum diagnostic markers.

    PubMed

    Maeda, Masahiro; Hino, Okio

    2006-11-01

    Mesothelioma is an aggressive tumor arising from the mesothelium, and is usually associated with previous exposure to asbestos. The incubation period of the tumor may be described as 30-40 years, and the prognosis is dismal. In addition to immunohistochemical markers, recently, serum markers for the diagnosis of mesothelioma have been reported as candidates. In contrast, the expression in renal carcinoma (ERC) gene has been discovered in the Eker rat model (Tsc2 gene mutant), which is a homolog of the human mesothelin/megakaryocyte potentiating factor gene, and a novel ELISA system (N-ERC/mesothelin) has been developed. It has also been found that N-ERC/mesothelin is very stable and plentiful in the blood. In the present paper the potential utility of molecular diagnostic markers is reviewed, including ELISA systems for asbestos-related mesothelioma. PMID:17040286

  4. Toward diagnostic and phenotype markers for genetically transmitted speech delay.

    PubMed

    Shriberg, Lawrence D; Lewis, Barbara A; Tomblin, J Bruce; McSweeny, Jane L; Karlsson, Heather B; Scheer, Alison R

    2005-08-01

    Converging evidence supports the hypothesis that the most common subtype of childhood speech sound disorder (SSD) of currently unknown origin is genetically transmitted. We report the first findings toward a set of diagnostic markers to differentiate this proposed etiological subtype (provisionally termed speech delay-genetic) from other proposed subtypes of SSD of unknown origin. Conversational speech samples from 72 preschool children with speech delay of unknown origin from 3 research centers were selected from an audio archive. Participants differed on the number of biological, nuclear family members (0 or 2+) classified as positive for current and/or prior speech-language disorder. Although participants in the 2 groups were found to have similar speech competence, as indexed by their Percentage of Consonants Correct scores, their speech error patterns differed significantly in 3 ways. Compared with children who may have reduced genetic load for speech delay (no affected nuclear family members), children with possibly higher genetic load (2+ affected members) had (a) a significantly higher proportion of relative omission errors on the Late-8 consonants; (b) a significantly lower proportion of relative distortion errors on these consonants, particularly on the sibilant fricatives /s/, /z/, and //; and (c) a significantly lower proportion of backed /s/ distortions, as assessed by both perceptual and acoustic methods. Machine learning routines identified a 3-part classification rule that included differential weightings of these variables. The classification rule had diagnostic accuracy value of 0.83 (95% confidence limits = 0.74-0.92), with positive and negative likelihood ratios of 9.6 (95% confidence limits = 3.1-29.9) and 0.40 (95% confidence limits = 0.24-0.68), respectively. The diagnostic accuracy findings are viewed as promising. The error pattern for this proposed subtype of SSD is viewed as consistent with the cognitive-linguistic processing deficits

  5. Molecular markers in oral lichen planus: A systematic review.

    PubMed

    Sagari, Shitalkumar; Sanadhya, Sudhanshu; Doddamani, Mallikarjun; Rajput, Rajan

    2016-01-01

    Oral lichen planus (OLP) is a chronic inflammatory mucosal disease that is usually detected in 0.5-2.2% of the human population. Among these, only 0.5-2.9% of the lesions progress to carcinoma. However, there are no prognostic markers available presently to recognize the increased risk in malignant transformation of the lesions. Selected markers for cell proliferation, adhesion, apoptosis and lymphocytic infiltration were analyzed by immunohistochemistry in addition to static cytometry for DNA content. The concept linking OLP and oral squamous cell carcinoma states that chronic inflammation results in crucial DNA damage, which further progresses to development of carcinoma. Even though in the past decade, enormous information has been accumulated on malignant potential of OLP, its transformation still remains unclear. Hence, the purpose of this article was to review cellular and molecular markers to understand the pathogenesis of OLP and its progression toward malignancy. PMID:27194873

  6. Molecular cladistic markers in New World monkey phylogeny (Platyrrhini, Primates).

    PubMed

    Singer, Silke S; Schmitz, Jürgen; Schwiegk, Claudia; Zischler, Hans

    2003-03-01

    Transpositions of primate-specific Alu elements were applied as molecular cladistic markers in a phylogenetic analysis of South American primates. Seventy-four human and platyrrhine loci containing intronic Alu elements were PCR screened in various New World monkeys and the human outgroup to detect the presence of orthologous retrotransposons informative of New World monkey phylogeny. Six loci revealed size polymorphism in the amplification pattern, indicating a shared derived character state due to the presence of orthologous Alu elements confirmed by subsequent sequencing. Three markers corroborate (1) New World monkey monophyly and one marker supports each of the following callitrichine relationships: (2) Callithrix and Cebuella are more closely related to each other than to any other callitrichine, (3) the callitrichines form a monophyletic clade including Callimico, and (4) the next living relatives to the callitrichines are Cebus, Saimiri, and Aotus. PMID:12644406

  7. Molecular markers in oral lichen planus: A systematic review

    PubMed Central

    Sagari, Shitalkumar; Sanadhya, Sudhanshu; Doddamani, Mallikarjun; Rajput, Rajan

    2016-01-01

    Oral lichen planus (OLP) is a chronic inflammatory mucosal disease that is usually detected in 0.5–2.2% of the human population. Among these, only 0.5–2.9% of the lesions progress to carcinoma. However, there are no prognostic markers available presently to recognize the increased risk in malignant transformation of the lesions. Selected markers for cell proliferation, adhesion, apoptosis and lymphocytic infiltration were analyzed by immunohistochemistry in addition to static cytometry for DNA content. The concept linking OLP and oral squamous cell carcinoma states that chronic inflammation results in crucial DNA damage, which further progresses to development of carcinoma. Even though in the past decade, enormous information has been accumulated on malignant potential of OLP, its transformation still remains unclear. Hence, the purpose of this article was to review cellular and molecular markers to understand the pathogenesis of OLP and its progression toward malignancy. PMID:27194873

  8. Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.).

    PubMed

    Peng, Ze; Gallo, Maria; Tillman, Barry L; Rowland, Diane; Wang, Jianping

    2016-02-01

    Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in

  9. Identification of Turkish and standard apple rootstocks by morphological and molecular markers.

    PubMed

    Koc, A; Akbulut, M; Orhan, E; Celik, Z; Bilgener, S; Ercisli, S

    2009-01-01

    Two local (Vezir-1 and Vezir-2) and two standard (M9 and MM106) clonal apple rootstocks were compared using both morphological and molecular markers. International Union for the Protection of New Varieties of Plants criteria were used for morphological evaluation, which did not clearly separate these rootstocks. We tested 47 random decamer primers for random amplified polymorphic DNA analysis; 15 of them gave reproducible polymorphic patterns, yielding 109 bands, which showed 78% polymorphism. Based on a dendrogram obtained by unweighted pair group method using arithmetic average analysis, three clusters were obtained. The highest genetic similarities were found between M9 and Vezir-2 (0.670). The random amplified polymorphic DNA markers proved to be more efficient than the standard morphological markers for the identification of rootstocks. PMID:19551628

  10. Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

    PubMed

    Rahmani, Mohammad-Shafie; Shabanian, Naghi; Khadivi-Khub, Abdollah; Woeste, Keith E; Badakhshan, Hedieh; Alikhani, Leila

    2015-11-01

    Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability. PMID:26143753

  11. Molecular Genetics of Tooth Development

    PubMed Central

    Bei, Marianna

    2009-01-01

    Organogenesis depends upon a well-ordered series of inductive events involving coordination of molecular pathways that regulate the generation and patterning of specific cell types. Key questions in organogenesis involve the identification of the molecular mechanisms by which proteins interact to organize distinct pattern formation and cell fate determination. Tooth development is an excellent context for investigating this complex problem because of the wealth of information emerging from studies of model organisms and human mutations. Since there are no obvious sources of stem cells in adult human teeth, any attempt to create teeth de novo will likely require the re-programming of other cell types. Thus, the fundamental understanding of the control mechanisms responsible for normal tooth patterning in the embryo will help us understand cell fate specificity and may provide valuable information towards tooth organ regeneration. PMID:19875280

  12. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers

    PubMed Central

    Xu, Chaoqun; Gao, Jiao; Du, Zengfeng; Li, Dengke; Wang, Zhe; Li, Yingyue; Pang, Xiaoming

    2016-01-01

    Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources. PMID:27531220

  13. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers.

    PubMed

    Xu, Chaoqun; Gao, Jiao; Du, Zengfeng; Li, Dengke; Wang, Zhe; Li, Yingyue; Pang, Xiaoming

    2016-01-01

    Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources. PMID:27531220

  14. [Molecular markers of carcinogenesis in the diagnostics of cervical cancer].

    PubMed

    Bedkowska, Grazyna Ewa; Ławicki, Sławomir; Szmitkowski, Maciej

    2009-01-01

    Cervical carcinoma is the most frequent disease of the reproductive organ and is the second most common cancer in women after breast cancer. As it is characterized by high mortality, new diagnostic methods are needed, for example tumor markers, enabling earlier diagnosis and rapid detection of recurrence after therapy. Different tumor markers may be useful in the diagnostics of cervical cancer, for example squamous cell carcinoma antigen (SCC-Ag), tissue polypeptide antigen (TPA), and CYFRA 21-1, as well as some cytokines such as vascular endothelial growth factor (VEGF), granulocyte colony-stimulating factor, and macrophage colony-stimulating factor (M-CSF). About 150 genes connected with the carcinogenesis of cervical carcinoma have been identified. This paper is devoted to evaluating the diagnostic usefulness of molecular markers of carcinogenesis, especially P53, Bcl-2, Brn-3a, and MCM, and comparing the results with those of typical tumor markers or cytokines useful in diagnosing this type of cancer. It was shown that telomerase and Brn-3a proteins demonstrate usefulness in screening examination, P53 in monitoring the effectiveness of therapy, and Bcl-2 as a survival prognostic factor. In summary, it is evident that molecular makers of carcinogenesis are helpful in the diagnostics of cervical cancer, but further investigation and confirmation by a prospective study is necessary. PMID:19252468

  15. Molecular genetics of febrile seizures.

    PubMed

    Nakayama, Junko; Arinami, Tadao

    2006-08-01

    Febrile seizures (FSs) represent the most common form of childhood seizures, occurring in 2-5% of infants in Europe and North America and in 6-9% in Japan. It has been recognized that there is a significant genetic component for susceptibility to this type of seizure. Six susceptibility FS loci have been identified on chromosomes 8q13-q21 (FEB1), 19p (FEB2), 2q23-q24 (FEB3), 5q14-q15 (FEB4), 6q22-q24 (FEB5), and 18p11 (FEB6). Furthermore, mutations in the voltage-gated sodium channel alpha-1, alpha-2 and beta-1 subunit genes (SCN1A, SCN2A and SCN1B) and the GABA(A) receptor gamma-2 subunit gene (GABRG2) have been identified in families with a clinical subset of seizures termed "generalized epilepsy with febrile seizure plus (GEFS+)". However, the causative genes have not been identified in most patients with FSs or GEFS+. Common forms of FSs are genetically complex disorders believed to be influenced by variations in several susceptibility genes. Recently, several association studies in FSs have been reported, but the results vary among different groups and no consistent or convincing FS susceptibility genes have emerged. To find a true association, larger sample size and newer methodologic refinements are recommended. PMID:16887333

  16. Genetic diversity of cultivated and wild tomatoes revealed by morphological traits and SSR markers.

    PubMed

    Zhou, R; Wu, Z; Cao, X; Jiang, F L

    2015-01-01

    In the current study, morphological traits and molecular markers were used to assess the genetic diversity of 29 cultivated tomatoes, 14 wild tomatoes and seven introgression lines. The three components of the principal component analysis (PCA) explained 78.54% of the total morphological variation in the 50 tomato genotypes assessed. Based on these morphological traits, a three-dimensional PCA plot separated the 50 genotypes into distinct groups, and a dendrogram divided them into six clusters. Fifteen polymorphic genomic simple- sequence repeat (genomic-SSR) and 13 polymorphic expressed sequence tag-derived SSR (EST-SSR) markers amplified 1115 and 780 clear fragments, respectively. Genomic-SSRs detected a total of 64 alleles, with a mean of 4 alleles per primer, while EST-SSRs detected 52 alleles, with a mean of 4 alleles per primer. The polymorphism information content was slightly higher in genomic-SSRs (0.49) than in EST-SSRs (0.45). The mean similarity coefficient among the wild tomatoes was lower than the mean similarity coefficient among the cultivated tomatoes. The dendrogram based on genetic distance divided the 50 tomato genotypes into eight clusters. The Mantel test between genomic-SSR and EST-SSR matrices revealed a good correlation, whereas the morphological matrices and the molecular matrices were weakly correlated. We confirm the applicability of EST-SSRs in analyzing genetic diversity among cultivated and wild tomatoes. High variability of the 50 tomato genotypes was observed at the morphological and molecular level, indicating valuable tomato germplasm, especially in the wild tomatoes, which could be used for further genetic studies. PMID:26535702

  17. Use of Molecular Markers for Catfish Production and Product Quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Channel catfish are a diploid species native to North America and the primary product of U.S. aquaculture, and molecular genetic research supports selective breeding of catfish for commercial production. To date, short tandem repeat loci have been used to characterize DNA sequence variation within ...

  18. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory

    PubMed Central

    Slankster, Eryn E.; Chase, Jillian M.; Jones, Lauren A.; Wendell, Douglas L.

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology. PMID:22675329

  19. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory.

    PubMed

    Slankster, Eryn E; Chase, Jillian M; Jones, Lauren A; Wendell, Douglas L

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology. PMID:22675329

  20. Genetic divergence among sweet corn lines estimated by microsatellite markers.

    PubMed

    Lopes, A D; Scapim, C A; Mangolin, C A; Machado, M F P S

    2014-01-01

    The purpose of this study was to analyze the genetic diversity of 15 sugary-1 sweet corn lines by microsatellite markers. One hundred pairs of simple sequence repeat primers that were mapped for field corn were tested. Of these primers, 15% were polymorphic, and all were selected for the evaluation. These primers identified a total of 39 alleles among the 15 loci that were evaluated. The number of alleles per locus in the genotypes ranged from 2 to 4, with an average of 2.60 alleles per locus; the highest number of alleles was observed at the loci Bnlg1083, Umc1241, and Umc1590. The occurrence of null alleles at locus Umc1363 was evident only in line DN44. The proportion of polymorphic loci was the highest in lines DN17.1 and DN6 (73.33%), whereas lines DN47, DN23, and DN28 were more monomorphic than other lines. The loci Bnlg1083 and Umc1506 were polymorphic in 8 and 7 lines, respectively, indicating that these loci might be effective and promising for the identification of polymorphism in other sweet corn lines. The genetic diversity calculated by Rogers' genetic distances indicated the lowest genetic similarity between lines DN9 and DN28 (0.7603) and the highest similarity between lines DN19 and DN6 (0.3724). The dendrogram obtained by the unweighted pair-group method based on arithmetic averages indicated the formation of 4 major groups, showing the crossing of the genotypes DN19 and DN6 with DN8 as a possible alternative for the expression of heterozygosis. PMID:25511025

  1. Evaluation of Pakistan wheat germplasms for stripe rust resistance using molecular markers.

    PubMed

    Sobia, Tabassum; Muhammad, Ashraf; Chen, XianMing

    2010-09-01

    Wheat production in Pakistan is seriously constrained due to rust diseases and stripe rust (yellow) caused by Puccinia striiformis f. sp. tritici, which could limit yields. Thus development and cultivation of genetically diverse and resistant varieties is the most sustainable solution to overcome these diseases. The first objective of the present study was to evaluate 100 Pakistan wheat cultivars that have been grown over the past 60 years. These cultivars were inoculated at the seedling stage with two virulent stripe rust isolates from the United States and two from Pakistan. None of the wheat cultivars were resistant to all tested stripe rust isolates, and 16% of cultivars were susceptible to the four isolates at the seedling stage. The data indicated that none of the Pakistan wheat cultivars contained either Yr5 or Yr15 genes that were considered to be effective against most P. striiformis f. sp. tritici isolates from around the world. Several Pakistan wheat cultivars may have gene Yr10, which is effective against isolate PST-127 but ineffective against PST-116. It is also possible that these cultivars may have other previously unidentified genes or gene combinations. The second objective was to evaluate the 100 Pakistan wheat cultivars for stripe rust resistance during natural epidemics in Pakistan and Washington State, USA. It was found that a higher frequency of resistance was present under field conditions compared with greenhouse conditions. Thirty genotypes (30% of germplasms) were found to have a potentially high temperature adult plant (HTAP) resistance. The third objective was to determine the genetic diversity in Pakistan wheat germplasms using molecular markers. This study was based on DNA fingerprinting using resistance gene analog polymorphism (RGAP) marker analysis. The highest polymorphism detected with RGAP primer pairs was 40%, 50% and 57% with a mean polymorphism of 36%. A total of 22 RGAP markers were obtained in this study. RGAP, simple

  2. Genetic diversity of bovine Neospora caninum determined by microsatellite markers.

    PubMed

    Salehi, N; Gottstein, B; Haddadzadeh, H R

    2015-10-01

    Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed. PMID:25988829

  3. New molecular markers in resistant B-CLL.

    PubMed

    Bouley, Julien; Deriano, Ludovic; Delic, Jozo; Merle-Béral, Hélène

    2006-05-01

    B-chronic lymphocytic leukemia (B-CLL) is characterized by a highly variable clinical course which has long remained a stumbling block for clinicians. This variability appears to arise from complex molecular alterations identified in malignant cells from patient subsets. Recent studies have focused in particular on identifying new molecular markers to help predict the most effective and adapted treatments. In addition to the mutation status of immunoglobulin variable heavy-chain region (IgVH) genes, which is a well-established predictive factor in B-CLL, these new markers include defects of cell factors involved in the maintenance of genome stability, such as telomere function, DNA repair, ATM and p53. Other predictive factors, such as tyrosine kinase Zap-70 and soluble factors found in patient sera, may be associated with B-cell receptor signal transduction. Interestingly, an alteration of these factors fits closely, though not strikingly, with the absence of somatic mutations in IgVH genes, suggesting that the latter may be due either to epigenetic events leading to an unstable genome or to an inherited defect in the immune response of malignant B-cells. Recent lessons from Zap-70 expression/phosphorylation suggest that some of these markers may reflect the defective pathways in B-CLL cells rather than being markers of cell malignancy per se. Furthermore, specific subsets of markers are found in patient cells resistant to treatment. Current studies on gene expression profiling and proteomic analyses should soon lead to a better understanding of how these pathways are affected, especially in multi-drug resistant B-CLL. PMID:16753863

  4. Molecular genetics of febrile seizures.

    PubMed

    Iwasaki, Nobuaki; Nakayama, Junko; Hamano, Kenzo; Matsui, Akira; Arinami, Tadao

    2002-01-01

    Febrile seizures are the most common form of convulsion, occurring in 2-5% of infants in Europe and North America and in 6-9% in Japan. In large families, the febrile seizure (FS) susceptibility trait is inherited by the autosomal dominant pattern with reduced penetrance. Two putative FS loci, FEB1 (chromosome 8q13-q21) and FEB2 (chromosome 19p13.3) have been mapped. A clinical subset of FS, termed generalized epilepsy with febrile seizures plus (GEFS+), was reported. In GEFS+ families, a mutation in the voltage-gated sodium channel beta1 subunit gene (SCN1B) at chromosome 19q13.1 and two mutations of the same alpha1 subunit gene (SCN1A) at chromosome 2q24 were identified. These loci are linked to febrile convulsions in large families. We conducted a genome-wide linkage search for FS in one large family with subsequent linkage confirmation in 39 nuclear families using nonparametric allele-sharing methods, and found a new FS susceptibility locus, FEB4 (chromosome 5q14-q15). In contrast to the FEB1, FEB2, and GEFS+ genetic loci, linkage to FEB4 was suggested in nuclear FS families, indicating that FEB4 may be the most common linkage locus in FS families. PMID:12383277

  5. Molecular advances in genetic skin diseases.

    PubMed

    Siegel, Dawn H; Howard, Renee

    2002-08-01

    The genes for several genetic skin diseases have been identified in recent years. This development improves diagnostic capabilities and genetic counseling, and investigators can now turn to the molecular mechanisms involved in the pathogenesis of these diseases. The identification of the causative genes has led to the generation of mouse models for some genetic skin diseases. A study of the keratin 10 deficient mouse, a model for epidermolytic hyperkeratosis, and a mouse model for Bloom syndrome are reviewed in this article. Several studies also evaluate the relation between genotype and phenotype. In this article, the clinical findings and molecular advances in tuberous sclerosis complex, neurofibromatosis type 1, Bloom syndrome, epidermolytic hyperkeratosis, X-linked ichthyosis, Netherton syndrome, and Hermansky-Pudlak syndrome are reviewed. PMID:12130905

  6. Analysis of the genetic diversity of super sweet corn inbred lines using SSR and SSAP markers.

    PubMed

    Ko, W R; Sa, K J; Roy, N S; Choi, H-J; Lee, J K

    2016-01-01

    In this study, we compared the efficiency of simple sequence repeat (SSR) and sequence specific amplified polymorphism (SSAP) markers for analyzing genetic diversity, genetic relationships, and population structure of 87 super sweet corn inbred lines from different origins. SSR markers showed higher average gene diversity and Shannon's information index than SSAP markers. To assess genetic relationships and characterize inbred lines using SSR and SSAP markers, genetic similarity (GS) matrices were constructed. The dendrogram using SSR marker data showed a complex pattern with nine clusters and a GS of 53.0%. For SSAP markers, three clusters were observed with a GS of 50.8%. Results of combined marker data showed six clusters with 53.5% GS. To analyze the genetic population structure of SSR and SSAP marker data, the 87 inbred lines were divided into groups I, II, and admixed based on the membership probability threshold of 0.8. Using combined marker data, the population structure was K = 3 and was divided into groups I, II, III, and admixed. This study represents a comparative analysis of SSR and SSAP marker data for the study of genetic diversity and genetic relationships in super sweet corn inbred lines. Our results would be useful for maize-breeding programs in Korea. PMID:26909914

  7. Genetic structure of the Korean black scraper Thamnaconus modestus inferred from microsatellite marker analysis.

    PubMed

    An, Hye Suck; Lee, Jang Wook; Park, Jung Yeon; Jung, Hyung Taek

    2013-05-01

    The Korean black scraper, Thamnaconus modestus, is one of the most economically important maricultural fish species in Korea. However, the annual catch of this fish has been continuously declining over the past several decades. In this study, the genetic diversity and relationships among four wild populations and two hatchery stocks of Korean black scraper were assessed based on 16 microsatellite (MS) markers. A total of 319 different alleles were detected over all loci with an average of 19.94 alleles per locus. The hatchery stocks [mean number of alleles (N(A)) = 12, allelic richness (A(R)) = 12, expected heterozygosity (He) = 0.834] showed a slight reduction (P > 0.05) in genetic variability in comparison with wild populations (mean N(A) = 13.86, A(R) = 12.35, He = 0.844), suggesting a sufficient level of genetic variation in the hatchery populations. Similarly low levels of inbreeding and significant Hardy-Weinberg equilibrium deviations were detected in both wild and hatchery populations. The genetic subdivision among all six populations was low but significant (overall F(ST) = 0.008, P < 0.01). Pairwise F(ST), a phylogenetic tree, and multidimensional scaling analysis suggested the existence of three geographically structured populations based on different sea basin origins, although the isolation-by-distance model was rejected. This result was corroborated by an analysis of molecular variance. This genetic differentiation may result from the co-effects of various factors, such as historical dispersal, local environment and ocean currents. These three geographical groups can be considered as independent management units. Our results show that MS markers may be suitable not only for the genetic monitoring of hatchery stocks but also for revealing the population structure of Korean black scraper populations. These results will provide critical information for breeding programs, the management of cultured stocks and the conservation of this species. PMID

  8. Mining associations between genetic markers, phenotypes, and covariates.

    PubMed

    Sevon, P; Ollikainen, V; Onkamo, P; Toivonen, H T; Mannila, H; Kere, J

    2001-01-01

    We used Haplotype Pattern Mining, HPM [Toivonen et al., Am J Hum Genet 67:133-45, 2000], for gene localization in Genetic Analysis Workshop (GAW) 12 isolate data. In HPM, association is analyzed by searching all trait-associated haplotype patterns. Data mining algorithms are utilized to make the search efficient. The strength of the haplotype-trait associations is measured by a linear model, into which a pre-seelected set of covariates is incorporated. Marker-wise patterns of association are used for predicting the disease gene location. Genome-wide scans of susceptibility genes for affection status as well as for the quantitative traits (Q1-Q5) were performed. First analyses were made with small sample sizes, 63-94 trios per trait, which is compared with a pilot study of a larger complex disease-mapping project. Subsequently, the analysis was repeated with approximately 600 cases and 600 controls per trait to give higher power to the analyses. With small sample sizes, only the susceptibility genes having the strongest effects on the traits could be localized. The larger sample size gave very good results: all susceptibility genes, except one, could be correctly localized. First experiments on candidate genes suggested that HPM is applicable even to fine mapping of mutations in DNA sequence. PMID:11793743

  9. Genetic and molecular alterations across medulloblastoma subgroups.

    PubMed

    Skowron, Patryk; Ramaswamy, Vijay; Taylor, Michael D

    2015-10-01

    Medulloblastoma is the most common malignant brain tumour diagnosed in children. Over the last few decades, advances in radiation and chemotherapy have significantly improved the odds of survival. Nevertheless, one third of all patients still succumb to their disease, and many long-term survivors are afflicted with neurocognitive sequelae. Large-scale multi-institutional efforts have provided insight into the transcriptional and genetic landscape of medulloblastoma. Four distinct subgroups of medulloblastoma have been identified, defined by distinct transcriptomes, genetics, demographics and outcomes. Integrated genomic profiling of each of these subgroups has revealed distinct genetic alterations, driving pathways and in some instances cells of origin. In this review, we highlight, in a subgroup-specific manner, our current knowledge of the genetic and molecular alterations in medulloblastoma and underscore the possible avenues for future therapeutic intervention. PMID:26350064

  10. Short Communication Development of microsatellite markers and genetic diversity analysis for Pelodiscus sinensis.

    PubMed

    Li, T; Zhao, J; Li, W; Shi, Y; Hong, X Y; Zhu, X P

    2016-01-01

    Pelodiscus sinensis is a common freshwater soft-shell turtle found in China, and is an important aquaculture species. In this study, 20 polymorphic microsatellite primers were developed from the transcriptome. The genetic diversity of three populations of P. sinensis was evaluated, using 72 individuals. The number of alleles per locus ranged from 3 to 26. The observed and expected heterozygosities varied from 0.208 to 0.958, and from 0.302 to 0.963, respectively. The polymorphic information content varied from 0.283 to 0.953. No significant linkage disequilibrium was detected. These markers will be useful for future population genetic studies and molecular breeding of P. sinensis. PMID:27525890

  11. The Promise of Novel Molecular Markers in Bladder Cancer

    PubMed Central

    Miremami, Jahan; Kyprianou, Natasha

    2014-01-01

    Bladder cancer is the fourth most common malignancy in the US and is associated with the highest cost per patient. A high likelihood of recurrence, mandating stringent surveillance protocols, has made the development of urinary markers a focus of intense pursuit with the hope of decreasing the burden this disease places on patients and the healthcare system. To date, routine use of markers is not recommended for screening or diagnosis. Interests include the development of a single urinary marker that can be used in place of or as an adjunct to current screening and surveillance techniques, as well identifying a molecular signature for an individual’s disease that can help predict progression, prognosis, and potential therapeutic response. Markers have shown potential value in improving diagnostic accuracy when used as an adjunct to current modalities, risk-stratification of patients that could aid the clinician in determining aggressiveness of surveillance, and allowing for a decrease in invasive surveillance procedures. This review discusses the current understanding of emerging biomarkers, including miRNAs, gene signatures and detection of circulating tumor cells in the blood, and their potential clinical value in bladder cancer diagnosis, as prognostic indicators, and surveillance tools, as well as limitations to their incorporation into medical practice. PMID:25535079

  12. Evaluation of insertion-deletion markers suitable for genetic diversity studies and marker-trait correlation analyses in cultivated peanut (Arachis hypogaea L.).

    PubMed

    Meng, S; Yang, X L; Dang, P M; Cui, S L; Mu, G J; Chen, C Y; Liu, L F

    2016-01-01

    Peanut is one of the most important oil crops worldwide. We used insertion-deletion (InDel) markers to assess the genetic diversity and population structure in cultivated peanut. Fifty-four accessions from North China were genotyped using 48 InDel markers. The markers amplified 61 polymorphic loci with 1 to 8 alleles and an average of 2.6 alleles per marker. The polymorphism information content values ranged from 0.0364 to 0.9030, with an average of 0.5038. Population structure and neighbor-joining (NJ) tree analyses suggested that all accessions could be divided into four clusters (A1-A4), using the NJ method. Likewise, four subpopulations (G1-G4) were identified using STRUCTURE analysis. A principal component analysis was also used and results concordant with the other analysis methods were found. A multi-linear stepwise regression analysis revealed that 13 InDel markers correlated with five measured agronomical traits. Our results will provide important information for future peanut molecular breeding and genetic research. PMID:27525935

  13. Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers.

    PubMed

    Verma, Priyanka; Sharma, Tilak R; Srivastava, Prem S; Abdin, M Z; Bhatia, Sabhyata

    2014-09-01

    Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement. PMID:24893599

  14. Identification of Novel Genetic Markers of Breast Cancer Survival

    PubMed Central

    Guo, Qi; Schmidt, Marjanka K.; Kraft, Peter; Canisius, Sander; Chen, Constance; Khan, Sofia; Tyrer, Jonathan; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Michailidou, Kyriaki; Lush, Michael; Kar, Siddhartha; Beesley, Jonathan; Dunning, Alison M.; Shah, Mitul; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Lambrechts, Diether; Weltens, Caroline; Leunen, Karin; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Blomqvist, Carl; Aittomäki, Kristiina; Fagerholm, Rainer; Muranen, Taru A.; Couch, Fergus J.; Olson, Janet E.; Vachon, Celine; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Mulligan, Anna Marie; Broeks, Annegien; Hogervorst, Frans B.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Hopper, John L.; Tsimiklis, Helen; Apicella, Carmel; Southey, Melissa C.; Cox, Angela; Cross, Simon S.; Reed, Malcolm W. R.; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Hooning, Maartje J.; Hollestelle, Antoinette; Martens, John W. M.; van den Ouweland, Ans M. W.; Marme, Federik; Schneeweiss, Andreas; Yang, Rongxi; Burwinkel, Barbara; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Holleczek, Bernd; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Li, Jingmei; Brand, Judith S.; Humphreys, Keith; Devilee, Peter; Tollenaar, Rob A. E. M.; Seynaeve, Caroline; Radice, Paolo; Peterlongo, Paolo; Bonanni, Bernardo; Mariani, Paolo; Fasching, Peter A.; Beckmann, Matthias W.; Hein, Alexander; Ekici, Arif B.; Chenevix-Trench, Georgia; Balleine, Rosemary; Phillips, Kelly-Anne; Benitez, Javier; Zamora, M. Pilar; Arias Perez, Jose Ignacio; Menéndez, Primitiva; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Hamann, Ute; Kabisch, Maria; Ulmer, Hans Ulrich; Rüdiger, Thomas; Margolin, Sara; Kristensen, Vessela; Nord, Silje; Evans, D. Gareth; Abraham, Jean E.; Earl, Helena M.; Hiller, Louise; Dunn, Janet A.; Bowden, Sarah; Berg, Christine; Campa, Daniele; Diver, W. Ryan; Gapstur, Susan M.; Gaudet, Mia M.; Hankinson, Susan E.; Hoover, Robert N.; Hüsing, Anika; Kaaks, Rudolf; Machiela, Mitchell J.; Willett, Walter; Barrdahl, Myrto; Canzian, Federico; Chin, Suet-Feung; Caldas, Carlos; Hunter, David J.; Lindstrom, Sara; García-Closas, Montserrat; Hall, Per; Easton, Douglas F.; Eccles, Diana M.; Rahman, Nazneen; Nevanlinna, Heli; Pharoah, Paul D. P.

    2015-01-01

    Background: Survival after a diagnosis of breast cancer varies considerably between patients, and some of this variation may be because of germline genetic variation. We aimed to identify genetic markers associated with breast cancer–specific survival. Methods: We conducted a large meta-analysis of studies in populations of European ancestry, including 37954 patients with 2900 deaths from breast cancer. Each study had been genotyped for between 200000 and 900000 single nucleotide polymorphisms (SNPs) across the genome; genotypes for nine million common variants were imputed using a common reference panel from the 1000 Genomes Project. We also carried out subtype-specific analyses based on 6881 estrogen receptor (ER)–negative patients (920 events) and 23059 ER-positive patients (1333 events). All statistical tests were two-sided. Results: We identified one new locus (rs2059614 at 11q24.2) associated with survival in ER-negative breast cancer cases (hazard ratio [HR] = 1.95, 95% confidence interval [CI] = 1.55 to 2.47, P = 1.91 x 10–8). Genotyping a subset of 2113 case patients, of which 300 were ER negative, provided supporting evidence for the quality of the imputation. The association in this set of case patients was stronger for the observed genotypes than for the imputed genotypes. A second locus (rs148760487 at 2q24.2) was associated at genome-wide statistical significance in initial analyses; the association was similar in ER-positive and ER-negative case patients. Here the results of genotyping suggested that the finding was less robust. Conclusions: This is currently the largest study investigating genetic variation associated with breast cancer survival. Our results have potential clinical implications, as they confirm that germline genotype can provide prognostic information in addition to standard tumor prognostic factors. PMID:25890600

  15. Genetic diversity analysis of tree peony germplasm using iPBS markers.

    PubMed

    Duan, Y B; Guo, D L; Guo, L L; Wei, D F; Hou, X G

    2015-01-01

    We examined the genetic diversity of 10 wild species (populations) and 55 varieties of tree peony using inter-primer binding site (iPBS) markers. From a total of 36 iPBS primers, 16 were selected based on polymorphic amplification. The number of bands amplified by each primer ranged from 9 to 19, with an average of 12.88 bands per primer. The length of bands ranged from 100 to 2000 bp, concentrated at 200 to 1800 bp. Sixteen primers amplified 206 bands in total, of which 173 bands were polymorphic with a polymorphism ratio of 83.98%. Each primer amplified 10.81 polymorphic bands on average. The data were then used to construct a phylogenetic tree using unweighted pair group method with arithmetic mean methods. Clustering analysis showed that the genetic relationships among the varieties were not only related to the genetic background or geographic origin, but also to the flowering phase, flower color, and flower type. Our data also indicated that iPBS markers were useful tools for classifying tree peony germplasms and for tree peony breeding, and the specific bands were helpful for molecular identification of tree peony varieties. PMID:26214434

  16. Genetic diversity revealed by morphological traits and ISSR markers in 48 Okras (Abelmoschus escullentus L.).

    PubMed

    Yuan, Cong-Ying; Wang, Ping; Chen, Pang-Pang; Xiao, Wen-Jun; Zhang, Cheng; Hu, Shuai; Zhou, Ping; Chang, Hong-Ping; He, Zhuang; Hu, Rong; Lu, Xiu-Tao; Ye, Jia-Zhuo; Guo, Xin-Hong

    2015-07-01

    Okra is a widely distributed crop in the tropics, subtropics, and warmer areas of the temperate zones. Its major potential uses as a vegetable, oil and protein source, and source of paper pulp and fuel, or biomass are compatible. It is expected to have high value of exploitation and application. Due to the limited number of molecular studies focused on okras, the methods of morphological and ISSR markers were used to analysis the genetic diversity of 48 okras in the present study. The 22 primers were picked for ISSR-PCR, and a total of 154 fragments were amplified with an overall average polymorphism of 54.55 %. We used the 154 markers to construct the dendrogram based on the unweighted pair group method with arithmetic means (UPGMA). A high level of genetic diversity was found among 48 individuals. The 48 Okras was divided into four clusters at Dice's coefficient of 0.19 with clustering analysis. Based on these data of the genetic diversity, it will be possible to exploit the available resources of okra in more valuable ways. PMID:26261400

  17. A consensus linkage map for molecular markers and quantitative trait loci associated with economically important traits in melon (Cucumis melo L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in ...

  18. Genetic neurological channelopathies: molecular genetics and clinical phenotypes

    PubMed Central

    Spillane, J; Kullmann, D M; Hanna, M G

    2016-01-01

    Evidence accumulated over recent years has shown that genetic neurological channelopathies can cause many different neurological diseases. Presentations relating to the brain, spinal cord, peripheral nerve or muscle mean that channelopathies can impact on almost any area of neurological practice. Typically, neurological channelopathies are inherited in an autosomal dominant fashion and cause paroxysmal disturbances of neurological function, although the impairment of function can become fixed with time. These disorders are individually rare, but an accurate diagnosis is important as it has genetic counselling and often treatment implications. Furthermore, the study of less common ion channel mutation-related diseases has increased our understanding of pathomechanisms that is relevant to common neurological diseases such as migraine and epilepsy. Here, we review the molecular genetic and clinical features of inherited neurological channelopathies. PMID:26558925

  19. Genetic neurological channelopathies: molecular genetics and clinical phenotypes.

    PubMed

    Spillane, J; Kullmann, D M; Hanna, M G

    2016-01-01

    Evidence accumulated over recent years has shown that genetic neurological channelopathies can cause many different neurological diseases. Presentations relating to the brain, spinal cord, peripheral nerve or muscle mean that channelopathies can impact on almost any area of neurological practice. Typically, neurological channelopathies are inherited in an autosomal dominant fashion and cause paroxysmal disturbances of neurological function, although the impairment of function can become fixed with time. These disorders are individually rare, but an accurate diagnosis is important as it has genetic counselling and often treatment implications. Furthermore, the study of less common ion channel mutation-related diseases has increased our understanding of pathomechanisms that is relevant to common neurological diseases such as migraine and epilepsy. Here, we review the molecular genetic and clinical features of inherited neurological channelopathies. PMID:26558925

  20. Genetic Diversity Analysis of Sugarcane Parents in Chinese Breeding Programmes Using gSSR Markers

    PubMed Central

    You, Qian; Xu, Liping; Zheng, Yifeng; Que, Youxiong

    2013-01-01

    Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use. PMID:23990759

  1. Genetics of asthma: a molecular biologist perspective

    PubMed Central

    Kumar, Amrendra; Ghosh, Balaram

    2009-01-01

    Asthma belongs to the category of classical allergic diseases which generally arise due to IgE mediated hypersensitivity to environmental triggers. Since its prevalence is very high in developed or urbanized societies it is also referred to as "disease of civilizations". Due to its increased prevalence among related individuals, it was understood quite long back that it is a genetic disorder. Well designed epidemiological studies reinforced these views. The advent of modern biological technology saw further refinements in our understanding of genetics of asthma and led to the realization that asthma is not a disorder with simple Mendelian mode of inheritance but a multifactorial disorder of the airways brought about by complex interaction between genetic and environmental factors. Current asthma research has witnessed evidences that are compelling researchers to redefine asthma altogether. Although no consensus exists among workers regarding its definition, it seems obvious that several pathologies, all affecting the airways, have been clubbed into one common category called asthma. Needless to say, genetic studies have led from the front in bringing about these transformations. Genomics, molecular biology, immunology and other interrelated disciplines have unearthed data that has changed the way we think about asthma now. In this review, we center our discussions on genetic basis of asthma; the molecular mechanisms involved in its pathogenesis. Taking cue from the existing data we would briefly ponder over the future directions that should improve our understanding of asthma pathogenesis. PMID:19419542

  2. Genetics of asthma: a molecular biologist perspective.

    PubMed

    Kumar, Amrendra; Ghosh, Balaram

    2009-01-01

    Asthma belongs to the category of classical allergic diseases which generally arise due to IgE mediated hypersensitivity to environmental triggers. Since its prevalence is very high in developed or urbanized societies it is also referred to as "disease of civilizations". Due to its increased prevalence among related individuals, it was understood quite long back that it is a genetic disorder. Well designed epidemiological studies reinforced these views. The advent of modern biological technology saw further refinements in our understanding of genetics of asthma and led to the realization that asthma is not a disorder with simple Mendelian mode of inheritance but a multifactorial disorder of the airways brought about by complex interaction between genetic and environmental factors. Current asthma research has witnessed evidences that are compelling researchers to redefine asthma altogether. Although no consensus exists among workers regarding its definition, it seems obvious that several pathologies, all affecting the airways, have been clubbed into one common category called asthma. Needless to say, genetic studies have led from the front in bringing about these transformations. Genomics, molecular biology, immunology and other interrelated disciplines have unearthed data that has changed the way we think about asthma now. In this review, we center our discussions on genetic basis of asthma; the molecular mechanisms involved in its pathogenesis. Taking cue from the existing data we would briefly ponder over the future directions that should improve our understanding of asthma pathogenesis. PMID:19419542

  3. Construction of a Genetic Linkage Map Based on Amplified Fragment Length Polymorphism Markers and Development of Sequence-Tagged Site Markers for Marker-Assisted Selection of the Sporeless Trait in the Oyster Mushroom (Pleurotus eryngii)

    PubMed Central

    Ueda, Jun; Obatake, Yasushi; Murakami, Shigeyuki; Fukumasa, Yukitaka; Matsumoto, Teruyuki

    2012-01-01

    A large number of spores from fruiting bodies can lead to allergic reactions and other problems during the cultivation of edible mushrooms, including Pleurotus eryngii (DC.) Quél. A cultivar harboring a sporulation-deficient (sporeless) mutation would be useful for preventing these problems, but traditional breeding requires extensive time and labor. In this study, using a sporeless P. eryngii strain, we constructed a genetic linkage map to introduce a molecular breeding program like marker-assisted selection. Based on the segregation of 294 amplified fragment length polymorphism markers, two mating type factors, and the sporeless trait, the linkage map consisted of 11 linkage groups with a total length of 837.2 centimorgans (cM). The gene region responsible for the sporeless trait was located in linkage group IX with 32 amplified fragment length polymorphism markers and the B mating type factor. We also identified eight markers closely linked (within 1.2 cM) to the sporeless locus using bulked-segregant analysis-based amplified fragment length polymorphism. One such amplified fragment length polymorphism marker was converted into two sequence-tagged site markers, SD488-I and SD488-II. Using 14 wild isolates, sequence-tagged site analysis indicated the potential usefulness of the combination of two sequence-tagged site markers in cross-breeding of the sporeless strain. It also suggested that a map constructed for P. eryngii has adequate accuracy for marker-assisted selection. PMID:22210222

  4. [Specific molecular markers of the rust resistance gene M4 in flax].

    PubMed

    Bo, Tian-Yue; Ye, Hua-Zhi; Wang, Shi-Quan; Yang, Jian-Chun; Li, Xiao-Bing; Zhai, Wen-Xue

    2002-10-01

    Flax (Linum usitatissimum L.) is an important fiber and oil-producing crop. Flax rust, caused by Melampsora lini Ehrenb. Lev., occurs worldwide and can cause severe losses in seed yield and fiber quality. In order to identify molecular markers linked to the flax rust resistant gene M4, RAPD analysis of NM4, a near-isogenic line containing the M4 gene, and the recurrent parent Bison was carried out with 540 decamer primers. The primer OPA18 could stably amplify a specific fragment, OPA18(432), in the NM4 line. The OPA18(432) marker was testified to be closely linked to the M4 gene with a genetic distance of 2.1 cM through the analysis of the F2 mapping population derived from a cross of Bison x NM4. Based on the sequence of OPA18(432), the specific PCR primers were designed, and a SCAR marker for the M4 gene was produced. Amplification of different resistant materials proved that the maker is specific for the M4 gene. This marker has been used successfully in marker-assisted selection in the flax breeding program. PMID:12561479

  5. Molecular Genetic Manipulation of Vector Mosquitoes

    PubMed Central

    Terenius, Olle; Marinotti, Osvaldo; Sieglaff, Douglas; James, Anthony A.

    2008-01-01

    Genetic strategies for reducing populations of vector mosquitoes or replacing them with those that are not able to transmit pathogens benefit greatly from molecular tools that allow gene manipulation and transgenesis. Mosquito genome sequences and associated EST (Expressed Sequence Tags) databases enable large-scale investigations to provide new insights into evolutionary, biochemical, genetic, metabolic and physiological pathways. Additionally, comparative genomics reveals the bases for evolutionary mechanisms with particular focus on specific interactions between vectors and pathogens. We discuss how this information may be exploited for the optimization of transgenes that interfere with the propagation and development of pathogens in their mosquito hosts. PMID:18996342

  6. Questionable Specificity of Genetic Total Faecal Pollution Markers for Integrated Water Quality Monitoring and Source Tracking

    NASA Astrophysics Data System (ADS)

    Vierheilig, Julia; Reischer, Georg H.; Farnleitner, Andreas H.

    2010-05-01

    Characterisation of microbial faecal hazards in water is a fundamental aspect for target-orientated water resources management to achieve appropriate water quality for various purposes like water supply or agriculture and thus to minimize related health risks. Nowadays the management of water resources increasingly demands detailed knowledge on the extent and the origin of microbial pollution. Cultivation of standard faecal indicator bacteria, which has been used for over a century to test the microbiological water quality, cannot sufficiently meet these challenges. The abundant intestinal bacterial populations are very promising alternative targets for modern faecal indication systems. Numerous assays for the detection of genetic markers targeting source-specific populations of the phylum Bacteroidetes have been developed in recent years. In some cases markers for total faecal pollution were also proposed in order to relate source-specific marker concentrations to general faecal pollution levels. However, microbial populations in intestinal and non-intestinal systems exhibit a dazzling array of diversity and molecular analysis of microbial faecal pollution has been based on a fragmentary puzzle of very limited sequence information. The aim of this study was to test the available qPCR-based methods detecting genetic Bacteroidetes markers for total faecal pollution in terms of their value and specificity as indicators of faecal pollution. We applied the AllBac (Layton et al., 2006) the BacUni (Kildare et al., 2007) and the Bacteroidetes (Dick and Field, 2004) assays on soil DNA samples. Samples were collected in well characterised karst spring catchments in Austria's Eastern Calcareous Alps. They were at various levels of altitude between 800 and 1800 meters above sea level and from several different habitats (woodland, alpine pastures, krummholz). In addition we tried to choose sampling sites representing a presumptive gradient of faecal pollution levels. For

  7. Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies.

    PubMed

    García-Lor, Andrés; Luro, François; Navarro, Luis; Ollitrault, Patrick

    2012-01-01

    Genetic stratification associated with domestication history is a key parameter for estimating the pertinence of genetic association study within a gene pool. Previous molecular and phenotypic studies have shown that most of the diversity of cultivated citrus results from recombination between three main species: C. medica (citron), C. reticulata (mandarin) and C. maxima (pummelo). However, the precise contribution of each of these basic species to the genomes of secondary cultivated species, such as C. sinensis (sweet orange), C. limon (lemon), C. aurantium (sour orange), C. paradisi (grapefruit) and recent hybrids is unknown. Our study focused on: (1) the development of insertion-deletion (InDel) markers and their comparison with SSR markers for use in genetic diversity and phylogenetic studies; (2) the analysis of the contributions of basic taxa to the genomes of secondary species and modern cultivars and (3) the description of the organisation of the Citrus gene pool, to evaluate how genetic association studies should be done at the cultivated Citrus gene pool level. InDel markers appear to be better phylogenetic markers for tracing the contributions of the three ancestral species, whereas SSR markers are more useful for intraspecific diversity analysis. Most of the genetic organisation of the Citrus gene pool is related to the differentiation between C. reticulata, C. maxima and C. medica. High and generalised LD was observed, probably due to the initial differentiation between the basic species and a limited number of interspecific recombinations. This structure precludes association genetic studies at the genus level without developing additional recombinant populations from interspecific hybrids. Association genetic studies should also be affordable at intraspecific level in a less structured pool such as C. reticulata. PMID:22160318

  8. Genetic and molecular changes in ovarian cancer

    PubMed Central

    Hollis, Robert L; Gourley, Charlie

    2016-01-01

    Epithelial ovarian cancer represents the most lethal gynecological malignancy in the developed world, and can be divided into five main histological subtypes: high grade serous, endometrioid, clear cell, mucinous and low grade serous. These subtypes represent distinct disease entities, both clinically and at the molecular level. Molecular analysis has revealed significant genetic heterogeneity in ovarian cancer, particularly within the high grade serous subtype. As such, this subtype has been the focus of much research effort to date, revealing molecular subgroups at both the genomic and transcriptomic level that have clinical implications. However, stratification of ovarian cancer patients based on the underlying biology of their disease remains in its infancy. Here, we summarize the molecular changes that characterize the five main ovarian cancer subtypes, highlight potential opportunities for targeted therapeutic intervention and outline priorities for future research. PMID:27458531

  9. Genetic stability of micropropagated plants of Crambe abyssinica Hochst using ISSR markers.

    PubMed

    Werner, E T; Soares, T C B; Gontijo, A B P L; Souza Neto, J D; do Amaral, J A T

    2015-01-01

    Crambe (Crambe abyssinica) is a non-edible annual herb, which was first cultivated to extract oil for industry, and now has great potential for biodiesel production. The objective of this investigation was to evaluate the genetic stability of micropropagated plants of the C. abyssinica Hochst cultivar 'FMS brilhante' using polymerase chain reaction techniques based on inter-simple sequence repeat (ISSR) molecular markers. The aim was to develop a protocol for the in vitro regeneration of these plants with low genetic variation as compared to the donor plant. For micropropagation, shoot tips from in vitro germinated seedlings were used as explants and were initially cultivated for 90 days on MS medium with 5.0 μM 6-benzylaminopurine (BAP), which at 90 days, led to the highest number of shoots per explant (NSE) (12.20 shoots) being detected. After 120 days, the interaction between BAP concentration and naphthalene acetic acid (NAA) was tested, and the highest NSE was observed following exposure to 0.0/0.5 μM BAP/NAA (11.40 shoots) and 1.0/0.0 μM BAP/NAA (11.00 shoots). The highest proportion of rooting phase were observed following exposure to 0.5 μM NAA (30%). The 13 ISSR primers used to analyze genetic stability produced 91 amplification products, of which only eight bands were polymorphic and 83 were monomorphic for all 10 regenerated crambe plants, compared to the donor plant explant. These results indicate that crambe shoot tips are a highly reliable explant that can be used to micropropagate genetically true-to-type plants or to maintain genetic stability, as verified using ISSR markers. PMID:26662443

  10. Variability analysis of 'Persian' acid lime tree selections using agronomic and molecular markers.

    PubMed

    Santos, M G; Passos, O S; Soares Filho, W S; Girardi, E A; Gesteira, A S; Ferreira, C F

    2013-01-01

    'Persian' acid lime (PAL) is the most important triploid commercial citrus crop planted in the world. Little is known about the genetic variability of the selections used in Brazil. Therefore, 25 genotypes originating from the PAL, and three control species, Citrus sunki, C. limon, and C. aurantiifolia, were assessed using inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) molecular markers and agronomic traits of the fruit. The dendrograms were designed using the mean Euclidean distance for the physicochemical attributes of the fruit (weight, length, diameter, peel color, peel thickness, number of seeds, juice yield, titratable acidity, soluble solids, and ratio) and the Jaccard distances using the data from the ISSR and IRAP molecular markers. In the physicochemical analysis, the genotypes were grouped according to species. The trait that contributed most to the diversity among accessions was the number of seeds. The 17 ISSR primers produced 69 polymorphic bands in the molecular analysis, and the seven IRAP primers generated 30 polymorphic bands. The markers detected polymorphisms within and among the PALs; two groups were formed within the PALs. PMID:24222236

  11. Use of molecular markers to compare Fusarium verticillioides pathogenic strains isolated from plants and humans.

    PubMed

    Chang, S C; Macêdo, D P C; Souza-Motta, C M; Oliveira, N T

    2013-01-01

    Fusarium verticillioides is a pathogen of agriculturally important crops, especially maize. It is considered one of the most important pathogens responsible for fumonisin contamination of food products, which causes severe, chronic, and acute intoxication in humans and animals. Moreover, it is recognized as a cause of localized infections in immunocompetent patients and disseminated infections among severely immunosuppressed patients. Several molecular tools have been used to analyze the intraspecific variability of fungi. The objective of this study was to use molecular markers to compare pathogenic isolates of F. verticillioides and isolates of the same species obtained from clinical samples of patients with Fusarium mycoses. The molecular markers that we used were inter-simple sequence repeat markers (primers GTG5 and GACA4), intron splice site primer (primer EI1), random amplified polymorphic DNA marker (primer OPW-6), and restriction fragment length polymorphism-internal transcribed spacer (ITS) from rDNA. From the data obtained, clusters were generated based on the UPGMA clustering method. The amplification products obtained using primers ITS4 and ITS5 and loci ITS1-5.8-ITS2 of the rDNA yielded fragments of approximately 600 bp for all the isolates. Digestion of the ITS region fragment using restriction enzymes such as EcoRI, DraI, BshI, AluI, HaeIII, HinfI, MspI, and PstI did not permit differentiation among pathogenic and clinical isolates. The inter-simple sequence repeat, intron splice site primer, and random amplified polymorphic DNA markers presented high genetic homogeneity among clinical isolates in contrast to the high variability found among the phytopathogenic isolates of F. verticillioides. PMID:24065642

  12. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    PubMed Central

    2012-01-01

    Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest. PMID:23036012

  13. Associations of genetic markers in cattle receiving differing implant protocols.

    PubMed

    King, D A; Shackelford, S D; McDaneld, T G; Kuehn, L A; Kemp, C M; Smith, T P L; Wheeler, T L; Koohmaraie, M

    2012-07-01

    The potential interaction of growth-promoting implants and genetic markers previously reported to be associated with growth, carcass traits, and tenderness was evaluated. Two implant protocols were applied to subsets of steers (n = 383) and heifers (n = 65) that were also genotyped for 47 SNP reported to be associated with variation in growth, fat thickness, LM area, marbling, or tenderness. The "mild" protocol consisted of a single terminal implant [16 mg estradiol benzoate (EB), 80 mg trenbalone acetate (TBA) or 8 mg EB, 80 mg TBA given to steers and heifers, respectively]. The "aggressive" protocol consisted of both a growing implant (8 mg EB, 40 mg TBA) for the lightest half of the animals on the aggressive protocol and 2 successive implants (28 mg EB, 200 mg TBA) given to all animals assigned to the aggressive treatment. Implant protocol had measurable impact on BW and ADG (P < 0.05), with the aggressive protocol increasing these traits before the terminal implant (relative to the mild protocol), whereas the mild protocol increased ADG after the terminal implant so that the final BW and ADG over the experimental period were similar between protocols. Animals on the aggressive protocol had significantly increased (P < 0.05) LM area (1.9 cm(2)), slice shear force (1.4 kg), and intact desmin (0.05 units), but decreased (P < 0.05) marbling score (49 units) and adjusted fat thickness (0.1 cm), and yield grade (0.15 units). Among both treatments, 8 of 9 growth-related SNP were associated with BW or ADG, and 6 of 17 tenderness-related SNP were associated with slice shear force or intact desmin. Favorable growth alleles generally were associated with increased carcass yield traits but decreased tenderness. Similarly, favorable tenderness genotypes for some markers were associated with decreased BW and ADG. Some interactions of implant protocol and genotype were noted, with some growth SNP alleles increasing the effect of the aggressive protocol. In contrast, putative

  14. Development of novel SCAR markers for genetic characterization of Lonicera japonica from high GC-RAMP-PCR and DNA cloning.

    PubMed

    Cheng, J L; Li, J; Qiu, Y M; Wei, C L; Yang, L Q; Fu, J J

    2016-01-01

    Sequence-characterized amplified region (SCAR) markers were further developed from high-GC primer RAMP-PCR-amplified fragments from Lonicera japonica DNA by molecular cloning. The four DNA fragments from three high-GC primers (FY-27, FY-28, and FY-29) were successfully cloned into a pGM-T vector. The positive clones were sequenced; their names, sizes, and GenBank numbers were JYHGC1-1, 345 bp, KJ620024; YJHGC2-1, 388 bp, KJ620025; JYHGC7-2, 1036 bp, KJ620026; and JYHGC6-2, 715 bp, KJ620027, respectively. Four novel SCAR markers were developed by designing specific primers, optimizing conditions, and PCR validation. The developed SCAR markers were used for the genetic authentication of L. japonica from its substitutes. This technique provides another means of developing DNA markers for the characterization and authentication of various organisms including medicinal plants and their substitutes. PMID:27173286

  15. Microbial Biofilms: from Ecology to Molecular Genetics

    PubMed Central

    Davey, Mary Ellen; O'toole, George A.

    2000-01-01

    Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development. PMID:11104821

  16. Genetic Variability and Geographic Diversity of the Common Bed Bug (Hemiptera: Cimicidae) Populations from the Midwest Using Microsatellite Markers.

    PubMed

    Narain, Ralph B; Lalithambika, Sreedevi; Kamble, Shripat T

    2015-07-01

    With the recent global resurgence of the bed bugs (Cimex lectularius L.), there is a need to better understand its biology, ecology, and ability to establish populations. Bed bugs are domestic pests that feed mainly on mammalian blood. Although bed bugs have not been implicated as vectors of pathogens, their biting activity inflicts severe insomnia and allergic reactions. Moreover, they have recently developed resistance to various insecticides, which requires further molecular research to determine genetic variation and appropriate interventions. Population dynamics, including genetic differentiation and genetic distance of 10 populations from the Midwest were analyzed in this study. The bed bug samples collected by pest control companies were genotyped using eight species-specific microsatellite markers. Results showed all eight markers were polymorphic, with 8-16 alleles per locus, suggesting high genetic diversity. The FST values were >0.25, signifying pronounced genetic differentiation. The G-test results also indicated high genetic differentiation among populations. The frequency of the most common allele across all eight loci was 0.42. The coefficient of relatedness between each of the populations was >0.5, indicative of sibling or parent-offspring relationships, while the FIS and its confidence interval values were statistically insignificant within the populations tested. The populations departed from Hardy-Weinberg equilibrium, possibly because of high heterozygosity. The genetic distance analysis using a neighbor-joining tree showed that the populations from Kansas City, MO, were genetically separate from most of those from Nebraska, indicating a geographic pattern of genetic structure. Our study demonstrated the effectiveness of using microsatellite markers to study bed bugs population structure, thereby improving our understanding of bed bug population dynamics in the Midwest. Overall, this study showed a high genetic diversity and identified several

  17. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    NASA Astrophysics Data System (ADS)

    Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

    2014-01-01

    Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (`K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.

  18. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    PubMed Central

    Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

    2016-01-01

    Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (‘K13-propeller’) with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242

  19. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa.

    PubMed Central

    Choi, Hong-Kyu; Kim, Dongjin; Uhm, Taesik; Limpens, Eric; Lim, Hyunju; Mun, Jeong-Hwan; Kalo, Peter; Penmetsa, R Varma; Seres, Andrea; Kulikova, Olga; Roe, Bruce A; Bisseling, Ton; Kiss, Gyorgy B; Cook, Douglas R

    2004-01-01

    A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an F(2) population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene analogs, covering 513 cM. In the case of EST-based markers we used an intron-targeted marker strategy with primers designed to anneal in conserved exon regions and to amplify across intron regions. Polymorphisms were significantly more frequent in intron vs. exon regions, thus providing an efficient mechanism to map transcribed genes. Genetic and cytogenetic analysis produced eight well-resolved linkage groups, which have been previously correlated with eight chromosomes by means of FISH with mapped BAC clones. We anticipated that mapping of conserved coding regions would have utility for comparative mapping among legumes; thus 60 of the EST-based primer pairs were designed to amplify orthologous sequences across a range of legume species. As an initial test of this strategy, we used primers designed against M. truncatula exon sequences to rapidly map genes in M. sativa. The resulting comparative map, which includes 68 bridging markers, indicates that the two Medicago genomes are highly similar and establishes the basis for a Medicago composite map. PMID:15082563

  20. Molecular Genetic of Atopic dermatitis: An Update

    PubMed Central

    Al-Shobaili, Hani A.; Ahmed, Ahmed A.; Alnomair, Naief; Alobead, Zeiad Abdulaziz; Rasheed, Zafar

    2016-01-01

    Atopic dermatitis (AD) is a chronic multifactorial inflammatory skin disease. The pathogenesis of AD remains unclear, but the disease results from dysfunctions of skin barrier and immune response, where both genetic and environmental factors play a key role. Recent studies demonstrate the substantial evidences that show a strong genetic association with AD. As for example, AD patients have a positive family history and have a concordance rate in twins. Moreover, several candidate genes have now been suspected that play a central role in the genetic background of AD. In last decade advanced procedures similar to genome-wide association (GWA) and single nucleotide polymorphism (SNP) have been applied on different population and now it has been clarified that AD is significantly associated with genes of innate/adaptive immune systems, human leukocyte antigens (HLA), cytokines, chemokines, drug-metabolizing genes or various other genes. In this review, we will highlight the recent advancements in the molecular genetics of AD, especially on possible functional relevance of genetic variants discovered to date. PMID:27004062

  1. Development of microsatellite markers for Manilkara maxima T.D. Penn. (Sapotaceae) and their use in conservation genetics.

    PubMed

    Silva-Junior, José Audenor; de Souza França, Daniele; Moraes, Ramiris César Souza; Gaiotto, Fernanda Amato

    2016-06-01

    Manilkara maxima is an endemic tree species of the Atlantic Forest in southern Bahia, Brazil. It is considered important for forest conservation due to its mutualistic interactions with endemic and endangered animals. Our aim was to develop microsatellite markers to estimate genetic diversity in order to provide information for effectiveness of future conservation programs. We used next generation sequencing technology to develop the first specific microsatellite markers for M. maxima. Seventeen new microsatellite loci were applied in 72 individuals sampled in three natural populations. On average, the number of alleles per loci was 8.8. The expected heterozygosity varied between 0.72 and 0.77, indicating that the developed set of molecular markers is useful for genetic diversity studies. Additionally, the estimated value for the combined probability of exclusion (Q) was greater than 0.999, which indicates the powerful of these molecular tools for paternity and kinship analysis. Our results demonstrate that the set of microsatellites developed in this work is a powerful tool for population genetics, molecular ecology and conservation biology purposes. PMID:27061192

  2. Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis.

    PubMed

    Cyriac, Anu; Paul, Ritto; Anupama, K; Senthil Kumar, R; Sheeja, T E; Nirmal Babu, K; Parthasarathy, V A

    2016-04-01

    Microsatellite markers in small cardamom (Elettaria cardamomum Maton) were developed using the selective hybridization enrichment method. A total of 140 microsatellite repeats were identified from 270 clones. Primers were designed for 58 microsatellites and 44 primer pairs amplified products of expected size in cardamom. These markers were used for studying the diversity of 20 important small cardamom genotypes, and six markers were found to be polymorphic. The number of alleles ranged from 2 to 7 with an average of 3.6 per locus. Polymorphic information content values ranged from 0.14 to 0.38 based on dominant scoring. The two markers ECM 47a and ECMG 28 generated specific banding patterns for the genotypes MCC7 (Pink tiller) and APG434 (MA18) respectively. Dendrogram illustrated the genetic similarity between different genotypes of Kerala and Karnataka regions. It differentiated the closely related genotypes and released varieties into separate groups. Principal coordinate analysis revealed PV1 and ICRI 1 as the most divergent genotypes. The study demonstrated that these markers are informative and can be further utilized for generating reliable molecular data for assisting the crop improvement of small cardamom. Cross generic transferability (71.4 %) of the developed primers proved that they are useful for phylogenetic studies in the family Zingiberaceae. This is the first report of de novo isolation, characterisation and utilization of microsatellite markers for the genetic diversity analysis of small cardamom. PMID:27436913

  3. Genetic, epigenetic, and molecular landscapes of multifocal and multicentric glioblastoma.

    PubMed

    Liu, Qun; Liu, Yuexin; Li, Wenliang; Wang, Xiaoguang; Sawaya, Raymond; Lang, Frederick F; Yung, W K Alfred; Chen, Kexin; Fuller, Gregory N; Zhang, Wei

    2015-10-01

    Ten to twenty percent of newly diagnosed glioblastoma (GBM) patients initially present with multiple lesions, termed multifocal or multicentric GBM (M-GBM). The prognosis of these patients is poorer than that of solitary GBM (S-GBM) patients. However, it is unknown whether multifocality has a genetic, epigenetic, or molecular basis. Here, we identified the genetic and epigenetic characteristics of M-GBM by performing a comprehensive analysis of multidimensional data, including imaging, genetic, epigenetic, and gene expression profiles, from 30 M-GBM cases in The Cancer Genome Atlas database and comparing the results with those of 173 S-GBM cases. We found that M-GBMs had no IDH1, ATRX, or PDGFRA mutations and were significantly associated with the mesenchymal subtype. We also identified the CYB5R2 gene to be hypo-methylated and overexpressed in M-GBMs. The expression level of CYB5R2 was significantly associated with patient survival in two major independent GBM cohorts, totaling 758 cases. The IDH1 mutation was markedly associated with CYB5R2 promoter methylation, but the survival influence of CYB5R2 was independent of IDH1 mutation status. CYB5R2 expression was significantly associated with collagen maturation and the catabolic process and immunoregulation pathways. These results reveal that M-GBMs have some underlying genetic and epigenetic characteristics that are associated with poor prognosis and that CYB5R2 is a new epigenetic marker for GBM prognosis. PMID:26323991

  4. Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR.

    PubMed

    Korbin, Małgorzata; Kuras, Anita; Zurawicz, Edward

    2002-01-01

    The genotypes of the strawberry (Fragaria x ananassa), apple (Malus domestica) and Ribes species (R. nigrum, R. rubrum and R. glossularia), maintained in our Institute's collection and used in breeding programs, were screened for DNA markers. Twenty primers for RAPD (among 60 tested) and seven for ISSR (among 10 tested) were chosen as creating polymorphic DNA bands differentiating the investigated genotypes. Based on those identity markers, the genetic distance between genotypes was determined, and their relatedness was estimated. In many cases, both RAPD- and ISSR-based genetic similarity confirmed relatedness connected with biological origin and with the place where the cultivar was developed. However, some diversity connected with the technique used for molecular marker generation was observed. Generally, the similarity values based on ISSR data were higher than those based on RAPD. Parallel study using two data sets seems to enable a reduction in the number of potential mistakes connected with each method's, technical limitations and ensures more precise relatedness determination. PMID:12378239

  5. Genetic diversity analysis of Capparis spinosa L. populations by using ISSR markers.

    PubMed

    Liu, C; Xue, G P; Cheng, B; Wang, X; He, J; Liu, G H; Yang, W J

    2015-01-01

    Capparis spinosa L. is an important medicinal species in the Xinjiang Province of China. Ten natural populations of C. spinosa from 3 locations in North, Central, and South Xinjiang were studied using morphological trait inter simple sequence repeat (ISSR) molecular markers to assess the genetic diversity and population structure. In this study, the 10 ISSR primers produced 313 amplified DNA fragments, with 52% of fragments being polymorphic. Unweighted pair-group method with arithmetic average (UPGMA) cluster analysis indicated that 10 C. spinosa populations were clustered into 3 geographically distinct groups. The Nei gene of C. spinosa populations in different regions had Diversity and Shannon's information index ranges of 0.1312-0.2001 and 0.1004-0.1875, respectively. The 362 markers were used to construct the dendrogram based on the UPGMA cluster analysis. The dendrogram indicated that 10 populations of C. spinosa were clustered into 3 geographically distinct groups. The results showed these genotypes have high genetic diversity, and can be used for an alternative breeding program. PMID:26662446

  6. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity present in crop landraces represents a valuable genetic resource for breeding and genetic studies. Bottle gourd (Lagenaria siceraria) landraces in Turkey are highly genetically diverse. However, the limited genomic resources available for this crop hinder the molecular characte...

  7. Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and interactions cannot be accurately estimated when minor marker allele frequencies (MAF) are low. To increase the accuracy of estimation for three marker systems in commercial use, an Angus population at USMARC was subjected to marker assisted-selection for multiple years t...

  8. Species boundaries of Astreopora corals (Scleractinia, Acroporidae) inferred by mitochondrial and nuclear molecular markers.

    PubMed

    Suzuki, Go; Nomura, Keiichi

    2013-08-01

    The genus Astreopora is a small but ancestral group in Acroporidae, which is one of the most diverse and dominant families of scleractinian coral in Indo-Pacific reefs. We estimated the species boundaries of Astreopora corals using two molecular markers: a mitochondrial non-coding region and a nuclear ribosomal 5.8S region. Seven species (59 specimens) commonly observed around Japan (Astreopora expansa, A. gracilis, A. incrustans, A. listeri, A. myriophthalma, A. cf. suggesta, and Astreopora sp.1) were investigated, and we observed no genetic divergence in the mitochondrial marker, suggesting that these species are closely related, consistent with a species complex or recent divergence, although genotyping by the marker is not so sensitive. In the nuclear 5.8S region, 121 clones consisted of six species were divided into the four major genetic groups. Although there were no monophyletic clades, the two dominant species A. myriophthalma and A. gracilis rarely shared the same haplotypes, suggesting that gene flow is limited between them. However, A. incrustans frequently shared the same haplotypes with A. gracilis although the distributions do not overlap. We found that the ancestral genus Astreopora in Acroporidae shows less genetic variation than traditionally identified morphospecies. Although further research on fertilization rate among these species is required to determine if there are reproductive barriers, the low level of genetic diversification in this genus hints that some ecological differences among acroporid corals play a role in the evolution of scleractinian corals, considering that the other members of this family, Acropora and Montipora, are highly diversified. PMID:23915155

  9. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    PubMed Central

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  10. Recent trends and perspectives of molecular markers against fungal diseases in wheat

    PubMed Central

    Goutam, Umesh; Kukreja, Sarvjeet; Yadav, Rakesh; Salaria, Neha; Thakur, Kajal; Goyal, Aakash K.

    2015-01-01

    Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40–60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases. PMID:26379639

  11. Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication.

    PubMed

    Shen, X L; Zhang, Y M; Xue, J Y; Li, M M; Lin, Y B; Sun, X Q; Hang, Y Y

    2016-01-01

    Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource. PMID:27173238

  12. Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae)

    PubMed Central

    Douaihy, Bouchra; Sobierajska, Karolina; Jasińska, Anna Katarzyna; Boratyńska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boratyński, Adam

    2012-01-01

    Background and aims Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. Methodology We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability. Principal results The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. Conclusions Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection. PMID:22822421

  13. Autism and genetics: Clinical approach and association study with two markers of HRAS gene

    SciTech Connect

    Herault, J.; Petit, E.; Cherpi, C.

    1995-08-14

    Twin studies and familial aggregation studies indicate that genetic factors could play a role in infantile autism. In an earlier study, we identified a possible positive association between autism and a c-Harvey-ras (HRAS) oncogene marker at the 3{prime} end of the coding region. In an attempt to confirm this finding, we studied a larger population, well-characterized clinically and genetically. We report a positive association between autism and two HRAS markers, the 3{prime} marker used in the initial study and an additional marker in exon 1. 46 refs., 1 fig., 2 tabs.

  14. Construction of a genetic linkage map for cultivated peanut and development of QTLs/markers for marker-assisted breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid peanut recently. The marker density, however, is still very low especially in context of large genome size (2,800Mb/1C) and 20 linkage groups (LGs). Therefore, improvement of...

  15. Molecular genetic approaches to understanding disease.

    PubMed Central

    Savill, J.

    1997-01-01

    Molecular genetics has greatly increased the understanding of diseases in which there is a single gene defect such as cystic fibrosis. Discovering the gene responsible and its function not only helps determine the pathogenesis of the disease but also offers a possible treatment-gene therapy. Polygenic disorders such as diabetes may soon yield their secrets to the same approach. Animal models of genetic diseases are proving useful research tools, and transgenesis has made xenografting possible. Furthermore, antisense technology allows specific inhibition of undesirably overexpressed genes such as those driving unwanted vascular cell proliferation and restenosis after angioplasty. The completion of the human genome project should make the search for "disease" gene much quicker and will increase still further the importance of these gene based approaches toward diseases. PMID:9006475

  16. Characterization of Molecular Markers Indicative of Cervical Cancer Progression

    PubMed Central

    Arnouk, Hilal; Merkley, Mark A.; Podolsky, Robert H.; Stöppler, Hubert; Santos, Carlos; Álvarez, Manuel; Mariategui, Julio; Ferris, Daron; Lee, Jeffrey R.; Dynan, William S.

    2009-01-01

    Cervical cancer originates with human papillomavirus (HPV) infection and progresses via histologically-defined premalignant stages. Here we compare normal cervical epithelium and patient-matched high grade squamous intraepithelial lesions (HSIL) with cervical carcinoma tissue from the same patient population (n=10 per group). Specimens were analyzed by combined laser capture microdissection and 2D-DIGE. Significant expression changes were seen with 53 spots resulting in identification of 23 unique proteins at the molecular level. These include eight that uniquely distinguish normal epithelium and HSIL and four that uniquely distinguish HSIL and carcinoma. In addition, one protein, cornulin, distinguishes all three states. Other identified proteins included differentiation markers, oncogene DJ-1, serpins, stress and interferon-responsive proteins, detoxifying enzymes, and serum transporters. A literature review, performed for all identified proteins, allowed most changes to be assigned to one of three causes: direct or indirect HPV oncoprotein interactions, growth selection during latency, or interactions in the lesion microenvironment. Selected findings were confirmed by immunohistochemistry using either frozen sections from the same cohort or formalin fixed paraffin embedded samples from a tissue microarray. Novel markers described here have potential applications for increasing the predictive value of current screening methods. PMID:19834583

  17. Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers

    PubMed Central

    Koedrith, Preeyaporn; Seo, Young Rok

    2011-01-01

    Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-κB, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression. PMID:22272150

  18. Genetics and molecular biology of hypotension

    NASA Technical Reports Server (NTRS)

    Robertson, D.

    1994-01-01

    Major strides in the molecular biology of essential hypertension are currently underway. This has tended to obscure the fact that a number of inherited disorders associated with low blood pressure exist and that these diseases may have milder and underrecognized phenotypes that contribute importantly to blood pressure variation in the general population. This review highlights some of the gene products that, if abnormal, could cause hypotension in some individuals. Diseases due to abnormalities in the catecholamine enzymes are discussed in detail. It is likely that genetic abnormalities with hypotensive phenotypes will be as interesting and diverse as those that give rise to hypertensive disorders.

  19. Psychobiology and molecular genetics of resilience.

    PubMed

    Feder, Adriana; Nestler, Eric J; Charney, Dennis S

    2009-06-01

    Every individual experiences stressful life events. In some cases acute or chronic stress leads to depression and other psychiatric disorders, but most people are resilient to such effects. Recent research has begun to identify the environmental, genetic, epigenetic and neural mechanisms that underlie resilience, and has shown that resilience is mediated by adaptive changes in several neural circuits involving numerous neurotransmitter and molecular pathways. These changes shape the functioning of the neural circuits that regulate reward, fear, emotion reactivity and social behaviour, which together are thought to mediate successful coping with stress. PMID:19455174

  20. Psychobiology and molecular genetics of resilience

    PubMed Central

    Feder, Adriana; Nestler, Eric J.; Charney, Dennis S.

    2010-01-01

    Every individual experiences stressful life events. In some cases acute or chronic stress leads to depression and other psychiatric disorders, but most people are resilient to such effects. Recent research has begun to identify the environmental, genetic, epigenetic and neural mechanisms that underlie resilience, and has shown that resilience is mediated by adaptive changes in several neural circuits involving numerous neurotransmitter and molecular pathways. These changes shape the functioning of the neural circuits that regulate reward, fear, emotion reactivity and social behaviour, which together are thought to mediate successful coping with stress. PMID:19455174

  1. Molecular Pathogenesis and Diagnostic, Prognostic and Predictive Molecular Markers in Sarcoma.

    PubMed

    Mariño-Enríquez, Adrián; Bovée, Judith V M G

    2016-09-01

    Sarcomas are infrequent mesenchymal neoplasms characterized by notable morphological and molecular heterogeneity. Molecular studies in sarcoma provide refinements to morphologic classification, and contribute diagnostic information (frequently), prognostic stratification (rarely) and predict therapeutic response (occasionally). Herein, we summarize the major molecular mechanisms underlying sarcoma pathogenesis and present clinically useful diagnostic, prognostic and predictive molecular markers for sarcoma. Five major molecular alterations are discussed, illustrated with representative sarcoma types, including 1. the presence of chimeric transcription factors, in vascular tumors; 2. abnormal kinase signaling, in gastrointestinal stromal tumor; 3. epigenetic deregulation, in chondrosarcoma, chondroblastoma, and other tumors; 4. deregulated cell survival and proliferation, due to focal copy number alterations, in dedifferentiated liposarcoma; 5. extreme genomic instability, in conventional osteosarcoma as a representative example of sarcomas with highly complex karyotype. PMID:27523972

  2. The molecular basis of genetic dominance.

    PubMed Central

    Wilkie, A O

    1994-01-01

    Studies of mutagenesis in many organisms indicate that the majority (over 90%) of mutations are recessive to wild type. If recessiveness represents the 'default' state, what are the distinguishing features that make a minority of mutations give rise to dominant or semidominant characters? This review draws on the rapid expansion in knowledge of molecular and cellular biology to classify the molecular mechanisms of dominant mutation. The categories discussed include (1) reduced gene dosage, expression, or protein activity (haploinsufficiency); (2) increased gene dosage; (3) ectopic or temporally altered mRNA expression; (4) increased or constitutive protein activity; (5) dominant negative effects; (6) altered structural proteins; (7) toxic protein alterations; and (8) new protein functions. This provides a framework for understanding the basis of dominant genetic phenomena in humans and other organisms. Images PMID:8182727

  3. Molecular Genetic Analysis of Phototropism in Arabidopsis

    PubMed Central

    Sakai, Tatsuya; Haga, Ken

    2012-01-01

    Plant life is strongly dependent on the environment, and plants regulate their growth and development in response to many different environmental stimuli. One of the regulatory mechanisms involved in these responses is phototropism, which allows plants to change their growth direction in response to the location of the light source. Since the study of phototropism by Darwin, many physiological studies of this phenomenon have been published. Recently, molecular genetic analyses of Arabidopsis have begun to shed light on the molecular mechanisms underlying this response system, including phototropin blue light photoreceptors, phototropin signaling components, auxin transporters, auxin action mechanisms and others. This review highlights some of the recent progress that has been made in further elucidating the phototropic response, with particular emphasis on mutant phenotypes. PMID:22864452

  4. Development of Microsatellite Markers and Detection of Genetic Variation between Goniozus Wasp Populations

    PubMed Central

    Khidr, Sahand K.; Hardy, Ian C.W.; Zaviezo, Tania; Mayes, Sean

    2014-01-01

    Molecular genetic markers reveal differences between genotypes according to the presence of alleles (the same or different) at target loci. Microsatellite markers are especially useful codominant markers that have been used in a wide range of studies to elucidate the population structure and dynamics of a range of organisms, including agriculturally beneficial insects such as parasitic wasps (parasitoids). In the present study, twelve primer pairs were designed for the south Asian , Goniozus nephantidis (Muesebeck) (Hymenoptera: Bethylidae), and 24 for its New World congener, Goniozus legneri Gordh, parasitoids of the larvae of the lepidopteran coconut pest Opisina arenosella Walker (Lepidoptera: Crytophasidae) and other lepidopteran pests, respectively, in order to investigate polymorphism within and between populations. The wasps fingerprinted were a total of 85 G. nephantidis and G. legneri, including individuals belonging to three putatively different strains of G. legneri. Annealing gradient tests (50–65°C) were conducted to study the quality of the PCR amplification across an annealing temperature gradient using a mixed genotype DNA template from each species separately. Seven primer pairs, which amplified clear products of approximately the expected size of G. nephantidis and 18 of G. legneri, were then selected for capillary analysis for fragment size determination on a Beckmann CEQ 8000. Neither G. nephantidis nor G. legneri were polymorphic within populations. However, there were six primer pairs that did show polymorphism between G. legneri populations that originated from different geographical areas within South America (Uruguay and Chile). Furthermore, one primer pair revealed diversity between the two strains collected within Chile. One of the markers was subsequently used to provide unbiased assessment of primary sex ratio in G. legneri. PMID:25373190

  5. Molecular genetics of Alzheimer's disease and aging.

    PubMed

    Cacabelos, Ramon; Fernandez-Novoa, Lucia; Lombardi, Valter; Kubota, Yasuhiko; Takeda, Masatoshi

    2005-07-01

    , accumulation of aberrant or misfolded proteins, protofibril formation, ubiquitin-proteasome system dysfunction, excitotoxic reactions, oxidative and nitrosative stress, mitochondrial injury, synaptic failure, altered metal homeostasis, dysfunction of axonal and dendritic transport, and chaperone misoperation may converge in pathogenic pathways leading to premature death and neurodegeneration. Some of these mechanisms are common to several neurodegenerative disorders, which differ depending upon the gene(s) affected and the involvement of specific genetic networks, together with epigenetic factors and environmental events. Many genes potentially associated with Alzheimer's disease in some studies cannot be confirmed as candidate genes in replication studies, indicating that methodological problems and genomic complexity are leading to erroneous conclusions. A different approach to Alzheimer's disease functional genomics is to integrate individual genetic information in polygenic genotypes (haplotype-like model) and to investigate genotype-phenotype correlations and genotype-related pharmacogenomic behaviors. The application of functional genomics to Alzheimer's disease can be a suitable strategy for molecular diagnosis and for understanding pathophysiological mechanisms associated with Alzheimer's disease-related neurodegeneration. Furthermore, the pharmacogenomics of Alzheimer's disease may contribute in the future to optimize drug development and therapeutics, increasing efficacy and safety, and reducing side-effects and unnecessary costs. PMID:16470248

  6. Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

    PubMed

    Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

    2011-01-01

    Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources. PMID:22146370

  7. Molecular Genetics of Pediatric Soft Tissue Tumors

    PubMed Central

    Chang, Chung-Che; Shidham, Vinod B.

    2003-01-01

    The application of molecular genetics to pediatric soft tissue tumors has grown tremendously over the last decade. It has resulted in the identification of novel genes that have provided us with an increased understanding of oncogenesis. Furthermore, these findings have identified diagnostic and potentially prognostic factors for patient management. Molecular diagnostic techniques, such as reverse transcription PCR (RT-PCR) and fluorescence in situ hybridization (FISH), have become important tools for evaluating pediatric soft tissue tumors. By detecting characteristic fusion genes, these techniques have greatly increased the diagnostic accuracy of histopathological classification. One of the exciting promises of the development of these molecular techniques is their ability to detect micrometastasis and minimal residual disease. Monitoring of minimal residual disease in pediatric soft tissue tumors by quantitative RT-PCR may provide important prognostic information. Furthermore, the potential development of targeted therapy based on the understanding of the molecular pathology of a specific soft tissue tumor may complement existing treatments and improve disease outcome. PMID:12876204

  8. Genome-wide identification of novel genetic markers from RNA sequencing assembly of diverse Aegilops tauschii accessions.

    PubMed

    Nishijima, Ryo; Yoshida, Kentaro; Motoi, Yuka; Sato, Kazuhiro; Takumi, Shigeo

    2016-08-01

    The wild species in the Triticeae tribe are tremendous resources for crop breeding due to their abundant natural variation. However, their huge and highly repetitive genomes have hindered the establishment of physical maps and the completeness of their genome sequences. To develop molecular markers for the efficient utilization of their valuable traits while avoiding their genome complexity, we assembled RNA sequences of ten representative accessions of Aegilops tauschii, the progenitor of the wheat D genome, and estimated single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). The deduced unigenes were anchored to the chromosomes of Ae. tauschii and barley. The SNPs and indels in the anchored unigenes, covering entire chromosomes, were sufficient for linkage map construction, even in combinations between the genetically closest accessions. Interestingly, the resolution of SNP and indel distribution on barley chromosomes was slightly higher than on Ae. tauschii chromosomes. Since barley chromosomes are regarded as virtual chromosomes of Triticeae species, our strategy allows capture of genetic markers arranged on the chromosomes in order based on the conserved synteny. The resolution of these genetic markers will be comparable to that of the Ae. tauschii whose draft genome sequence is available. Our procedure should be applicable to marker development for Triticeae species, which have no draft sequences available. PMID:27142109

  9. Genetic Structure of the Endangered Plant Neolitsea sericea (Lauraceae) from the Zhoushan Archipelago Using RAPD Markers

    PubMed Central

    WANG, ZHONG-SHENG; AN, SHU-QING; LIU, HONG; LENG, XIN; ZHENG, JIAN-WEI; LIU, YU-HONG

    2004-01-01

    • Background and Aims The Zhoushan archipelago is the largest archipelago in China. It separated from the mainland about 9000 years ago due to rising sea levels and climate change. Because of the long-term influences of human activities, the original forest vegetation on the large islands has been badly damaged and its plant diversity reduced. • Methods Levels and patterns of genetic diversity in 114 individuals from six natural populations and four cultivated populations of the insular endangered plant Neolitsea sericea (Lauraceae) on the Zhoushan archipelago were assessed using random amplified polymorphic DNA (RAPD) markers. • Key Results A total of 99 discernible loci were obtained for all populations using ten primers, 50·5 % of which were polymorphic [percentage of polymorphic bands (PPB) = 50·5 %]. Despite being a woody, long-lived, perennial, outcrossing and insect-pollinated plant, N. sericea exhibited low levels of genetic variation. The cultivated populations (PPB = 18·9 %, HE = 0·060, S = 0·092) were genetically less diverse than the natural populations (PPB = 23·1 %, HE = 0·082, S = 0·123). Based on analysis of molecular variance, a high degree of among-population differentiation was revealed for both natural (0·387) and cultivated populations (0·598). • Conclusions Removal of plants from the wild for horticulture purposes has eroded the level of genetic variation of N. sericea. Low levels of genetic diversity and a high degree of population differentiation indicate that management strategies should include conservation of natural habitats occupied by all six wild populations, and sampling of germplasm resources from multiple seed sources. PMID:15546928

  10. [Relationship of the course of nephrotuberculosis in patients to various combinations of genetic markers].

    PubMed

    Khakimov, M A; Ubaĭdullaev, A M; Kazakov, K S

    2007-01-01

    To examine the body's responsiveness in different forms of nepthrotuberculosis, 237 patients underwent comprehensive clinical laboratory studies. To reveal various combinations of genetic markers, the authors determine the phenotypes of haptoglobin, the activity of red blood cell glucose-6-phosphate dehydrogenase, the type of inactivation of isonicotinic acid hydrazide. According to the combinations of a complex of these genetic markers, the authors identified 4 combinations: poor, good, relatively poor, and relatively good. The studies indicated the high incidence of common forms of nephrotuberculosis in subjects with poor and relatively poor combinations of genetic markers. The determination of various chronic renal failure-associated combinations of genetic markers may be used to identify risk groups for this disease. PMID:18080530

  11. [Progress on biosafety assessment of marker genes in genetically modified foods].

    PubMed

    Yang, Lichen; Yang, Xiaoguang

    2003-05-01

    Marker genes are useful in facilitating the detection of genetically modified organisms(GMO). These genes play an important role during the early identification stage of GMO development, but they exist in the mature genetically modified crops. So the safety assessment of these genes could not be neglected. In this paper, all the study on the biosafety assessment of marker genes were reviewed, their possible hazards and risks were appraised, and the marker genes proved safe were list too. GMO Labeling the is one important regulations for the development of genetically modified foods in the market. The accurate detecting techniques for GMO are the basis for setting up labeling regulation. In addition, some methods used to remove marker genes in genetically modified foods were introduced in the paper, which can eliminate their biosafety concern thoroughly. PMID:12914289

  12. Genetic variation in wild populations of the tuber crop Amorphophallus konjac (Araceae) in central China as revealed by AFLP markers.

    PubMed

    Pan, C; Gichira, A W; Chen, J M

    2015-01-01

    Amorphophallus konjac is an economically important crop. In order to provide baseline information for sustainable development and conservation of the wild plant resources of A. konjac, we studied the genetic diversity and population structure of this species using amplified fragment length polymorphism (AFLP) molecular markers. We sampled 139 individuals from 10 wild populations of A. konjac in central China. Using five AFLP primer combinations, we scored a total of 270 DNA fragments, most of which were polymorphic (98.2%). Percentage of polymorphic loci, Nei's genetic diversity index, and Shannon's information index showed high levels of genetic variation within A. konjac populations. Analysis of molecular variance indicated that most of the variance (68%) resided within populations. The coefficient of genetic differentiation between populations was 0.348 and the estimated gene flow was 0.469, indicating that there was limited gene flow among the populations. Unweighted pair group method with arithmetic mean cluster analysis and principal coordinates analysis indicated that geographically close populations were more likely to cluster together. The Mantel test revealed a significant correlation between geographic and genetic distances (R2 = 0.2521, P < 0.05). The special insect-pollination system of A. konjac and the complex geography of central China are likely to have contributed to the current pattern of genetic variation of this species. In the present study, we provide several suggestions on the future protection of the wild plant genetic resources of A. konjac. PMID:26782525

  13. Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalum genus

    PubMed Central

    2013-01-01

    Background Paspalum (Poaceae) is an important genus of the tribe Paniceae, which includes several species of economic importance for foraging, turf and ornamental purposes, and has a complex taxonomical classification. Because of the widespread interest in several species of this genus, many accessions have been conserved in germplasm banks and distributed throughout various countries around the world, mainly for the purposes of cultivar development and cytogenetic studies. Correct identification of germplasms and quantification of their variability are necessary for the proper development of conservation and breeding programs. Evaluation of microsatellite markers in different species of Paspalum conserved in a germplasm bank allowed assessment of the genetic differences among them and assisted in their proper botanical classification. Results Seventeen new polymorphic microsatellites were developed for Paspalum atratum Swallen and Paspalum notatum Flüggé, twelve of which were transferred to 35 Paspalum species and used to evaluate their variability. Variable degrees of polymorphism were observed within the species. Based on distance-based methods and a Bayesian clustering approach, the accessions were divided into three main species groups, two of which corresponded to the previously described Plicatula and Notata Paspalum groups. In more accurate analyses of P. notatum accessions, the genetic variation that was evaluated used thirty simple sequence repeat (SSR) loci and revealed seven distinct genetic groups and a correspondence of these groups to the three botanical varieties of the species (P. notatum var. notatum, P. notatum var. saurae and P. notatum var. latiflorum). Conclusions The molecular genetic approach employed in this study was able to distinguish many of the different taxa examined, except for species that belong to the Plicatula group, which has historically been recognized as a highly complex group. Our molecular genetic approach represents a

  14. Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii

    PubMed Central

    Zhang, Shouan; Gao, Muqiang; Zaitlin, David

    2012-01-01

    Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a “modified backcross” involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062 cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina. PMID

  15. Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

  16. Usefulness of WRKY gene-derived markers for assessing genetic diversity of Florida coconut cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of the genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm representing eight cultivars was previously described using 15 microsatellite (simple sequence repeat, SSR) markers. Here we report on the analysis of the same genotypes using 13 markers d...

  17. GENETIC LINKAGE MAP FOR WATERMELON: SEGREGATION AND DISTRIBUTION OF DNA MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic linkage map is being constructed for watermelon based on a testcross population and an F2 population. About 51.0% and 31.8% of the markers in the testcross and F2 populations are skewed from the expected segregation ratios. AFLP markers appeared to be clustered on linkage regions, while IS...

  18. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia.

    PubMed

    Moges, Asmare D; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R

    2016-01-01

    Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

  19. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

    PubMed Central

    Moges, Asmare D.; Admassu, Belayneh; Belew, Derbew; Yesuf, Mohammed; Njuguna, Joyce; Kyalo, Martina; Ghimire, Sita R.

    2016-01-01

    Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia. PMID:26978654

  20. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study.

    PubMed

    de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

    2013-03-01

    Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings. PMID:23569417

  1. Molecular genetic diversity in populations of the stingless bee Plebeia remota: A case study

    PubMed Central

    de Oliveira Francisco, Flávio; Santiago, Leandro Rodrigues; Arias, Maria Cristina

    2013-01-01

    Genetic diversity is a major component of the biological diversity of an ecosystem. The survival of a population may be seriously threatened if its genetic diversity values are low. In this work, we measured the genetic diversity of the stingless bee Plebeia remota based on molecular data obtained by analyzing 15 microsatellite loci and sequencing two mitochondrial genes. Population structure and genetic diversity differed depending on the molecular marker analyzed: microsatellites showed low population structure and moderate to high genetic diversity, while mitochondrial DNA (mtDNA) showed high population structure and low diversity in three populations. Queen philopatry and male dispersal behavior are discussed as the main reasons for these findings. PMID:23569417

  2. Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.).

    PubMed

    Gujaria, Neha; Kumar, Ashish; Dauthal, Preeti; Dubey, Anuja; Hiremath, Pavana; Bhanu Prakash, A; Farmer, Andrew; Bhide, Mangla; Shah, Trushar; Gaur, Pooran M; Upadhyaya, Hari D; Bhatia, Sabhyata; Cook, Douglas R; May, Greg D; Varshney, Rajeev K

    2011-05-01

    A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here

  3. Distribution of Genetic Marker Concentrations for Fecal Indicator Bacteria in Sewage and Animal Feces

    PubMed Central

    Kelty, Catherine A.; Varma, Manju; Sivaganesan, Mano; Haugland, Richard A.

    2012-01-01

    Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log10 copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications. PMID:22504809

  4. Distribution of genetic marker concentrations for fecal indicator bacteria in sewage and animal feces.

    PubMed

    Kelty, Catherine A; Varma, Manju; Sivaganesan, Mano; Haugland, Richard A; Shanks, Orin C

    2012-06-01

    Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log(10) copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications. PMID:22504809

  5. Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design

    PubMed Central

    Diaz-Cano, Salvador J.

    2012-01-01

    Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning. PMID:22408433

  6. Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.

    PubMed

    Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Cho, Young-Il; Lee, Hye-Eun; Kim, Do-Sun; Woo, Jong-Gyu; Cho, Myeong-Cheoul

    2014-01-10

    Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies. PMID:24125952

  7. Delimitation of Russula Subgenus Amoenula in Korea Using Three Molecular Markers

    PubMed Central

    Park, Myung Soo; Fong, Jonathan J.; Lee, Hyun; Oh, Seung-Yoon; Jung, Paul Eunil; Min, Young Ju; Seok, Soon Ja

    2013-01-01

    Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula. PMID:24493939

  8. Phylogenetic analysis of heterocystous cyanobacteria (Subsections IV and V) using highly iterated palindromes as molecular markers.

    PubMed

    Singh, Prashant; Kaushik, Manish Singh; Srivastava, Meenakshi; Mishra, Arun Kumar

    2014-07-01

    Highly iterated palindromes (HIP) have been used as high resolution molecular markers for assessing the genetic variability and phylogenetic relatedness of heterocystous cyanobacteria (subsections IV and V) representing 12 genera of heterocystous cyanobacteria, collected from different geographical areas of India. DNA fingerprints generated using four HIP markers viz. HIP-AT, HIP-CA, HIP-GC, and HIP-TG showed 100 % polymorphism in all the heterocystous cyanobacteria studied and each marker produced unique and strain-specific banding pattern. Furthermore, phylogenetic affinities based on the dendrogram constructed using HIP DNA profiles of heterocystous cyanobacteria suggest the monophyletic origin of this entire heterocystous clade along with a clear illustration of the polyphyletic origin of the branched Stigonematalean order (Subsection V). In addition, phylogenetic affinities were validated by principal component analysis of the HIP fingerprints. The overall data obtained by both the phylogeny and principal component assessments proved that the entire heterocystous clade was intermixed, and there are immediate needs for classificatory reforms that satisfy morphological plasticity and environmental concerns. PMID:25049460

  9. Genetics

    MedlinePlus

    Homozygous; Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  10. Genetics

    MedlinePlus

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  11. An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

    PubMed Central

    2011-01-01

    Background Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. Results The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. Conclusions Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with Uni

  12. Isolation and characterization of microsatellite markers and analysis of genetic diversity in Chinese jujube (Ziziphus jujuba Mill.).

    PubMed

    Wang, Siqi; Liu, Ying; Ma, Liying; Liu, Huabo; Tang, Yan; Wu, Liping; Wang, Zhe; Li, Yingyue; Wu, Rongling; Pang, Xiaoming

    2014-01-01

    Chinese jujube (Ziziphus jujuba Mill, 2n = 2× = 24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba 'Dongzao' using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for 'Dongzao'. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars. PMID:24932973

  13. Molecular markers for identifying municipal, domestic and agricultural sources of organic matter in natural waters.

    PubMed

    Harwood, John J

    2014-01-01

    Molecular markers can be used to determine the sources of organic pollution in water. This review summarizes progress made during the last two decades in identifying reliable molecular markers to distinguish pollution from sewage, animal production, and other sources. Two artificial sweeteners, sucralose and acesulfame-K, are sufficiently stable to be molecular markers and easily associated with domestic wastewater. Waste from different animal species may be distinguished by profiling fecal sterols and bile acids. Other markers which have been evaluated, including caffeine, detergent components, and compounds commonly leached from landfills are discussed. PMID:24200048

  14. Molecular and immunologic markers of kidney cancer-potential applications in predictive, preventive and personalized medicine.

    PubMed

    Mickley, Amanda; Kovaleva, Olga; Kzhyshkowska, Julia; Gratchev, Alexei

    2015-01-01

    Kidney cancer is one of the deadliest malignancies due to frequent late diagnosis (33 % or renal cell carcinoma are metastatic at diagnosis) and poor treatment options. There are two major subtypes of kidney cancer: renal cell carcinoma (RCC) and renal pelvis carcinoma. The risk factors for RCC, accounting for more than 90 % of all kidney cancers, are smoking, obesity, hypertension, misuse of pain medication, and some genetic diseases. The most common molecular markers of kidney cancer include mutations and epigenetic inactivation of von Hippel-Lindau (VHL) gene, genes of vascular endothelial growth factor (VEGF) pathway, and carbonic anhydrase IX (CIAX). The role of epigenetic pathways, including DNA methylation and chromatin structure remodeling, was also demonstrated. Immunologic properties of RCC enable this type of tumor to escape immune response effectively. An important role in this process is played by tumor-associated macrophages that demonstrate mixed M1/M2 phenotype. In this review, we discuss molecular and cellular aspects for RCC development and current state of knowledge allowing personalized approaches for diagnostics and prognostic prediction of this disease. A set of macrophage markers is suggested for the analysis of the association of macrophage phenotype and disease prognosis. PMID:26500709

  15. Advances in Research to Improve Selection for Beef Production and Quality Using Genetic Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker technology for selection of beef cattle has changed and continues to change. Some ideas about how this technology would be used and how much of the genetic differences could easily be identified have changed. New approaches based on what we have learned so far and on new genotyping ...

  16. Bottlenecks in molecular testing for rare genetic diseases.

    PubMed

    Willems, Patrick J

    2008-06-01

    Despite the impressive progress in our understanding of the genetic causes of genetic diseases over the past decade, molecular diagnosis for rare genetic disorders is still in its infancy, being slow, expensive, unreliable, insufficient, and ill-organized in many countries. This leaves the gap between the hype of the current genomic research and the hope for a simple genetic diagnosis too large for patients and families affected with genetic disease. The bottlenecks in the molecular testing for rare genetic disorders are discussed below. PMID:18412107

  17. Influence of wastewater disinfection on densities of culturable fecal indicator bacteria and genetic markers.

    PubMed

    Chern, Eunice C; Brenner, Kristen; Wymer, Larry; Haugland, Richard A

    2014-09-01

    The US Environmental Protection Agency has proposed the use of quantitative polymerase chain reaction (qPCR) as a rapid alternative analytical method for monitoring recreational water quality at beaches. For qPCR to be considered for other Clean Water Act purposes, such as inclusion in discharge permits and use in Total Maximum Daily Load calculations, it is necessary to understand how qPCR detectable genetic markers are influenced by wastewater disinfection. This study investigated genetic markers for Escherichia coli, Enterococcus, Clostridium spp., Bacteroides, total Bacteroidales, as well as the human-associated Bacteroides markers, HF183 and HumM2, to determine which, if any, were influenced by disinfection (chlorination or ultraviolet light) of effluents from secondary wastewater treatment in different seasons. The effects of disinfection on culturable enterococci, E. coli, Bacteroides, and C. perfringens were also compared to their associated genetic markers. Disinfection of secondary treatment effluents significantly reduced culturable fecal indicator bacteria (FIB) but not genetic marker densities. No significant differences were observed in the responses of FIB culture and genetic marker densities to type of disinfection (chlorination vs UV) or season. Results of this study provide evidence that qPCR may not be suitable for monitoring efficacy of wastewater disinfection on the inactivation of bacterial pathogens. PMID:25252344

  18. Development of 10 microsatellite markers from Pantala flavescens and their applicability in studying genetics diversity.

    PubMed

    Cao, Lingzhen; Fu, Xiaowei; Wu, Kongming

    2015-08-01

    Pantala flavescens (Fabricius 1798) is one of the most common species among migration dragonflies. It is often encountered in large swarms during migration or directed dispersal flights. For a better understanding of its gene flow, genetic structure and migration patterns throughout the world, 10 polymorphic microsatellite markers were isolated in this study. We respectively collected 32 P. flavescens from three places (Hunan, Liaoning and Heilongjiang) and 20 P. flavescens from Beijing. Partial genomic libraries containing microsatellite sequences were constructed with magnetic-bead enrichment method. By screening, sequence analysis, PCR amplification and so on, ten 10 polymorphic microsatellite markers were isolated. In order to assess their applicability, genetic diversity of these novel markers was tested in 96 individuals from three populations in China (Hunan, Liaoning and Heilongjiang). These markers were highly polymorphic, with 3-12 alleles per markers. The observed (Ho) and expected (He) heterozygosities ranged 0.321-0.667 and from 0.531 to 0.948 respectively. The genetic difference between Hunan and Liaoning is 0.429, while the genetic difference between Liaoning and Heilongjiang is 0.0508. These microsatellite markers for P. flavescens were developed for the first time, and will be a powerful tool for studying population genetic diversity and dispersal behavior of P. flavescens in China and worldwide. PMID:25788247

  19. Analysis of Genetic Diversity and Development of SCAR Markers in a Mycogone perniciosa Population.

    PubMed

    Wang, Wei; Li, Xiao; Chen, Bingzhi; Wang, Shuang; Li, Chenghuan; Wen, Zhiqiang

    2016-07-01

    The fungus Mycogone perniciosa is a major pathogen of the common button mushroom Agaricus bisporus. Analysis of genetic diversity in M. Perniciosa may assist in developing methods for prophylaxis and treatment of M. Perniciosa infections. For this, it is necessary to classify M. Perniciosa into relevant class groups quickly and efficiently. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and sequence-related amplified polymorphism (SRAP) markers were used to obtain genetic fingerprints and assess the genetic variation among 49 strains of M. perniciosa collected from different areas of Fujian Province in China. Analysis of DNA sequence polymorphism revealed two major distinct groups (Group I and Group II). Specific DNA fragments that were identified through RAPD, ISSR, and SRAP markers were sequenced and used for the designing of stable sequence-characterized amplified region (SCAR) markers. The resulting SCAR markers were then validated against the classified groups of M. perniciosa. PMID:26960290

  20. [Glucotransporters: clinical, molecular and genetic aspects].

    PubMed

    Sandoval-Muñiz, Roberto de Jesús; Vargas-Guerrero, Belinda; Flores-Alvarado, Luis Javier; Gurrola-Díaz, Carmen Magdalena

    2016-01-01

    Oxidation of glucose is the major source of obtaining cell energy, this process requires glucose transport into the cell. However, cell membranes are not permeable to polar molecules such as glucose; therefore its internalization is accomplished by transporter proteins coupled to the cell membrane. In eukaryotic cells, there are two types of carriers coupled to the membrane: 1) cotransporter Na+-glucose (SGLT) where Na+ ion provides motive power for the glucose´s internalization, and 2) the glucotransporters (GLUT) act by facilitated diffusion. This review will focus on the 14 GLUT so far described. Despite the structural homology of GLUT, different genetic alterations of each GLUT cause specific clinical entities. Therefore, the aim of this review is to gather the molecular and biochemical available information of each GLUT as well as the particular syndromes and pathologies related with GLUT´s alterations and their clinical approaches. PMID:27595260

  1. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations

    PubMed Central

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express–in the form of dendrograms–the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  2. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations.

    PubMed

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express--in the form of dendrograms--the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  3. Expression of Molecular Markers of Angiogenesis, Lymphangiogenesis, and Proliferation Depending on the Stage of Skin Melanoma.

    PubMed

    Bgatova, N P; Lomakin, A I; Fursov, S A; Kachesov, I V; Chepko, S A; Isakova, N B; Borodin, Yu I; Voytsitsky, V E; Konenkov, V I

    2016-08-01

    The expression of molecular markers characterizing activity of the tumor process and metastases (proliferation marker Ki-67, angiogenesis marker CD34, and lymphangiogenesis markers podoplanin and LYVE-1) was assessed by immunohictochemical method in the primary tumor specimens collected during surgery for cutaneous melanoma (40 patients). Proliferative activity of the tumor tissue and volume density of peritumoral blood and lymph vessels increased with increasing tumor malignancy, which could indicate the risk of metastases. PMID:27590758

  4. Assessment of genetic diversity in Mucuna species of India using randomly amplified polymorphic DNA and inter simple sequence repeat markers.

    PubMed

    Patil, Ravishankar R; Pawar, Kiran D; Rane, Manali R; Yadav, Shrirang R; Bapat, Vishwas A; Jadhav, Jyoti P

    2016-04-01

    Genus Mucuna which is native to China and Eastern India comprises of perennial climbing legume with long slender branches, trifoliate leaves and bear green or brown pod covered with soft or rigid hairs that cause intense irritation. The plants of this genus are agronomically and economically important and commercially cultivated in India, China and other regions of the world. The high degrees of taxonomical confusions exist in Mucuna species that make authentic identification and classification difficult. In the present study, the genetic diversity among the 59 accessions of six species and three varieties of M. pruriens has been assessed using DNA fingerprinting based molecular markers techniques namely randomly amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and combined dataset of RAPD and ISSR. Also, genetic relationship among two endemic species of Mucuna namely M. imbricata and M. macrocarpa and two varieties namely IIHR hybrid (MHR) and Dhanwantari (MD) with other species under study was investigated by using cluster analysis and principal coordinate analysis. The cluster analysis of RAPD, ISSR and combined dataset of RAPD and ISSR clearly demonstrated the existence of high interspecific variation than intra-specific variation in genus Mucuna. The utility and efficacy of RAPD and ISSR for the study of intra species and interspecies genetic diversity was evident from AMOVA and PCoA analysis. This study demonstrates the genetic diversity in Mucuna species and indicates that these markers could be successfully used to assess genetic variation among the accessions of Mucuna species. PMID:27436912

  5. Potential of Start Codon Targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions.

    PubMed

    Zhang, Junchao; Xie, Wengang; Wang, Yanrong; Zhao, Xuhong

    2015-01-01

    Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT) markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB) of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) showed that genetic variation was greater within geographical regions (50.99%) than between them (49.01%). Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions. PMID:25853316

  6. Molecular and comparative genetics of mental retardation.

    PubMed Central

    Inlow, Jennifer K; Restifo, Linda L

    2004-01-01

    Affecting 1-3% of the population, mental retardation (MR) poses significant challenges for clinicians and scientists. Understanding the biology of MR is complicated by the extraordinary heterogeneity of genetic MR disorders. Detailed analyses of >1000 Online Mendelian Inheritance in Man (OMIM) database entries and literature searches through September 2003 revealed 282 molecularly identified MR genes. We estimate that hundreds more MR genes remain to be identified. A novel test, in which we distributed unmapped MR disorders proportionately across the autosomes, failed to eliminate the well-known X-chromosome overrepresentation of MR genes and candidate genes. This evidence argues against ascertainment bias as the main cause of the skewed distribution. On the basis of a synthesis of clinical and laboratory data, we developed a biological functions classification scheme for MR genes. Metabolic pathways, signaling pathways, and transcription are the most common functions, but numerous other aspects of neuronal and glial biology are controlled by MR genes as well. Using protein sequence and domain-organization comparisons, we found a striking conservation of MR genes and genetic pathways across the approximately 700 million years that separate Homo sapiens and Drosophila melanogaster. Eighty-seven percent have one or more fruit fly homologs and 76% have at least one candidate functional ortholog. We propose that D. melanogaster can be used in a systematic manner to study MR and possibly to develop bioassays for therapeutic drug discovery. We selected 42 Drosophila orthologs as most likely to reveal molecular and cellular mechanisms of nervous system development or plasticity relevant to MR. PMID:15020472

  7. Molecular genetics of testicular germ cell tumors

    PubMed Central

    Sheikine, Yuri; Genega, Elizabeth; Melamed, Jonathan; Lee, Peng; Reuter, Victor E.; Ye, Huihui

    2012-01-01

    Testicular germ cell tumors (TGCT) are the most common malignancy in young men. While most TGCT are potentially curable, approximately 5% of patients with TGCT may develop chemoresistance and die from the disease. This review article summarizes current knowledge in genetics underlying the development, progression and chemoresistance of TGCT. Most post-pubertal TGCT originate from intratubular germ cell neoplasia unclassified (IGCNU), which are transformed fetal gonocytes. Development of IGCNU may involve aberrantly activated KITLG/KIT pathway and overexpression of embryonic transcription factors such as NANOG and POU5F1, which leads to suppression of apoptosis, increased proliferation, and accumulation of mutations in gonocytes. Invasive TGCT consistently show gain of chromosome 12p, typically isochromosome 12p. Single gene mutations are uncommon in TGCT. KIT, TP53, KRAS/NRAS, and BRAF are genes most commonly mutated in TGCT and implicated in their pathogenesis. Different histologic subtypes of TGCT possess different gene expression profiles that reflect different directions of differentiation. Their distinct gene expression profiles are likely caused by epigenetic regulation, in particular DNA methylation, but not by gene copy number alterations. Resistance of TGCT to chemotherapy has been linked to karyotypic aberrations, single-gene mutations, and epigenetic regulation of gene expression in small-scale studies. The study of TGCT genetics could ultimately translate into development of new molecular diagnostic and therapeutic modalities for these tumors and improve the care of patients with these malignancies. PMID:22432056

  8. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    PubMed Central

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  9. Genetic linkage map of Chinese native variety faba bean (Vicia faba L.) based on simple sequence repeat markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Simple sequence repeat (SSR) marker is a powerful tool for construction of genetic linkage map which can be applied for locating quantitative trait loci (QTL) and marker-assisted selection (MAS). In this study, a genetic map of faba bean was constructed with SSR markers using a population of 129 F2 ...

  10. Genetic and molecular alterations in meningiomas.

    PubMed

    Alexiou, George A; Markoula, Sofia; Gogou, Pinelopi; Kyritsis, Athanasios P

    2011-05-01

    Meningiomas are the most common benign intracranial tumors in adults arising from the dura matter. The etiology of meningiomas is mostly unknown, although several risk factors have been described, such as ionizing radiation, head injury, hormones and genetic factors. According to WHO they are classified into 3 grades, grade I, grade II and grade III. Meningiomas express various hormonal and growth factor receptors, such as progesterone, estrogen, somatostatin, transforming growth factor alpha (TGF-alpha) and epidermal growth factor (EGF) receptors, which may be related to their biological behavior and response to treatment. Chromosomal abnormalities linked to meningiomas involve chromosomes 22, 1p, 9p, 10p, 11, 14q, 15, 17, and 18q. In addition, genes that may be involved in the formation of meningiomas include NF2, DAL-1, p14 (ARF), p53, MDM2, Rb, p16 and c-myc. It is likely that detailed molecular information will aid in establishing a molecular grading of these tumors and predict response to treatment and survival. PMID:21227570

  11. Molecular Genetics of Supernumerary Tooth Formation

    PubMed Central

    Wang, Xiu-Ping; Fan, Jiabing

    2011-01-01

    Summary Despite advances in the knowledge of tooth morphogenesis and differentiation, relatively little is known about the aetiology and molecular mechanisms underlying supernumerary tooth formation. A small number of supernumerary teeth may be a common developmental dental anomaly, while multiple supernumerary teeth usually have a genetic component and they are sometimes thought to represent a partial third dentition in humans. Mice, which are commonly used for studying tooth development, only exhibit one dentition, with very few mouse models exhibiting supernumerary teeth similar to those in humans. Inactivation of Apc or forced activation of Wnt/β(catenin signalling results in multiple supernumerary tooth formation in both humans and in mice, but the key genes in these pathways are not very clear. Analysis of other model systems with continuous tooth replacement or secondary tooth formation, such as fish, snake, lizard, and ferret, is providing insights into the molecular and cellular mechanisms underlying succesional tooth development, and will assist in the studies on supernumerary tooth formation in humans. This information, together with the advances in stem cell biology and tissue engineering, will pave ways for the tooth regeneration and tooth bioengineering. PMID:21309064

  12. LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers.

    PubMed

    Tam, Sheh May; Lefebvre, Véronique; Palloix, Alain; Sage-Palloix, Anne-Marie; Mhiri, Corinne; Grandbastien, Marie-Angèle

    2009-10-01

    Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution. PMID:19618162

  13. Widespread utility of highly informative AFLP molecular markers across divergent shark species.

    PubMed

    Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

    2006-01-01

    Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks. PMID:17150982

  14. Assessment of genetic diversity and relationships among wild and cultivated Tunisian plums (Prunus spp) using random amplified microsatellite polymorphism markers.

    PubMed

    Ben Tamarzizt, H; Ben Mustapha, S; Baraket, G; Abdallah, D; Salhi-Hannachi, A

    2015-01-01

    The usefulness of random amplified microsatellite polymorphism markers to study the genetic diversity and relationships among cultivars belonging to Prunus salicina and P. domestica and their wild relatives (P. insititia and P. spinosa) was investigated. A total of 226 of 234 bands were polymorphic (96.58%). The 226 random amplified microsatellite polymorphism markers were screened using 15 random amplified polymorphic DNA and inter-simple sequence repeat primers combinations for 54 Tunisian plum accessions. The percentage of polymorphic bands (96.58%), the resolving power of primers values (135.70), and the polymorphic information content demonstrated the efficiency of the primers used in this study. The genetic distances between accessions ranged from 0.18 to 0.79 with a mean of 0.24, suggesting a high level of genetic diversity at the intra- and interspecific levels. The unweighted pair group with arithmetic mean dendrogram and principal component analysis discriminated cultivars efficiently and illustrated relationships and divergence between spontaneous, locally cultivated, and introduced plum types. These procedures showed continuous variation that occurs independently of the status of the species and geographical origin of the plums. In this study, random amplified microsatellite polymorphism was found to be as a reliable molecular marker for fingerprinting and for examining the diversity study of the plum and its relatives. PMID:25867340

  15. Biomedical wellness monitoring system based upon molecular markers

    NASA Astrophysics Data System (ADS)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  16. Measuring the genetic diversity of Arabian Oryx using microsatellite markers: implication for captive breeding.

    PubMed

    Arif, Ibrahim A; Khan, Haseeb A; Shobrak, Mohammad; Homaidan, Ali A Al; Sadoon, Mohammad Al; Farhan, Ahmad H Al

    2010-04-01

    Arabian oryx (Oryx leucoryx) is an endangered antelope that is being protected by captive breeding programs. However, the long term success of these programs mainly depends on the prudent use of molecular information for conservation management. We have used an array of seven microsatellite loci to examine the molecular diversity in a representative population of 24 captive-bred and reintroduced Arabian oryx. The locus-wise mean observed heterozygosity (0.601) was found to be comparatively higher than the mean expected heterozygosity (0.565). The specimen-wise observed heterozygosity ranged from 0.143 to 1.00 with an average of 0.60 whereas the mean d(2) varied from 0.57 to 1023.428 with an average value of 223.357. The results of Shannon information index (I = 0.898) also indicated a high level of within population genetic diversity. The average gene flow was 0.298, ranging between 0.204 and 0.424 for different loci. In conclusion, the information about the extent of heterozygosity, allelic diversity and inbreeding/outbreeding depression using microsatellite markers could be of potential relevance for the management of captive breeding programs for the conservation of Arabian oryx. PMID:20558900

  17. Genetic variant as a marker for bladder cancer therapy

    Cancer.gov

    Patients who have inherited a specific common genetic variant develop bladder cancer tumors that strongly express a protein known as prostate stem cell antigen (PSCA), which is also expressed in many pancreatic and prostate tumors, according to research a

  18. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

    PubMed Central

    Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  19. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    PubMed

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  20. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    PubMed

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  1. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

    PubMed Central

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  2. The origin of the Japanese race based on genetic markers of immunoglobulin G

    PubMed Central

    Matsumoto, Hideo

    2009-01-01

    This review addresses the distribution of genetic markers of immunoglobulin G (Gm) among 130 Mongoloid populations in the world. These markers allowed the populations to be clearly divided into 2 groups, the northern and southern groups. The northern group is characterized by high frequencies of 2 marker genes, ag and ab3st, and an extremely low frequency of the marker gene afb1b3; and the southern group, in contrast, is indicated by a remarkably high frequency of afb1b3 and low frequencies of ag and ab3st. Based on the geographical distribution of the markers and gene flow of Gm ag and ab3st (northern Mongoloid marker genes) from northeast Asia to the Japanese archipelago, the Japanese population belongs basically to the northern Mongoloid group and is thus suggested to have originated in northeast Asia, most likely in the Baikal area of Siberia. PMID:19212099

  3. Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.

    PubMed

    Öz, M H; Vurgun, H; Bakir, M; Büyük, İ; Yüksel, C; Ünlü, H M; Çukadar, K; Karadoğan, B; Köse, Ö; Ergül, A

    2013-01-01

    We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars. PMID:24301792

  4. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

    PubMed Central

    Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2013-01-01

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

  5. Dinucleotide repeat loci contribute highly informative genetic markers to the human chromosome 2 linkage map

    SciTech Connect

    Todd, S. ); Sherman, S.L. ); Naylor, S.L. )

    1993-06-01

    Microsatellite repeat loci can provide informative markers for genetic linkage. Currently, the human chromosome 2 genetic linkage map has very few highly polymorphic markers. Being such a large chromosome, it will require a large number of informative markers for the dense coverage desired to allow disease genes to be mapped quickly and accurately. Dinucleotide repeat loci from two anonymous chromosome 2 genomic DNA clones were sequenced so that oligonucleotide primers could be designed for amplifying each locus using the polymerase chain reaction (PCR). Five sets of PCR primers were also generated from nucleotide sequences in the GenBank Database of chromosome 2 genes containing dinucleotide repeats. In addition, one PCR primer pair was made that amplifies a restriction fragment length polymorphism on the TNP1 gene. These markers were placed on the CEPH genetic linkage map by screening the CEPH reference DNA panel with each primer set, combining these data with those of other markers previously placed on the map, and analyzing the combined data set using CRI-MAP and LINKAGE. The microsatellite loci are highly informative markers and the TNP1 locus, as expected, is only moderately informative. A map was constructed with 38 ordered loci (odds [ge] 1000:1) spanning 296 cM (male) and 476 cM (female) of chromosome 2 compared with 306 cM (male) and 529 cM (female) for a previous map of 20 markers. 32 refs., 2 figs., 3 tabs.

  6. Reasoning across Ontologically Distinct Levels: Students' Understandings of Molecular Genetics

    ERIC Educational Resources Information Center

    Duncan, Ravit Golan; Reiser, Brian J.

    2007-01-01

    In this article we apply a novel analytical framework to explore students' difficulties in understanding molecular genetics--a domain that is particularly challenging to learn. Our analytical framework posits that reasoning in molecular genetics entails mapping across ontologically distinct levels--an information level containing the genetic…

  7. Child Development and Molecular Genetics: 14 Years Later

    ERIC Educational Resources Information Center

    Plomin, Robert

    2013-01-01

    Fourteen years ago, the first article on molecular genetics was published in this journal: "Child Development, Molecular Genetics, and What to Do With Genes Once They Are Found" (R. Plomin & M. Rutter, 1998). The goal of the article was to outline what developmentalists can do with genes once they are found. These new directions for developmental…

  8. Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note

    PubMed Central

    2013-01-01

    Background Plasmodium vivax is the most widespread of the human malaria parasites in terms of geography, and is thought to present unique challenges to local efforts aimed at control and elimination. Parasite molecular markers can provide much needed data on P. vivax populations, but few such markers have been critically evaluated. One marker that has seen extensive use is the gene encoding merozoite surface protein 3-alpha (MSP-3α), a blood-stage antigen known to be highly variable among P. vivax isolates. Here, a sample of complete msp-3α gene sequences is analysed in order to assess its utility as a molecular marker for epidemiologic investigations. Methods Amplification, cloning and sequencing of additional P. vivax isolates from different geographic locations, including a set of Venezuelan field isolates (n = 10), yielded a sample of 48 complete msp-3α coding sequences. Characterization of standard population genetic measures of diversity, phylogenetic analysis, and tests for recombination were performed. This allowed comparisons to patterns inferred from the in silico simulation of a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) protocol used widely. Results The larger sample of MSP-3α diversity revealed incongruence between the observed levels of nucleotide polymorphism, which were high in all populations, and the pattern of PCR-RFLP haplotype diversity. Indeed, PCR-RFLP haplotypes were not informative of a population’s genetic diversity and identical haplotypes could be produced from analogous bands in the commonly used protocol. Evidence of frequent and variable insertion-deletion mutations and recurrent recombination between MSP-3α haplotypes complicated the inference of genetic diversity patterns and reduced the phylogenetic signal. Conclusions The genetic diversity of P. vivax msp-3α involves intragenic recombination events. Whereas the high genetic diversity of msp-3α makes it a promising marker for some

  9. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

    PubMed

    Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

  10. Identification of QTLs Associated with Callogenesis and Embryogenesis in Oil Palm Using Genetic Linkage Maps Improved with SSR Markers

    PubMed Central

    Ting, Ngoot-Chin; Jansen, Johannes; Nagappan, Jayanthi; Ishak, Zamzuri; Chin, Cheuk-Weng; Tan, Soon-Guan; Cheah, Suan-Choo; Singh, Rajinder

    2013-01-01

    Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm. PMID:23382832

  11. Molecular Markers of Lung Cancer in MAYAK Workers

    SciTech Connect

    Steven A. Belinsky, PhD

    2007-02-15

    The molecular mechanisms that result in the elevated risk for lung cancer associated with exposure to radiation have not been well characterized. Workers from the MAYAK nuclear enterprise are an ideal cohort in which to study the molecular epidemiology of cancer associated with radiation exposure and to identify the genes targeted for inactivation that in turn affect individual risk for radiation-induced lung cancer. Epidemiology studies of the MAYAK cohort indicate a significantly higher frequency for adenocarcinoma and squamous cell carcinoma (SCC) in workers than in a control population and a strong correlation between these tumor types and plutonium exposure. Two hypotheses will be evaluated through the proposed studies. First, radiation exposure targets specific genes for inactivation by promoter methylation. This hypothesis is supported by our recent studies with the MAYAK population that demonstrated the targeting of the p16 gene for inactivation by promoter methylation in adenocarcinomas from workers (1). Second, genes inactivated in tumors can serve as biomarkers for lung cancer risk in a cancer-free population of workers exposed to plutonium. Support for this hypothesis is based on exciting preliminary results of our nested, case-control study of persons from the Colorado cohort. In that study, a panel of methylation markers for predicting lung cancer risk is being evaluated in sputum samples from incident lung cancer cases and controls. The first hypothesis will be tested by determining the prevalence for promoter hypermethylation of a panel of genes shown to play a critical role in the development of either adenocarcinoma and/or SCC associated with tobacco. Our initial studies on adenocarcinoma in MAYAK workers will be extended to evaluate methylation of the PAX5 {alpha}, PAX5 {beta}, H-cadherin, GATA5, and bone morphogenesis 3B (BMP3B) genes in the original sample set described under Preliminary studies. In addition, studies will be initiated in SCC

  12. Overview of molecular, cellular, and genetic neurotoxicology.

    PubMed

    Wallace, David R

    2005-05-01

    It has become increasingly evident that the field of neurotoxicology is not only rapidly growing but also rapidly evolving, especially over the last 20 years. As the number of drugs and environmental and bacterial/viral agents with potential neurotoxic properties has grown, the need for additional testing has increased. Only recently has the technology advanced to a level that neurotoxicologic studies can be performed without operating in a "black box." Examination of the effects of agents that are suspected of being toxic can occur on the molecular (protein-protein), cellular (biomarkers, neuronal function), and genetic (polymorphisms) level. Together, these areas help to elucidate the potential toxic profiles of unknown (and in some cases, known) agents. The area of proteomics is one of the fastest growing areas in science and particularly applicable to neurotoxicology. Lubec et al, provide a review of the potential and limitations of proteomics. Proteomics focuses on a more comprehensive view of cellular proteins and provides considerably more information about the effects of toxins on the CNS. Proteomics can be classified into three different focuses: post-translational modification, protein-expression profiling, and protein-network mapping. Together, these methods represent a more complete and powerful image of protein modifications following potential toxin exposure. Cellular neurotoxicology involves many cellular processes including alterations in cellular energy homeostasis, ion homeostasis, intracellular signaling function, and neurotransmitter release, uptake, and storage. The greatest hurdle in cellular neurotoxicology has been the discovery of appropriate biomarkers that are reliable, reproducible, and easy to obtain. There are biomarkers of exposure effect, and susceptibility. Finding the appropriate biomarker for a particular toxin is a daunting task. The appropriate biomarker for a particular toxin is a daunting task. The advantage to biomarker

  13. Development of DArT Marker Platforms and Genetic Diversity Assessment of the U.S. Collection of the New Oilseed Crop Lesquerella and Related Species

    PubMed Central

    Cruz, Von Mark V.; Kilian, Andrzej; Dierig, David A.

    2013-01-01

    The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa. PMID:23724020

  14. Genetic markers reveal a gradient of hybridization between cape hakes (Merluccius capensis and Merluccius paradoxus) in their sympatric geographic distribution

    NASA Astrophysics Data System (ADS)

    Miralles, Laura; Machado-Schiaffino, Gonzalo; Garcia-Vazquez, Eva

    2014-02-01

    The cape hakes Merluccius capensis and Merluccius paradoxus are important fishing resources for African countries such as Namibia and South Africa. In this study we have genetically analyzed adult samples from the overlapping distribution of these species. Eight microsatellite loci, the nuclear 5S rDNA locus and the Cytochrome Oxidase subunit I (COI) gene were employed as molecular markers. A North-South gradient of interspecific hybridization was found, with discordant mitochondrial and nuclear genotypes at the northernmost edge of M. paradoxus distribution. These results suggest intense introgression in North Benguela off the Namibian coast. Independent hake stock assessment is recommended in this region for sustainable management of this valuable resource.

  15. Molecular genetics at the Fort Collins Science Center

    USGS Publications Warehouse

    Oyler-McCance, S.J.; Stevens, P.D.

    2011-01-01

    The Fort Collins Science Center operates a molecular genetic and systematics research facility (FORT Molecular Ecology Laboratory) that uses molecular genetic tools to provide genetic information needed to inform natural resource management decisions. For many wildlife species, the data generated have become increasingly important in the development of their long-term management strategies, leading to a better understanding of species diversity, population dynamics and ecology, and future conservation and management needs. The Molecular Ecology Lab serves Federal research and resource management agencies by developing scientifically rigorous research programs using nuclear, mitochondrial and chloroplast DNA to help address many of today's conservation biology and natural resource management issues.

  16. Using genetic markers to orient the edges in quantitative trait networks: The NEO software

    PubMed Central

    Aten, Jason E; Fuller, Tova F; Lusis, Aldons J; Horvath, Steve

    2008-01-01

    Background Systems genetic studies have been used to identify genetic loci that affect transcript abundances and clinical traits such as body weight. The pairwise correlations between gene expression traits and/or clinical traits can be used to define undirected trait networks. Several authors have argued that genetic markers (e.g expression quantitative trait loci, eQTLs) can serve as causal anchors for orienting the edges of a trait network. The availability of hundreds of thousands of genetic markers poses new challenges: how to relate (anchor) traits to multiple genetic markers, how to score the genetic evidence in favor of an edge orientation, and how to weigh the information from multiple markers. Results We develop and implement Network Edge Orienting (NEO) methods and software that address the challenges of inferring unconfounded and directed gene networks from microarray-derived gene expression data by integrating mRNA levels with genetic marker data and Structural Equation Model (SEM) comparisons. The NEO software implements several manual and automatic methods for incorporating genetic information to anchor traits. The networks are oriented by considering each edge separately, thus reducing error propagation. To summarize the genetic evidence in favor of a given edge orientation, we propose Local SEM-based Edge Orienting (LEO) scores that compare the fit of several competing causal graphs. SEM fitting indices allow the user to assess local and overall model fit. The NEO software allows the user to carry out a robustness analysis with regard to genetic marker selection. We demonstrate the utility of NEO by recovering known causal relationships in the sterol homeostasis pathway using liver gene expression data from an F2 mouse cross. Further, we use NEO to study the relationship between a disease gene and a biologically important gene co-expression module in liver tissue. Conclusion The NEO software can be used to orient the edges of gene co

  17. Pathology and Molecular Genetics of Meningioma: Recent Advances

    PubMed Central

    SHIBUYA, Makoto

    2015-01-01

    Meningiomas are the most common intracranial primary neoplasm in adults. Although the spectrum of clinical and molecular genetic issues regarding meningiomas remains undefined, novel genetic alterations that are associated with tumor morphology, malignancy, or location have recently been discovered. This review focuses on recent advances in understanding of the heterogenous pathology of meningiomas, particularly on associations between the clinical, histological, etiological, epidemiological, and molecular genetical aspects of the neoplasm. PMID:25744347

  18. [Advance in molecular genetic research on primary congenital glaucoma].

    PubMed

    Li, Xiulan; Liu, Haotian; Zhang, Dingding

    2016-04-01

    Primary congenital glaucoma (PCG) is one of the major diseases causing blindness in children, but its pathogenesis has remained unclear. Genetic factors play an important role in the pathogenesis of PCG. Molecular genetics of candidate genes such as CYP1B1, MYOC, LTBP2 and FOXC1 has so far been explored, but no disease-causing gene has been identified. Molecular genetic research on PCG including candidate gene screening and research strategies are reviewed here. PMID:27060330

  19. Genetic diversity analysis in Piper species (Piperaceae) using RAPD markers.

    PubMed

    Sen, Sandeep; Skaria, Reby; Abdul Muneer, P M

    2010-09-01

    The genetic diversity of eight species of Piper (Piperaceae) viz., P. nigrum, P. longum, P. betle, P. chaba, P. argyrophyllum, P. trichostachyon, P. galeatum, and P. hymenophyllum from Kerala state, India were analyzed by Random amplified polymorphic DNA (RAPD). Out of 22 10-mer RAPD primers screened, 11 were selected for comparative analysis of different species of Piper. High genetic variations were found among different Piper species studied. Among the total of 149 RAPD fragments amplified, 12 bands (8.05%) were found monomorphic in eight species. The remaining 137 fragments were found polymorphic (91.95%). Species-specific bands were found in all eight species studied. The average gene diversity or heterozygosity (H) was 0.33 across all the species, genetic distances ranged from 0.21 to 0.69. The results of this study will facilitate germplasm identification, management, and conservation. PMID:20383613

  20. Genetic Marker Analysis of a Global Collection of Isolates of Citrus tristeza virus: Characterization and Distribution of CTV Genotypes and Association with Symptoms.

    PubMed

    Hilf, Mark E; Mavrodieva, Vessela A; Garnsey, Stephen M

    2005-08-01

    ABSTRACT Genetic markers amplified from three noncontiguous regions by sequence specific primers designed from the partial or complete genome sequences of Citrus tristeza virus (CTV) isolates T3, T30, T36, and VT were used to assess genetic relatedness of 372 isolates in an international collection. Eighty-five isolates were judged similar to the T3 isolate, 81 to T30, 11 to T36, and 89 to VT. Fifty-one isolates were mixed infections by two or more identifiable viral genotypes, and 55 isolates could not be assigned unequivocally to a group defined by marker patterns. Maximum parsimony analysis of aligned marker sequences supported the grouping of isolates on the basis of marker patterns only. Specific disease symptoms induced in select citrus host plants were shared across molecular groups, although symptoms were least severe among isolates grouped by markers with the T30 isolate and were most severe among isolates grouped by markers with the T3 isolate. Isolates assigned the same genotype showed variable symptoms and symptom severity. A classification strategy for CTV isolates is proposed that combines genetic marker patterns and nucleotide sequence data. PMID:18944413

  1. Pollen genetic markers for detection of mutagens in the environment

    SciTech Connect

    Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

    1981-01-01

    To utilize pollen for in situ monitoring of the genetic hazards of environmental pollutants, the range of genetic traits in pollen must be identified and analyzed. These include ornamentation, shape and form, male sterility viability, intraspecific incompatibility, proteins, and starch deposition. Several proteins that meet the necessary criteria for mutagen detection systems are discussed. At Washington State Univ., a waxy pollen system is being developed in barley for in situ mutagen monitoring. Studies are being conducted to develop data concerning the nature of the mutations induced by various environmental mutagens.

  2. A molecular approach towards the taxonomy of fresh water prawns Macrobrachium striatum and M. equidens (Decapoda, Palaemonidae) using mitochondrial markers.

    PubMed

    Jose, Deepak; Nidhin, B; Anil Kumar, K P; Pradeep, P J; Harikrishnan, M

    2016-07-01

    Genus Macrobrachium includes freshwater prawns which inhabit most diverse habitats ranging from low saline areas to inland hill streams and impounded water bodies. Being morphologically conserved, this genus has been exposed to severe disputes related to their taxonomy, systematics and phylogeny. Macrobrachium striatum and M. equidens represent two morphologically related congeneric species within this genus. Earlier, M. striatum was considered as a striped form of M. equidens. Though these species are now well-described morphologically and differentiated into two species, no molecular level investigation has been carried out in support of their speciation. We report a study on M. striatum and M. equidens with emphasis to their molecular data through mitochondrial markers (16S ribosomal RNA and cytochrome oxidase subunit I). Results obtained from developed molecular markers of the two species revealed considerable genetic differentiation between them. Phylogram generated using Minimum evolution and Neighbour joining analyses differentiated M. striatum and M. equidens as two independent species. Genetic distance data showed high interspecific divergence (ranging from 3.9% to 17.0% for 16S rRNA sequences and 13.8% to 21.0% for COI sequences) between M. striatum and M. equidens confirming the findings of phylogram. Hence, it could be delineated that M. striatum and M. equidens represent two distinct species within genus Macrobrachium with emphasis to their morphology and genetics. PMID:26119113

  3. Genetic evaluation by best linear unbiased prediction using marker and trait information in a multibreed population.

    PubMed Central

    Wang, T; Fernando, R L; Grossman, M

    1998-01-01

    Genetic evaluation by best linear unbiased prediction (BLUP) requires modeling genetic means, variances, and covariances. This paper presents theory to model means, variances, and covariances in a multibreed population, given marker and breed information, in the presence of gametic disequilibrium between the marker locus (ML) and linked quantitative trait locus (MQTL). Theory and algorithms are presented to construct the matrix of conditional covariances between relatives (Gv) for the MQTL effects in a multibreed population and to obtain the inverse of Gv efficiently. Theory presented here accounts for heterogeneity of variances among pure breeds and for segregation variances between pure breeds. A numerical example was used to illustrate how the theory and algorithms can be used for genetic evaluation by BLUP using marker and trait information in a multibreed population. PMID:9475759

  4. Integration of genetic and epigenetic markers for risk stratification: opportunities and challenges

    PubMed Central

    Pashayan, Nora; Reisel, Daniel; Widschwendter, Martin

    2016-01-01

    Summary Common genetic susceptibility variants could be used for risk stratification in risk-tailored cancer screening and prevention programmes. Combining genetic variants with environmental risk factors would improve risk stratification. Epigenetic changes are surrogate markers of environmental exposures during individual’s lifetime. Integrating epigenetic markers, in lieu of environmental exposure data, with genetic markers would potentially improve risk stratification. Epigenetic changes are reversible and acquired gradually, providing potentials for prevention and early detection strategies. The epigenetic changes are tissue-specific and stage-of-development-specific, raising challenges in choice of sample and timing for evaluation of cancer-associated changes. The Horizon 2020 funded research programme, FORECEE, using empirical data, will investigate the value of integration of epigenomics with genomics for risk prediction and prevention of women-specific cancers. PMID:27053939

  5. Breakpoint analysis: Precise localization of genetic markers by means of nonstatistical computation using relatively few genotypes

    SciTech Connect

    Elsner, T.I.; Albertsen, H.; Gerken, S.C.; Cartwright, P.; White, R.

    1995-02-01

    Placing new markers on a previously existing genetic map by using conventional methods of multilocus linkage analysis requires that a large number of reference families be genotyped. This paper presents a methodology for placing new markers on existing genetic maps by genotyping only a few individuals in a selected subset of the reference panel. We show that by identifying meiotic breakpoint events within existing genetic maps and genotyping individuals who exhibit these events, along with one nonrecombinant sibling and their parents, we can determine precise locations for new markers even within subcentimorgan chromosomal regions. This method also improves detection of errors in genotyping and assists in the observation of chromosome behavior in specific regions. 31 refs., 9 figs.

  6. Assessing genetic diversity in Valencia peanut germplasm using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Valencia peanuts (Arachis hypogaea L.ssp. fastigiata var. fastigiata) are well known for their in-shell market value. Assessment of genetic diversity of the available Valencia germplasm is key to the success of developing improved cultivars with desirable agronomic and quality traits. In the pres...

  7. Genetic manipulation of Aedes aegypti: incorporation and maintenance of a genetic marker and a chromosomal translocation in natural populations*

    PubMed Central

    Rai, K. S.; Grover, K. K.; Suguna, S. G.

    1973-01-01

    Studies with Aedes aegypti were undertaken to determine if an alien genotype can be (1) incorporated into a natural population and (2) maintained for several generations on its own without any subsequent introductions. Such information is an essential prerequisite for successful application of any genetic control method. Data from a walk-in, field population cage and from field releases of a genetic marker and a chromosomal translocation have demonstrated both genetic incorporation and persistence for at least three successive generations. This is the first demonstration of its type with any vector species. PMID:4541148

  8. Molecular and genetic control of plant thermomorphogenesis.

    PubMed

    Quint, Marcel; Delker, Carolin; Franklin, Keara A; Wigge, Philip A; Halliday, Karen J; van Zanten, Martijn

    2016-01-01

    Temperature is a major factor governing the distribution and seasonal behaviour of plants. Being sessile, plants are highly responsive to small differences in temperature and adjust their growth and development accordingly. The suite of morphological and architectural changes induced by high ambient temperatures, below the heat-stress range, is collectively called thermomorphogenesis. Understanding the molecular genetic circuitries underlying thermomorphogenesis is particularly relevant in the context of climate change, as this knowledge will be key to rational breeding for thermo-tolerant crop varieties. Until recently, the fundamental mechanisms of temperature perception and signalling remained unknown. Our understanding of temperature signalling is now progressing, mainly by exploiting the model plant Arabidopsis thaliana. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) has emerged as a critical player in regulating phytohormone levels and their activity. To control thermomorphogenesis, multiple regulatory circuits are in place to modulate PIF4 levels, activity and downstream mechanisms. Thermomorphogenesis is integrally governed by various light signalling pathways, the circadian clock, epigenetic mechanisms and chromatin-level regulation. In this Review, we summarize recent progress in the field and discuss how the emerging knowledge in Arabidopsis may be transferred to relevant crop systems. PMID:27250752

  9. Genetic Diversity of Five Local Swedish Chicken Breeds Detected by Microsatellite Markers

    PubMed Central

    Abebe, Abiye Shenkut; Mikko, Sofia; Johansson, Anna M.

    2015-01-01

    This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (FST) was 0.440, and the global inbreeding of individuals within breed (FIS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results

  10. Genetic variation within and among populations of Rhodiola alsia (Crassulaceae) native to the Tibetan Plateau as detected by ISSR markers.

    PubMed

    Xia, Tao; Chen, Shilong; Chen, Shengyun; Ge, Xuejun

    2005-04-01

    Genetic variation of 10 Rhodiola alsia (Crassulaceae) populations from the Qinghai-Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai-Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible. PMID:15932059

  11. Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius.

    PubMed

    Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot Hm; Rengel, Zed

    2016-06-01

    Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. PMID:27049020

  12. Root trait diversity, molecular marker diversity, and trait-marker associations in a core collection of Lupinus angustifolius

    PubMed Central

    Chen, Yinglong; Shan, Fucheng; Nelson, Matthew N; Siddique, Kadambot HM; Rengel, Zed

    2016-01-01

    Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions. PMID:27049020

  13. Serological and biochemical genetic markers and their associations with psychiatric disorders : a review.

    PubMed

    Balgir, R S

    1983-10-01

    The studies pertaining to associations of serological and biochemical genetic markers (blood groups in particular and scrum proteins and enzymes in general) with the psychiatric disorders such as psychoses in general, Schizophrenia, manic-depressive psychosis including unipolar and bipolar affective disorders and neuroses have been critically examined. The reasons for inconsistent findings of various investigators have been pointed out to assist the future researchers to overcome the previous drawbacks. Implications of associations of genetic markers with the psychiatric disorders have been discussed and future areas of research suggested. PMID:21847304

  14. SEROLOGICAL AND BIOCHEMICAL GENETIC MARKERS AND THEIR ASSOCIATIONS WITH PSYCHIATRIC DISORDERS : A REVIEW

    PubMed Central

    Balgir, R.S.

    1983-01-01

    SUMMARY The studies pertaining to associations of serological and biochemical genetic markers (blood groups in particular and scrum proteins and enzymes in general) with the psychiatric disorders such as psychoses in general, Schizophrenia, manic-depressive psychosis including unipolar and bipolar affective disorders and neuroses have been critically examined. The reasons for inconsistent findings of various investigators have been pointed out to assist the future researchers to overcome the previous drawbacks. Implications of associations of genetic markers with the psychiatric disorders have been discussed and future areas of research suggested. PMID:21847304

  15. Prediction of total genetic value using genome-wide dense marker in Holstein breed by Bayesian method

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Marker-assisted selection (MAS) can be based on molecular markers in linkage equilibrium with quantitative trait loci, molecular markers in linkage disequilibrium with QTL, or on selection of the actual mutations causing the QTL effect. However, one problem in relation to all of them is that only a ...

  16. Genetic Markers of Cardiovascular Disease in Rheumatoid Arthritis

    PubMed Central

    Rodríguez-Rodríguez, Luis; López-Mejías, Raquel; García-Bermúdez, Mercedes; González-Juanatey, Carlos; González-Gay, Miguel A.; Martín, Javier

    2012-01-01

    Cardiovascular (CV) disease is the most common cause of premature mortality in patients with rheumatoid arthritis (RA). It is the result of an accelerated atherosclerotic process. Both RA and atherosclerosis are complex polygenic diseases. Besides traditional CV risk factors and chronic inflammation, a number of studies have confirmed the role of genetic factors in the development of the atherogenesis observed in RA. In this regard, besides a strong association between the HLA-DRB1∗04 shared epitope alleles and both endothelial dysfunction, an early step in the atherosclerotic process, and clinically evident CV disease, other polymorphisms belonging to genes implicated in inflammatory and metabolic pathways, located inside and outside the HLA region, such as the 308 variant (G > A, rs1800629) of the TNFA locus, the rs1801131 polymorphism (A > C; position + 1298) of the MTHFR locus, or a deletion of 32 base pairs on the CCR5 gene, seem to be associated with the risk of CV disease in patients with RA. Despite considerable effort to decipher the genetic basis of CV disease in RA, further studies are required to better establish the genetic influence in the increased risk of CV events observed in patients with RA. PMID:22927710

  17. Genetic diversity of Cosmos species revealed by RAPD and ISSR markers.

    PubMed

    Rodríguez-Bernal, A; Piña-Escutia, J L; Vázquez-García, L M; Arzate-Fernández, A M

    2013-01-01

    The genus Cosmos is native of America and is constituted by 34 species; 28 of them are endemic of Mexico. The cosmos are used as a nematicide, antimalarial, and antioxidative agent. The aim of this study was to estimate the genetic diversity among 7 cosmos species based on random amplified polymorphic DNA (RAPD) and inter-simple sequences repeats (ISSR) markers. With RAPD markers, the obtained polymorphism was 91.7 % and the genetic diversity was 0.33, whereas these values were 65.6%, and 0.22 from ISSR markers, respectively, indicating the presence of high genetic diversity among the Cosmos species that were analyzed. The unweighted pair group method with arithmetic mean dendrograms that were obtained with both markers were notably similar, revealing 2 clusters and indicating a clear genetic differentiation among the Cosmos species that were assessed. The first cluster comprised the species Cosmos sulphureus, Cosmos pacificus, and Cosmos diversifolius, while the second cluster included the species Cosmos purpureus, Cosmos crithmifolius, Cosmos bipinnatus, and Cosmos parviflorus. Besides this, the Cosmos species were clustered according to their collection sites. The Mantel test corroborates the correlation between the genetic distance and the geographic altitude of each Cosmos species. The results suggest that it is necessary to preserve the Cosmos species in their natural habitat in addition to the germoplasm collection for ex situ conservation. PMID:24338421

  18. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    PubMed Central

    Seo, Dongwon; Bhuiyan, Md. Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-01-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  19. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    PubMed

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market. PMID:26949947

  20. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.

    PubMed

    Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K; Gopalakrishnan, S; Singh, Ashok K; Rao, Atmakuri R; Agarwal, Pinky; Parida, Swarup K; Tyagi, Akhilesh K

    2016-01-01

    We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17-79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9-21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, "Oryza ISM-ILP marker" database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

  1. Association of cancer stem cell markers genetic variants with gallbladder cancer susceptibility, prognosis, and survival.

    PubMed

    Yadav, Anu; Gupta, Annapurna; Rastogi, Neeraj; Agrawal, Sushma; Kumar, Ashok; Kumar, Vijay; Mittal, Balraj

    2016-02-01

    Genes important to stem cell progression have been involved in the genetics and clinical outcome of cancers. We investigated germ line variants in cancer stem cell (CSC) genes to predict susceptibility and efficacy of chemoradiotherapy treatment in gallbladder cancer (GBC) patients. In this study, we assessed the effect of SNPs in CSC genes (surface markers CD44, ALCAM, EpCAM, CD133) and (molecular markers NANOG, SOX-2, LIN-28A, ALDH1A1, OCT-4) with GBC susceptibility and prognosis. Total 610 GBC patients and 250 controls were genotyped by using PCR-RFLP, ARMS-PCR, and TaqMan allelic discrimination assays. Chemotoxicity graded 2-4 in 200 patients and tumor response was recorded in 140 patients undergoing neoadjuvant chemotherapy (NACT). Differences in genotype and haplotype frequency distributions were calculated by binary logistic regression. Gene-gene interaction model was analyzed by generalized multifactor dimensionality reduction (GMDR). Overall survival was assessed by Kaplan-Meier survival curve and multivariate Cox-proportional methods. ALCAM Ars1157Crs10511244 (P = 0.0035) haplotype was significantly associated with GBC susceptibility. In GMDR analysis, ALCAM rs1157G>A, EpCAM rs1126497T>C emerged as best significant interaction model with GBC susceptibility and ALDH1A1 rs13959T>G with increased risk of grade 3-4 hematological toxicity. SOX-2 rs11915160A>C, OCT-4 rs3130932T>G, and NANOG rs11055786T>C were found best gene-gene interaction model for predicting response to NACT. In both Cox-proportional and recursive partitioning ALCAM rs1157GA+AA genotype showed higher mortality and hazard ratio. ALCAM gene polymorphisms associated with GBC susceptibility and survival while OCT-4, SOX-2, and NANOG variants showed an interactive role with treatment response. PMID:26318430

  2. Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum

    PubMed Central

    Gräser, Y.; Kühnisch, J.; Presber, W.

    1999-01-01

    Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin. PMID:10523582

  3. Genetic Diversity of Japanese Strawberry Species Based on Microsatellite Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The strawberry collection at the United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, consists of 1769 accessions from 17 species and 37 countries. Molecular techniques which include DNA-Based methods...

  4. HUMAN GENETIC MARKER FOR RESISTANCE TO RADIATIONS AND CHEMICALS

    EPA Science Inventory

    The overall objective of this research is to characterize the human RAD9 gene at molecular and cellular levels, and use the information and materials gained to develop a predictive assay for assessing risks posed to individuals involved in toxic waste clean-up.Fission yeast Sch...

  5. Population Genetic Effects of Urban Habitat Fragmentation in the Perennial Herb Viola pubescens (Violaceae) using ISSR Markers

    PubMed Central

    Culley, Theresa M.; Sbita, Sarah J.; Wick, Anne

    2007-01-01

    Background and Aims Fragmentation of natural habitats can negatively impact plant populations by leading to reduced genetic variation and increased genetic distance as populations become geographically and genetically isolated from one another. To test whether such detrimental effects occur within an urban landscape, the genetic structure of six populations of the perennial herb Viola pubescens was characterized in the metropolitan area of Greater Cincinnati in southwestern Ohio, USA. Methods Using three inter-simple sequence repeat (ISSR) markers, 51 loci amplified across all urban populations. For reference, four previously examined agricultural populations in central/northern Ohio and a geographically distant population in Michigan were also included in the analysis. Key Results Urban populations retained high levels of genetic variation (percentage of polymorphic loci, Pp = 80·7 %) with similar genetic distances among populations and an absence of unique alleles. Geographic and genetic distances were correlated with one another, and all populations grouped according to region. Individuals from urban populations clustered together and away from individuals from agricultural populations and from the Michigan population in a principle coordinates analysis. Hierarchical analysis of molecular variance (AMOVA) revealed that most of the genetic variability was partitioned within populations (69·1 %) and among groups (22·2 %) of southwestern Ohio, central/northern Ohio and Michigan groups. Mean Fst was 0·308, indicating substantial population differentiation. Conclusions It is concluded that urban fragmentation does not appear to impede gene flow in V. pubescens in southwestern Ohio. These results are consistent with life history traits of this species and the possibility of high insect abundance in urban habitats due to diverse floral resources and nesting sites. Combined with the cleistogamous breeding system of this species, pollinator availability in the urban

  6. Assessment of genetic diversity of landraces of Dendrocalamus hamiltonii using AFLP markers and association with biochemical traits.

    PubMed

    Waikhom, S D; Ghosh, S; Talukdar, N C; Mandi, S S

    2012-01-01

    Fermented bamboo shoots are popular traditional food items of various ethnic groups of the northeastern India, especially in Manipur State. Dendrocalamus hamiltonii is an economically important bamboo species used to produce fermented bamboo shoots. We studied genetic variability of this bamboo species in Chandel and Imphal-East (commercial production districts), using AFLP molecular markers. Each of the selected primers detected polymorphisms and 1614 (95.8%) were found to be polymorphic. Cluster analysis based on Dice similarity coefficients using UPGMA differentiated the populations into two major groups. Principal coordinate analysis based on the AFLP data clearly separated the populations according to their genetic diversity and antioxidant activity. Four primers were tested through multiple regression analysis to identify marker-trait association between AFLP data and biochemical attributes, i.e., antioxidant activity and total cyanide content. The 273 bp generated by EcoRI-AAG(Joe)/MseI-CTC showed high positive correlation with antioxidant activity (r = 0.729, P < 0.01). The 396 bp generated by EcoRI-AAC(Ned)/MseI-CTG were negatively correlated with cyanide content (r = -0.694, P < 0.01). Thus, we found association of DNA markers with antioxidant activities and total cyanide content. These results could be of use for the identification of superior genotypes with desirable traits. PMID:22782634

  7. Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of Endangered Polyporus umbellatus.

    PubMed

    Zhang, Yuejin; Chen, Yuanyuan; Wang, Ruihong; Zeng, Ailin; Deyholos, Michael K; Shu, Jia; Guo, Hongbo

    2015-01-01

    A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences in Ganoderma lucidum obtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 natural Polyporus umbellatus accessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13 P. umbellatus accessions showed relatively high genetic diversity. The expected heterozygosity, Nei's gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups. PMID:26146636

  8. De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

    PubMed Central

    Huang, Xiu; Yan, Hai-Dong; Zhang, Xin-Quan; Zhang, Jian; Frazier, Taylor P.; Huang, De-Jun; Lu, Lu; Huang, Lin-Kai; Liu, Wei; Peng, Yan; Ma, Xiao; Yan, Yan-Hong

    2016-01-01

    Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa “Yaan” and H. altissima “1110.” Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for “Yaan” and “1110,” respectively. In addition, a total of 86,731 “Yaan” and 48,645 “1110” unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11–87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus. PMID:27148320

  9. Genetic Map of Triticale Integrating Microsatellite, DArT and SNP Markers.

    PubMed

    Tyrka, Mirosław; Tyrka, Dorota; Wędzony, Maria

    2015-01-01

    Triticale (×Triticosecale Wittm) is an economically important crop for fodder and biomass production. To facilitate the identification of markers for agronomically important traits and for genetic and genomic characteristics of this species, a new high-density genetic linkage map of triticale was constructed using doubled haploid (DH) population derived from a cross between cultivars 'Hewo' and 'Magnat'. The map consists of 1615 bin markers, that represent 50 simple sequence repeat (SSR), 842 diversity array technology (DArT), and 16888 DArTseq markers mapped onto 20 linkage groups assigned to the A, B, and R genomes of triticale. No markers specific to chromosome 7R were found, instead mosaic linkage group composed of 1880 highly distorted markers (116 bins) from 10 wheat chromosomes was identified. The genetic map covers 4907 cM with a mean distance between two bins of 3.0 cM. Comparative analysis in respect to published maps of wheat, rye and triticale revealed possible deletions in chromosomes 4B, 5A, and 6A, as well as inversion in chromosome 7B. The number of bin markers in each chromosome varied from 24 in chromosome 3R to 147 in chromosome 6R. The length of individual chromosomes ranged between 50.7 cM for chromosome 2R and 386.2 cM for chromosome 7B. A total of 512 (31.7%) bin markers showed significant (P < 0.05) segregation distortion across all chromosomes. The number of 8 the segregation distorted regions (SDRs) were identified on 1A, 7A, 1B, 2B, 7B (2 SDRs), 5R and 6R chromosomes. The high-density genetic map of triticale will facilitate fine mapping of quantitative trait loci, the identification of candidate genes and map-based cloning. PMID:26717308

  10. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars

    PubMed Central

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938–0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars. PMID:27379163

  11. Development of SSR Markers and Assessment of Genetic Diversity in Medicinal Chrysanthemum morifolium Cultivars.

    PubMed

    Feng, Shangguo; He, Renfeng; Lu, Jiangjie; Jiang, Mengying; Shen, Xiaoxia; Jiang, Yan; Wang, Zhi'an; Wang, Huizhong

    2016-01-01

    Chrysanthemum morifolium, is a well-known flowering plant worldwide, and has a high commercial, floricultural, and medicinal value. In this study, simple-sequence repeat (SSR) markers were generated from EST datasets and were applied to assess the genetic diversity among 32 cultivars. A total of 218 in silico SSR loci were identified from 7300 C. morifolium ESTs retrieved from GenBank. Of all SSR loci, 61.47% of them (134) were hexa-nucleotide repeats, followed by tri-nucleotide repeats (17.89%), di-nucleotide repeats (12.39%), tetra-nucleotide repeats (4.13%), and penta-nucleotide repeats (4.13%). In this study, 17 novel EST-SSR markers were verified. Along with 38 SSR markers reported previously, 55 C. morifolium SSR markers were selected for further genetic diversity analysis. PCR amplification of these EST-SSRs produced 1319 fragments, 1306 of which showed polymorphism. The average polymorphism information content of the SSR primer pairs was 0.972 (0.938-0.993), which showed high genetic diversity among C. morifolium cultivars. Based on SSR markers, 32 C. morifolium cultivars were separated into two main groups by partitioning of the clusters using the unweighted pair group method with arithmetic mean dendrogram, which was further supported by a principal coordinate analysis plot. Phylogenetic relationship among C. morifolium cultivars as revealed by SSR markers was highly consistent with the classification of medicinal C. morifolium populations according to their origin and ecological distribution. Our results demonstrated that SSR markers were highly reproducible and informative, and could be used to evaluate genetic diversity and relationships among medicinal C. morifolium cultivars. PMID:27379163

  12. Genetic Map of Triticale Integrating Microsatellite, DArT and SNP Markers

    PubMed Central

    Tyrka, Mirosław; Tyrka, Dorota; Wędzony, Maria

    2015-01-01

    Triticale (×Triticosecale Wittm) is an economically important crop for fodder and biomass production. To facilitate the identification of markers for agronomically important traits and for genetic and genomic characteristics of this species, a new high-density genetic linkage map of triticale was constructed using doubled haploid (DH) population derived from a cross between cultivars ‘Hewo’ and ‘Magnat’. The map consists of 1615 bin markers, that represent 50 simple sequence repeat (SSR), 842 diversity array technology (DArT), and 16888 DArTseq markers mapped onto 20 linkage groups assigned to the A, B, and R genomes of triticale. No markers specific to chromosome 7R were found, instead mosaic linkage group composed of 1880 highly distorted markers (116 bins) from 10 wheat chromosomes was identified. The genetic map covers 4907 cM with a mean distance between two bins of 3.0 cM. Comparative analysis in respect to published maps of wheat, rye and triticale revealed possible deletions in chromosomes 4B, 5A, and 6A, as well as inversion in chromosome 7B. The number of bin markers in each chromosome varied from 24 in chromosome 3R to 147 in chromosome 6R. The length of individual chromosomes ranged between 50.7 cM for chromosome 2R and 386.2 cM for chromosome 7B. A total of 512 (31.7%) bin markers showed significant (P < 0.05) segregation distortion across all chromosomes. The number of 8 the segregation distorted regions (SDRs) were identified on 1A, 7A, 1B, 2B, 7B (2 SDRs), 5R and 6R chromosomes. The high-density genetic map of triticale will facilitate fine mapping of quantitative trait loci, the identification of candidate genes and map-based cloning. PMID:26717308

  13. Genetic Structure and Inferences on Potential Source Areas for Bactrocera dorsalis (Hendel) Based on Mitochondrial and Microsatellite Markers

    PubMed Central

    Shi, Wei; Kerdelhué, Carole; Ye, Hui

    2012-01-01

    Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan. PMID:22615898

  14. Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis).

    PubMed

    Ong, P W; Maizura, I; Abdullah, N A P; Rafii, M Y; Ooi, L C L; Low, E T L; Singh, R

    2015-01-01

    The genetic evaluation of oil palm germplasm collections is required for insight into the variability among populations. The information obtained is also useful for incorporating new genetic materials into current breeding programs. Single nucleotide polymorphisms (SNPs) have been widely used in many plant genetic studies due to the availability of large numbers of genomic sequences and expressed sequence tags. The present study examined 219 oil palms collected from two natural Angolan populations, a few hundred kilometers apart. A total of 62 SNPs were designed from oil palm genomic sequences and converted to cleaved amplified polymorphic sequence (CAPS). Of these, nine were found to be informative across the two populations. The nine informative SNPs revealed mean major allele frequency of 0.693. The average expected and observed heterozygosities were 0.398 and 0.400, respectively. The mean polymorphism information content was 0.315 (ranging between 0.223 and 0.375). None of the loci deviated from Hardy-Weinberg equilibrium and no rare alleles were detected. In cluster analysis using unweighted pair group method with arithmetic, the 219 oil palms fell into two clusters. This was further supported by the population structure analysis result (K = 2), suggesting that the samples were divided into two main genetic groups. However, the two groups did not coincide with the geographic populations. Analysis of molecular variance indicated that within-population variation contributed 93% of the total genetic variation. This study showed that SNP-based CAPS markers are useful for studying the genetic diversity of oil palm and have potential application for marker-trait association studies. PMID:26505369

  15. IDENTIFICATION OF SEX CHROMOSOME MOLECULAR MARKERS USING RAPDS AND FLUORESCENT IN SITU HYBRIDIZATION IN RAINBOW TROUT

    EPA Science Inventory

    The goal of this work is to identify molecular markers associated with the sex chromosomes in rainbow trout to study the mode of sex determination mechanisms in this species. Using the RAPD assay and bulked segregant analysis, two markers were identified that generated polymorphi...

  16. Molecular Screening of Blast Resistance Genes in Rice using SSR Markers

    PubMed Central

    Singh, A. K.; Singh, P. K.; Arya, Madhuri; Singh, N. K.; Singh, U. S.

    2015-01-01

    Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1–24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106

  17. Relationships among pest flour beetles of the genus Tribolium (Tenebrionidae) inferred from multiple molecular markers

    PubMed Central

    Angelini, David R.; Jockusch, Elizabeth L.

    2008-01-01

    Model species often provide initial hypotheses and tools for studies of development, genetics, and molecular evolution in closely related species. Flour beetles of the genus Tribolium MacLeay (1825) are one group with potential for such comparative studies. Tribolium castaneum (Herbst 1797) is an increasingly useful developmental genetic system. The convenience with which congeneric and other species of tenebrionid flour beetles can be reared in the laboratory makes this group attractive for comparative studies on a small phylogenetic scale. Here we present the results of phylogenetic analyses of relationships among the major pest species of Tribolium based on two mitochondrial and three nuclear markers (cytochrome oxidase 1, 16S ribosomal DNA, wingless, 28S ribosomal DNA, histone H3). The utility of partitioning the dataset in a manner informed by biological structure and function is demonstrated by comparing various partitioning strategies. In parsimony and partitioned Bayesian analyses of the combined dataset, the castaneum and confusum species groups are supported as monophyletic and as each other’s closest relatives. However, a sister group relationship between this clade and Tribolium brevicornis (Leconte 1859) is not supported. Therefore, we suggest transferring brevicornis group species to the genus Aphanotus Leconte (1862). The inferred phylogeny provides an evolutionary framework for comparative studies using flour beetles. PMID:18024090

  18. Apocalypse...now? Molecular epidemiology, predictive genetic tests, and social communication of genetic contents.

    PubMed

    Castiel, L D

    1999-01-01

    The author analyzes the underlying theoretical aspects in the construction of the molecular watershed of epidemiology and the concept of genetic risk, focusing on issues raised by contemporary reality: new technologies, globalization, proliferation of communications strategies, and the dilution of identity matrices. He discusses problems pertaining to the establishment of such new interdisciplinary fields as molecular epidemiology and molecular genetics. Finally, he analyzes the repercussions of the social communication of genetic content, especially as related to predictive genetic tests and cloning of animals, based on triumphal, deterministic metaphors sustaining beliefs relating to the existence and supremacy of concepts such as 'purity', 'essence', and 'unification' of rational, integrated 'I's/egos'. PMID:10089550

  19. Human genetic marker for resistance to radiations and chemicals. 1997 annual progress report

    SciTech Connect

    Lieberman, H.B.

    1997-01-01

    'The specific aims listed in the original application will essentially be pursued as indicated. The major goal of the grant is to characterize a human homologue of the fission yeast Schizosaccharomyces pombe rad9 checkpoint control, radioresistance and chemoresistance gene, which is called HRAD9. The purpose is to gain information about the gene, including its structure and function, such that it can potentially be developed as a human genetic marker indicative of hypersensitivity to the deleterious effects associated with exposure to radiations or certain chemicals. The specific aims are divided into two major sections. The first section includes experiments designed to characterize the HRAD9 gene at the molecular level. Specifically, the genomic version of the gene will be isolated and its DNA sequence determined, in vitro mutagenesis will be used to assess structure/function relationships, and expression in cells and tissues will be examined. The second major set of aims focuses on determining the role of HRAD9 in radio/chemoresponsiveness and cancer. For this aim, human HRAD9 mutants will be constructed and characterized. In addition, the status of HRAD9 in cancer cells and tissues will be assessed.'

  20. Expanding Possibilities for Intervention against Small Ruminant Lentiviruses through Genetic Marker-Assisted Selective Breeding

    PubMed Central

    White, Stephen N.; Knowles, Donald P.

    2013-01-01

    Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a strong genetic component in susceptibility to infection by OvLV in sheep. A genetic marker test for susceptibility to OvLV has been developed recently based on the TMEM154 gene with validation data from over 2,800 sheep representing nine cohorts. While no single genotype has been shown to have complete resistance to OvLV, consistent association in thousands of sheep from multiple breeds and management conditions highlight a new strategy for intervention by selective breeding. This genetic marker-assisted selection (MAS) has the potential to be a useful addition to existing viral control measures. Further, the discovery of multiple additional genomic regions associated with susceptibility to or control of OvLV suggests that additional genetic marker tests may be developed to extend the reach of MAS in the future. This review will cover the strengths and limitations of existing data from host genetics as an intervention and outline additional questions for future genetic research in sheep, goats, small ruminant lentiviruses, and their host-pathogen interactions. PMID:23771240

  1. Genetic diversity in the germplasm of black pepper determined by EST-SSR markers.

    PubMed

    Wu, B D; Fan, R; Hu, L S; Wu, H S; Hao, C Y

    2016-01-01

    This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding. PMID:27050963

  2. Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population.

    PubMed

    Sorkheh, Karim; Amirbakhtiar, Nazanin; Ercisli, Sezai

    2016-08-01

    Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement. PMID:27056191

  3. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    PubMed Central

    Aranguren-Méndez, José; Jordana, Jordi; Gomez, Mariano

    2001-01-01

    Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE) over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P < 0.01). Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, except HMS5 that showed agreement in all analysed populations. The cumulative exclusion probability (PE) was 0.999 in each breed, suggesting that the loci would be suitable for donkey parentage testing. The constructed dendrogram from the DA distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans. PMID:11559485

  4. Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner

    PubMed Central

    Achar, Devaraja; Awati, Mallikarjuana G.; Udayakumar, M.; Prasad, T. G.

    2015-01-01

    Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection. PMID:25821599

  5. Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner.

    PubMed

    Achar, Devaraja; Awati, Mallikarjuana G; Udayakumar, M; Prasad, T G

    2015-01-01

    Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection. PMID:25821599

  6. Molecular genetics of facioscapulohumeral muscular dystrophy (FSHD).

    PubMed

    Fisher, J; Upadhyaya, M

    1997-01-01

    Facioscapulohumeral muscular dystrophy (FSHD; MIM 158900), is an autosomal dominant neuromuscular disorder. The disease is characterized by the weakness of the muscles of the face, upper-arm and shoulder girdle. The gene for FSHD has been mapped to 4q35 (FSHD1A) and is closely linked to D4F1O4S1, which detects two highly polymorphic loci (located at 4q35 and 10q26), with restriction enzyme EcoRI. The polymorphic EcoRI fragment detected with D4F1O4S1 is composed almost entirely of D4Z4 (3.3 kb) tandem repeats. In FSHD patients a deletion of the integral number of D4Z4 repeats generates a fragment which is usually smaller than 35 kb, whereas in normal controls, the size usually ranges from 50 to 300 kb. These 'small' EcoRI fragments segregate with FSHD in families but appear as de novo deletions in the majority of sporadic cases. Each 3.3 kb repeat contains two homeobox domains neither of which has yet been proven to encode a protein. D4Z4 is located adjacent to the 4q telomere and cross hybridizes to several different regions of the genome. Although D4Z4 probably does not encode a protein with any direct association to FSHD, a clear correlation has been shown between the deletion size at this locus and the age at onset of the disease in FSHD patients. In approximately 5-10% of FSHD families the disease locus is unlinked to 4q35 (locus designated FSHD1B), however, none of the non 4q35 loci for FSHD have yet been chromosomally located. Thus so far, only one gene, FRG1 (FSHD region gene 1) has been identified from the FSHD candidate region on 4q35. The apparent low level of expressed sequences from within this region, the integral deletions of D4Z4 repeats observed in FSHD patients and the close proximity of these repeats to the 4q telomere, all suggest that the disease may be the result of position effect variegation. To date, the molecular diagnosis of FSHD with D4F104S1 has been most secure in those families which are linked to other 4q35 markers. Recent studies

  7. Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis.

    PubMed

    Ul Haq, Shamshad; Kumar, Pradeep; Singh, R K; Verma, Kumar Sambhav; Bhatt, Ritika; Sharma, Meenakshi; Kachhwaha, Sumita; Kothari, S L

    2016-01-01

    Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks. PMID:27340568

  8. Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis

    PubMed Central

    Ul Haq, Shamshad; Kumar, Pradeep; Singh, R. K.; Verma, Kumar Sambhav; Bhatt, Ritika; Sharma, Meenakshi; Kachhwaha, Sumita; Kothari, S. L.

    2016-01-01

    Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks. PMID:27340568

  9. Molecular characterization of an International cocoa collection using microsallte markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High levels of redundancy and limited information on genetic structure hinder the efficient conservation and utilization of cacao germplasm. The present study targeted the assessment of genetic identity and population structure in an international cocoa collection maintained in Costa Rica. Using a c...

  10. Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers

    SciTech Connect

    Rosen, D.R.; Sapp, P.; O`Regan, J.; McKenna-Yasek, D.; Schlumpf, K.S.; Haines, J.L.; Gusella, J.F.; Horvitz, H.R.; Brown, R.H. Jr.

    1994-05-15

    Amyotrophic lateral sclerosis (ALS; Lou Gehrig`s Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS familes for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers reveal recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219. The only characterized gene within this segment was SOD-1, the structural gene for Cu, Zn SOD. 30 refs., 4 figs., 4 tabs.

  11. An empirical review: Characteristics of plant microsatellite markers that confer higher levels of genetic variation1

    PubMed Central

    Merritt, Benjamin J.; Culley, Theresa M.; Avanesyan, Alina; Stokes, Richard; Brzyski, Jessica

    2015-01-01

    During microsatellite marker development, researchers must choose from a pool of possible primer pairs to further test in their species of interest. In many cases, the goal is maximizing detectable levels of genetic variation. To guide researchers and determine which markers are associated with higher levels of genetic variation, we conducted a literature review based on 6782 genomic microsatellite markers published from 1997–2012. We examined relationships between heterozygosity (He or Ho) or allele number (A) with the following marker characteristics: repeat type, motif length, motif region, repeat frequency, and microsatellite size. Variation across taxonomic groups was also analyzed. There were significant differences between imperfect and perfect repeat types in A and He. Dinucleotide motifs exhibited significantly higher A, He, and Ho than most other motifs. Repeat frequency and motif region were positively correlated with A, He, and Ho, but correlations with microsatellite size were minimal. Higher taxonomic groups were disproportionately represented in the literature and showed little consistency. In conclusion, researchers should carefully consider marker characteristics so they can be tailored to the desired application. If researchers aim to target high genetic variation, dinucleotide motif lengths with large repeat frequencies may be best. PMID:26312192

  12. Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers.

    PubMed

    Liu, Xiao Bin; Feng, Bang; Li, Jing; Yan, Chen; Yang, Zhu L

    2016-10-10

    Flammulina velutipes is one of the most widely cultivated mushroom species in China. However, its genetic background remains poorly understood due to the limited sampling and poor molecular markers used. In this study, 124 F. velutipes strains were employed, including 110 cultivars and 14 wild strains, and 25 new SSR markers were developed based on the genome of F. velutipes. A total of 153 alleles were detected in 124 strains to investigate the improper cultivar naming, genetic diversity and breeding history of F. velutipes in China. Our fingerprinting analyses indicated that 65 strains can be differentiated from the total of 124 strains, and over 53% of the strains are labeled with improper commercial names. The genetic diversities of wild strains are higher than those of the cultivars, suggesting that wild strains may harbor a large "arsenal" gene pool in nature available for strain breeding. The white cultivars in China were originally introduced from Japan, while the yellow cultivars were directly domesticated from wild strains isolated from southeastern China or hybridized between the white cultivars and yellow strains. PMID:27393649

  13. Genetic diversity of the endemic flat-needle pine Pinus krempfii (Pinaceae) from Vietnam revealed by SSR markers.

    PubMed

    Phong, D T; Lieu, T T; Hien, V T T; Hiep, N T

    2015-01-01

    Pinus krempfii Lecomte (Pinaceae) is an endemic tree to Vietnam with restricted habitats at higher altitudes in the highlands. In this study, genetic variation of four populations of P. krempfii was assessed using 17 microsatellite markers (single sequence repeats). Of these 17 markers, eight were polymorphic, and among the 42 putative alleles amplified, 32 were polymorphic (accounting for 76.19%). The Cong Troi population was found to be the most genetically diverse (Shannon's information index, I = 0.415, and percentage of polymorphic bands, PPB = 52.95%), whereas the Hon Giao population was found to have the lowest diversity (I = 0.330 and PPB = 47.06%). The genetic diversity at species level was also estimated (I = 0.414, PPB = 76.19%). Molecular variance was found to be low among populations (11.94%) and high among individuals within the populations (88.06%). Private alleles were not detected in the Hon Giao population. The Yang Ly population had a positive FIS (inbreeding coefficient) value of 0.071, while the three remaining populations had negative values (-0.116 for Cong Troi, -0.316 for Chu Yang Sin, and -0.350 for Hon Giao). The results obtained show an excess of homozygosity in the Yang Ly population, and also suggest a deficiency of heterozygosity for this population. Several approaches and measures of conservation for P. krempfii are discussed and proposed. PMID:26214454

  14. Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India.

    PubMed

    Singh, Nripendra Vikram; Abburi, Venkata Lakshmi; Ramajayam, D; Kumar, Ravinder; Chandra, Ram; Sharma, Kuldeep Kumar; Sharma, Jyotsana; Babu, K Dhinesh; Pal, Ram Krishna; Mundewadikar, Dhananjay M; Saminathan, Thangasamy; Cantrell, Robert; Nimmakayala, Padma; Reddy, Umesh K

    2015-08-01

    This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate collections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies. PMID:25675870

  15. Workshop on molecular methods for genetic diagnosis. Final technical report

    SciTech Connect

    Rinchik, E.M.

    1997-07-01

    The Sarah Lawrence College Human Genetics Program received Department of Energy funding to offer a continuing medical education workshop for genetic counselors in the New York metropolitan area. According to statistics from the National Society of Genetic Counselors, there are approximately 160 genetic counselors working in the tri-state area (New York, New Jersey, and Connecticut), and many of them had been working in the field for more than 10 years. Thus, there was a real need to offer these counselors an in-depth opportunity to learn the specifics of the major advances in molecular genetics, and, in particular, the new approaches to diagnostic testing for genetic disease. As a result of the DOE Award DE-FG02-95ER62048 ($20,583), in July 1995 we offered the {open_quotes}Workshop on Molecular Methods for Genetic Diagnosis{close_quotes} for 24 genetic counselors in the New York metropolitan area. The workshop included an initial review session on the basics of molecular biology, lectures and discussions on past and current topics in molecular genetics and diagnostic procedures, and, importantly, daily laboratory exercises. Each counselor gained not only background, but also firsthand experience, in the major techniques of biochemical and molecular methods for diagnosing genetic diseases as well as in mathematical and computational techniques involved in human genetics analyses. Our goal in offering this workshop was not to make genetic counselors experts in these laboratory diagnostic techniques, but to acquaint them, by hands-on experience, about some of the techniques currently in use. We also wanted to provide them a technical foundation upon which they can understand and appreciate new technical developments arising in the near future.

  16. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential.

    PubMed

    Biswas, Manosh Kumar; Liu, Yuxuan; Li, Chunyu; Sheng, Ou; Mayer, Christoph; Yi, Ganjun

    2015-01-01

    The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species. PMID:26121637

  17. [Progress in molecular genetics of epilepsy].

    PubMed

    Tang, Beisha; Zhang, Yuhu

    2002-12-01

    Epilepsy is a group of disorders characterized by recurrent seizures. The etiologies of idiopathic epilepsy commonly have a genetic basis. Gene mutations causing several of the inherited epilepsies have been mapped. In this review, the authors summarize the available information on the genetic basis of human epilepsies and epilepsy syndromes, emphasizing how genetic defects may correlate with the pathophysiological mechanisms of brain hyperexcitability and gene defects can lead to epilepsy by altering multiple and diverse aspects of neuronal function. PMID:12476426

  18. Miniature inverted-repeat transposable element identification and genetic marker development in Agrostis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Creeping bentgrass (Agrostis stolonifera L.) is an important species to the turfgrass industry because of its adaptation for use in high quality turf stands such as golf course putting greens, tees, and fairways. A. stolonifera is a highly outcrossing allotetraploid making genetic marker developmen...

  19. Mitochondrial genomes of Bremia lactucae and development of haplotype markers for population and genetic studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bremia lactucae, the causative agent of lettuce downy mildew, is the most important pathogen of lettuce in the US and worldwide. In order to identify cytoplasmic markers for use in population and genetic studies the reference mitochondrial genome of B. lactucae isolate SF5 was assembled from Illumi...

  20. Application of marker selection to enhance estimation of genetic effects and gene interaction in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection on important genetic markers can improve estimates of additive and dominance association effects. A composite population of beef cattle was selected for intermediate frequencies of myostatin (GDF8) F94L and µ-calpain (CAPN1) polymorphisms. Important additive associations of the GDF8 locu...

  1. Genetic management of broodstock populations with DNA markers in rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA markers are very useful for aquaculture and fisheries broodstock management. They have been used for parentage assignment when spawning families share common environments, and to evaluate genetic parameters in broodstock populations. The selective breeding program at the National Center for Cool...

  2. Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

  3. Assessment of genetic diversity in Saccharum using SSR markers and capillary electrophoresis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to assess the genetic diversity amongst 12 Saccharum clones from 3 species using SSR markers and CE (capillary electrophoresis). Genomic DNA of 12 sugarcane cultivars was amplified with 19 SSR primer pairs. A total of 229 bands generated with a size range between 100 and 26...

  4. Genetic Diversity of Lablab (L. purpureus) Germplasm Assessed by SSR Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of the USDA Lablab purpureus germplasm collection is unknown and was assessed by using polymorphic simple sequence repeat (SSR) markers derived from Medicago, soybean and cowpea. Phylogenetic analysis partitioned 47 representative accessions into two main clades (wild clade pr...

  5. Genetic markers that influence feed efficiency phenotypes also affect cattle temperament as measured by flight speed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The measure of flight speed for cattle has been shown to be a predictive indicator of temperament and has also been associated with feed efficiency phenotypes, thus, genetic markers associated with both traits may assist with the selection of animals with calmer disposition and economic value. Chrom...

  6. Genetic characterization of four strains of Nile tilapia (Oreochromis niloticus L.) using microsatellite markers.

    PubMed

    Rutten, M J M; Komen, H; Deerenberg, R M; Siwek, M; Bovenhuis, H

    2004-04-01

    Four domesticated strains of Nile tilapia (Oreochromis niloticus L.) were genetically characterized using 14 microsatellite markers and 64 animals per strain. Two strains, Chitralada (AIT) and International Development Research Centers (IDRC) were obtained from the AIT institute, Bangkok, Thailand. The GIFT strain (5th generation) came from NAGRI, Thailand, and the GOTT strain was supplied by the University of Göttingen, Germany. The average numbers of alleles per marker were 5.0 (GOTT), 5.4 (AIT), 5.6 (IDRC) and 7.5 (GIFT). Private alleles were found at all markers with the exception of two. No fixation of alleles was found at any marker. Population differentiation, FST, was 0.178 (great genetic differentiation) and confirmed grouping of the animals in strains. The expected level of heterozygosity ranged from 0.624 to 0.711, but the observed level of heterozygosity significantly deviated from the expected level in three strains. This was probably because of small population size. Moderate to great genetic differentiation was found between strains. A phylogenetic tree reflected the strains known histories. Application of the Weitzman approach showed that all strains have added value for the total genetic diversity and thus should be retained. PMID:15025567

  7. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    EPA Science Inventory

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  8. Evaluation of Genetic Diversity of the USDA Lablab Purpureus Germplasm Collection Using Simple Sequence Repeat Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of the USDA Lablab purpureus germplasm collection is unknown and was assessed by using polymorphic simple sequence repeat (SSR) markers derived from Medicago, soybean and cowpea. Phylogenetic analysis paritioned 47 representative accessions into two main clades (wild clade prod...

  9. Genetic diversity assessment of Saccharum species and elite cultivars from China using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity amongst 52 sugarcane clones including Saccharum species and cultivars (used for breeding and commercial production since the beginning of 20th century) has been assessed using 21 Simple Sequence Repeat (SSR) markers and capillary electrophoresis (CE) technique. Use of 21 SSR primer...

  10. Preliminary Genetic Map of Hydrangea macrophylla Using SSR Markers and a Pseudo-Testcross Strategy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We used a “two-way pseudo-testcross” mapping strategy in combination with simple sequence repeat (SSR) markers to construct a genetic map of Hydrangea macrophylla. Mapping populations were developed from reciprocal crosses between two divergent cultivars, “Bailmer” and “Veitchii”. “Bailmer”, which i...

  11. Genetic markers in bovine chromosome 14 are significant for residual feed intake in steers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic selection for animals that require less feed while still achieving acceptable levels of production could result in substantial cost savings for cattle producers. The purpose of this study was to identify DNA markers with predictive merit for differences among cattle for traits associated wit...

  12. Diverse Genetic Markers Concordantly Identify Bovine Origin Escherichia coli O157 Genotypes Underrepresented in Human Disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic markers previously reported to occur at significantly different frequencies in isolates of Escherichia coli O157:H7 obtained from cattle and from clinically affected humans are congruent and delineate at least five groups. Isolates in three of these groups consistently carry one or more mark...

  13. Pollen genetic markers for detection of mutagens in the environment

    SciTech Connect

    Nilan, R.A.; Rosichan, J.L.; Arenaz, P.; Hodgdon, A.L.; Kleinhofs, A.

    1980-01-01

    To utilize and exploit pollen for in situ mutagen monitoring, screening and toxicology, the range of genetic traits in pollen must be identified and analyzed. To be useful for the development of mutagen detection systems proteins should be: (1) activity stainable or immunologically identifiable in the pollen, (2) the products of one to three loci; and (3) gametophytic and nuclear in origin. Several proteins, including alcohol dehydrogenase in maize, which meet these criteria are discussed. The waxy locus in barley and maize which controls starch deposition for pollen screening and mutant detection. Thirty waxy mutant lines, induced by sodium azide and gamma-rays are characterized for spontaneous and induced reversion frequencies, allelism, karyotype, amylose content, and UDPglucose glucosyltransferase (waxy gene product) activity. Twelve mutant alleles are being mapped by recombinant frequencies.

  14. mazF as a counter-selectable marker for unmarked genetic modification of Pichia pastoris.

    PubMed

    Yang, Junjie; Jiang, Weihong; Yang, Sheng

    2009-06-01

    In this study, we demonstrate a novel method for unmarked genetic modification of the methylotrophic yeast Pichia pastoris, in which the Escherichia coli toxin gene mazF was used as a counter-selectable marker. mazF was placed under the tightly controlled AOX1 promoter, and the induced expression of MazF in P. pastoris halted cell growth. A modular plasmid was constructed in which mazF and a Zeocin resistance gene acted as counter-selectable and active-selectable markers, respectively, and the MazF-ZeoR cassette was flanked by two direct repeats for marker recycling. Linearized delivery vectors constructed from the modular plasmid were integrated into the P. pastoris genome via homologous recombination, introducing genetic modifications. Upon counter-selection with methanol medium, which induces the AOX1 promoter, the markers were recycled efficiently via homologous recombination between the direct repeats. We used this method successfully to knock-out the ARG1 and MET2 genes, knock-in a green fluorescent protein expression cassette, and perform site-directed mutagenesis on the ARG1 gene, all without introducing unwanted selection markers. The novel method allows repeated use of the selectable marker gene for multiple modifications and will be a useful tool for P. pastoris studies. PMID:19416369

  15. An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)

    PubMed Central

    Pandey, Manish K.; Moretzsohn, Márcio C.; Sujay, Venkataswamy; Qin, Hongde; Hong, Yanbin; Faye, Issa; Chen, Xiaoping; BhanuPrakash, Amindala; Shah, Trushar M.; Gowda, Makanahally V. C.; Nigam, Shyam N.; Liang, Xuanqiang; Hoisington, Dave A.; Guo, Baozhu; Bertioli, David J.; Rami, Jean-Francois; Varshney, Rajeev K.

    2012-01-01

    Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut. PMID:22815973

  16. Molecular Evaluation of Genetic Diversity in Wild-Type Mastic Tree (Pistacia lentiscus L.).

    PubMed

    Abuduli, Alimu; Aydin, Yıldız; Sakiroglu, Muhammet; Onay, Ahmet; Ercisli, Sezai; Uncuoglu, Ahu Altinkut

    2016-10-01

    In this study, the patterns of genetic variation and phylogenetic relationships of mastic tree (Pistacia lentiscus L.) genotypes including 12 males and 12 females were evaluated using SSR, RAPD, ISSR, and ITS markers yielding 40, 703, 929 alleles, and 260-292 base pairs for ITS1 region, respectively. The average number of alleles produced from SSR, RAPD, and ISSR primers were 5.7, 14, and 18, respectively. The grouping pattern obtained from Bayesian clustering method based on each marker dataset was produced. Principal component analyses (PCA) of molecular data was investigated and neighbor joining dendrograms were subsequently created. Overall, the results indicated that ISSR and RAPD markers were the most powerful to differentiate the genotypes in comparison with other types of molecular markers used in this study. The ISSR results indicated that male and female genotypes were distinctly separated from each other. In this frame, M9 (Alaçatı) and M10 (Mesta Sakız Adası-Chios) were the closest genotypes and while F11 (Seferihisar) and F12 (Bornova/Gökdere) genotypes fall into same cluster and showing closer genetic relation. The RAPD pattern indicated that M8 (Urla) and M10 (Mesta Sakız Adası-Chios), and F10 (Mesta Sakız Adası-Chios) and F11 (Seferihisar) genotypes were the closest male and female genotypes, respectively. PMID:27246402

  17. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

    PubMed Central

    2011-01-01

    Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in

  18. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice

    PubMed Central

    Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K.; Gopalakrishnan, S.; Singh, Ashok K.; Rao, Atmakuri R.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

    2016-01-01

    We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

  19. Recent advances in molecular genetic linkage maps of cultivated peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and deficiency of polymorphic DNA markers had severely hi...

  20. Genetic diversity and relationship of chicory (Cichorium intybus L.) using sequence-related amplified polymorphism markers.

    PubMed

    Liang, X Y; Zhang, X Q; Bai, S Q; Huang, L K; Luo, X M; Ji, Y; Jiang, L F

    2014-01-01

    Chicory is a crop with economically important roles and is cultivated worldwide. The genetic diversity and relationship of 80 accessions of chicories and endives were evaluated by sequence-related amplified polymorphism (SRAP) markers to provide a theoretical basis for future breeding programs in China. The polymorphic rate was 96.83%, and the average polymorphic information content was 0.323, suggesting the rich genetic diversity of chicory. The genetic diversity degree of chicory was higher (GS = 0.677) than that of endive (GS = 0.701). The accessions with the highest genetic diversity (effective number of alleles, NE = 1.609; Nei's genetic diversity, H = 0.372; Shannon information index, I = 0.556) were from Italy. The richest genetic diversity was revealed in a chicory line (NE = 1.478, H = 0.289, I = 0.443) among the 3 types (line, wild, and cultivar). The chicory genetic structure of 8 geographical groups showed that the genetic differentiation coefficient (GST) was 14.20% and the number of immigrants per generation (Nm) was 3.020. A GST of 6.80% and an Nm of 6.853 were obtained from different types. This observation suggests that these chicory lines, especially those from the Mediterranean region, have potential for providing rich genetic resources for further breeding programs, that the chicory genetic structure among different countries obviously differs with a certain amount of gene flow, and that SRAP markers could be applied to analyze genetic relationships and classifications of Cichorium intybus and C. endivia. PMID:25299087

  1. Identifying molecular markers associated with stigma characteristics in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stigma characteristics play essential roles in hybrid seed production of rice and marker-assisted breeding plays essential role because they are quantitatively inherited with single-flowered perfect spikelet. Ninety four accessions originated from 47 countries were selected from the USDA rice core c...

  2. Development of a genetic linkage map for Louisiana sugarcane: New microsatellite (SSR) DNA markers identified for LCP 85-384

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Application of the recently developed genetic linkage map of sugarcane (Saccharum spp.) cultivar LCP 85-384 has been limited due to the small number of DNA markers, in particular microsatellite (SSR) DNA markers, on the map. Adding DNA markers to the map improves its usefulness in identifying assoc...

  3. Gains in reliability from combining subsets of 500, 5,000, 50,000 or 500,000 genetic markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    More genetic markers can increase both reliability and cost of genomic selection. Fewer markers can be used to trace chromosome segments within a population once identified by high-density haplotyping. Combinations of marker densities can improve reliability at lower cost. As of January 2010, 33,414...

  4. Genetically encoded dendritic marker sheds light on neuronal connectivity in Drosophila

    PubMed Central

    Nicolaï, Laura J. J.; Ramaekers, Ariane; Raemaekers, Tim; Drozdzecki, Andrzej; Mauss, Alex S.; Yan, Jiekun; Landgraf, Matthias; Annaert, Wim; Hassan, Bassem A.

    2010-01-01

    In recent years, Drosophila melanogaster has emerged as a powerful model for neuronal circuit development, pathology, and function. A major impediment to these studies has been the lack of a genetically encoded, specific, universal, and phenotypically neutral marker of the somatodendritic compartment. We have developed such a marker and show that it is effective and specific in all neuronal populations tested in the peripheral and central nervous system. The marker, which we name DenMark (Dendritic Marker), is a hybrid protein of the mouse protein ICAM5/Telencephalin and the red fluorescent protein mCherry. We show that DenMark is a powerful tool for revealing novel aspects of the neuroanatomy of developing dendrites, identifying previously unknown dendritic arbors, and elucidating neuronal connectivity. PMID:21059961

  5. Genetic Characterization of Green Bean (Phaseolus vulgaris L.) Accessions from Turkey with SCAR and SSR Markers.

    PubMed

    Madakbaş, Seher Yıldız; Sarıkamış, Gölge; Başak, Hakan; Karadavut, Ufuk; Özmen, Canan Yüksel; Daşçı, Mete Gürhan; Çayan, Selin

    2016-08-01

    Characterization, conservation, and utilization of genetic resources is essential for the sustainability in agriculture. Plant genetic resources are important for breeding efforts designed for the generation of new cultivars or for the improvement of existing ones. Green bean has been cultivated extensively in Turkey giving rise to local accessions through selection over time and adaptation to various environmental conditions. The objective of the present study was to determine the genetic relationships of green bean accessions collected from Kırşehir Province of Turkey, located at the central Anatolia. Within a population of 275 green bean accessions, 50 accessions were selected on the basis of morphological observations for further evaluation with SSR and STS/SCAR markers together with 4 reference cultivars of Andean and Mesoamerican origin. SSR markers selected on the basis of high polymorphism information content revealed the genetic relatedness of selected green bean accessions. STS/SCAR markers associated with bean anthracnose, common bacterial blight, white mold, halo blight, and phaseolin protein demonstrated the inheritance of resistance traits of local accessions at the selected loci. These findings may help better utilize genetic resources and furthermore are expected to facilitate forthcoming breeding studies for the generation of novel cultivars well adapted to the region. PMID:27156082

  6. Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium

    PubMed Central

    Pochon, Xavier; Putnam, Hollie M.; Burki, Fabien; Gates, Ruth D.

    2012-01-01

    Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A–H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A–H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available. PMID:22238660

  7. Distribution and localization of microsatellites in the Perigord black truffle genome and identification of new molecular markers.

    PubMed

    Murat, C; Riccioni, C; Belfiori, B; Cichocki, N; Labbé, J; Morin, E; Tisserant, E; Paolocci, F; Rubini, A; Martin, F

    2011-06-01

    The level of genetic diversity and genetic structure in the Perigord black truffle (Tuber melanosporum Vittad.) has been debated for several years, mainly due to the lack of appropriate genetic markers. Microsatellites or simple sequence repeats (SSRs) are important for the genome organisation, phenotypic diversity and are one of the most popular molecular markers. In this study, we surveyed the T. melanosporum genome (1) to characterise its SSR pattern; (2) to compare it with SSR patterns found in 48 other fungal and three oomycetes genomes and (3) to identify new polymorphic SSR markers for population genetics. The T. melanosporum genome is rich in SSRs with 22,425 SSRs with mono-nucleotides being the most frequent motifs. SSRs were found in all genomic regions although they are more frequent in non-coding regions (introns and intergenic regions). Sixty out of 135 PCR-amplified mono-, di-, tri-, tetra, penta, and hexa-nucleotides were polymorphic (44%) within black truffle populations and 27 were randomly selected and analysed on 139 T. melanosporum isolates from France, Italy and Spain. The number of alleles varied from 2 to 18 and the expected heterozygosity from 0.124 to 0.815. One hundred and thirty-two different multilocus genotypes out of the 139 T. melanosporum isolates were identified and the genotypic diversity was high (0.999). Polymorphic SSRs were found in UTR regulatory regions of fruiting bodies and ectomycorrhiza regulated genes, suggesting that they may play a role in phenotypic variation. In conclusion, SSRs developed in this study were highly polymorphic and our results showed that T. melanosporum is a species with an important genetic diversity, which is in agreement with its recently uncovered heterothallic mating system. PMID:20965267

  8. Marker-based estimation of genetic parameters in genomics.

    PubMed

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing 'big' genomic data sets. PMID:25025305

  9. Marker-Based Estimation of Genetic Parameters in Genomics

    PubMed Central

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

  10. Analysis of Molecular Genetics Content in Spanish Secondary School Textbooks

    ERIC Educational Resources Information Center

    Martinez-Gracia, M. V.; Gil-Quilez, M. J.; Osada, J.

    2006-01-01

    The treatment of molecular biology in thirty-four Spanish high school biology textbooks has been analysed using a check-list made up of twenty-three items. The study showed a tendency to confuse the genetic code with genetic information. The treatment of DNA transcription, regulation of gene expression and translation were presented as masses of…

  11. Genetic relationships of ethnic minorities in Southwest China revealed by microsatellite markers.

    PubMed

    Lin, Hongbin; Fan, Hao; Zhang, Feng; Huang, Xiaoqin; Lin, Keqin; Shi, Lei; Hu, Songnian; Chu, Jiayou; Wang, Duen-Mei

    2010-01-01

    Population migrations in Southwest and South China have played an important role in the formation of East Asian populations and led to a high degree of cultural diversity among ethnic minorities living in these areas. To explore the genetic relationships of these ethnic minorities, we systematically surveyed the variation of 10 autosomal STR markers of 1,538 individuals from 30 populations of 25 ethnic minorities, of which the majority were chosen from Southwest China, especially Yunnan Province. With genotyped data of the markers, we constructed phylogenies of these populations with both D(A) and D(C) measures and performed a principal component analysis, as well as a clustering analysis by structure. Results showed that we successfully recovered the genetic structure of analyzed populations formed by historical migrations. Aggregation patterns of these populations accord well with their linguistic affiliations, suggesting that deciphering of genetic relationships does in fact offer clues for study of ethnic differentiation. PMID:20360948

  12. Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers.

    PubMed

    Liu, M P; Du, H Y; Zhu, G P; Fu, D L; Tana, W Y

    2015-01-01

    Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters. PMID:26345904

  13. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  14. First haploid genetic map based on microsatellite markers in Senegalese sole (Solea senegalensis, Kaup 1858).

    PubMed

    Molina-Luzón, Ma Jesús; Hermida, Miguel; Navajas-Pérez, Rafael; Robles, Francisca; Navas, José Ignacio; Ruiz-Rejón, Carmelo; Bouza, Carmen; Martínez, Paulino; de la Herrán, Roberto

    2015-02-01

    The Senegalese sole (Solea senegalensis, Kaup 1858) is a flatfish species of great value for aquaculture. In this study, we develop the first linkage map in this species based on microsatellite markers characterized from genomic DNA libraries and EST databases of Senegalese sole and from other flatfish species. Three reference gynogenetic families were obtained by chromosome-manipulation techniques: two haploid gynogenetics, used to assign and order microsatellites to linkage groups and another diploid gynogenetic family, used for estimating marker-centromere distances. The consensus map consists of 129 microsatellites distributed in 27 linkage groups (LG), with an average density of 4.7 markers per LG and comprising 1,004 centimorgans (cM). Additionally, 15 markers remained unlinked. Through half-tetrad analysis, we were able to estimate the centromere distance for 81 markers belonging to 24 LG, representing an average of 3 markers per LG. Comparative mapping was performed between flatfish species LG and model fish species chromosomes (stickleback, Tetraodon, medaka, fugu and zebrafish). The usefulness of microsatellite markers and the genetic map as tools for comparative mapping and evolution studies is discussed. PMID:25107689

  15. Using genetic markers to estimate the pollen dispersal curve.

    PubMed

    Austerlitz, Frederic; Dick, Christopher W; Dutech, Cyril; Klein, Etienne K; Oddou-Muratorio, Sylvie; Smouse, Peter E; Sork, Victoria L

    2004-04-01

    Pollen dispersal is a critical process that shapes genetic diversity in natural populations of plants. Estimating the pollen dispersal curve can provide insight into the evolutionary dynamics of populations and is essential background for making predictions about changes induced by perturbations. Specifically, we would like to know whether the dispersal curve is exponential, thin-tailed (decreasing faster than exponential), or fat-tailed (decreasing slower than the exponential). In the latter case, rare events of long-distance dispersal will be much more likely. Here we generalize the previously developed TWOGENER method, assuming that the pollen dispersal curve belongs to particular one- or two-parameter families of dispersal curves and estimating simultaneously the parameters of the dispersal curve and the effective density of reproducing individuals in the population. We tested this method on simulated data, using an exponential power distribution, under thin-tailed, exponential and fat-tailed conditions. We find that even if our estimates show some bias and large mean squared error (MSE), we are able to estimate correctly the general trend of the curve - thin-tailed or fat-tailed - and the effective density. Moreover, the mean distance of dispersal can be correctly estimated with low bias and MSE, even if another family of dispersal curve is used for the estimation. Finally, we consider three case studies based on forest tree species. We find that dispersal is fat-tailed in all cases, and that the effective density estimated by our model is below the measured density in two of the cases. This latter result may reflect the difficulty of estimating two parameters, or it may be a biological consequence of variance in reproductive success of males in the population. Both the simulated and empirical findings demonstrate the strong potential of TWOGENER for evaluating the shape of the dispersal curve and the effective density of the population (d(e)). PMID:15012767

  16. Alu repeats as markers for human population genetics

    SciTech Connect

    Batzer, M.A.; Alegria-Hartman, M.; Bazan, H.

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  17. Genetic characterization of European-Zebu composite bovine using RFLP markers.

    PubMed

    Marson, Erica Perez; Ferraz, José Bento Sterman; Meirelles, Flávio Vieira; Balieiro, Júlio César de Carvalho; Eler, Joanir Pereira; Figueiredo, Luís Gustavo Girardi; Mourão, Gerson Barreto

    2005-01-01

    A population of 370 European-Zebu composite beef heifers, consisting of six different breed compositions (A-F), were characterized genetically, using RFLP markers of luteinizing hormone receptor (LHR) and follicle-stimulating hormone receptor (FSHR) genes. Our objectives were to genetically characterize this population and to determine the structure and the genetic variability of this hybrid herd. The genotypes were determined through PCR, followed by digestion with restriction endonucleases. The PCR-RFLP analysis made it possible to identify the LHR and FSHR genotypes, as well as to characterize the degree of heterozygosis, which was high for all of the breed compositions, for both loci, except for two combinations for LHR (B and C). The observed heterozygosity (Ho) was lower than the expected heterozygosity (He) for compositions C (for LHR) and A and D (for FSHR); however, for the population as a whole, Ho was above He (with a mean of 57 versus 46%, respectively), reflecting the elevated genetic variability in this population and also the informative value of the RFLP markers, which could be useful for population genetic characterization studies. The analysis of the degree of genetic structure of this population, estimated by the Nei's statistic, for both loci, indicated an elevated total genetic diversity (HT = 47%), with most of this variability being due to intrapopulational diversity (HS = 46%), with a low degree of genetic differentiation among the six breed compositions (GST = 1.2%). The estimates generated by the Wright's F statistic indicated a non-endogamic population, with excess heterozygotes (FIT = -0.22), which was also observed at the intrapopulational level (FIS = -0.23). The results gave evidence that the genetic selection applied to this European-Zebu composite population did not affect the expected high genetic variability for this type of crossbreeding, which makes it possible to use these animals to obtain economically valuable productive and

  18. Genetic variation and population genetic structure of Rhizophora apiculata (Rhizophoraceae) in the Greater Sunda Islands, Indonesia using microsatellite markers.

    PubMed

    Yahya, Andi Fadly; Hyun, Jung Oh; Lee, Jae Ho; Kim, Yong Yul; Lee, Kyung Mi; Hong, Kyung Nak; Kim, Seung-Chul

    2014-03-01

    Genetic variations within and among Rhizophora apiculata populations in the Greater Sunda Islands of Indonesia were studied using microsatellite markers. The study found 38 alleles on five loci in 15 populations. The observed (H(o)) and expected (H(e)) heterozygosity values are 0.338 and 0.378, respectively. Inbreeding effect from self-pollination might explain its heterozygote deficiency. Population genetic differentiation (F(ST) = 0.381) was similar to other mangrove species. The genetic diversity of R. apiculata populations along the coastline inside the archipelago (e.g., Buleleng, Donggala, Mamuju, and Takalar) was higher than those of population along the coastline outside the archipelago, especially northern Sumatra populations (i.e., Langkat, Tapanuli Tengah, Dumai, and Padang). The isolation by distances and sea currents directions as well as their connectivity might affect the gene flow and genetic exchange. The more isolated with fewer connections by sea currents, the smaller gene flow and genetic exchange observed between populations. The higher genetic exchange, on the contrary, occurred when population location was closer to the meeting point of the sea currents. The study also showed that the patterns of sea current movement seemed to have influence genetic clustering of populations which fell into three main groups (Sunda Shelf Mangroves) and one isolated population (New Guinea Mangroves). PMID:24323307

  19. DNA markers in molecular diagnostics for hepatocellular carcinoma

    PubMed Central

    Su, Ying-Hsiu; Lin, Selena Y; Song, Wei; Jain, Surbhi

    2015-01-01

    Hepatocellular carcinoma (HCC) is the one of the leading causes of cancer mortality in the world, mainly due to the difficulty of early detection and limited therapeutic options. The implementation of HCC surveillance programs in well-defined, high-risk populations were only able to detect about 40–50% of HCC at curative stages (Barcelona Clinic Liver Cancer stages 0 & 1) due to the low sensitivities of the current screening methods. The advance of sequencing technologies has identified numerous modifications as potential candidate DNA markers for diagnosis/surveillance. Here we aim to provide an overview of the DNA alterations that result in activation of cancer pathways known to potentially drive HCC carcinogenesis and to summarize performance characteristics of each DNA marker in the periphery (blood or urine) for HCC screening. PMID:25098554

  20. The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.

    EPA Science Inventory

    Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...

  1. Varietal Discrimination and Genetic Variability Analysis of Cymbopogon Using RAPD and ISSR Markers Analysis.

    PubMed

    Bishoyi, Ashok Kumar; Sharma, Anjali; Kavane, Aarti; Geetha, K A

    2016-06-01

    Cymbopogon is an important genus of family Poaceae, cultivated mainly for its essential oils which possess high medicinal and economical value. Several cultivars of Cymbopogon species are available for commercial cultivation in India and identification of these cultivars was conceded by means of morphological markers and essential oil constitution. Since these parameters are highly influenced by environmental factors, in most of the cases, it is difficult to identify Cymbopogon cultivars. In the present study, Random amplified polymorphic DNA (RAPD) and Inter-simple sequence repeat (ISSR) markers were employed to discriminate nine leading varieties of Cymbopogon since prior genomic information is lacking or very little in the genus. Ninety RAPD and 70 ISSR primers were used which generated 63 and 69 % polymorphic amplicons, respectively. Similarity in the pattern of UPGMA-derived dendrogram of RAPD and ISSR analysis revealed the reliability of the markers chosen for the study. Varietal/cultivar-specific markers generated from the study could be utilised for varietal/cultivar authentication, thus monitoring the quality of the essential oil production in Cymbopogon. These markers can also be utilised for the IPR protection of the cultivars. Moreover, the study provides molecular marker tool kit in both random and simple sequence repeats for diverse molecular research in the same or related genera. PMID:26922722

  2. Molecular Pathology: Prognostic and Diagnostic Genomic Markers for Myeloid Neoplasms.

    PubMed

    Kuo, Frank C

    2016-09-01

    Application of next-generation sequencing (NGS) on myeloid neoplasms has expanded our knowledge of genomic alterations in this group of diseases. Genomic alterations in myeloid neoplasms are complex, heterogeneous, and not specific to a disease entity. NGS-based panel testing of myeloid neoplasms can complement existing diagnostic modalities and is gaining acceptance in the clinics and diagnostic laboratories. Prospective, randomized trials to evaluate the prognostic significance of genomic markers in myeloid neoplasms are under way in academic medical centers. PMID:27523973

  3. Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica

    PubMed Central

    Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

    2015-01-01

    Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

  4. Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica.

    PubMed

    Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

    2015-01-01

    Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the "candidate genes" and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

  5. Small-scale field test of the genetically engineered lacZY marker

    SciTech Connect

    Hattemer-Frey, H.A.; Brandt, E.J.; Travis, C.C. )

    1990-06-01

    Commercial genetic engineering is advancing into areas that require the small-scale introduction of genetically engineered microorganisms (GEMs) to better quantify variables that affect microorganism distribution and survival and to document potential long-term consequences. A recombinant DNA marker system, the lacZY marker, developed by the Monsanto Agricultural Co., enables the distribution and fate of marked fluorescent pseudomonad organisms to be monitored under actual field conditions. Critical evaluation of GEMs under field conditions is imperative if plant-beneficial effects are to be correlated with organism release. This paper evaluates the effectiveness of this marker system and its ability to facilitate the assessment of risks associated with deliberate environmental introductions of genetically engineered microorganisms. Results of prerelease contained growth chamber and field experiments demonstrated that: (1) the scientific risk assessment methodology adopted by Monsanto and approved by the U.S. Environmental Protection Agency was appropriate and comprehensive; (2) the deliberate introduction of a GEM did not pose unacceptable or unforeseen risks to human health or the environment; (3) the lacZY marker is an effective environmental tracking tool; and (4) regulatory oversight should reflect the expected risk and not be excessively burdensome for all GEMs.

  6. Competitive Metagenomic DNA Hybridization Identifies Host-Specific Microbial Genetic Markers in Cow Fecal Samples†

    PubMed Central

    Shanks, Orin C.; Santo Domingo, Jorge W.; Lamendella, Regina; Kelty, Catherine A.; Graham, James E.

    2006-01-01

    Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities. PMID:16751515

  7. Genetic diversity of the Hungarian Gidran horse in two mitochondrial DNA markers.

    PubMed

    Sziszkosz, Nikolett; Mihók, Sándor; Jávor, András; Kusza, Szilvia

    2016-01-01

    The Gidran is a native Hungarian horse breed that has approached extinction several times. Phylogenetic analysis of two mitochondrial markers (D-loop and cytochrome-b) was performed to determine the genetic characterization of the Gidran for the first time as well as to detect errors in the management of the Gidran stud book. Sequencing of 686 bp of CYTB and 202 bp of the D-loop in 260 mares revealed 24 and 32 haplotypes, respectively, among 31 mare families. BLAST analysis revealed six novel CYTB and four D-loop haplotypes that have not been previously reported. The Gidran mares showed high haplotype (CYTB: 0.8735 ± 0.011; D-loop: 0.9136 ± 0.008) and moderate nucleotide (CYTB: 0.00472 ± 0.00017; D-loop: 0.02091 ± 0.00068) diversity. Of the 31 Gidran mare families, only 15 CYTB (48.4%) and 17 D-loop (54.8%) distinct haplotypes were formed using the two markers separately. Merged markers created 24 (77.4%) mare families, which were in agreement with the mare families in the stud book. Our key finding was that the Gidran breed still possesses high genetic diversity despite its history. The obtained haplotypes are mostly consistent with known mare families, particularly when the two mtDNA markers were merged. Our results could facilitate conservation efforts for preserving the genetic diversity of the Gidran. PMID:27168959

  8. Genetic diversity of the Hungarian Gidran horse in two mitochondrial DNA markers

    PubMed Central

    Sziszkosz, Nikolett; Mihók, Sándor; Jávor, András

    2016-01-01

    The Gidran is a native Hungarian horse breed that has approached extinction several times. Phylogenetic analysis of two mitochondrial markers (D-loop and cytochrome-b) was performed to determine the genetic characterization of the Gidran for the first time as well as to detect errors in the management of the Gidran stud book. Sequencing of 686 bp of CYTB and 202 bp of the D-loop in 260 mares revealed 24 and 32 haplotypes, respectively, among 31 mare families. BLAST analysis revealed six novel CYTB and four D-loop haplotypes that have not been previously reported. The Gidran mares showed high haplotype (CYTB: 0.8735 ± 0.011; D-loop: 0.9136 ± 0.008) and moderate nucleotide (CYTB: 0.00472 ± 0.00017; D-loop: 0.02091 ± 0.00068) diversity. Of the 31 Gidran mare families, only 15 CYTB (48.4%) and 17 D-loop (54.8%) distinct haplotypes were formed using the two markers separately. Merged markers created 24 (77.4%) mare families, which were in agreement with the mare families in the stud book. Our key finding was that the Gidran breed still possesses high genetic diversity despite its history. The obtained haplotypes are mostly consistent with known mare families, particularly when the two mtDNA markers were merged. Our results could facilitate conservation efforts for preserving the genetic diversity of the Gidran. PMID:27168959

  9. Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow.

    PubMed

    O'Malley, Kathleen G; Jacobson, Dave P; Kurth, Ryon; Dill, Allen J; Banks, Michael A

    2013-12-01

    Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing. PMID:24478800

  10. Comparison of two molecular weight markers used in DNA-profiling.

    PubMed

    Eriksen, B; Svensmark, O

    1992-01-01

    DNA-profiling was performed on DNA from human blood samples. Restriction was performed with HinfI and the fragments were analysed with the single locus probes MS1, MS31, MS43a, and YNH24. Calculations of the sizes of DNA-fragments in the range from 1.4 to 22 kilobase pairs (kb) were performed with two different size markers: the Amersham marker SJ5000 and the Gibco BRL marker 4401SA. The standard deviation of the difference between duplicate determinations was significantly lower with the Gibco BRL marker than with the Amersham marker. Calculation of the fragment lengths with the two markers differed significantly, especially in the high molecular weight region (> 8 kb). Fragment lengths were 3-8% (kb) higher with the Amersham marker than with the Gibco BRL marker which corresponds to a difference of 1.0-1.8 mm in migration distance. The difference was enhanced in the presence of ethidium bromide. The consequences of the replacement of the Amersham marker by the Gibco BRL marker in practical casework is discussed. PMID:1358177

  11. Evaluation of the genetic diversity of microsatellite markers among four strains of Oreochromis niloticus.

    PubMed

    Dias, M A D; de Freitas, R T F; Arranz, S E; Villanova, G V; Hilsdorf, A W S

    2016-06-01

    Different strains of Nile tilapia can be found worldwide. To successfully use them in breeding programs, they must be genetically characterized. In this study, four strains of Nile tilapia - UFLA, GIFT, Chitralada and Red-Stirling - were genetically characterized using 10 noncoding microsatellite loci and two microsatellites located in the promoter and first intron of the growth hormone gene (GH). The two microsatellites in the GH gene were identified at positions -693 to -679 in the promoter [motif (ATTCT)8 ] and in intron 1 at positions +140 to +168 [motif (CTGT)7 ]. Genetic diversity was measured as mean numbers of alleles and expected heterozygosity, which were 4 and 0.60 (GIFT), 3.5 and 0.71 (UFLA), 4.5 and 0.57 (Chitralada) and 2.5 and 0.42 (Red-Stirling) respectively. Genetic differentiation was estimated both separately and in combination for noncoding and GH microsatellites markers using Jost's DEST index. The UFLA and GIFT strains were the least genetically divergent (DEST  = 0.10), and Chitralada and Red-Stirling were the most (DEST  = 0.58). The UFLA strain was genetically characterized for the first time and, because of its unique origin and genetic distinctness, may prove to be an important resource for genetic improvement of Nile tilapia. This study shows that polymorphisms found in coding gene regions might be useful for assessing genetic differentiation among strains. PMID:26932188

  12. Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers

    PubMed Central

    Suh, Sangwon; Sharma, Aditi; Lee, Seunghwan; Cho, Chang-Yeon; Kim, Jae-Hwan; Choi, Seong-Bok; Kim, Hyun; Seong, Hwan-Hoo; Yeon, Seong-Hum; Kim, Dong-Hun; Ko, Yeoung-Gyu

    2014-01-01

    The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds PMID:25178290

  13. Assessment of genetic diversity in Chinese eared pheasant using fluorescent-AFLP markers.

    PubMed

    Li, Xiujuan; Zhu, Yaohong; Liu, Panqi; Zhuge, Zengyu; Su, Guosheng; Wang, Jiufeng

    2010-10-01

    The eared pheasant consists of four species: white eared pheasant (Crossoptilon crossoptilon), Tibetan eared pheasant (Crossoptilon harmani), blue eared pheasant (Crossoptilon auritum), and brown eared pheasant (Crossoptilon mantchuricum). These species are found only in China, and are also on the list of the world's threatened species. In this paper, 74 individuals from the four eared pheasant species were assessed for population genetic diversity by means of fluorescent-AFLP markers. A total of 429 AFLP peaks were amplified by 11 pairs of fluorescent EcoRI/TaqI primer combinations. Out of all markers, 329 AFLPs were polymorphic. Each primer combination produced in reactions from 19 to 72 fragments and the polymorphic peaks percentage ranged from 53.33% to 86.11% with an average of 74.36% polymorphic bands. Genetic distance between species and genetic diversity within species were evaluated using Jaccard's similarity coefficients (SC) and the corresponding dendrogram. It was found that there was a moderate genetic distance between the four species (SC=0.674-0.832). Brown eared pheasant was genetically closely related to blue eared pheasant (SC=0.832), while white eared pheasant was more closely related to Tibetan eared pheasant (SC=0.812). Genetic diversity was lower in brown eared pheasant (SC=0.913) and Tibetan eared pheasant (SC=0.903) than in white eared pheasant (SC=0.832) and blue eared pheasant (SC=0.853). PMID:20595068

  14. Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum).

    PubMed

    Badigannavar, Ashok; Myers, Gerald O

    2015-03-01

    Cottonseed contains 16% seed oil and 23% seed protein by weight. High levels of palmitic acid provides a degree of stability to the oil, while the presence of bound gossypol in proteins considerably changes their properties, including their biological value. This study uses genetic principles to identify genomic regions associated with seed oil, protein and fibre content in upland cotton cultivars. Cotton association mapping panel representing the US germplasm were genotyped using amplified fragment length polymorphism markers, yielding 234 polymorphic DNA fragments. Phenotypic analysis showed high genetic variability for the seed traits, seed oil range from 6.47-25.16%, protein from 1.85-28.45% and fibre content from 15.88-37.12%. There were negative correlations between seed oil and protein content.With reference to genetic diversity, the average estimate of FST was 8.852 indicating a low level of genetic differentiation among subpopulations. The AMOVA test revealed that variation was 94% within and 6% among subpopulations. Bayesian population structure identified five subpopulations and was in agreement with their geographical distribution. Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic relationships and their utilization in breeding programmes. PMID:25846880

  15. [Developing and applying of a parentage identification approach based on high density genetic markers].

    PubMed

    Zhang, Zhe; Luo, Yuanyu; Li, Qingqing; He, Jinlong; Gao, Ning; Zhang, Hao; Ding, Xiangdong; Zhang, Qin; Li, Jiaqi

    2014-08-01

    Pedigree is an important information source in the studies on human genetics and animal/plant breeding. Pedigree error is a common data error in breeding practice. It can affect the reliability of results from researches such as gene mapping, genetic or phenotypic value prediction. By using genetic markers, several approaches can identify the suspected pedigrees, but most of them are complex and the allowed number of genetic markers is limited, such as Cervus. Since the wide use of high density single nucleotide polymorphisms (SNPs) in human genetic and animal/plant breeding, a new parentage identification approach (named EasyPC, Easy Pedigree Checking) based on whole genome genetic data was proposed in this study. EasyPC was compared with Cervus on efficiency, and validated with a Chinese Holstein cattle (n=2180) and a Duroc swine (n=191) population. Results showed that EasyPC was much less time demanding than Cervus, and pedigree error rates were 20% for cattle and 6% for swine. Result from the cattle population is in accordance with previous study. By analyzing the empirical distribution of Mendelian error rate calculated in a population using all available SNPs, EasyPC not only can identify the correctness of a pedigree in a simple, fast, and accurate manner, but also can correct the wrong pedigree. EasyPC provides a promising alternative solution to traditional pedigree correction approaches and eases the data analysis of whole genome related studies. PMID:25143282

  16. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.

    PubMed

    Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

    2012-03-01

    Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), a non-coding nuclear DNA region (the ITS region), and a novel marker for G. pallida, a ∼3.4 kb non-coding mitochondrial DNA (mtDNA) region. Multiple phylogenetic analysis methods were performed on the three DNA regions separately, and on a data set of these three regions combined. The analyses of the combined data set were similar to that of the sole mtDNA marker; resolving more populations as monophyletic groups, relative to that of the ITS region and rbp-1 gene region. This suggests that individual markers may be inadequate for distinguishing populations of G. pallida. The use of this new non-coding mtDNA marker may provide further insights into the historical distribution of G. pallida, as well as enable the development of more sensitive diagnostic methods. PMID:23482966

  17. Genetic and molecular distinctions in spinal ependymomas: A review.

    PubMed

    Connolly, Ian D; Ali, Rohaid; Li, Yingmei; Gephart, Melanie Hayden

    2015-12-01

    While gross total resection of spinal ependymomas prevents recurrence, this surgical result is not always possible. Increasing evidence suggests that ependymomas occurring in the spine are genetically distinct from those originating in the brain. Herein we review the most recent developments detailing the molecular and genetic characteristics of spinal ependymomas, which may inform more effective and personalized adjuvant therapies for spinal ependymomas that are ineligible for gross total resection. We performed a key-word search for articles published on the molecular, genetic, chromosomal, and epigenetic transformations inherent in spinal ependymomas. We reviewed appropriate articles and their relevant citations. While resection can often achieve favorable outcomes in the treatment of spinal ependymoma, more research on the unique molecular, genetic, chromosomal and epigenetic traits must be conducted in order to tailor treatment and intervention for those patients for whom total resection is not possible. PMID:26519890

  18. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

    PubMed Central

    Fan, Guang Yao; Ye, Yi; Hou, Yi Ping

    2016-01-01

    Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry