WorldWideScience

Sample records for aflp molecular markers

  1. Molecular mapping of the Pinus monticola Cr2 gene using AFLP and SCAR markers

    Directory of Open Access Journals (Sweden)

    A.K.M. Ekramoddoullah

    2013-12-01

    Full Text Available White pine blister rust (WPBR, caused by Cronartium ribicola, is a devastating disease in five-needle pines. Genetic resistance is an important component of integrated strategies to control WPBR. The major resistance gene Cr2, discovered by Kinloch etal.(1999, is also effective against British Columbia (BC isolates of WPBR (Hunt et al. 2004. Pyramiding Cr2 gene with other resistancegenes is being pursued as a strategy in BC white pine breeding. To facilitate this strategy, we have recently identified a few RAPD markerslinked to Cr2 at one side (Liu et al. 2006. The objective of the present study was to identify amplified fragment length polymorphism(AFLP markers linked to both sides of Cr2 for its more precise apping. Use of the AFLP technique combined with bulked segregant analysis (BSA and haploid segregation analysis allowed the identification of five AFLP markers. Of these five AFLP markers in the Cr2 linkage, markers EacccMccgat-365, EactgMcccac- 290, and EacagEacag-750 werelinked in coupling and EacagMcccag-160r and EacccMccgat-180r in repulsion. Following cloning and sequencing of the AFLP andRAPD markers, specific PCR primers were designed and used in the amplification of sequence characterized amplified region(SCAR markers at both sides of Cr2. EacccMccgat- 365 and RAPD marker U570-843 reported previously were converted into SCARmarkers. These two SCARs segregated in a 1:1 (presence:absence ratio and the scoring cosegregated with their respective AFLP orRAPD marker. The SCAR marker EacccMccgat- 365-scar was positioned at 3.1 Kosambi cM from one side of Cr2 and U570-843-scarlocalized at 1.4 Kosambi cM from other side. Both SCAR markers can be useful in breeding programs with marker-assisted selection procedureto screen for resistance. This study represents the first report of the development of PCR-based sequence-specific markers linkedto blister rust resistance in five-needle pines. These findings may

  2. AFLP molecular marker and crop improvement%AFLP分子标记与作物改良

    Institute of Scientific and Technical Information of China (English)

    李爱丽; 马峙英

    2001-01-01

    Molecular markers based on DNA play a very important role in crop improvement. Amplified fragment length polymorphism (AFLP) technology is a novel and powerful DNA fingerprinting technique. It is based on the selective amplification of restriction fragments from a total digest of genomic DNA. The AFLP approach is particularly powerful because it requires no prior sequence characterization of the target genome, and it is readily applicable to a wide variety of crops. This paper mainly discussed the application of AFLP in main crops to cultivars identification, genetic map construction, gene location, and assisted selection.%建立于DNA基础之上的分子标记对于作物改良具有重要作用。 AFLP(Amplified fragment length polytism, 简称AFtP)国内译为扩增片段长度多态性,是一种DNA分子标记技术。利用这一方法,在不需要预先知道DNA序列信息的情况下就可以同时进行多数DNA酶切片断的PCR扩增。目前,该技术不仅在小麦、玉米、棉花和大豆等主要农作物上得以应用,而且在蔬菜(番茄、马铃薯、鹰嘴豆等)以及植物基因组研究的模式植物拟南芥上广泛应用。讨论了AFLP在主要作物的品种鉴定、遗传多样性分析、遗传作图、基因定位以及辅助选择等方面的应用进展。

  3. Optimizing AFLP Molecular Marker System for Leucaena%银合欢AFLP分子标记体系的优化

    Institute of Scientific and Technical Information of China (English)

    吴成贡; 邹冬梅; 张景千; 蒋昌顺

    2011-01-01

    DNA was extracted from the materials of Leucaena seedlings with CTAB and kit. The suitable AFLP molecular marker system was established for Leucaena diversity analysis after AFLP reaction had been optimized with DNA samples in different digestion time and primers screening. This work provided a basic knowledge on AFLP molecular marker for studying Leucaena molecular biology and molecular breeding.%以银合欢幼苗为材料,采用CTAB区室法和试剂盒法2种方法提取DNA,通过对影响AFLP反应关键因子,如DNA样品酶切时间、引物等进行优化,建立了适合银合欢AFLP分子标记的反应体系,为利用AFLP标记对银合欢进行分子生物学研究及分子育种奠定基础.

  4. Development of Molecular Marker Linked to Cf-10 Gene Using SSR and AFLP Method in Tomato

    Institute of Scientific and Technical Information of China (English)

    Li Ning; Jiang Jing-bin; Li Jing-fu; Xu Xiang-yang

    2012-01-01

    The leaf mould resistance gene Cf-10 on tomato confered resistant or immune to all prevalent physiological races of Cladosporium fulvum presented in three northeastern provinces of China in inoculation test. In order to better utilize Cf-10 gene in a marker-assisted selection program and to permit the pyramiding of one or several resistance genes in a cultivar, tightly linked SSR and AFLP markers were obtained by the bulked segregant analysis method. One SSR marker and three AFLP markers were identified linked to Cf-10 gene, with the distance of 9.73, 5.8, 8.5, and 10.6 cM, respectively. These markers will facilitate the selection of resistant tomato germplasm containing Cf-10 gene.

  5. High Lycopene AFLP- SCAR Molecular Marker of Fresh Tomato%鲜食番茄茄红素基因的AFLP-SCAR分子标记

    Institute of Scientific and Technical Information of China (English)

    侯丽霞; 刘淑梅; 王施慧; 吕鑫

    2011-01-01

    Lycopene (LYC) is a function of the natural pigment, because of its high antioxidant functions have attracted much attention. For screening high-lycopene varieties of fresh tomatoes to accelerate the process of molecular marker-assisted breeding, AFLP-SCAR marks of high lycopene were studied by using materials high-lycopene selling line F-516F8 and low-lycopene selfing line Nor. Using genetical population of Ft and F2, AFLP and BAS techniques with 64 pairs of E/M primers screening, we obtained one AFLP marker E-AG/M-CAT. Through recovery, and sequencing of idio-fragment, transformation of SCAR, BLAST, marker E-AG/M-CAT was locating on the eighth chromosome. Utilizing SCAR makers can evaluate the content of lycopene at DNA level when the tomato materials are in seedling period, which greatly reducing the workload of field screening. SCAR makers can also be used on molecular marker assisted selection, improving the breeding efficiency.%番茄红素(Lycopene)是功能性天然色素,因其高抗氧化功能而备受关注.为筛选高番茄红素品种,加速鲜食番茄分子标记辅助育种进程,本试验以高茄红素番茄骨干系F-516F8和低茄红素骨干系Nor作为试验材料,研究了鲜食番茄高茄红素基因的AFLP-SCAR分子标记.利用杂交F1代、自交F2代遗传群体,通过64对E/M引物组合的筛选,采用AFLP分析技术和改良BAS法,获得1个与高番茄红素基因连锁的AFLP标记E-AG/M-CAT.通过特异片段回收、测序、SCAR转化、BLAST比对分析,该标记定位在番茄第8染色体.利用SCAR标记可在苗期从DNA水平上对番茄材料的番茄红素含量高低进行鉴定,大大减少了田间筛选工作量,并可用于分子标记辅助育种,提高育种效率.

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

    Science.gov (United States)

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

    2016-02-19

    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.

  7. Molecular Markers for Leaf Rust Resistance Gene Lr45 in Wheat Based on AFLP Analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Na; YANG Wen-xiang; YAN Hong-fei; LIU Da-qun; CHU Dong; MENG Qing-fang; ZHANG Ting

    2006-01-01

    Amplified fragment length polymorphism (AFLP) analysis was carried out in Thatcher, near isogenic lines (NILs) carrying different genes conferring resistance against wheat leaf rust, and TcLr45×Thatcher F2 progenies were used to develop markers for Lr45 gene. Sixty AFLP primer combinations were screened and most of them provided clear amplification products, 31 primer combinations displayed polymorphism of TcLr45 in 23 NILs. Two AFLP markers closely linked to the gene Lr45 were acquired: P-AGG/M-GAG261 bp, which was found closely linked to the Lr45 locus at a distance of 0.6 cM on one side, and P-ACA/M-GGT105 bp, which was found at a distance of 1.3 cM on the other side. The specific bands were cloned and subsequently sequenced. The 261-bp fragment produced by P-AGG/M-GAG showed 86% similarity with the sequence of Vulgare Hort Ⅰ gene; the 105-bp fragment produced by P-ACA/M-GGT showed 96% similarity with the phosphatidylserine decarboxylase gene of the Triticum monococcum. Both included an open reading frame (ORF).

  8. Genetic diversity and relationship in American and African oil palm as revealed by RFLP and AFLP molecular markers

    Directory of Open Access Journals (Sweden)

    Barcelos Edson

    2002-01-01

    Full Text Available The objective of this work was to evaluate the genetic diversity, its organization and the genetic relationships within oil palm (Elaeis oleifera (Kunth Cortés, from America, and E. guineensis (Jacq., from Africa germplasm using Restriction Fragment Length Polymorphism (RFLP and Amplified Fragment Length Polymorphism (AFLP. In complement to a previous RFLP study on 241 E. oleifera accessions, 38 E. guineensis accessions were analyzed using the same 37 cDNA probes. These accessions covered a large part of the geographical distribution areas of these species in America and Africa. In addition, AFLP analysis was performed on a sub-set of 40 accessions of E. oleifera and 22 of E. guineensis using three pairs of enzyme/primer combinations. Data were subjected to Factorial Analysis of Correspondence (FAC and cluster analysis, with parameters of genetic diversity being also studied. Results appeared congruent between RFLP and AFLP. In the E. oleifera, AFLP confirmed the strong structure of genetic diversity revealed by RFLP, according to geographical origin of the studied material, with the identification of the same four distinct genetic groups: Brazil, French Guyana/Surinam, Peru, north of Colombia/Central America. Both markers revealed that genetic divergence between the two species is of the same magnitude as that among provenances of E. oleifera. This finding is in discrepancy with the supposed early tertiary separation of the two species.

  9. Widespread utility of highly informative AFLP molecular markers across divergent shark species.

    Science.gov (United States)

    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.

  10. Statistical analysis of the associations between phenolic monoterpenes and molecular markers, AFLPs and SAMPLs in the spice plant Oregano

    Directory of Open Access Journals (Sweden)

    Azizi Ali

    2016-06-01

    Full Text Available Introduction: Molecular markers are the examples of the contribution of genome technology to medicinal plant breeding through marker-assisted selection (MAS for pharmaceutical quality.

  11. AFLP molecular marker of Salix spp.based on apillary electrophoresis%基于毛细管电泳的柳树AFLP分子标记研究

    Institute of Scientific and Technical Information of China (English)

    吕金辉; 胡建军; 卢孟柱

    2012-01-01

    为构建柳树遗传图谱、进行分子育种等奠定基础,以柳树为材料,基于毛细管电泳技术体系建立并优化了AFLP分子标记技术,简化了AFLP分析流程。首先提取高质量的柳树基因组DNA,对基因组进行酶切与接头连接、预扩增和选择性扩增,最后通过毛细管电泳分析各因素的影响。基因组DNA提取采用改进的CTAB法,酶切模板DNA用量450ng,EcoRⅠ酶切2h,MseⅠ酶切2h,接头过夜连接,选择性扩增时dNTP浓度0.3mmol/L,Mg2+浓度1.5mmol/L,引物浓度0.125μmol/L,DNA聚合酶浓度0.025U/μL,预扩增产物最适稀释倍数20倍。经过重复实验,证明建立的AFLP-毛细管反应体系适用于柳树AFLP分析。%In this paper,we established and optimized the AFLP molecular marker technology of Salix spp.based on capillary electrophoresis as well as simplify analysis flow of AFLP in order to construct Salix spp.linkage mapping and the implement of molecular breeding.First,the high-quality genomic DNA was extracted for AFLP analysis.Then the genomic DNA was completely digested by restriction enzyme and ligased with oligonucleotide adapters successfully.We got the products via pre-amplification and selective amplification.At last,the selective amplification products were analyzed by capillary electrophoresis.Results showed that improved CTAB method was selected to extract genomic DNA,450 ng of genomic DNA was used in digestion with EcoRⅠ and MseⅠ for 2 hours respectively,and ligased overnight.In selective amplification,0.3 mmol/L dNTP,1.5 mmol/L Mg2+,0.125 μmol/L primers,0.025 U/μL polymerase and 20 times dilution of pre-amplification products were desirable.Through many repeats,this system has been proved to be feasible in Salix spp.AFLP-capillary electrophoresis analysis.

  12. Genetic diversity of Cuban pineapple germplasm assessed by AFLP Markers

    Directory of Open Access Journals (Sweden)

    Ermis Yanes Paz

    2012-01-01

    Full Text Available The Cuban pineapple germplasm collection represents the genetic diversity of pineapple cultivated in that country and includes other important genotypes obtained from the germplasm collections in Brazil and Martinique. The collection has previously been characterized with morphological descriptors but a molecular characterization has been lacking. With this aim, 56 six genotypes of A. comosus and one of Bromelia pinguin were analyzed with a total of 191 AFLP markers. A dendrogram that represents the genetic relationships between these samples based on the AFLP results showed a low level of diversity in the Cuban pineapple collection. All Ananas comosus accessions, being the majority obtained from farmers in different regions in Cuba, are grouped at distances lower than 0.20. Molecular characterization was in line with morphological characterization. These results are useful for breeding and conservation purposes.

  13. Study on the sex-related AFLP marker of the Yangtze finless porpoise

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The sex-related molecular marker of the Yangtze finless porpoise was screened using Amplified Fragment Length Polymorphism (AFLP) technique combined with the bulked segregant analysis. Totally 36 AFLP primer combinations were used to detect the genome DNA bulks of the female and male porpoises, and one sex-related AFLP marker was finally obtained. The marker can be applied to sex identification, and provides a base for further cloning of sex-related genes and analyzing of Y chromosome haplotypes of the Yangtze finless porpoise.

  14. AFLP marker linked to water-stress-tolerant bulks in barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    A. Altinkut

    2003-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP assay is an efficient method for the identification of molecular markers, useful in the improvement of numerous crop species. Bulked Segregant Analysis (BSA was used to identify AFLP markers associated with water-stress tolerance in barley, as this would permit rapid selection of water-stress tolerant genotypes in breeding programs. AFLP markers linked to water-stress tolerance was identified in two DNA pools (tolerant and sensitive, which were established using selected F2 individuals resulting from a cross between water-stress-tolerant and sensitive barley parental genotypes, based on their paraquat (PQ tolerance, leaf size, and relative water content (RWC. All these three traits were previously shown to be associated with water-stress tolerance in segregating F2 progeny of the barley cross used in a previous study. AFLP analysis was then performed on these DNA pools, using 40 primer pairs to detect AFLP fragments that are present/absent, respectively, in the two pools and their parental lines. One separate AFLP fragment, which was present in the tolerant parent and in the tolerant bulk, but absent in the sensitive parent and in the sensitive bulk, was identified. Polymorphism of the AFLP marker was tested among tolerant and sensitive F2 individuals. The presence of this marker that is associated with water-stress tolerance will greatly enhance selection for paraquat and water-stress tolerant genotypes in future breeding programs.

  15. Molecular characterization of cultivated species of the genus Pachyrhizus Rich. ex DC. by AFLP markers

    DEFF Research Database (Denmark)

    Santayana, Monica; Rossel, Genoveva; Núñez, Jorge;

    2014-01-01

    Yam beans (Pachyrhizus DC.) are legume root crops that have attracted scientific interest because of high contents of starch, protein, and iron in their roots. In this study, 58 accessions of three cultivated Pachyrhizus species were characterized by amplified fragment length polymorphism (AFLP) ...

  16. Association of AFLP and SSR markers with agronomic and fibre quality traits in Gossypium hirsutum L.

    Indian Academy of Sciences (India)

    Arunita Rakshit; S. Rakshit; J. Singh; S. K. Chopra; H. S. Balyan; P. K. Gupta; Shripad R. Bhat

    2010-08-01

    Molecular markers linked to QTL contributing to agronomic and fibre quality traits would be useful for cotton improvement. We have attempted to tag yield and fibre quality traits with AFLP and SSR markers using F2 and F3 populations of a cross between two Gossypium hirsutum varieties, PS56-4 and RS2013. Out of 50 AFLP primer combinations and 177 SSR primer pairs tested, 32 AFLP and four SSR primers were chosen for genotyping F2 individuals.Marker-trait associations were studied for eight agronomic and five fibre quality traits through simple and multiple regression analysis (MRA) using a set of 92 AFLP polymorphic loci and four SSR markers. Simple linear regression analysis (SLRA) identified 23 markers for eight different traits whereas multiple regression analysis identified 30 markers for at least one of the 13 traits. SSR marker BNL 3502 was consistently identified to be associated with fibre strength. While all the markers identified in SLRA were also detected in MRA, as many as 16 of the 30 markers were identified to be associated with respective traits in both F2 and F3 generations. The markers explained up to 41 per cent of phenotypic variation for individual traits. A number of markers were found to be associated with multiple traits suggesting clustering of QTLs for fibre quality traits in cotton.

  17. Variabilidade genética de Colletotrichum guaranicola usando marcadores AFLP Variability of Colletotrichum guaranicola using AFLP markers

    Directory of Open Access Journals (Sweden)

    Jânia Lilia da Silva Bentes

    2011-01-01

    Full Text Available Foi detectada a variabilidade genética de vinte isolados de Colletotrichum guaranicola (Albuq. provenientes de diferentes localidades produtoras de guaraná no Amazonas, utilizando-se marcadores moleculares AFLP. Foi possível separar os isolados em dois grupos. O coeficiente de variação genética entre os isolados foi de 0,0216 e a similaridade genética foi de 94,95%, confirmando que os isolados pertencem à mesma espécie, no entanto, foi observada variabilidade intra-específica.The genetic variability of twenty Colletotrichum guaranicola (Albuq. isolates from different fields of guarana in Amazonas, was studied using molecular AFLP markers. The isolates were separated into two groups. The genetic variability coefficient was 0.0216 and the genetic similarity was 94.5%, confirming that the isolates belongs to the same species, however, an intra-specific variability was observed.

  18. Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

    Directory of Open Access Journals (Sweden)

    Bianca W. Bertoni

    2010-01-01

    Full Text Available Jacaranda decurrens (Bignoniaceae is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD and amplified fragment length polymorphism (AFLP. Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2% polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006 between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.

  19. Discussion on AFLP Molecular Markers in Piper methysticum and Pepper%卡瓦胡椒及胡椒的AFLP分子标记探讨

    Institute of Scientific and Technical Information of China (English)

    施江; 辛莉; 杨彦; 郑学勤

    2007-01-01

    The aim of the research was to discuss the genetic relationships between Pier methysticum.Pepper and other wild species in Pepper genus.DNA Was extracted from leaves which belonged tp 28 germplasras including 6 materials of P. methysticum,21 ma+ erials of cultivated and wild Pepper,1 material of Peperomia pellucida belonged to different genus.Premiers with good band-type and high polymorphism and resolution were selected from 64 pairs of Drimers for AFLP amplification and the clustering analysis was conducted with MVSP3.13f software.191 bands were amplified by 4 pairs of premiers,189 of which had polymorphism,being 98.6%. 28 germplasms were classified into 6 different groups al the genetic similarity coefficient of 0.52 by silver staining AFLP,in which 6 materials of Piper methysticum were clustered into a single group,indicating that P. methysticum belonged to Pepper family of Pepper genus but were distantly related to the others.The research provided the basis for selecting rootstocks for P. methysticum graft,molecular identification of P. methysticum and the fingerprint construction of P.methysticum.

  20. Genetic Relationships among Prunus mume var. pendula Using AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    Ming Jun; Zhang Qixiang; Ru Guangxin; Mao Qingshan; Yan Xiaolan; Lan Yanping

    2003-01-01

    Genetic relationships among Prunus mume var. pendula were studied by using AFLP markers. 18 accessions representing 14 cultivars ofPrunus murne var. pendula were selected from the germplasm collection at the Research Center of China Mci Flower. Seven Mse I-EcoR I AFLP primer combinations revealed 450 legible bands, and 269 of which were polymorphic markers. A similarity matrix was prepared using the simple matching coefficient of similarity and Nei's (72) distance coefficient. A UPGMA dendrogram demonstrated the genetic relationships of the cultivars. The information given by AFLP markers was basically consistent with the morphological classification and the evolutionary history of the morphotypes, and roughly supported the new revised classification system for Chinese Mci Cultivars. But there were still several exceptions: 1) the 'Guhong Chuizhi' inserted between the 'Tiaoxue Chuizhi' and the 'Danfen Chuizhi'; 2) the 'Wufu Chuizhi' kept off the Pink Pendant Form, and the 'Moshan Chuizhi' was removed from Viridiflora Pendant Form; 3) the 'Danbi Chuizhi' and the 'Shuangbi Chuizhi' of Viridiflora Pendant Form got together well but fell within the Pink Pendant Form.

  1. Genetic linkage map of Brassica campestris L. Using AFLP and RAPD markers

    Institute of Scientific and Technical Information of China (English)

    卢钢; 曹家树; 陈杭

    2002-01-01

    A genetic linkage map comprised of 131 loci was constructed with an F2 population derived from an inter-subspecific cross between Brassica 'qisihai'. The genetic map included 93 RAPD loci, 36 AFLP loci and 2 morphological loci organized into 10 main linkage groups (LGs) and 2 small groups, covering 1810.9cM with average distance between adjacent markers being approximately 13.8cM. The map is suitable for identification of molecular markers linked to important agronomic traits, QTL analysis, and even for marker-assisted selection in breeding programs of Chinese cabbage and turnip.

  2. Evolutionary analysis of allotetraploid hybrids of red crucian carp × common carp,based on ISSR,AFLP molecular markers and cloning of cyclins genes

    Institute of Scientific and Technical Information of China (English)

    LIU LiangGuo; YAN JinPeng; LIU ShaoJun; LIU Dong; YOU CuiPing; ZHONG Huan; TAO Min; LIU Yun

    2009-01-01

    The allotetraploid hybrids of red crucian carp × common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate.Using ISSR and AFLP markers and the cyclins genes,the genomes and cyclin gene sequence changes were analyzed between the allotetraploid hybrids and their parents.The results indicated that the allotetraploids inherited many genetic characteristics from their parents and the genetic characteristics were stable after 15 generations.However,the allotetraploids had a closer genetic relationship with their original female parents and represented a bias toward the maternal progenitor.DNA fingerprinting analysis showed that the allotetraploids had undergone sequences deletion from their original parents and that the deleted sequences were mostly from the male parent's genome.Some non-parental bands were found in the allotetraploid hybrids.Sequences analysis of the cyclin A1 and B1 genes showed nonsynonymous substitutions of single nucleotides in codons that were different from their original parents,leading to non-parental amino acid loci.We speculate that the non-additivity in the allotetraploids,compared with their progenitors,could be an adjustment to the genomic shock from heterozygosity and polyploidy, allowing maintenance of genetic stability.

  3. Comparison Between AFLP and RFLP Markers in Detecting the Diversity of Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    CHEN Liang; LIANG Chun-yang; SUN Chuan-qing; JIN De-min; JIANG Ting-bo; WANG Bin; WANG Xiang-kun

    2002-01-01

    AFLP and RFLP were used to study the diversity of 20 rice cultivars. 15 primer combinations were used in the AFLP analysis and 47 - 118 bands were amplified in each lane. A total of 107 polymorphic bands were detected in the RFLP analysis using 49 RFLP probes. The cluster analysis based on RFLP data showed that 20 rice cultivars could be divided into an indica group and a japonica group, as did the AFLP data; however AFLP is more suitable in detecting the difference of pedigree and ecotype among the 20 cultivars.The genetic distance based on AFLP and RFLP data showed the same tendency, but AFLP markers increased the measure of genetic distance among intra-subspecific cultivars and decreased the measure of genetic distance among inter-subspecific cultivars relative to RFLP markers. That indicated that AFLP is more suitable than RFLP in the diversity study and RFLP is more suitable to study the indica-japonica differentiation of cultivars.

  4. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers.

    Science.gov (United States)

    Ferriol, M; Picó, B; Nuez, F

    2003-07-01

    Cucurbita pepo is a highly polymorphic species. The cultivars can be grouped into eight morphotypes in two subspecies, ssp. pepo and ssp. ovifera. A collection of 69 accessions representative of the morphotypes and some unclassified types was used for analysing the morphological and molecular diversity of this species. This collection includes commercial cultivars and Spanish landraces, which represent the great diversification of types that have arisen in Europe after this species arrived from America. For the molecular variability studies, two PCR-based systems were employed, AFLP and SRAP, which preferentially amplify ORFs. Principal coordinates analysis and cluster analysis using the UPGMA method clearly separate the accessions into the two subspecies through the use of both markers. However, the gene diversity and the genetic identity values among morphotypes and subspecies varied between the two marker systems. The information given by SRAP markers was more concordant to the morphological variability and to the evolutionary history of the morphotypes than that of AFLP markers. In ssp. ovifera, the accessions of the different morphotypes were basically grouped according to the fruit colour. This may indicate different times of development and also the extent of breeding in the accessions used. This study has allowed identification of new types that can be employed for the development of new cultivars. The landraces of the spp. ovifera, used as ornamental in Europe, have proved to be of great interest for preserving the diversity of C. pepo.

  5. Genetic linkage map of Brassica campestris L.using AFLP and RAPD markers

    Institute of Scientific and Technical Information of China (English)

    卢钢; 陈杭; 等

    2002-01-01

    A genetic linkage map comprised of 131 loci was constructed with an F2 population derived from an inter-subspecific cross between Brassica campestris L.ssp.chinensis cv.aijiaohang” and ssp.rapifera cv.,”'isihai”.The genetic map included 93 RAPD loci,36 AFLP loci and 2 morphological loci organized into 10 main linkage groups(LGs) and 2 small groups,covering 1810.9cM with average distance between adjacent markers being approximately 13.8cM.The map is suitable for identification of molecular markers linked to important agronomic traits.QTL analysis,and even for marker-assisted selection in breeding programs of Chinese cabbage and turnip.

  6. 中国野生芒果种质资源及其AFLP分子标记%The Wild Mango Germplasm Resources in China and Their AFLP Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    雷新涛; 姚全胜; 徐雪荣; 王家保

    2009-01-01

    从生物学特性和AFLP标记两个方面对中国广西百色那坡县野生芒果资源进行了初步描述和研究.结果表明:那坡县野生芒果在形态学上与普通芒果较为相似;AFLP标记显示,包括部分栽培品种、林生芒果、广西百色那坡县野生芒果、泰国芒果等在内的92份芒果种质在相似系数0.63的水平上可分为14组,广西百色那坡县野生芒果虽然与林生芒果、泰国野生芒果等芒果属其它种较为接近,但仍处于栽培芒果的中间.不能与栽培芒果分开.这些证据表明分布在广西百色那坡县平盂镇的野生芒果属于普通芒果,可能是栽培芒果的野生种而不是芒果属的其它种.%The genus Mangifera contains 69 species. It is worthwhile to explore the origin of Mangifera indica. In this context the wild mango germplasm at Lapuo County, Guangxi, China were studied by using their biological characteristics and the amplified fragments length polymorphism (AFLP) molecular marker. These wild mangoes were found morphologically similar to Mangifera indica; and the AFLP markers showed that at the similarity coefficient of 0.63, 92 mangoes including cultivars, Mangifera sylvatica Roxb., wild mangoes, Mangifera. Siamensis Warbg. were divided into 14 groups and that the wild mangoes at Lapuo were close to M. sylvatica Roxb. and M. siamensis Warbg., but remained to fall in the middle of the cultivars and could not be separated from them. These evidences indicated that the wild mangoes belonged to M. indica, not other species of the genus Mangifera, and might be the wild species of the cultivar mangoes.

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

    Directory of Open Access Journals (Sweden)

    Víctor Pecina‑Quintero

    2012-08-01

    Full Text Available 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 revealed robust amplification profiles and were able to differentiate the 41 genotypes of sweet sorghum evaluated. Analysis of the frequency and distribution of polymorphic fragments allowed for the detection of unique (AFLP and rare (SSR alleles in several genotypes (RBSS‑8, RBSS‑9, RBSS‑25, RBSS‑32, and RBSS‑37, indicating that these markers may be associated with a feature that has not yet been determined or may be useful for the identification of these genotypes. The genetic relationships indicated the presence of at least two types of sweet sorghum: a group of modern genotypes used for sugar and biofuel production, and another group consisting of historic and modern genotypes used for the production of syrups. Sweet sorghum genotypes may be used to develop new varieties with higher sugar and juice contents.

  8. Chromosome landing at the ¤Mla¤ locus in barley (¤Hordeum vulgare¤ L.) by means of high-resolution mapping with AFLP markers

    DEFF Research Database (Denmark)

    Schwarz, G.; Michalek, W.; Mohler, V.

    1999-01-01

    to construct a high-resolution map of the Mla region. A fluorescence-based AFLP technique and bulked segregant analysis were applied to screen for polymorphic, tightly linked AFLP markers, Three AFLP markers were selected as suitable for a chromosome-landing strategy. One of these AFLP markers and a closely...

  9. Genetic diversity revealed by AFLP markers in Albanian goat breeds

    Directory of Open Access Journals (Sweden)

    Hoda Anila

    2012-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei’s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright’s FST index, Nei’s unbiased genetic distance and Reynolds’ genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds’ genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard’s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

  10. The molecular characterization of maize B chromosome specific AFLPs

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The origin and evolution of B chromosomes could be explained by the specific DNA sequence on them.But the specific sequences known were quite limited. To investigate maize B chromosome sqicific DNA sequeces, maize genomes with and without B chromosomes were analyzed by AFLP. Only 5 markers were found specific to genomes with B chromosomes among about 2000 AFLP markers. Southern hybridization and sequence analysis revealed that only the sequence of M8-2D was a B chromosome specific sequence.This sequence contained the telomeric repeat unit AGGGTTT conserved in plant chromosome telomeres.In addition, the sequence of M8-2D shared low homology to clones from maize chromosome 4 centromere as well. M8-2D were localized to B chromosome centromeric and telomeric regions.

  11. AFLP markers for the assessment of genetic diversity in european and North American potato varieties cultivated in Iran

    Directory of Open Access Journals (Sweden)

    Saeed Tarkesh Esfahani

    2009-01-01

    Full Text Available Information about the genetic diversity of potato germplasm in Iran is important for variety identification andto enhance the classification of germplasm collections and exploit them in breeding programs and for the development andintroduction of new varieties. AFLP fingerprinting was applied to a group of cultivated potato varieties to find if there is anygeographical differentiation in potato diversity from Europe and North America. The high level of polymorphism within potatovarieties and the high number of variety-specific bands suggest that AFLPs are powerful markers for diversity analysis inpotato varieties. No region-specific AFLP markers were found (present in varieties from the same origin and absent inothers. The UPGMA dendrogram revealed four distinct clusters corresponding almost to the geographical origin of thevarieties. However, the bootstrap support for branches was rather weak. No clusters clearly distinguished varieties fromEurope and North America. Varieties from the same geographical origins however tended to group together within eachcluster. The mean similarity and the UPGMA dendrogram both suggest that North American varieties have nearly identicalgenetic diversity to European varieties. The results of AMOVA revealed large within-region variations which accounted for94.5% of the total molecular variance. The between-region variation, although accounting for only 5.5% of the total variation,was statistically significant. AFLP technology was successfully used to evaluate diversity between different geographicalgroups of potatoes and is recommended for potato genetic studies.

  12. Identification of AFLP and STS markers closely linked to the def locus in pea.

    Science.gov (United States)

    von Stackelberg, M; Lindemann, S; Menke, M; Riesselmann, S; Jacobsen, H-J

    2003-05-01

    The recessive mutation of the def gene of pea (Pisum sativum L.) leads to the loss of the hilum, the abscission zone between the seed and the pod. Thereby, it reduces the free dispersal of the seeds through pod shattering. As a prerequisite for a gene isolation via a map-based cloning approach, bulked segregant analysis followed by single plant analyses of over 200 homozygous individuals of a population of 476 F2 plants derived from a cross between 'DGV' (def wild-type) and 'PF' (def mutant), were used to detect markers closely linked to the def locus. The AFLP technique in combination with silver staining was used to maximize numbers of reproducible marker loci. Fifteen AFLP loci showed a genetic distance less than 5 and two of them less than 1 centiMorgans (cM) to the gene of interest. AFLPs were converted into sequence tagged sites (STSs) and into a newly refined AFLP-based single locus marker named the 'sequence specified AFLP' (ssAFLP).

  13. A Genetic Linkage Map of Brassica rapa Based on AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jian-jun; WANG Xiao-wu; Guusje Bonnema; SUN Ri-fei; XU Ze-yong; Dick Vreugdenhi; Maarten Koornneef

    2005-01-01

    A F2 mapping population was developed by crossing a Chinese cabbage-pe-tsai variety CC156 and an oil type Rapid cycling RC144 which were different from each other in morphology, maturity, self-compatibility, plant height, etc. Using 244 AFLP markers a map was constructed containing 10 main linkage groups covering a total distance of 857 cM,corresponding to 3.5 cM per marker. Length of linkage groups varied from 43 to 125 cM and the number of AFLP markers linkage to each group ranged from 7 to 41.

  14. Isolation, cloning and sequencing of AFLP markers related to disease-resistance traits in Fenneropenaeus chinensis

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Amplified fragment length polymorphisms (AFLP) technique was used to analyze the fingerprinting of four successive generations of Fenneropenaeus chinensis to reveal their disease-resistance traits. Some loci showed quite different genetic frequencies due to artificial selection, which implied that these fragments were putative markers related to the disease-resistance trait. We developed a simple and effective method to further characterize these AFLP fragments. Specific AFLP bands were cut directly from polyacrylamide gels,re-amplified, cloned and sequenced. Eight putative genetic markers were sequenced and their sizes ranged from 63 to 209 bp. The sequences were submitted to dbGSS (database of Genome Sequence Survey); and the BLAST analysis showed low similarity to the function genes, indicating these markers were tightly linked to a disease-resistance trait but were not functional genes.

  15. Genetic structure and distribution of pythium aphanidermatum populations in Pennsylvania greenhouses based on analysis of AFLP and SSR markers.

    Science.gov (United States)

    Lee, Seonghee; Garzón, Carla D; Moorman, Gary W

    2010-01-01

    Pythium aphanidermatum is one of the most aggressive species in the genus and has a wide host range, but little is known about its population genetic structure. We tested 123 P. aphanidermatum isolates with six AFLP primer combinations and four SSR markers. The genetic diversity of P. aphanidermatum was 0.34 with AFLP and 0.55 with SSR markers. SSR genotypes totaled 3-8 for each locus, and a total of 14 SSR genotypes were found among all isolates. Three major genetic groups were identified with the combination of AFLP and SSR marker data. The genetic structure observed among P. aphanidermatum isolates was related to location and mefenoxam fungicide resistance instead of host. Four genotypes (PA1, PA2, PA5 and PA7) were found in the population from a commercial greenhouse, and the genetic diversity of a greenhouse population was similar to that found in the whole sample. The molecular tools for P. aphanidermatum isolates identified the possible gene flow within and among populations in Pennsylvania greenhouses.

  16. Association of AFLP and SCAR markers with common leafspot resistance in autotetraploid alfalfa (Medicago sativa).

    Science.gov (United States)

    Wang, Y; Bi, B; Yuan, Q H; Li, X L; Gao, J M

    2012-03-14

    To identify amplified fragment length polymorphism (AFLP) markers associated with resistance or susceptibility of alfalfa to common leafspot (CLS) caused by the fungus Pseudopeziza medicaginis (Dermateaceae), bulked segregant analysis was conducted based on an F(1(M × M)) population of 93 plants and a BC(1)S population of 91 plants. Three AFLP markers, ACTCAA(R206), TAGCAC(R185), and GGACTA(S264), were found to be associated with CLS resistance or susceptibility. All three markers were found at significantly different frequencies (71.9, 80.3 and 91.8%) compared to resistant or susceptible plants in the original population. Subsequently, these three AFLP markers were converted into three SCAR markers, ACTCAA(R136), TAGCAC(R128) and GGACTA(S254), which are easier to employ in breeding programs. The three SCAR markers were used in a randomly selected population with 50% resistance; the probability of finding one resistant plant was increased to 67.3, 66.7 and 90.0% with markers ACTCAA(R136), TAGCAC(R128) and GGACTA(S254), independently. If two of the SCAR markers were used simultaneously, the probability would be higher than 89%. The three SCAR markers identified in this study would be applicable for selection for CLS resistance in alfalfa breeding programs. Moreover, the genetic analysis indicated that CLS resistance in alfalfa is conferred by a single dominant gene.

  17. Using AFLP markers and the Geneland program for the inference of population genetic structure

    DEFF Research Database (Denmark)

    Guillot, Gilles; Santos, Filipe

    2010-01-01

    The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how the comp......The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how...... such as single nucleotide polymorphisms (SNP) markers but this difference becomes negligible for data sets of common size (number of individuals n≥100, number of markers L≥200). The latest Geneland version (3.2.1) handling dominant markers is freely available as an R package with a fully clickable graphical...

  18. AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu stricto (Solanaceae)

    NARCIS (Netherlands)

    Manoko, M.L.K.; Berg, R.G. van den; Feron, R.M.C.; Weerden, G.M. van der; Mariani, C.

    2007-01-01

    This study was aimed at examining the relationships between the African material of Solanum americanum (also designated as S. nodiflorum), accessions of this taxon from other geographical areas, and American S. americanum using AFLP markers. 96 individuals representing 39 accessions of S. americanum

  19. AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu strictio (Solanaceae)

    NARCIS (Netherlands)

    Manoko, M.L.K.; Berg, van den R.G.; Feron, R.M.C.; Weerden, van der G.M.; Mariani, C.

    2007-01-01

    This study was aimed at examining the relationships between the African material of Solanum americanum (also designated as S. nodiflorum), accessions of this taxon from other geographical areas, and American S. americanum using AFLP markers. 96 individuals representing 39 accessions of S. americanum

  20. Genetic Relationships of Aglaonema Species and Cultivars Inferred from AFLP Markers

    OpenAIRE

    Chen, Jianjun; DEVANAND, PACHANOOR S.; Norman, David J; HENNY, RICHARD J.; CHAO, CHIH‐CHENG T.

    2004-01-01

    • Background and Aims Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers.

  1. A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatelite markers

    NARCIS (Netherlands)

    Hanley, S.; Barker, J.H.A.; Ooijen, van J.W.; Aldam, C.; Harris, S.L.; Ahman, I.; Larsson, S.; Karp, A.

    2002-01-01

    The genus Salix (willow) contains a number of species of great value as biomass crops. Efforts to breed varieties with improved biomass yields and resistances to pests and diseases are limited by the lack of knowledge on the genetic basis of the traits. We have used AFLP and microsatellite markers t

  2. Genetic structure of Pilosocereus gounellei (Cactaceae) as revealed by AFLP marker to guide proposals for improvement and restoration of degraded areas in Caatinga biome.

    Science.gov (United States)

    Monteiro, E R; Strioto, D K; Meirelles, A C S; Mangolin, C A; Machado, M F P S

    2015-12-15

    Amplified fragment length polymorphism (AFLP) analysis was used to evaluate DNA polymorphism in Pilosocereus gounellei with the aim of differentiating samples grown in different Brazilian semiarid regions. Seven primer pairs were used to amplify 703 AFLP markers, of which 700 (99.21%) markers were polymorphic. The percentage of polymorphic markers ranged from 95.3% for the primer combination E-AAG/M-CTT to 100% for E-ACC/M-CAT, E-ACC/M-CAA, E-AGC/M-CAG, E-ACT/M-CTA, and E-AGG/M-CTG. The largest number of informative markers (126) was detected using the primer combination E-AAC/M-CTA. Polymorphism of the amplified DNA fragments ranged from 72.55% (in sample from Piauí State) to 82.79% (in samples from Rio Grande Norte State), with an average of 75.39%. Despite the high genetic diversity of AFLP markers in xiquexique, analysis using the STRUCTURE software identified relatively homogeneous clusters of xiquexique from the same location, indicating a differentiation at the molecular level, among the plant samples from different regions of the Caatinga biome. The AFLP methodology identified genetically homogeneous and contrasting plants, as well as plants from different regions with common DNA markers. Seeds from such plants can be used for further propagation of plants for establishment of biodiversity conservation units and restoration of degraded areas of the Caatinga biome.

  3. A new image of plantain diversity assessed by SSR, AFLP and MSAP markers.

    Science.gov (United States)

    Noyer, J L; Causse, S; Tomekpe, K; Bouet, A; Baurens, F C

    2005-05-01

    Using both SSR and AFLP markers, the genetic diversity of 30 plantains constituting a representative sample of the phenotypic diversity was assessed. The results confirmed a very narrow genetic base of this cultivar group. SSR and AFLP data support the hypothesis that these cultivars may have arisen from vegetative multiplication of a single seed. MSAP were used to survey cytosine methylation status at CCGG sites in order to obtain an alternative source of diversity data. A higher degree of polymorphism was revealed allowing the classification of the samples into three clusters. No correlation was observed between the phenotypic classification and methylation diversity. Implications for breeding programs are discussed.

  4. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  5. Identification of AFLP Markers Linked to Lr19 Resistance to Wheat Leaf Rust

    Institute of Scientific and Technical Information of China (English)

    LI Xing; YANG Wen-xiang; LI Ya-ning; LIU Da-qun; YAN Hong-fei; MENG Qing-fang; ZHANG Ting

    2007-01-01

    AFLP analyses were carried out on Thatcher, 23 near-isogenic lines and F2 generation of TcLrl9 × Thatcher, to develop molecular markers for gene Lr19 resistance to wheat leaf rust. Seven markers linked to Lr19 resistance trait were obtained,which were P-AGT/M-GAG289 bp (3.3 cM), P-ACA/M-GGT102 bp (4.1 cM), P-ACA/M-GGT106 bp (4.1 cM), P-AAC/M-CAG123 bp(4.9 cM), P-AAC/M-GGT203 bp (5.0 cM), P-ACA/M-GGT290 bp (5.7 cM), and P-ATC/M-GAG293 bp (9.6 cM). All of these specific fragments were isolated from the polyacrylamide gels, reamplified, cloned, and sequenced. The research may facilitate genetic mapping, physical mapping, and the eventual cloning of Lr19.

  6. Molecular characterisation of Aspergillus flavus isolates from peanut fields in India using AFLP

    Directory of Open Access Journals (Sweden)

    Diwakar Singh

    2015-09-01

    Full Text Available Aflatoxin contamination of peanut, due to infection by Aspergillus flavus, is a major problem of rain-fed agriculture in India. In the present study, molecular characterisation of 187 Aspergillus flavus isolates, which were sampled from the peanut fields of Gujarat state in India, was performed using AFLP markers. On a pooled cluster analysis, the markers could successfully discriminate among the ‘A’, ‘B’ and ‘G’ group A. flavus isolates. PCoA analysis also showed equivalent results to the cluster analysis. Most of the isolates from one district could be clustered together, which indicated genetic similarity among the isolates. Further, a lot of genetic variability was observed within a district and within a group. The results of AMOVA test revealed that the variance within a population (84% was more than that between two populations (16%. The isolates, when tested by indirect competitive ELISA, showed about 68.5% of them to be atoxigenic. Composite analysis between the aflatoxin production and AFLP data was found to be ineffective in separating the isolate types by aflatoxigenicity. Certain unique fragments, with respect to individual isolates, were also identified that may be used for development of SCAR marker to aid in rapid and precise identification of isolates.

  7. Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.).

    Science.gov (United States)

    Ipek, Meryem; Ipek, Ahmet; Simon, Philipp W

    2006-10-01

    Linkage mapping and genetic diversity studies with DNA markers in plant species assume that comigrating bands are identical, or at least that they have homologous sequences. To test this assumption in a plant with a large genome, sequence identities of 7 polymorphic amplified fragment length polymorphism (AFLP) markers of garlic, previously used to estimate similarity in genetic diversity studies, were characterized. Among 37 diverse garlic clones, 87 bands from these 7 polymorphisms were excised, amplicons were cloned, and 2 to 6 colonies were sequenced from each band, to yield a total of 191 DNA amplicons. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band; only 4 bands contained amplicons with little homology to the same-sized amplicons of other garlic clones. Of these 83 bands, 64 (73.6%) contained only highly homologous amplicons (>90% sequence identity), whereas 19 (21.8%) contained both homologous and nonhomologous amplicons, with sequence identities less than 60%. Of the 37 nonhomologous amplicons identified, 25 (67.5%) differed in length from other amplicons in the band. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones, making them useful for developing simple PCR-based markers in genetic mapping and diversity assessment.

  8. Comparative analysis of genetic diversity in sacred lotus (Nelumbo nucifera Gaertn.) using AFLP and SSR markers.

    Science.gov (United States)

    Hu, Jihong; Pan, Lei; Liu, Honggao; Wang, Shuzhen; Wu, Zhihua; Ke, Weidong; Ding, Yi

    2012-04-01

    The sacred lotus (Nelumbo nucifera Gaertn.) is an aquatic plant of economic and ornamental importance in China. In this study, we developed twenty novel sacred lotus SSR markers, and used AFLP and SSR markers to investigate the genetic diversity and genetic relationships among 58 accessions of N. nucifera including 15 seed lotus, 12 rhizome lotus, 24 flower lotus and 7 wild lotus. Our results showed that sacred lotus exhibited a low level of genetic diversity, which may attribute to asexual reproduction and long-term artificial selection. A dendrogram based on both AFLP and SSR clustering data showed that: (1) the seed lotus accessions and rhizome lotus accessions were distinctly clustered into different groups, which indicated the significant genetic differentiation between them. This may be attributed to the two modes of reproduction and lack of genetic exchange; (2) the accessions of Thailand wild lotus were separated from other wild lotus accessions. This implied that the Thailand lotus might be genetically differentiated from other wild lotuses. In addition, Mantel test conducted gave highly significant correlation between AFLP-SSR data and each of the AFLP and SSR ones, with the values of r = 0.941 and r = 0.879, respectively, indicating the higher efficiency of the combination of these techniques (AFLP and SSR) in estimation and validation of the genetic diversity among the accession of sacred lotus. This knowledge of the genetic diversity and genetic relatedness of N. nucifera is potentially useful to improve the current strategies in breeding and germplasm conservation to enhance the ornamental and economic value of sacred lotus.

  9. AFLP Marker Linked to Turnip Mosaic Virus Susceptible Gene in Chinese Cabbage (Brassica rapa L.ssp.pekinensis)

    Institute of Scientific and Technical Information of China (English)

    HAN He-ping; SUN Ri-fei; ZHANG Shu-jiang; LI Fei; ZHANG Shi-fan; NIU Xin-ke

    2004-01-01

    Turnip mosaic virus (TuMV) which has several strains causes the most important virusdisease in Chinese cabbage in terms of crop damage. In China, Chinese cabbage is infectedby a mixture of strains, breeding of cultivar for the TuMV resistance has become themajor aim. Screening the molecular marker linked to the TuMV-resistance gene formolecular assisted selection is the major method to improve the breeding efficiency. Inthis study, we used AFLP technique and the method of bulked segregant analysis(BSA) tostudy the progeny of Brp0058 x Brp0108, and identified two DNA molecular marker linked toTurnip mosaic virus-resistance gene with a recombination frequency 7.5 cM and 8.4 cM.

  10. Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers

    Directory of Open Access Journals (Sweden)

    Sandra Bibiana Aguilar

    2007-01-01

    Full Text Available The Andean blackberry belongs to the genus Rubus, the largest of the Rosaceae family and one of the mostdiverse of the plant kingdom. In Colombia Rubus glaucus Benth, known as the Andean raspberry or blackberry, is one of thenine edible of the genus out of forty-four reported species. In this study wild and cultivated genotypes, collected in the CentralAndes of Colombia were analyzed by AFLP and SSR markers. Sexual reproduction seems to play an important role inmaintaining the genetic variability in R. glaucus, and the viability of using the SSR of Rubus alceifolius to characterizeColombian Rubus species was clearly demonstrated. All species evaluated produced very specific banding patterns,differentiating them from the others. Both AFLP and SSR produced bands exclusive to each of the following species: R.robustus, R. urticifolius, R. glaucus, and R. rosifolius. The SSR markers differentiated diploid and tetraploid genotypes of R.glaucus.

  11. AFLP and SRAP markers linked to the mj gene for root-knot nematode resistance in cucumber Marcadores AFLP e SRAP ligados ao gene mj para resistência a nematóides causadores de galhas em pepino

    Directory of Open Access Journals (Sweden)

    Zübeyir Devran

    2011-02-01

    Full Text Available Root-knot nematodes (Meloidogyne spp. are an important worldwide pest of cucumber (Cucumis sativus L.. Molecular markers linked to the Javanese root-knot nematode (M. javanica resistance gene mj in cucumber may aid marker assisted selection. One-hundred AFLP (EcoRI-MseI and 112 SRAP were used to screen resistant and susceptible parents for polymorphisms to develop molecular markers linked to the mj gene. Of the 100 AFLP primers, 92 produced bands and two yielded candidate markers (E-ATT/M-CAA and E-AAC/M-CTG. These two bands were cut off from polyacrylamide gel, cloned and sequenced. Primers designed from the sequences did not yield polymorphic bands between the parents. In addition, the sequences did not contain any restriction site or indel to be used to convert them to CAPS or SCAR markers. The two sequences obtained from polymorphic AFLP markers were used primarily to design D1F, D1R, D17F and D17R primers. SRAP forward and reverse primers were used in combination with these four specific primers to search for polymorphisms between parents. Of the 112 primer combinations 11 yielded polymorphisms between parents. MapMaker Exp 3.0 software was used to analyze the 11 markers. Two markers were identified that flanked the mj gene at distance of 16.3 and 19.3 cM. The results indicated that these markers should be useful to develop molecular markers flanking the mj gene.Nematóides causadores de galhas (Meloidogyne spp. em raízes de pepino Cucumis sativus L. são de ocorrência mundial. Marcadores moleculares ligados ao gene mj que confere resistência a M. javanica em pepino podem auxiliar na seleção de plantas em programas de melhoramento genético. Cem AFLP (EcoRI-MseI e 112 SRAP foram usados para a seleção de parentais resistentes e susceptíveis, por meio de polimorfismos, para o desenvolvimento de marcadores moleculares ligados ao gene mj. Entre 100 oligonucleotídeos iniciadores para AFLP, 92 geraram fragmentos amplificados de DNA e

  12. A genetic linkage map of quinoa ( Chenopodium quinoa) based on AFLP, RAPD, and SSR markers.

    Science.gov (United States)

    Maughan, P J; Bonifacio, A; Jellen, E N; Stevens, M R; Coleman, C E; Ricks, M; Mason, S L; Jarvis, D E; Gardunia, B W; Fairbanks, D J

    2004-10-01

    Quinoa ( Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines 'Ku-2' and '0654', a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F(2) mapping population. The genetic map is based on 80 F(2) individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations.

  13. Population genetic structure in Phyla scaberrima from Mexico and Colombia assessed by AFLP markers and implications for conservation.

    Science.gov (United States)

    Androcioli, L G; Ruas, E A; Rodrigues, L A; Ruas, C F; Perilla, H E R; Ruas, P M

    2015-12-02

    Phyla scaberrima (Verbenaceae) is a herbaceous perennial species that is distributed from Mexico (center of origin) to Colombia, growing in forest and swamp edges or grasslands from sea level up to an altitude of 1800 m. The chemical properties and uses in popular medicine have drastically affected the population size of this species. In this study, we investigated genetic variability in populations of P. scaberrima using AFLP markers. Three AFLP primer combinations rendered a total of 997 markers in a sample of 131 individuals from five populations, including two populations from Mexico and three from Colombia. The average percentage of polymorphic loci, gene diversity and Shannon-Wiener index were 46.62, 0.0695, and 0.119, respectively. Analysis of molecular variance showed that the distribution of the genetic variability within populations (85.41%) was higher than between groups (8.11%) and between populations (6.48%). Principal coordinate analysis and Bayesian analysis for the K number of clusters showed that the individuals were dispersed in five (K= 5) clusters. The low levels of genetic diversity observed in these populations demonstrated that the populations from Mexico and Colombia need urgent management to recover their genetic variability.

  14. A preliminary study for identification of candidate AFLP markers under artificial selection for shell color in pearl oyster Pinctada fucata.

    Science.gov (United States)

    Zou, Keshu; Zhang, Dianchang; Guo, Huayang; Zhu, Caiyan; Li, Min; Jiang, Shigui

    2014-05-25

    Pearl oyster Pinctada fucata is widely cultured to produce seawater pearl in South China, and the quality of pearl is significantly affected by its shell color. Thus the Pearl Oyster Selective Breeding Program (POSBP) was carried out for the shell color and growth traits. The black (B), gold (G), red (R) and white (W) shell strains with fast growth trait were achieved after five successive generation selection. In this study, AFLP technique was used to scan genome of four strains with different shell colors to identify the candidate markers under artificial selection. Eight AFLP primer combinations were screened and yielded 688 loci, 676 (98.26%) of which were polymorphic. In black, gold, red and white strains, the percentage of polymorphic loci was 90.41%, 87.79%, 93.60% and 93.31%, respectively, Nei's gene diversity was 0.3225, 0.2829, 0.3221 and 0.3292, Shannon's information index was 0.4801, 0.4271, 0.4825 and 0.4923, and the value of FST was 0.1805. These results suggested that the four different shell color strains had high genetic diversity and great genetic differentiation among strains, which had been subjected to the continuous selective pressures during the artificial selective breeding. Furthermore, six outlier loci were considered as the candidate markers under artificial selection for shell color. This study provides a molecular evidence for the inheritance of shell color of P. fucata.

  15. Marcadores fAFLP na caracterização de três genótipos de umezeiro selecionados como porta-enxertos para pessegueiro fAFLP markers to characterize three mume genotypes selected as rootstocks for peach tree

    Directory of Open Access Journals (Sweden)

    Ester Wickert

    2007-12-01

    Full Text Available O objetivo deste trabalho foi caracterizar a diversidade genética existente em três genótipos de umezeiro (Clone 05, cv. Rigitano e Clone 15 e identificar marcadores moleculares fAFLP (fluorescent Amplified Fragment Lenght Polymorphism passíveis de serem utilizados na discriminação dos três genótipos de umezeiro selecionados como porta-enxertos para pessegueiro. Foram utilizadas 24 diferentes combinações de primers seletivos fAFLP que geraram 648 marcas, das quais 272 foram diferenciadoras dos três genótipos entre si. As marcas diferenciadoras permitiram o agrupamento dos clones de umezeiro de acordo com sua similaridade através do Método da Distância e algorítmo Neighbour Joining. As mesmas marcas foram utilizadas para calcular a distância genética entre os clones. Com o uso de marcadores fAFLP foi possível discriminar os três genótipos de umezeiro entre si, destacando-se as combinações Fam ACT/CAT, Joe AGG/CTT e Ned AGC/CAA, que permitiram a diferenciação individual de cada um dos clones. A maior distância genética foi encontrada entre a cv. Rigitano e o Clone 15. Os marcadores fAFLP revelaram maior proximidade genética entre o Clone 05 e a cv. Rigitano.The objective of this work was the identification of fAFLP markers to be used in molecular characterization of three mume genotypes selected as rootstocks for peach tree. Twenty-four different fAFLP primer combinations were used and allowed the recognition of 648 markers, comprising 272 markers which were able to discriminate the three clones one from the other. These markers were used to calculate the groupment of the clones according to their similarities with the distance method and neighbour joining algorithm. The same markers were also used to calculate the genetic distance among the clones. The fAFLP markers were efficient to identify the clones, mainly by the combinations of selective primers Fam ACT/CAT, Joe AGG/CTT and Ned AGC/CAA. fAFLP markers allowed the

  16. 基于AFLP分子标记的核桃核心种质的构建%A Construction of the Core-Collection of Juglans regia L. Based on AFLP Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    王红霞; 赵书岗; 高仪; 玄立春; 张志华

    2013-01-01

    [目的]构建核桃核心种质以便更好地保存、评价和利用丰富的核桃种质资源。[方法]利用 AFLP 分子标记,对131份核桃原始种质采用逐步聚类法建立候选核心种质,比较不同候选核心种质的多态性位点数、多态性位点百分率,结合形态学指标及地理来源,最终确定核桃核心种质,并进行评价。[结果]建立的核桃核心种质保留了原始种质10%的样品,分别为河北的天桥1号、陕西的西洛2号和西林1号、山西的晋龙1号、山东的丰辉、辽宁的辽宁8号和辽73013、新疆的温185、河南的绿波、北京的北京746、美国引进品种维纳、日本引进品种清香和朝鲜的品种安边1号。根据遗传多样性评价结果,与原始种质相比,核心种质的多态性位点保留率为75.4%。[结论]构建的核桃核心种质能较大程度地代表原始种质的遗传信息,符合核心种质要求。%[Objective] Walnut is an important economic tree species in China, and its germplasm resources are very rich. There were many problems in the processing of germplasm preservation such as large area occupied, higher management costs, which brought great difficulties to the conservation, utilization and evaluation. Therefore, construction of walnut core collection is very important for preservation, study and application of Juglans regia L. germplasm resources.[Method]Based on AFLP markers, candidate core collections were constructed by using proportional strategy and UPGMA clustering sampling method within subgroups after dividing 131 Juglans regia germplasm into 45 subgroups. The core collection was eventually identified by comparison of the genetic diversity parameters of these candidate core collections, such as the number of polymorphic loci, percentage of polymorphic loci, and morphological indicators. [Result]The core collections including Tianqiao1 from Hebei province, Xiluo2 and Xilin1 from Shaanxi province, Jinglong1

  17. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-01-01

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future. PMID:27488242

  18. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers.

    Science.gov (United States)

    Arias, Marina; Hernandez, Monica; Remondegui, Naroa; Huvenaars, Koen; van Dijk, Peter; Ritter, Enrique

    2016-08-04

    Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.

  19. Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers.

    Directory of Open Access Journals (Sweden)

    Licia Colli

    Full Text Available BACKGROUND: During the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection. METHODOLOGY/PRINCIPAL FINDINGS: Landscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with Matsam software, based on a correlative approach (SAM, and with Mcheza and Bayescan, two FST based software able to detect markers carrying signatures of natural selection. Matsam identified four loci possibly under natural selection--also confirmed by FST-outlier methods--and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation. CONCLUSIONS/SIGNIFICANCE: These results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.

  20. Genetic map of triticale compiling DArT, SSR, and AFLP markers.

    Science.gov (United States)

    Tyrka, M; Bednarek, P T; Kilian, A; Wędzony, M; Hura, T; Bauer, E

    2011-05-01

    A set of 90 doubled haploid (DH) lines derived from F(1) plants that originated from a cross between × Triticosecale Wittm. 'Saka3006' and ×Triticosecale Wittm. 'Modus', via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

  1. Molecular marker databases.

    Science.gov (United States)

    Lai, Kaitao; Lorenc, Michał Tadeusz; Edwards, David

    2015-01-01

    The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.

  2. The Core-Collection Construction of Flower Lotus Based on AFLP Molecular Markers%利用AFLP分子标记技术构建花莲核心种质资源

    Institute of Scientific and Technical Information of China (English)

    杨美; 付杰; 向巧彦; 刘艳玲

    2011-01-01

    [目的]构建花莲核心种质,以利于对花莲种质资源的保存、研究和利用.[方法]利用AFLP分子标记,对395份花莲原始种质按照种属来源分组后采用组内简单比例法和聚类抽样法建立候选核心种质,比较不同候选核心种质的多态性位点数、多态性位点百分率、观测等位基因数、有效等位基因数、Nei's遗传多样性指数和Shannon's信息指数等参数,最终确定花莲核心种质,并进行核心种质与原始种质的遗传多样性比较和t检验.[结果]所获得88个品种的花莲核心种质包括60份中国花莲品种,3份美洲黄莲,16份中美杂交莲和9份日本莲品种.核心种质保留了原始种质22.270%的样品,多态性位点和多态性位点百分率保留率为99.27%,观测等位基因数、有效等位基因数、Nei's遗传多样性指数、Shannon's信息指数的保留率分别为100.00%、101.72%、110.00%、106.67%.t测验结果表明,核心种质的遗传多样性指数与原始种质差异不显著.[结论]根据聚类分析结果剔除原始种质中的冗余种质后,建立的核心种质以最少的花莲资源可代表原始种质最大的遗传多样性.本文所构建的花莲核心种质在遗传上能最大程度地代表原始种质资源.%[Objective] The construction of the core collection is very important for preservation, study and application of flower lotus (Nelumbo Adans.) germplasm resources. [Method] Based on AFLP markers, candidate core collections were constructed by using proportional strategy and UPGMA clustering sampling method within subgroups after dividing 395 flower lotus germplasm into 4 subgroups. By comparison of the genetic diversity parameters of these candidate core collection, such as the number of polymorphic loci, percentage of polymorphic loci, observed number of alleles, effective number of alleles, Nei's gene diversity and Shannon's information index, the core collection of flower lotus were screened, and

  3. AFLP and SCAR markers associated with the sex in Gracilaria lemaneiformis (Rhodophyta).

    Science.gov (United States)

    Huan, Li; He, Linwen; Zhang, Baoyu; Niu, Jianfeng; Lin, Apeng; Wang, Guangce

    2013-08-01

    Gracilaria lemaneiformis (Bory de Saint-Vincent) Greville, an important marine alga, has great economic and nutritional value. However, during the nonreproductive period, it is difficult to distinguish the sporophyte, male gametophyte, and female gametophyte from each other by appearance. Amplified fragment length polymorphism (AFLP) is a multilocus marker technique, which was used in this study to identify markers associated with G. lemaneiformis sex type. By applying 80 primer combinations in the screening process, three fragments were found that were specific to male or female forms of the alga. A 173 bp band and an 89 bp band were found in the sporophyte and the male gametophyte by using primer E-AGG/M-CGT. E-ACC/M-CGG was used to amplify a 118 bp specific fragment in the sporophyte and the female gametophyte. Sequence characterized amplified region (SCAR) primers were designed and showed the expected bands at the corresponding stages. This suggested that the SCAR markers that had been developed were successful. The joint use of the three primer pairs allowed us to characterize sex and the G. lemaneiformis developmental phase in the nondescript stages. Rapid gender testing is expected to improve cross-breeding experiments and other genetic research in this economically important seaweed.

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

    Directory of Open Access Journals (Sweden)

    Juliana Morini Küpper Cardoso Perseguini

    2011-01-01

    Full Text Available 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.

  5. Species phylogeny and diversification process of Northeast Asian Pungitius revealed by AFLP and mtDNA markers

    DEFF Research Database (Denmark)

    Takahashi, Hiroshi; Møller, Peter Rask; Shedko, Sergei V.;

    2016-01-01

    Pungitius is a highly diversified genus of sticklebacks (Gasterosteidae) occurring widely in northern parts of the Northern Hemisphere. Several ecologically and genetically divergent types that are largely isolated reproductively but occasionally hybridize in sympatry have been discovered...... in Northeast Asia, although the taxonomy and evolutionary relationships among them remain unclear. We used amplified fragment length polymorphism (AFLP) and mitochondrial DNA (mtDNA) markers to infer phylogenies among individuals collected from sympatric and allopatric populations, including the type...

  6. Highly informative single-copy nuclear microsatellite DNA markers developed using an AFLP-SSR approach in black spruce (Picea mariana and red spruce (P. rubens.

    Directory of Open Access Journals (Sweden)

    Yong-Zhong Shi

    Full Text Available Microsatellites or simple sequence repeats (SSRs are highly informative molecular markers for various biological studies in plants. In spruce (Picea and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana and red spruce (Picea rubens using a simple but efficient method based on a combination of AFLP and microsatellite technologies.A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67 in black spruce and from 0.161 to 0.851 (mean = 0.62 in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies.The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for

  7. Assessment of the Genetic Diversity of Pummelo Germplasms Using AFLP and SSR Markers

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The genetic diversities of 110 pummelo germplasms and 12 of their relatives were analyzed by SSR and AFLP methods. Approximately 99.1% of the 335 SSR loci were polymorphic, and 9.85 alleles per SSR locus were identified. The gene diversity values changed from 0.1939 to 0.9073, and 46 SSR polymorphic bands were scored. 72% of the 343 AFLP loci were polymorphic, and 82 polymorphic loci per AFLP were identified. Heterozygosity changed from 0.21863 to 0.28445,and 44 AFLP polymorphic bands were scored. The UPGMA result showed that 122 pummelo genotypes and their relatives could be divided into eight groups, and the pummelo genotypes composed mainly of Shatian pummelo varieties group,Wendan pummelo vareties group and a huge hybrid pummelo varieties group. The classification result was expected to widen the genetic background of pummelos using various target varieties.

  8. [Genetic diversity of ancient tea gardens and tableland tea gardens from Yunnan Province as revealed by AFLP marker].

    Science.gov (United States)

    Ji, Peng-Zhang; Jiang, Hui-Bing; Huang, Xing-Qi; Zhang, Jun; Liang, Min-Zhi; Wang, Ping-Sheng

    2009-01-01

    This study was conducted to evaluate the genetic diversity within and among the plants of four ancient tea gardens and two tableland tea gardens form Yunnan Province, China by AFLP technique. The percentage of polymorphic loci (P) of the plants from six tea gardens was 92.31%. The genetic diversity within the six gardens demonstrated by Nei cents genetic diversity (He) was estimated to be 0.1366, while Shannon indices (Ho) were 0.2323. The percentage of polymorphic loci of the four ancient tea populations was 45.55% on average, with a range of 36.44% (Mengsong) to 59.11% (Mengla). But the percentages of polymorphic loci of the plants from two tableland gardens were 13.77% (Yunkang 10) and 24.2% (Menghai Daye), respectively. There was a great genetic difference between ancient tea gardens and tableland tea gardens. The genetic diversity among the plants of the ancient tea garden was higher than those of the sexual tableland tea garden and the clone tableland tea garden based on P valve. The four ancient tea gardens and two tableland gardens could be differentiated with AFLP markers. The results show that AFLP marker is an effective tool in the discrimination of tea germplasm, as well as sundried green tea.

  9. Identification of Heat Tolerance Linked Molecular Markers of Chinese Cabbage (Brassica campestris L.ssp. pekinensis)

    Institute of Scientific and Technical Information of China (English)

    ZHENG Xiao-ying; WANG Yong-jian; SONG Shun-hua; LI Li; YU Shuan-cang

    2002-01-01

    Genetically stable population of recombination inbred line (RIL) was derived from a cross between a heat tolerant line 177 and a heat sensitive line 276 of Chinese cabbage (Brassica campestris L. ssp.pekinensis ) by single seed descent. The RILs were analyzed using isozyme, RAPD and AFLP techniques in order to find molecular markers that are linked to heat tolerance quantitative trait loci (QTL). The results of variance analysis of single factor indicated that there were 9 molecular markers closely linked with heat tolerance QTL, including 5 AFLP markers, 3 RAPD markers and 1 PGM isozyme marker. Total genetic contribution of these makers to heat tolerance was 46.7%. Five of the nine markers distributed in one linkage group,the remaining 4 markers were located in separate groups. Thus the 9 heat tolerance linked markers distributed in 5 independent locations in the genome of Chinese cabbage.

  10. Comparison Analysis of Genetic Diversity of Indonesian Mangosteens (Garcinia mangostana L. and Related Species by Means Isozymes and AFLP Markers

    Directory of Open Access Journals (Sweden)

    RUDY LUKMAN

    2009-10-01

    Full Text Available Mangosteen (Garcinia mangostana belongs to a large genus of Garcinia that native in South East Asia, as well as Indonesia, and in order evaluate genetics diversity of mangosteen and their close relatives, we employed isoenzyme and AFLP marker on 13 accessions of mangosteen and their close relatives. Isoenzyme marker using four enzyme systems produced 25 bands and 88% out of them were polymorphic and elucidate genetic variability at similarity level ranged between 0.38-0.89. AFLP markers with three primer system produced 220 polymorphic bands and revealed genetic variability at similarity level ranged between 0.38-0.89 successfully produced high polymorphism bands and elucidates genetic variability at similarity coefficient ranged between 0.21-0.77. Both markers exhibited similar clustering pattern, and group successfully G. mangostana accessions in one clustering group. Furthermore G. malaccensis and G. porrecta consistently showed closer genetic relationship to G. mangostana clustering group in both markers, in comparison to G. hombroniana, which implies the assumption they may be the progenitor of G. mangostana, and should be reviewed with more accurate data.

  11. Development of AFLP and RAPD markers linked to a locus associated with twisted growth in corkscrew willow (Salix matsudana 'Tortuosa').

    Science.gov (United States)

    Lin, Juan; Gunter, Lee E; Harding, Scott A; Kopp, Richard F; McCord, Rachel P; Tsai, Chung-Jui; Tuskan, Gerald A; Smart, Lawrence B

    2007-11-01

    Salix matsudana Koidz. cultivar 'Tortuosa' (corkscrew willow) is characterized by extensive stem bending and curling of leaves. To investigate the genetic basis of this trait, controlled crosses were made between a corkscrew female (S. matsudana 'Tortuosa') and a straight-stemmed, wild-type male (Salix alba L. Clone 99010). Seventy-seven seedlings from this family (ID 99270) were grown in the field for phenotypic observation. Among the progeny, 39 had straight stems and leaves and 38 had bent stems and curled leaves, suggesting that a dominant allele at a single locus controls this phenotype. As a first step in characterizing the locus, we searched for amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD) markers linked to the tortuosa allele using bulked segregant analysis. Samples of DNA from 10 corkscrew individuals were combined to produce a corkscrew pool, and DNA from 10 straight progeny was combined to make a wild-type pool. Sixty-four AFLP primer combinations and 640 RAPD primers were screened to identify marker bands amplified from the corkscrew parent and progeny pool, but not from the wild-type parent or progeny pool. An AFLP marker and a RAPD marker linked to and flanking the tortuosa locus were placed on a preliminary linkage map constructed based on segregation among the 77 progeny. Sectioning and analysis of shoot tips revealed that the corkscrew phenotype is associated with vascular cell collapse, smaller cell size in regions near the cambium and less developed phloem fibers than in wild-type progeny. Identification of a gene associated with this trait could lead to greater understanding of the control of normal stem development in woody plants.

  12. Molecular markers: a potential resource for ginger genetic diversity studies.

    Science.gov (United States)

    Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

    2016-12-01

    Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

  13. Variabilidade genética do umbuzeiro no Semi-Árido brasileiro, por meio de marcadores AFLP Genetic variability of umbu trees in Brazilian Semi-Arid region, based on AFLP markers

    Directory of Open Access Journals (Sweden)

    Carlos Antonio Fernandes Santos

    2008-08-01

    Full Text Available O objetivo deste trabalho foi avaliar a distribuição da variabilidade genética do umbuzeiro (Spondias tuberosa, no Semi-Árido brasileiro, por meio de marcadores AFLP, para subsidiar estratégias de prospecção e conservação da espécie. Foram analisados 68 indivíduos de umbuzeiro de 15 ecorregiões, pelo dendrograma UPGMA e pela dispersão em escala multidimensional (MDS, com o coeficiente de Jaccard de 141 bandas polimórficas de AFLP. A análise da variância molecular foi realizada pela decomposição total entre e dentro das regiões ecogeográficas. O dendrograma apresentou valor cofenético de 0,96, e o gráfico MDS apresentou 0,25 para a falta de ajustamento. A variabilidade genética do umbuzeiro foi estimada em 0,3138, o que indica grande variação entre os grupos de indivíduos. Agrupamentos específicos foram observados em seis regiões ecogeográficas, enquanto nas demais regiões observaram-se pares entre alguns indivíduos, sem formação de agrupamentos específicos por local de amostragem, o que indica que a variabilidade genética do umbuzeironão está uniformemente distribuída no Semi-Árido. Sugerem-se estratégias para o estabelecimento de maior número de áreas para conservação in situ ou amostragens de menor número de indivíduos, em várias unidades de paisagens, para conservação ex situ da variabilidade genética do umbuzeiro.The objective of this work was to evaluate the genetic variability distribution of umbu tree (Spondias tuberosa, within Brazilian Semi-Arid region, based on AFLP markers, in order to suggest prospecting and preservation strategies for this species. Sixty-eight umbu trees of 15 ecogeographic regions were analyzed for 141 polymorphic AFLP bands, through the UPGMA dendrogram and the multidimensional scaling (MDS, based on Jaccard's coefficient . Analysis of molecular variance was accomplished by total decomposition among and within ecogeographic regions. The dendrogram presented co

  14. THE EFFECT OF INDIVIDUAL SELECTION FOR GENETIC DIVERSITY OF Acacia mangium SEEDLING SEED ORCHARD USING AFLP MARKERS

    Directory of Open Access Journals (Sweden)

    A. Y.P.B.C. Widyatmoko

    2006-07-01

    Full Text Available Establishment of seed orchard is aimed at producing good quality seeds which is an important activity for breeding program. Seed orchard is also a base population, thus its genetic diversity is depending on its design and composition (provenance, family and individual tree. Selection of an individual tree in seed orchard is needed for the enhancement of  retaining good-character trees. However, selection of individual tree can change the genetic diversity of seed orchard, and the degrees to which the genetic diversity will change depend on the used selection methods. In order to investigate the effects of selection methods, 4 simulations of selection methods based on height, diameter and stem performance of individual trees were used. The differences among the 4 methods were the ranking of individual trees those selected, and families and provenances those have been represented. Seedling seed orchard of Acacia mangium in Wonogiri, Central Java was used as materials. Analysis of genetic diversity was carried out using AFLP markers. Nine primer combinations were used to produce 1025 AFLP banding patterns. Among those banding patterns, only 109 were polymorphic markers. No significant effect of individual tree selection was revealed in this study. Even though the selection was done intensively, only 7.1% of genetic diversity was reduced. In other words, the selection activity did not reduce the genetic diversity of seed orchard significantly. The result is important for developing future tree improvement of A. mangium, including development of hybrid between A. mangium and A. auriculiformis.

  15. Cloning, characterization of two female-specific AFLP markers and development of PCR-based sex identification method for the half-smooth tongue sole Cynoglossus semilaevis

    Directory of Open Access Journals (Sweden)

    Hongyu MA, Songlin CHEN, Jing LI, Jin-Zhen BI, Tianjun XU

    2009-08-01

    Full Text Available Two female-specific AFLP (amplified fragment length polymorphism markers (named CseF464 and CseF136 were isolated by using one selective primer combination (E-AGC/M-CTG from the genomic DNA of 20 females and 20 males of the half-smooth tongue sole Cynoglossus semilaevis. Both the markers were re-amplified, recovered from the agarose gels, cloned and sequenced. Bioinformatics analysis indicated that the length of the two markers were 468bp and 134bp, respectively, and the sequences showed no similarity to each other, as well as to the known sequences deposited in the GenBank database using BLASTn. Two pairs of SCAR (sequence characterized amplified regions primers were designed based on the sequences of the two female-specific markers. Furthermore, PCR-based genetic sex identification method was developed in Cynoglossus semilaevis. A specific fragment was amplified in all females but not in any males by using these SCAR primers on the initial 20 female and 20 male individuals of Cynoglossus semilaevis. The feasibility of the two SCAR primer pairs was confirmed in additional 100 individuals (50 females and 50 males. This allowed for reliable, rapid molecular identification of genetic sex of the species, genetic mapping on the sex chromosomes and better understanding of the sex determination and sex differentiation in the half-smooth tongue sole [Current Zoology 55 (4: 309–314, 2009].

  16. Caracterização molecular de populações de Butia capitata (Arecaceae do Sul do Brasil através de marcadores AFLP Molecular characterization of Butia capitata populations (Arecaceae in Southern Brazil estimated by AFLP analysis

    Directory of Open Access Journals (Sweden)

    Miriam Valli Buttow

    2010-03-01

    Full Text Available O gênero Butia (Arecaceae é um pequeno gênero subtropical com espécies no sul da América do Sul, considerado ornamental. Além disso, seus frutos são apreciados pelo sabor e aroma peculiares. Porém, no Rio Grande do Sul, as populações naturais sofrem com o avanço das atividades rurais e da construção imobiliária. O objetivo deste trabalho foi caracterizar oito populações de Butia capitata ocorrentes no Rio Grande do Sul através de marcadores moleculares do tipo AFLP. Pela análise molecular da variância, foi possível verificar que 83,68% da variabilidade genética são atribuídos à variação entre populações e 13,67% são atribuídos a diferenças entre populações dentro de regiões. A análise comparativa entre as oito populações feita de duas a duas demonstrou que são significativas as diferenças entre 15 populações, com média de 14,72% da variação molecular atribuída às diferenças entre populações. Este resultado indica a presença de variabilidade genética distribuída entre todas as populações, sem subdivisão decorrente de isolamento geográfico.The Butia genus (Arecaceae is a small genus with subtropical species distributed in South America widely used as an ornamental plant. Besides, its fruits are appreciated for its unique flavor and aroma. But in some regions in Rio Grande do Sul State natural populations suffer with progress of building and rural activities. The aim of this study, therefore, was characterizing eight populations of Butia capitata through AFLP markers. By analysis of molecular variance was possible to verify that 83.68% of genetic variability is attributed to variation among populations and 13.67% is attributed to differences among populations within regions. In the pair-wise analysis, differences between 15 populations were significant, with an average of 14.72% of molecular variation attributed to differences between populations. This result indicates the presence of genetic

  17. Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi).

    Science.gov (United States)

    Gupta, S K; Gopalakrishna, T

    2009-02-01

    Genetic diversity in 20 elite blackgram (Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.

  18. Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis

    Institute of Scientific and Technical Information of China (English)

    LIU Yunguo; LI Junfeng; YE Naihao

    2011-01-01

    The genetic diversity of wild and hatchery populations of half-smooth tongue sole Cynoglossus semilaevis, based on observation of amplified fragment length polymorphism (AFLP) was described. Two hundred individuals from four wild populations, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ), and one hatchery population, Mingbo (MB), were screened using eight different AFLP primer combinations. A total of 384 loci were screened in the five studied populations. 48.4%, 51.3%,50.7%, 49.3% and 45.8% of these loci were polymorphic among the individuals tested in the LZ, WH,QD, RZ and MB populations, respectively. The number of polymorphic loci detected by single primer combinations ranged from 17 to 35. The average heterozygosity of the LZ, WH, QD, RZ and MB populations was 0.072, 0.093, 0.092, 0.090 and 0.063, respectively. The WH population showed the highest genetic diversity in terms of total number of AFLP bands, total number of polymorphic bands,average heterozygosity and percentage of low frequency (0-0.2) polymorphic loci among all the populations,while the LZ population was the lowest among the wild populations. Compared with the wild populations,the hatchery population showed a low genetic viability.

  19. Inheritance of Powdery Mildew Resistance in Cucumber (Cucumis sativus L.) and Development of an AFLP Marker for Resistance Detection

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Cucumber powdery mildew is one of the most destructive diseases of cucumber throughout the world. In the present study, inheritance of powdery mildew resistance in three crosses, and linkage of resistance with amplified fragment length polymorphism (AFLP) markers are studied to formulate efficient strategies for breeding cultivars resistant to powdery mildew. The joint analysis of multiple generations and AFLP technique has been applied in this study. The best model is the one with two major genes, additive, dominant, and epistatic effects, plus polygenes with additive, dominant, and epistatic effects (E-1-0 model). The heritabilities of the major genes varied from 64.26% to 97.82%, and susceptibility was incompletely dominant for the two major genes in the three crosses studied. The additive effects of the two major genes and the dominant effect of the second major gene were high, and the epistatic effect of the additive-dominant between the two major genes was the highest in cross Ⅰ. In cross Ⅱ, the absolute value of the additive effect, dominant effect, and potential ratio of the first major gene were far higher than those of the second major gene, and the epistatic effect of the additive-additive was the highest. The genetic parameters of the two major genes in cross Ⅲ were similar to those in cross Ⅱ. Correlation and regression analyses showed that marker E25/M63-103 was linked to a susceptible gene controlling powdery mildew resistance. The marker could account for 19.98% of the phenotypic variation. When the marker was tested on a diverse set of 29 cucumber lines, the correlation between phenotype and genotype was not significant, which suggested cultivar specialty of gene expression or different methods of resistance to powdery mildew. The target DNA fragment was 103 bp in length, and only a small part was found to be homologous to DNA in the other species evaluated,which indicated that it was unique to the cucumber genome.

  20. Molecular marker applications in plants.

    Science.gov (United States)

    Hayward, Alice C; Tollenaere, Reece; Dalton-Morgan, Jessica; Batley, Jacqueline

    2015-01-01

    Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.

  1. Identification of Common AFLP Markers Linked with Resistance to Bacterial Wilt in Potato%马铃薯青枯病抗性的共性AFLP标记的初步定位

    Institute of Scientific and Technical Information of China (English)

    郜刚; 金黎平; 屈冬玉; 连勇; 闫桂琴; 段江燕

    2005-01-01

    The bulked Segregant Analysis (BSA) was used to examine and evaluate the feasibility and the efficiency of the identification of markers linked to resistance to bacterial wilt (Ralstonia solanacearum) in potato. A highly resistant primitive cultivated species Solanum phureja was employed to generate a mapping population to perform the bulked segregant analysis for screening of AFLP markers linked with the resistance. Another population which had genetic similarity to the mapping population was used for testing of the markers achieved. A novel strategy named common AFLP marker was used to identify the genomic position of the molecular markers in the linkage map mapped before. Several informative primer combinations were employed in the detection and the common AFLP markers ATG/CTC 307.0, ATG/CTC 246.0, ATG/CTC 191.0 and AAC/CAC 79.0 were considered as markers that associated with the resistance and located on the relevant chromosome maps. The markers were located on chromosome 1 and 12 and may be used for other related studies.%利用集群分类法(bulked segregant analysis, BSA)对与马铃薯青枯病(Ralstonia solanacearum) 抗性连锁的分子标记进行了分析.以马铃薯青枯病高抗性的原始栽培种Solanum phureja获得的二倍体群体为作图群体进行AFLP标记的初步筛选,另选一个与作图群体有较大亲缘关系和相近遗传背景的二倍体群体对所获标记进行验证.在标记鉴定过程中使用了共性AFLP标记(common AFLP marker)的方法.通过与已构建的连锁图谱的比较分析,获得了4个与马铃薯青枯病抗性相关的4个AFLP标记ATG/CTC 307.0, ATG/CTC 246.0, ATG/CTC 191.0和AAC/CAC 79.0,将其分别定位于染色体1和12上,可望应用于其它相关研究.

  2. Assessing genetic diversity of wild populations of Japanese flounder using AFLP markers

    Institute of Scientific and Technical Information of China (English)

    XU Xiaofei; ZHANG Quanqi; WANG Zhigang; QI Jie; ZHANG Zhifeng; BAO Zhenmin; Heisuke Nakagawa

    2006-01-01

    Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic diversity of four wild geographical populations of Japanese flounder (Paralichthys olivaceus). A total of 775 loci (58.32% of which was polymorphic) in the range between 100 and 1 300 base pairs were detected from 110 individuals using seven primer combinations. The percentage of polymorphic loci detected by single primer combination for each population was calculated, ranging from 19.59% to 53.33%. Genetic similarities within and among the populations were calculated from the binary matrices of presence - absence. Phylogenetic tree of four populations was constructed by using the UPGMA method using PHYLIP Version 3.5. According to intrapopulation genetic similarities, CW population displayed the highest genetic diversity value and KY population had the lowest genetic diversity value.The distance between CW and CF populations was the farthest, which was possibly resulted from the farthest distance of Weihai of Shandong and Fujian of China compared with the geographical distance between other locations of populations. The subpopulation differentiation value ( Gst ) is 0.356 5, showing a certain extent of differentiation among the four geographical populations. AFLP technology was confirmed to be an effective tool to assess within- and among-population genetic diversity of Japanese flounder. The present survey provided significant insights for research in the Japanese flounder breeding program.

  3. Application of molecular markers in apple breeding

    Directory of Open Access Journals (Sweden)

    Marić Slađana

    2010-01-01

    Full Text Available Apple is economically the most important species of genus Malus Miller. In respect of production, trade and consumption, it ranks first among deciduous fruit and third on a global scale among all fruit species. Apple breeding is carried out on a large scale in several scientific institutes throughout the world. Due to this activity, apple is a fruit species with the highest number of described monogenic traits; 76 genes, encoding morphological traits, pest and disease resistance, as well as 69 genes encoding enzymes. The development of molecular markers (RFLPs, AFLPs, SCARs and SSRs has allowed the mapping of the apple genome and the development of several saturated genetic maps, to which genes controlling important traits are assigned. Markers flanking these genes not only play an important role in selecting parental combinations and seedlings with positive traits, but they are also particularly important in detecting recessive traits, such as seedless fruit. In addition they enable pre-selection for polygenic quantitative traits. In recent years, particular attention has been paid to biochemical and physiological processes involved in the pathway of important traits e.g., ripening and the storage capability of apple fruit.

  4. An AFLP marker linked to the Pm-1 gene that confers resistance to Podosphaera xanthii race 1 in Cucumis melo

    Directory of Open Access Journals (Sweden)

    Ana Paula Matoso Teixeira

    2008-01-01

    Full Text Available Brazil produced 330,000 metric tons of melons in 2005, principally in the Northeast region where one of the most important melon pathogens is the powdery mildew fungus Podosphaera xanthii. The disease is controlled mainly by incorporating single dominant resistance genes into commercial hybrids. We report on linkage analysis of the Pm-1 resistance gene, introgressed from the AF125Pm-1 Cantalupensis Charentais-type breeding line into the yellow-fleshed melon (Group Inodorus breeding line AF426-S by backcrossing to produce the resistant line AF426-R, and the amplified fragment length polymorphism (AFLP marker M75/H35_155 reported to be polymorphic between AF426-S and AF426-R. Segregation analysis of M75/H35_155 using a backcross population of 143 plants derived from [AF426-R x AF426-S] x AF426-S and screened for resistance to P. xanthii race 1 produced a recombination frequency of 4.9%, indicating close linkage between M75/H35_155 and Pm-1. Using the same segregating population, the M75/H35_155 marker had previously been reported to be distantly linked to Prv¹, a gene conferring resistance to papaya ringspot virus-type W. Since M75/H35_155 is linked to Prv¹ at a distance of 40.9 cM it is possible that Pm-1 and Prv¹ are also linked.

  5. AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague-mediated selection.

    Science.gov (United States)

    Tollenaere, C; Duplantier, J-M; Rahalison, L; Ranjalahy, M; Brouat, C

    2011-03-01

    The black rat (Rattus rattus) is the main reservoir of plague (Yersinia pestis infection) in Madagascar's rural zones. Black rats are highly resistant to plague within the plague focus (central highland), whereas they are susceptible where the disease is absent (low altitude zone). To better understand plague wildlife circulation and host evolution in response to a highly virulent pathogen, we attempted to determine genetic markers associated with plague resistance in this species. To this purpose, we combined a population genomics approach and an association study, both performed on 249 AFLP markers, in Malagasy R. rattus. Simulated distributions of genetic differentiation were compared to observed data in four independent pairs, each consisting of one population from the plague focus and one from the plague-free zone. We found 22 loci (9% of 249) with higher differentiation in at least two independent population pairs or with combining P-values over the four pairs significant. Among the 22 outlier loci, 16 presented significant association with plague zone (plague focus vs. plague-free zone). Population genetic structure inferred from outlier loci was structured by plague zone, whereas the neutral loci dataset revealed structure by geography (eastern vs. western populations). A phenotype association study revealed that two of the 22 loci were significantly associated with differentiation between dying and surviving rats following experimental plague challenge. The 22 outlier loci identified in this study may undergo plague selective pressure either directly or more probably indirectly due to hitchhiking with selected loci.

  6. [Identification of the wild germplasm of Prunus mume based on AFLP markers].

    Science.gov (United States)

    Li, Qingwei; Zhang, Qixiang; Chen, Junyu

    2012-08-01

    Mei (Prunus mume Sieb.et Zucc.) is traditionally not only a famous special ornamental plant but also a fruit tree origined in China. In order to conserve and ultilize scientifically the germplasm resources of wild mei, we identified and analysed the germplasm of mei flower in 65 samples collected from the habitat, using AFLP makers in combination with morphological anaylsis. This study amplified clearly 1 728 polymorphic bands, using the 8- pair-primer of Mse I -EcoR I screened totally from 64 -primer combination. According to the Nei' 72 distance coefficient clustering, all of the formas and varieties used in this study, including Prunus mume var. mume, P. mume, P. mume var. goethartiana, P. mume var. pallescens, P. mume var. microcarpa, P. mume var. cenrnus-sempervirens (newly recoeding variety), P. mume var. cernua, P. mume var. pallidus, P. mume var. taomei, were identified at the point of Nei' 72=0.26. Due to the genetic difference obviously among the formas and varieties, we suggested that wild germplasmtypes of all formas and varieties in P. mume should be conserved in their habitats in the furture.

  7. Assessment of genetic diversity in glandless cotton germplasm resources by using agronomic traits and molecular markers

    Institute of Scientific and Technical Information of China (English)

    Zhikun LI; Xingfen WANG; Yan ZHANG; Guiyin ZHANG; Liqiang WU; Jina CHI; Zhiying MA

    2008-01-01

    Seventy-one glandless cotton germplasm resources were firstly evaluated genetically by using nine agronomic traits,33 simple sequence repeat (SSR) primers and ten amplified fragment length polymorphism (AFLP)primer combinations.Principal component analysis (PCA) of the agronomic traits showed that the first six principal components (PCs) explained a total of 86.352% of the phenotypic variation.A total of 329 alleles were amplified for 33 SSR primers,and 232 polymorphic bands in a total of 389 bands were obtained by using ten AFLP primer combinations.The average polymorphic information content (PIC) value was 0.80 and 0.18 for SSR primers and AFLP primer combinations,respectively.The DIST (average taxonomic distance) and DICE (Nei and Li's pairwise distance) coefficients ranged from 0.373 to 3.164 and 0.786 to 0.948,respectively,for agronomic traits and SSR & AFLP data based on UPGMA analysis.This suggested that there was a higher diversity in the evaluated population for both agronomic traits and molecular markers.The Mantel's test showed that the correlation between the dendrograms based on agronomic traits and SSR & AFLP data was non-significant.

  8. Assessment of genetic diversity among Chinese upland cottons with Fusarium and/or Verticillium wilts resistance by AFLP and SSR markers

    Institute of Scientific and Technical Information of China (English)

    WANG Xingfen; MA Jun; YANG Shuo; ZHANG Guiyin; MA Zhiying

    2007-01-01

    Genetic diversity among 95 Chinese upland cottons with Fusarium and/or Verticillium wilts resistance was estimated using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers.Twenty EcoRI-MseI AFLP and 19 SSR primers with polymorphism were selected to perform the fingerprinting.The results showed that 20 AFLP primer pairs produced a total of 1 480 major bands among 95 genotypes,and 214 were polymorphic bands.The number of total bands per primer pair ranged from 47 to 109,with an average of 74.0.The polymorphism information content (PIC) values for the 20 primer pairs varied from 0.01 (E-ACT/M-CAT) to 0.24 (E-ACA/MCTA),and the average value was 0.09.Nineteen SSR primers generated 89 DNA bands,of which 61 were polymorphic.The total number of alleles per locus varied from 3 to 8,with an average of 4.7.The average PIC value for the SSR amplification products was 0.69.Genetic similarity estimates for the entire data set ranged from 0.978 to 0.998 based on AFLP and SSR bands.It was proved that the close genetic relationship and narrow genetic diversity existed in the tested cultivars.The clustering patterns could not be correlated to the geographic origin,the pedigree and common parentage of the cultivars.

  9. Diversity of garlic (Allium sativum L.) using SSR, EST and AFLP markers

    Science.gov (United States)

    Germplasm from the center of origin/diversity is important for the breeding and fingerprinting crop plants. In this study we utilized both dominant and co-dominant markers for the characterization of garlic samples from diverse geographic origins to assess the relative utility of these markers to id...

  10. Evaluation of genetically modified sugarcane lines carrying Cry 1AC gene using molecular marker techniques.

    Science.gov (United States)

    Ismail, Roba M

    2013-01-01

    Five genetically modified insect resistant sugarcane lines harboring the Bt Cry 1AC gene to produce insecticidal proteins were compared with non-transgenic control by using three types of molecular marker techniques namely, RAPD, ISSR and AFLP. These techniques were applied on transgenic and non-transgenic plants to investigate the genetic variations, which may appear in sugarcane clones. This variation might demonstrate the genomic changes associated with the transformation process, which could change important molecular basis of various biological phenomena. Genetic variations were screened using 22 different RAPD primers, 10 ISSR primers and 13 AFLP primer combinations. Analysis of RAPD and ISSR banding patterns gave no exclusive evidence for genetic variations. Meanwhile, the percentage of polymorphic bands was 0.45% in each of RAPD and ISSR, while the polymorphism generated by AFLP analysis was 1.8%. The maximum percentage of polymorphic bands was 1.4%, 1.1% and 5.5% in RAPD, ISSR and AFLP, respectively. These results demonstrate that most transgenic lines showed genomic homogeneity and verified minor genomic changes. Dendrograms revealing the relationships among the transgenic and control plants were developed from the data of each of the three marker types.

  11. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility

    NARCIS (Netherlands)

    Badali, H.; Yazdanparast, S.A.; Bonifaz, A.; Mousavi, B.; de Hoog, G.S.; Klaassen, C.H.W.; Meis, J.F.G.M.

    2013-01-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated in

  12. Genetic Diversity Within a Jackfruit(Artocarpus heterophyllus Lam.)Germplasm Collection in China Using AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    LI Ying-zhi; MAO Qi; FENG Feng; YE Chun-hai

    2010-01-01

    Jackfruit is cross-pollinated and mostly seed propagated,a wide range of variation exists in fruit quality.With the development of efficient vegetative propagation methods,excellent genotypes selected from these seed propagated seedlings will gradually replace other genotypes in jackfruit producing areas.In this study,genetic diversity of 50jackfruit accessions from three provinces in China was analyzed based on amplified fragment length polymorphic(AFLP)markers.A total of 320 unambiguous bands were produced by eight primer combinations,and 65(20.3%)of them were polymorphic.Genetic similarity coefficients ranged from 0 to 0.9841,with an average of 0.5000,indicating a moderate genetic diversity in this collection.The dendrogram derived by unweighted pair group method with arithmetic mean algorithm(UPGMA)analysis revealed five groups,and no correlation between genetic relationship and geographical origin were found.Accessions of soft and firm flesh type were not clustered into distinct groups,neither could yearly bearing once,or twice fruit accessions.This study has provided useful information for collection and preservation of jackfruit germplasm worldwide.

  13. Genetic differentiation in the winter pine processionary moth (Thaumetopoea pityocampa--wilkinsoni complex), inferred by AFLP and mitochondrial DNA markers.

    Science.gov (United States)

    Salvato, Paola; Battisti, Andrea; Concato, Silvia; Masutti, Luigi; Patarnello, Tomaso; Zane, Lorenzo

    2002-11-01

    The winter pine processionary moth has become an important pine pest in the last century, as a consequence of the spread of pine cultivation in the Mediterranean region. The pattern of genetic differentiation of this group, that includes two sibling species (Thaumetopoea pityocampa and Th. wilkinsoni), has been studied in nine populations using amplified fragment length polymorphism (AFLP) and single strand conformation polymorphism-sequence analysis (SSCP) of the mitochondrial cytochrome oxidase 1 (COI) and cytochrome oxydase 2 (COII). Results indicate the existence of strong genetic differentiation between the two species that became separated before the Quaternary ice ages. Moreover data indicate that Th. pityocampa has a strong geographical structure, particularly evident at the nuclear level, where all pairwise phiST resulted to be highly significant and individuals from the same population resulted to be strongly clustered when an individual tree was reconstructed. The estimates of the absolute number of migrants between populations (Nm), obtained from mitochondrial and nuclear DNA markers, suggest that gene flow is low and that a gender-related dispersal could occur in this species. The males appear to disperse more than females, contributing to the genetic diversity of populations on a relatively wide range, reducing the risks of inbreeding and the genetic loss associated with bottlenecks occurring in isolated populations.

  14. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    OpenAIRE

    2012-01-01

    Abstract Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating ...

  15. Divergência genética entre genótipos de alface por meio de marcadores AFLP Genetics divergence among lettuce genotypes by AFLP markers

    Directory of Open Access Journals (Sweden)

    Cristina Soares de Sousa

    2007-01-01

    Full Text Available Considerando a restrita diversidade de espécies disponíveis para nutrir a carência de vitaminas no Brasil, Kerr e colaboradores, desde 1981, vêm desenvolvendo pesquisas para melhoramento genético de hortaliças ricas em vitamina A. Dentre elas, obtiveram uma cultivar de alface, denominada Uberlândia 10.000 com 10.200 UI de vitamina A em 100 gramas de folha fresca. Este trabalho objetivou comparar o grau de divergência genética entre a cultivar Uberlândia 10.000 e seus parentais para avaliar a eficiência da seleção utilizada, por meio da técnica AFLP. Foram utilizados os seguintes genótipos de alface: Maioba, Salad Bowl-Mimosa, Moreninha-de-Uberlândia, Vitória de Santo Antão, Uberlândia 10.000 lisa 8.ª e 9.ª geração e Uberlândia 10.000 crespa 8.ª e 9.ª geração. A técnica AFLP foi eficiente para identificar genótipos muito próximos e para estudos de progênies em alface. O primer PR15 permitiu a separação da forma lisa e crespa com 1,8% de divergência genética e a oitava da nona geração com apenas 0,71%. Com o estudo da filogenia da cultivar pode-se observar que o programa de melhoramento foi desenvolvido com sucesso, pois a cultivar obtida Uberlândia 10.000 possui alto teor de vitamina A e 92% de similaridade com o parental Vitória de Santo Antão. O primer PR11 conseguiu identificar polimorfismo entre cultivares de alta e baixa resistência à septoriose, sugerindo a possibilidade destas bandas estarem relacionadas à resistência.Considering the restricted diversity of species available to counteract vitamin deficiencies in Brazil, Kerr and coworkers have been engaged since 1981, in developing genetic improved garden vegetables rich in vitamin A. One of these vegetables is the lettuce cultivar Uberlândia 10,000, which contains 10,200 UI of vitamin A per 100 grams of fresh leaves. This study compares the genetic diversity between Uberlândia 10,000 and its parental, evaluating selection efficiency through

  16. Duck (Anas platyrhynchos) linkage mapping by AFLP fingerprinting.

    Science.gov (United States)

    Huang, Chang-Wen; Cheng, Yu-Shin; Rouvier, Roger; Yang, Kuo-Tai; Wu, Chean-Ping; Huang, Hsiu-Lin; Huang, Mu-Chiou

    2009-03-17

    Amplified fragment length polymorphism (AFLP) with multicolored fluorescent molecular markers was used to analyze duck (Anas platyrhynchos) genomic DNA and to construct the first AFLP genetic linkage map. These markers were developed and genotyped in 766 F2 individuals from six families from a cross between two different selected duck lines, brown Tsaiya and Pekin. Two hundred and ninety-six polymorphic bands (64% of all bands) were detected using 18 pairs of fluorescent TaqI/EcoRI primer combinations. Each primer set produced a range of 7 to 29 fragments in the reactions, and generated on average 16.4 polymorphic bands. The AFLP linkage map included 260 co-dominant markers distributed in 32 linkage groups. Twenty-one co-dominant markers were not linked with any other marker. Each linkage group contained three to 63 molecular markers and their size ranged between 19.0 cM and 171.9 cM. This AFLP linkage map provides important information for establishing a duck chromosome map, for mapping quantitative trait loci (QTL mapping) and for breeding applications.

  17. Duck (Anas platyrhynchos linkage mapping by AFLP fingerprinting

    Directory of Open Access Journals (Sweden)

    Yang Kuo-Tai

    2009-03-01

    Full Text Available Abstract Amplified fragment length polymorphism (AFLP with multicolored fluorescent molecular markers was used to analyze duck (Anas platyrhynchos genomic DNA and to construct the first AFLP genetic linkage map. These markers were developed and genotyped in 766 F2 individuals from six families from a cross between two different selected duck lines, brown Tsaiya and Pekin. Two hundred and ninety-six polymorphic bands (64% of all bands were detected using 18 pairs of fluorescent TaqI/EcoRI primer combinations. Each primer set produced a range of 7 to 29 fragments in the reactions, and generated on average 16.4 polymorphic bands. The AFLP linkage map included 260 co-dominant markers distributed in 32 linkage groups. Twenty-one co-dominant markers were not linked with any other marker. Each linkage group contained three to 63 molecular markers and their size ranged between 19.0 cM and 171.9 cM. This AFLP linkage map provides important information for establishing a duck chromosome map, for mapping quantitative trait loci (QTL mapping and for breeding applications.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available 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.

  20. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories

    NARCIS (Netherlands)

    Jones, C.J.; Edwards, K.J.; Castiglione, S.; Winfield, M.O.; Sala, F.; Wiel, van de C.C.M.; Bredemeijer, G.M.M.; Vosman, B.; Matthes, M.; Daly, A.; Brettschneider, R.; Bettini, P.; Buiatti, M.; Maestri, E.; Malcevschi, A.; Marmiroli, N.; Aert, R.; Volckaert, G.; Ru, J.; eda,; Linacero, R.; Vazquez, A.; Karp, A.

    1997-01-01

    A number of PCR-based techniques can be used to detect polymorphisms in plants. For their wide-scale usage in germplasm characterisation and breeding it is important that these marker technologies can be exchanged between laboratories, which in turn requires that they can be standardised to yield re

  1. Identification of Amplified Fragment Length Polymorphism (AFLP) Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge.

    Science.gov (United States)

    Zhang, Yuejin; Guo, Lijun; Shu, Zhiming; Sun, Yiyue; Chen, Yuanyuan; Liang, Zongsuo; Guo, Hongbo

    2013-03-22

    Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs) of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006-2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246) was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357) was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10-93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1-5.

  2. Identification of Amplified Fragment Length Polymorphism (AFLP Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge

    Directory of Open Access Journals (Sweden)

    Hongbo Guo

    2013-03-01

    Full Text Available Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006–2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA and amplified fragment length polymorphism (AFLP with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246 was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357 was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10−93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1–5.

  3. Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit) in red raspberry (Rubus idaeus L.) using AFLP and microsatellite markers

    Science.gov (United States)

    Sargent, Daniel J; Fernández-Fernández, Felicidad; Rys, Alicja; Knight, Victoria H; Simpson, David W; Tobutt, Kenneth R

    2007-01-01

    Background Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus) F1 progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO), which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A1) and (dw) respectively. Results The progeny of 94 seedlings was scored for the segregation of 95 AFLP and 22 SSR markers and a linkage map was constructed that covers a total genetic distance of 505 cM over seven linkage groups. The average linkage group length was 72.2 cM and there was an average of 17 markers per linkage group, of which at least two were codominant SSRs, allowing comparisons with previously published maps of raspberry. The two phenotypic traits, A1 and dw, mapped to linkage groups 3 and 6 respectively. Conclusion The mapping of A1 will facilitate the discrimination of resistance genes from different sources and the pyramiding of aphid resistance genes in new raspberry cultivars; the mapping of dw will allow further investigations into the genetics of dwarfing habit in Rubus. PMID:17374159

  4. Mapping of A1 conferring resistance to the aphid Amphorophora idaei and dw (dwarfing habit in red raspberry (Rubus idaeus L. using AFLP and microsatellite markers

    Directory of Open Access Journals (Sweden)

    Knight Victoria H

    2007-03-01

    Full Text Available Abstract Background Raspberry breeding programmes worldwide aim to produce improved cultivars to satisfy market demands and within these programmes there are many targets, including increased fruit quality, yield and season, and improved pest and disease resistance and plant habit. The large raspberry aphid, Amphorophora idaei, transmits four viruses and vector resistance is an objective in raspberry breeding. The development of molecular tools that discriminate between aphid resistance genes from different sources will allow the pyramiding of such genes and the development of raspberry varieties with superior pest resistance. We have raised a red raspberry (Rubus idaeus F1 progeny from the cross 'Malling Jewel' × 'Malling Orion' (MJ × MO, which segregates for resistance to biotype 1 of the aphid Amphorophora idaei and for a second phenotypic trait, dwarf habit. These traits are controlled by single genes, denoted (A1 and (dw respectively. Results The progeny of 94 seedlings was scored for the segregation of 95 AFLP and 22 SSR markers and a linkage map was constructed that covers a total genetic distance of 505 cM over seven linkage groups. The average linkage group length was 72.2 cM and there was an average of 17 markers per linkage group, of which at least two were codominant SSRs, allowing comparisons with previously published maps of raspberry. The two phenotypic traits, A1 and dw, mapped to linkage groups 3 and 6 respectively. Conclusion The mapping of A1 will facilitate the discrimination of resistance genes from different sources and the pyramiding of aphid resistance genes in new raspberry cultivars; the mapping of dw will allow further investigations into the genetics of dwarfing habit in Rubus.

  5. Identification of antimony resistance markers in Leishmania tropica field isolates through a cDNA-AFLP approach.

    Science.gov (United States)

    Kazemi-Rad, Elham; Mohebali, Mehdi; Khadem-Erfan, Mohammad Bagher; Saffari, Mojtaba; Raoofian, Reza; Hajjaran, Homa; Hadighi, Ramtin; Khamesipour, Ali; Rezaie, Sassan; Abedkhojasteh, Hoda; Heidari, Mansour

    2013-10-01

    Pentavalent antimonial compounds have been the first line therapy for leishmaniasis; unfortunately the rate of treatment failure of anthroponotic cutaneous leishmaniasis (ACL) is increasing due to emerging of drug resistance. Elucidation of the molecular mechanisms operating in antimony resistance is critical for development of new strategies for treatment. Here, we used a cDNA-AFLP approach to identify gene(s) which are differentially expressed in resistant and sensitive Leishmania tropica field isolates. We identified five genes, aquaglyceroporin (AQP1) acts in drug uptake, ATP-binding cassette (ABC) transporter (MRPA) involved in sequestration of drug, phosphoglycerate kinase (PGK) implicated in glycolysis metabolism, mitogen activated protein kinase (MAPK) and protein tyrosine phosphatase (PTP) responsible for phosphorylation pathway. The results were confirmed using real time RT-PCR which revealed an upregulation of MRPA, PTP and PGK genes and downregulation of AQP1 and MAPK genes in resistant isolate. To our knowledge, this is the first report of identification of PTP and PGK genes potentially implicated in resistance to antimonials. Our findings support the idea that distinct biomolecules might be involved in antimony resistance in L. tropica field isolates.

  6. Molecular markers for biodiversity analysis of wildlife animals: a brief review

    Directory of Open Access Journals (Sweden)

    Arif, I. A.

    2009-06-01

    Full Text Available Molecular markers are indis­pensable tools for determining the genetic variation and biodiversity with high levels of accuracy and repro­ducibility. These markers are mainly classified into two types; mitochondrial and nuclear markers. The widely used mitochondrial DNA markers with decreasing order of conserved sequences are 12S rDNA > 16S rDNA > cytochrome b > control region (CR; thus the 12S rDNA is highly conserved and the CR is highly variable. The most commonly used nuclear markers for DNA fingerprinting include random amplified polymorphic DNA (RAPD, amplified fragment length polymorphism (AFLP and microsatellites. This short review narrates the application of these molecular markers for biodiversity analysis of wildlife animals.

  7. Sequence-Related Amplified Polymorphism (SRAP Markers: A Potential Resource for Studies in Plant Molecular Biology

    Directory of Open Access Journals (Sweden)

    Daniel W. H. Robarts

    2014-07-01

    Full Text Available 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.

  8. The Possible Physical Barrier and Coastal Dispersal Strategy for Japanese Grenadier Anchovy, Coilia nasus in the East China Sea and Yellow Sea: Evidence from AFLP Markers

    Directory of Open Access Journals (Sweden)

    Zhi-Qiang Han

    2015-02-01

    Full Text Available In order to ascertain the taxonomic status of the Ariake Sea population of Japanese grenadier anchovy, Coilia nasus, and assess the contemporary possible genetic barrier between the west and east coastal waters of the East China Sea, we used amplified fragment length polymorphism (AFLP markers to detect the genetic structure of C. nasus, in the East China Sea and Yellow Sea. Eighty-one individuals of C. nasus were collected from five locations and 12 individuals of Coilia mystus were sampled from the Yangtze River Estuary. A total of 371 loci were detected by five primer combinations, 310 of which were polymorphic (83.56%. Analysis of molecular variation (AMOVA and pairwise fixation index (FST revealed significant genetic differentiation among five samples, indicating limited gene flow among populations. The dendrogram for populations by neighbor-joining (NJ cluster analysis provided evidence of a clear relationship between genetic and geographic patterns, supporting significant genetic differentiation between China coastal populations and Ariake Sea populations. Compared to the genetic divergence between C. nasus and C. mystus, the level of genetic differentiation between China and the Ariake Sea populations of C. nasus is obvious below the species level, indicating isolated populations of C. nasus in the Ariake Sea. Isolation by distance analysis revealed that direct ocean distance with deep-water at the continental slope and high salinity between west and east coastal waters of the East China Sea served as major physical barrier to C. nasus, supporting the coastal dispersal pattern in this estuarine species, and rejecting offshore dispersal strategy.

  9. Caracterización molecular de introducciones colombianas de caña flecha utilizando la técnica AFLP Molecular characterization of colombian wild cane accesions with AFLP

    Directory of Open Access Journals (Sweden)

    Hernando Rivera Jiménez

    2008-12-01

    Full Text Available La fibra de la caña flecha Gynerium sagittatum (Aubl. se utiliza como materia prima para fabricar el "sombrero vueltiao", sombrero típico de la costa caribeña colombiana. Se realizó la caracterización molecular con AFLP para estimar variabilidad genética teniendo en cuenta criterios geográficos y morfológicos de 25 introducciones colombianas del banco de germoplasma de la Universidad de Córdoba. El análisis de correspondencia múltiple discriminó las introducciones en cuatro grupos, donde se identificaron características de importancia artesanal (comercial y atributos agronómicos. Se observó escasa correlación entre distancia geográfica y diferenciación genética, lo cual indicó flujos antrópicos por la reproducción asexual del material.Wild cane (Gynerium sagittatum Aubl. fiber is used as raw material for to make "hat vueltiao". A molecular characterization using AFLP was carriet out to estimate genetic variability of 25 accessions planted at the University of Cordoba, associated with geographical and morphological traits. Multiple discrimination correspondence analyses of introductions separated four groups, based on craft handling and agronomic attributes desirable. There was little correlation between geographic distance and genetic differentiation, indicating an anthropic flows by asexual reproduction.

  10. High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    Jiwen Yu; Shuxun Yu; Cairui Lu; Wu Wang; Shuli Fan; Meizhen Song; Zhongxu Lin; Xianlong Zhang; Jinfa Zhang

    2007-01-01

    A high-density linkage map was constructed for an F2 population derived from an interspecific cross of cultivated allotetraploid species between Gossyplum hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the interspecific cross of "CRI 36 × Hai 7124" were genotyped at 1 252 polymorphic loci including a novel marker system,target region amplification polymorphism (TRAP). The map consists of 1 097 markers, including 697 simple sequence repeats (SSRs), 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were identified in tetraplold cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

  11. An AFLP marker linked to the leaf rust resistanc gene LrBi16 and test of allelism with Lr14a on chromosome arm 7BL

    Institute of Scientific and Technical Information of China (English)

    Peipei; Zhang; Huixin; Zhou; Caixia; Lan; Zaifeng; Li; Daqun; Liu

    2015-01-01

    Leaf rust(LR), caused by Puccinia triticina, is one of the most widespread diseases of common wheat(Triticum aestivum L.) worldwide. The LR resistance gene Lr Bi16 has been mapped on chromosome arm 7BL in Chinese wheat cultivar Bimai 16 and was closely linked to SSR loci Xcfa2257 and Xgwm344 with genetic distances of 2.8 c M and 2.9 c M, respectively. In the present study, a total of 304 AFLP primer pairs were used to screen Bimai 16 and Thatcher and resistant and susceptible DNA bulks. The polymorphic AFLP marker P-ATT/M-CGC173 bp was used to genotype F2 and F3populations to identify markers more closely linked to Lr Bi16. Marker P-ATT/M-CGC173 bp was tightly linked to Lr Bi16 with a genetic distance of0.5 c M. As Lr Bi16 was mapped near the Lr14 a locus, 809 F2 plants from the Bimai 16/RL6013(Lr14a) cross were inoculated with the Pt pathotype FHNQ to test the allelism of Lr14 a and Lr Bi16. All of the F2 plants were resistant to FHNQ(IT between; and 2), suggesting that Lr14 a and Lr Bi16 are allelic.

  12. An AFLP marker linked to the leaf rust resistance gene LrBi16 and test of allelism with Lr14a on chromosome arm 7BL

    Directory of Open Access Journals (Sweden)

    Peipei Zhang

    2015-04-01

    Full Text Available Leaf rust (LR, caused by Puccinia triticina, is one of the most widespread diseases of common wheat (Triticum aestivum L. worldwide. The LR resistance gene LrBi16 has been mapped on chromosome arm 7BL in Chinese wheat cultivar Bimai 16 and was closely linked to SSR loci Xcfa2257 and Xgwm344 with genetic distances of 2.8 cM and 2.9 cM, respectively. In the present study, a total of 304 AFLP primer pairs were used to screen Bimai 16 and Thatcher and resistant and susceptible DNA bulks. The polymorphic AFLP marker P-ATT/M-CGC173 bp was used to genotype F2 and F3 populations to identify markers more closely linked to LrBi16. Marker P-ATT/M-CGC173 bp was tightly linked to LrBi16 with a genetic distance of 0.5 cM. As LrBi16 was mapped near the Lr14a locus, 809 F2 plants from the Bimai 16/RL6013 (Lr14a cross were inoculated with the Pt pathotype FHNQ to test the allelism of Lr14a and LrBi16. All of the F2 plants were resistant to FHNQ (IT between; and 2, suggesting that Lr14a and LrBi16 are allelic.

  13. Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

    DEFF Research Database (Denmark)

    Schwarz, G.; Herz, M.; Huang, X.Q.

    2000-01-01

    Genetic mapping and the selection of closely linked molecular markers for important agronomic traits require efficient, large-scale genotyping methods. A semi-automated multifluorophore technique was applied for genotyping AFLP marker loci in barley and wheat. In comparison to conventional P-33...

  14. Identification of molecular markers linked to the mildew resistance gene Pl-d in apple.

    Science.gov (United States)

    James, C M; Clarke, J B; Evans, K M

    2004-12-01

    Powdery mildew poses a serious problem for apple growers, and resistance to the disease is a major objective in breeding programmes for cultivar improvement. As selective pressure allows pathogens to overcome previously reliable resistances, there is a need for the introduction of novel resistance genes into new breeding lines. This investigation is concerned with the identification of the first set of molecular markers linked to the gene for mildew resistance, Pl-d, from the accession 'D12'. As no prior information on the map position or markers for Pl-d were available, a bulked-segregant approach was used to test 49 microsatellite primers, 176 amplified fragment length polymorphism (AFLP) primers and 80 random amplified polymorphic DNA (RAPD) primers in a progeny segregating for Pl-d resistance, 'Fiesta' (susceptible) x A871-14 ('Worcester Pearmain' x 'D12'). The segregations of the markers identified in the resistant and susceptible bulks were scored in the progeny, then the recombination fractions between Pl-d and the most tightly linked markers were calculated and a map prepared. Three AFLP, one RAPD and two microsatellite markers were identified. One AFLP was developed into a sequence-characterised amplified region marker, while the microsatellites CH03C02 and CH01D03 were flanking markers, 7 and 11 recombination units, respectively, from Pl-d. Two more distant microsatellites on the same linkage group, CH01D09 and CH01G12, confirmed the orientation of the markers on the linkage group. These microsatellites place Pl-d on the bottom of linkage group 12 in published apple maps, a region where a number of other disease resistance genes have been identified.

  15. Genetic diversity among some canola cultivars as revealed by RAPD, SSR and AFLP analyses.

    Science.gov (United States)

    Moghaieb, Reda E A; Mohammed, Etr H K; Youssief, Sawsan S

    2014-08-01

    To assess the genetic diversity among four canola cultivars (namely, Serw-3, Serw-4, Misser L-16 and Semu 249), random amplified polymorphic DNA (RAPD), simple sequence repeat polymorphism (SSR) and amplified fragment length polymorphism (AFLP) analyses were performed. The data indicated that all of the three molecular markers gave different levels of polymorphism. A total of 118, 31 and 338 markers that show 61, 67.7 and 81 % polymorphism percentages were resulted from the RAPD, SSR and AFLP analyses, respectively. Based on the data obtained the three markers can be used to differentiate between the four canola cultivars. The genotype-specific markers were determined, 18 out of the 72 polymorphic RAPD markers generated were found to be genotype-specific (25 %). The highest number of RAPD specific markers was scored for Semu 249 (15 markers), while Serw-4 scored two markers. On the other hand, Serw-3 scored one marker. The cultivar Semu 249 scored the highest number of unique AFLP markers, giving 57 unique markers, followed by Misser L-16 which was characterized by 40 unique AFLP markers, then Serw-3 giving 31 unique markers. While Serw-4 was characterized by the lowest number producing 14 unique positive markers. The dendrogram built on the basis of combined data from RAPD, SSR and AFLP analysis represents the genetic distances among the four canola cultivars. Understanding the genetic variability among the current canola cultivars opens up a possibility for developing a molecular genetic map that will lead to the application of marker-assisted selection tools in genetic improvement of canola.

  16. Advances in molecular marker techniques and their applications in plant sciences.

    Science.gov (United States)

    Agarwal, Milee; Shrivastava, Neeta; Padh, Harish

    2008-04-01

    Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation to phenotypes provide us with requisite landmarks for elucidation of genetic variation. Genetic or DNA based marker techniques such as RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA), SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) are routinely being used in ecological, evolutionary, taxonomical, phylogenic and genetic studies of plant sciences. These techniques are well established and their advantages as well as limitations have been realized. In recent years, a new class of advanced techniques has emerged, primarily derived from combination of earlier basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques. The newer methods also incorporate modifications in the methodology of basic techniques to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. The advanced marker techniques also utilize newer class of DNA elements such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The review details account of techniques used in identification of markers and their applicability in plant sciences.

  17. Screening of AFLP markers related to growth traits in Tegillarca granosa%泥蚶生长性状相关AFLP分子标记的筛选

    Institute of Scientific and Technical Information of China (English)

    董迎辉; 姚韩韩; 林志华; 肖国强; 柴雪良

    2012-01-01

    The bloody clam, Tegillarca granosa, is an important commercial bivalve which is extensively cultured from South Korea to Malaysia. Due to its economic value, it is important to cultivate rapid growth strains for the sustainable development of aquaculture industry of T. granosa. The emergence of molecular markers provides a rich theoretical basis for the rapid cultivation varieties. By the method of group selection, the rapid growth strains of T. granosa were bred though two generations. According to the comparison test, the rapid growth strains showed significant advantages in shell length, shell height, shell width and total weight than control group under the same environmental conditions. AFLP marker was applied in this study to evaluate the genetic variation of the rapid growth strains, and to screen the molecular markers associated with the traits of growth. A total of 2180 bands were amplified from 64 individuals of the rapid growth strain and control group by 40 primer combinations. The analysis of Nei's genetic diversity index and Shannon's genetic information index of two groups indicated that the genetic diversity of breeding group was slightly higher than the control group. The genetic distance between two groups was about 0.011 3, the value of GSt was 0.022 4 and Nm was 22.281 1, from which we concluded that there is a little genetic differentiation after selection. Of all amplified bands, 7 bands showed significant differences in frequency between two groups. 2 bands of all were only found in rapid growth strains, with the frequency of 0.812 5 and 0.343 8, respectively. And 2 bands showed significantly higher frequencies in rapid growth strains, while 3 bands showed significantly higher frequencies in control group. The bands with higher frequencies in rapid growth strains may be associated with the traits of growth. The unique AFLP markers associated with growth traits would be useful for growth-related gene cloning, quantitative trait locus (QTL

  18. Molecular linkage mapping and marker-trait associations with NlRPT, a downy mildew resistance gene in Nicotiana langsdorffii

    Directory of Open Access Journals (Sweden)

    Shouan eZhang

    2012-08-01

    Full Text Available 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 (SSR, 10 conserved orthologous sequence (COS markers, nine inter-simple sequence repeat (ISSR markers, and four target region amplification polymorphism (TRAP markers arranged in 12 linkage groups with a combined length of 1062 cM. NlRPT is located on linkage group 3, 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

  19. Veronaea botryosa: molecular identification with amplified fragment length polymorphism (AFLP) and in vitro antifungal susceptibility.

    Science.gov (United States)

    Badali, Hamid; Yazdanparast, Seyed Amir; Bonifaz, Alexandro; Mousavi, Bita; de Hoog, G Sybren; Klaassen, Corné H W; Meis, Jacques F

    2013-06-01

    Inter- and intraspecific genomic variability of 18 isolates of Veronaea botryosa originating from clinical and environmental sources was studied using amplified fragment length polymorphism (AFLP). The species was originally described from the environment, but several severe cases of disseminated infection in apparently healthy individuals have been reported worldwide. All tested strains of V. botryosa, identified on the basis of sequencing and phenotypic and physiological criteria prior to our study, were confirmed by AFLP analysis, yielding a clear separation of V. botryosa as a rather homogeneous group from related species. In vitro antifungal susceptibility testing resulted in MIC90s across all strains in increasing order posaconazole (0.25 μg/ml), itraconazole (1 μg/ml), voriconazole (4 μg/ml), terbinafine (4 μg/ml), caspofungin (8 μg/ml), anidulafungin (8 μg/ml), isavuconazole (16 μg/ml), amphotericin B (16 μg/ml), and fluconazole (32 μg/ml). Overall, the isolates showed a uniform pattern of low MICs of itraconazole and posaconazole, but high MICs for remaining agents. The echinocandins (caspofungin and anidulafungin) had no activity against V. botryosa. There was no statistically significant difference between susceptibilities of environmental (n = 11) and clinical (n = 7) isolates of V. botryosa (P > 0.05).

  20. Molecular Markers: an Introduction and Applications

    Directory of Open Access Journals (Sweden)

    Firas Rashad Al-Samarai

    2015-09-01

    Full Text Available The dramatic development of molecular genetics has laid the groundwork for genomics. It has introduced new generations of molecular markers for use in the genetic improvement of farm animals. These markers provide more accurate genetic information and better understanding of the animal genetic resources. Scientists, unfamiliar with the different molecular techniques tend to get lost as each has its own advantages and disadvantages. This review represents a trail to shade alight on the different types of molecular markers by introducing a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review could be helpful to better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.

  1. Assessment of Genetic Stability Among In Vitro Plants of Arachis retusa Using RAPD and AFLP Markers for Germplasm Preservation

    Institute of Scientific and Technical Information of China (English)

    Rachel Fatima Gagliardi; Luiz Ricardo Hanai; Georgia Pacheco; Carlos Alberto Oliveira; Leonardo Alves Carneiro; José Francisco Montenegro Valls; Elisabeth Mansur; Maria Lucia Carneiro Vieira

    2007-01-01

    Arachis retusa Krapov. et W. C. Gregory et Valls is endemic in the West-central region of Brazil, occurring in areas endangered by human actions. The establishment of in vitro preservation methods for wild species of Arachis isan alternative to seed banks for germplasm storage, multiplication and distribution. The risk of genetic changesinduced by tissue culture and the monitoring of the genetic stability of the biological material before, during andafter storage must be considered in the context of conservation. Random amplified polymorphic DNA (RAPD) andamplified fragment length polymorphism (AFLP) fingerprinting were used to evaluate the genetic stability of invitro plants originated from cotyledons and embryo axes of A. retusa. Cotyledons originated shoots through directorganogenesis and embryo axes displayed multishoot formation induced by 110 mmol/L and 8.8 mmol/L BAP,respectively. Ninety genomlc regions (loci) generated from RAPD and 372 from AFLP analyses were evaluated. Allamplified fragments detected by both techniques in plants derived from the two explant types were monomorphic.The results indicate that the recovered shoots are genetically stable at the assessed genomic regions.

  2. AFLP Fingerprint and SCAR Marker of Watermelon Core Collection%西瓜核心种质的AFLP指纹图谱和SCAR标记

    Institute of Scientific and Technical Information of China (English)

    车克鹏; 许勇; 梁春阳; 宫国义; 翁曼丽; 张海英; 金德敏; 王斌

    2003-01-01

    西瓜(Citrullus lanatus (Thunb.) Mansf.)种质资源的鉴定与评价是对其有效利用的基础.以往的研究表明, 西瓜是一种遗传资源特别狭窄的作物,在用同工酶、RAPD及SSR技术对西瓜种质资源进行鉴定时,发现很难将品种完全区分开来.本研究利用高效可靠的AFLP技术,对30个西瓜核心种质材料进行了遗传分析,最终建立了这30个材料的DNA指纹图谱.在该图谱中,每个材料均有其独特的"指纹",材料之间可以相互区分开来.为了进一步利用AFLP分子标记,将重要抗病种质材料"PI296341"的AFLP特异带转化成了生产上可以直接利用的SCAR标记.%The identification of germplasm is an important step for effective utilization of the available germplasm. In previous studies, isoenzyme, RAPD and SSR techniques had been used to conduct the genetic identification of watermelon (Citrullus lanatus (Thunb.) Mansf.), but their effectiveness was limited due to the extremely narrow genetic background among watermelon genotypes. In this research, amplified fragment length polymorphism (AFLP), which was reported as a reliable technique with high efficiency in detecting polymorphism, was used to conduct genetic analysis and variety identification of thirty genotypes of watermelon core collection that represent a wide range of breeding and commercially available germplasm. As a result, a DNA fingerprint based on 15 bands amplified with four primer combinations was developed. In this fingerprint, each genotype has its unique fingerprint pattern and can be distinguished from each other. Furthermore, in order to facilitate the utilization of AFLP marker in practice, one specific AFLP band of genotype "PI296341" coming from fragment amplified by primer combination E-AT/M-CAT was successfully converted into a sequence characterized amplified region (SCAR) marker.

  3. Diversidade genética entre híbridos de laranja-doce e tangor 'Murcott' avaliada por fAFLP e RAPD Genetic diversity among hybrids of sweet orange and 'Murcott' tangor evaluated by fAFLP and RAPD markers

    Directory of Open Access Journals (Sweden)

    Marinês Bastianel

    2006-05-01

    Full Text Available O objetivo deste trabalho foi avaliar a diversidade genética em uma população de 148 híbridos de tangor 'Murcott' (Citrus reticulata Blanco x C. sinensis L. Osbeck e laranja 'Pêra' (C. sinensis L. Osbeck obtidos por polinização controlada, pelo uso de marcadores fAFLP e RAPD. Marcadores polimórficos (416 marcadores fAFLP e 33 RAPD foram utilizados para avaliar a similaridade genética entre os híbridos, calculada com o coeficiente Jaccard pelo método UPGMA. A consistência de cada agrupamento foi determinada pelo programa BOOD. Houve alta similaridade genética entre os parentais. A laranja 'Pêra' apresentou maior número (132 de loci em heterozigose em relação ao tangor 'Murcott' (105, corroborando a teoria de origem híbrida para a laranja-doce. Observaram-se dois grupos distintos de plantas, e um deles abrangeu 80% dos híbridos com maior similaridade com a laranja 'Pêra'. A análise bootstrap não revelou consistência estatística entre esses grupos. Marcadores fAFLP são mais eficientes na avaliação do polimorfismo, sendo indicados para seleção de indivíduos híbridos mais próximos a um dos parentais.The objective of this work was to evaluate the genetic diversity in a population of 148 hybrids of 'Murcott' tangor (Citrus reticulata Blanco x C. sinensis L. Osbeck and 'Pêra' sweet orange (C. sinensis L. Osbeck, obtained by controlled polination, using fAFLP and RAPD markers. Polymorphic markers (416 fAFLP and 33 RAPD markers were used to evaluate genetic similarity among the hybrids, calculated by the coefficient of Jaccard, using the UPGMA method. The consistency of each group was determined by software BOOD. There was high genetic similarity within the parents. 'Pêra' sweet orange had a higher number of loci in heterozygosis (132 compared to 'Murcott' tangor (105, supporting the theory of hybrid origin for sweet oranges. Two distinct groups of plants were observed: one group had 80% of the hybrids that displayed

  4. Comparison of genetic diversity of the invasive weed Rubus alceifolius poir. (Rosaceae) in its native range and in areas of introduction, using amplified fragment length polymorphism (AFLP) markers.

    Science.gov (United States)

    Amsellem, L; Noyer, J L; Le Bourgeois, T; Hossaert-McKey, M

    2000-04-01

    Theory predicts that colonization of new areas will be associated with population bottlenecks that reduce within-population genetic diversity and increase genetic differentiation among populations. This should be especially true for weedy plant species, which are often characterized by self-compatible breeding systems and vegetative propagation. To test this prediction, and to evaluate alternative scenarios for the history of introduction, the genetic diversity of Rubus alceifolius was studied with amplified fragment length polymorphism (AFLP) markers in its native range in southeast Asia and in several areas where this plant has been introduced and is now a serious weed (Indian Ocean islands, Australia). In its native range, R. alceifolius showed great genetic variability within populations and among geographically close populations (populations sampled ranging from northern Vietnam to Java). In Madagascar, genetic variability was somewhat lower than in its native range, but still considerable. Each population sampled in the other Indian Ocean islands (Mayotte, La Réunion, Mauritius) was characterized by a single different genotype of R. alceifolius for the markers studied, and closely related to individuals from Madagascar. Queensland populations also included only a single genotype, identical to that found in Mauritius. These results suggest that R. alceifolius was first introduced into Madagascar, perhaps on multiple occasions, and that Madagascan individuals were the immediate source of plants that colonized other areas of introduction. Successive nested founder events appear to have resulted in cumulative reduction in genetic diversity. Possible explanations for the monoclonality of R. alceifolius in many areas of introduction are discussed.

  5. Identification of an AFLP marker linked to the stripe rust resistance gene Yr1O in wheat

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    AFLP analysis of near-isogenic lines of the stripe rust resistance gene Yr10 was carried out with 6 Pst Ⅰprimers and 10 Taq Ⅰ -primers with the donor parent of Yr10 gene as the check. A total of about 4200 distinguishable bands were amplified, of which 5 were stable. The genetic linkage of the 5 polymorphic DNA fragments with the target gene were tested preliminarily on a segregating F2 population derived from a cross between the gene donor parent "Moro" and susceptible cultivar "Mingxian 169". The DNA fragment PT0502 was found closely linked to the Yr10 gene and cloned and sequenced. Based on the sequence specific primers for PCR were designed and synthesized. Genetic linkage analysis with 195 segregating F2 plants indicated that the genetic distance was 05 cM between the main product SC200 fragment produced by PCR with the primers and the Yr10 gene. The primers can be used to detect the Yr10 gene quickly, effectively and exactly.``

  6. Investigating Genetic Diversity of Foeniculum Vulgare Mill using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Omid Jadidi

    2016-06-01

    Full Text Available Medicinal plants are considered valuable genetic resources in Iran. One of these medicinal as well as spice plants is Foeniculum Vulgare Mill from Umbellifetae family used in different industries such as food, medicine, and cosmetics. It seems that due to different climate conditions in Iran this plant represents a high and valuable genetic diversity; therefore, management of genetic resources protection and obtaining information about genetic diversity will help awareness of evolution processes as well as genetic erosion of this valuable plant. Genetic diversity in local masses of Foeniculum Vulgare Mill can be investigated using molecule markers such as AFLP, RAPD, ISSR, SRAP, RFLP, and so on. In investigation of over 30 ecotype of local Foeniculum Vulgare Mill, different markers have shown that mean polymorphic content (PIC is about 36% and mean genetic diversity is estimated about 40% in different samples. Data obtained from molecule software analyses help to categorize Foeniculum Vulgare Mill genotype in different groups based on climate and geographical conditions. Principle components analysis (PCOA has also confirmed the results of cluster analysis. Dendrogram obtained by cluster analysis based on similarity coefficient of simple matching (SM and UPGMA algorithm can also categorize population of Foeniculum Vulgare Mill in different groups. Results of molecular variance analysis (AMOVA have shown that most genetic variance between geographical groups can be seen in populations. In general, according to investigations, there is a significant genetic diversity regarding agronomic and molecular traits of Foeniculum Vulgare Mill masses in Iran and knowing this genetic diversity will help in breeding programs, complementary studies, categorization, and so on.

  7. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L. germplasm.

    Directory of Open Access Journals (Sweden)

    Matteo Busconi

    Full Text Available The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence and epigenetic (cytosine methylation level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12 effective different genotypes, the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28 different effective epigenotypes. The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real and accessions from the East (Cuenca and Teruel were clearly recognised.

  8. AFLP and MS-AFLP analysis of the variation within saffron crocus (Crocus sativus L.) germplasm.

    Science.gov (United States)

    Busconi, Matteo; Colli, Licia; Sánchez, Rosa Ana; Santaella, Marcela; De-Los-Mozos Pascual, Marcelino; Santana, Omar; Roldán, Marta; Fernández, José-Antonio

    2015-01-01

    The presence and extent of genetic variation in saffron crocus are still debated, as testified by several contradictory articles providing contrasting results about the monomorphism or less of the species. Remarkably, phenotypic variations have been frequently observed in the field, such variations are usually unstable and can change from one growing season to another. Considering that gene expression can be influenced both by genetic and epigenetic changes, epigenetics could be a plausible cause of the alternative phenotypes. In order to obtain new insights into this issue, we carried out a molecular marker analysis of 112 accessions from the World Saffron and Crocus Collection. The accessions were grown for at least three years in the same open field conditions. The same samples were analysed using Amplified Fragment Length Polymorphism (AFLP) and Methyl Sensitive AFLP in order to search for variation at the genetic (DNA sequence) and epigenetic (cytosine methylation) level. While the genetic variability was low (4.23% polymorphic peaks and twelve (12) effective different genotypes), the methyl sensitive analysis showed the presence of high epigenetic variability (33.57% polymorphic peaks and twenty eight (28) different effective epigenotypes). The pattern obtained by Factorial Correspondence Analysis of AFLP and, in particular, of MS-AFLP data was consistent with the geographical provenance of the accessions. Very interestingly, by focusing on Spanish accessions, it was observed that the distribution of the accessions in the Factorial Correspondence Analysis is not random but tends to reflect the geographical origin. Two clearly defined clusters grouping accessions from the West (Toledo and Ciudad Real) and accessions from the East (Cuenca and Teruel) were clearly recognised.

  9. MOLECULAR MARKERS FOR METASTATIC PROSTATE ADENOCARCINOMA

    Directory of Open Access Journals (Sweden)

    I. S. Kunin

    2012-01-01

    Full Text Available The search of molecular markers of metastasing and prognosis in prostate cancer remains an urgent task. In this study, we investigated the relationship of gene expression heparanase-1 (HPSE1 and D-glucuronil C5-epimerase (GLCE with early disease relapse and metastasis of a 2,5−3 years after diagnosis. It was shown that the ratio of the expression levels of genes HPSE1/GLCE > 1 may serve as a prognostic relapse marker and trends of the tumour to metastasis. The data obtained suggest to use this option as a molecular marker for the diagnostics of metastatic process and the disease prognosis.

  10. NABIC marker database: A molecular markers information network of agricultural crops

    OpenAIRE

    2013-01-01

    In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number...

  11. Ecological Epigenetics: Beyond MS-AFLP.

    Science.gov (United States)

    Schrey, Aaron W; Alvarez, Mariano; Foust, Christy M; Kilvitis, Holly J; Lee, Jacob D; Liebl, Andrea L; Martin, Lynn B; Richards, Christina L; Robertson, Marta

    2013-08-01

    Ecological Epigenetics studies the relationship between epigenetic variation and ecologically relevant phenotypic variation. As molecular epigenetic mechanisms often control gene expression, even across generations, they may impact many evolutionary processes. Multiple molecular epigenetic mechanisms exist, but methylation of DNA so far has dominated the Ecological Epigenetic literature. There are several molecular techniques used to screen methylation of DNA; here, we focus on the most common technique, methylation-sensitive-AFLP (MS-AFLP), which is used to identify genome-wide methylation patterns. We review studies that used MS-AFLP to address ecological questions, that describe which taxa have been investigated, and that identify general trends in the field. We then discuss, noting the general themes, four studies across taxa that demonstrate characteristics that increase the inferences that can be made from MS-AFLP data; we suggest that future MS-AFLP studies should incorporate these methods and techniques. We then review the short-comings of MS-AFLP and suggest alternative techniques that might address some of these limitations. Finally, we make specific suggestions for future research on MS-AFLP and identify questions that are most compelling and tractable in the short term.

  12. AFLP markers for the R-gene in the flea beetle, Phyllotreta nemorum, conferring resistance to defenses in Barbarea vulgaris

    NARCIS (Netherlands)

    Breuker, C.J.; Victoir, K.; Jong, de P.W.; Meijden, van der E.; Brakefield, P.M.; Vrieling, K.

    2005-01-01

    A so-called R-gene renders the yellow-striped flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae: Alticinae) resistant to the defenses of the yellow rocket Barbarea vulgaris R.Br. (Brassicacea) and enables it to use it as a host plant in Denmark. In this study, genetic markers for an auto

  13. AFLP fingerprinting for paternity testing in ducks.

    Science.gov (United States)

    Huang, C-W; Cheng, Y-S; Rouvier, R; Yang, K-T; Wu, C-P; Huang, M-C

    2007-06-01

    1. The accuracy and reproducibility of AFLP fingerprinting was investigated in the duck (Anas Platyrhynchos), using a multicolour fluorescent labeling technique. The fluorescent labelling fragments were separated on a capillary electrophoresis-base ABI PRISM 3100 Genetic Analyzer. 2. A total of 337 AFLP peaks with 103 of them being polymorphic markers were generated by 16 sets consisting of EcoRI/TaqI primer pair combinations. The number and size range of AFLP polymorphisms detected per primer pair varied from 3 to 11 and 58 to 290 bp, respectively. About 30.6% (103/337) of AFLP peaks were detected polymorphisms, with an average of 6.4 polymorphic markers per primer pair. 3. The clear polymorphic peaks were amplified with EcoR+AC/Taq+AC primer combinations. The AFLP peaks showed high reproducibility. From the family testing, we found that the fingerprints of all the offspring were derived from one or other parent. Therefore, we conclude that AFLP fingerprinting might be a suitable method for duck paternity testing.

  14. Molecular markers in pediatric neuro-oncology.

    Science.gov (United States)

    Ichimura, Koichi; Nishikawa, Ryo; Matsutani, Masao

    2012-09-01

    Pediatric molecular neuro-oncology is a fast developing field. A multitude of molecular profiling studies in recent years has unveiled a number of genetic abnormalities unique to pediatric brain tumors. It has now become clear that brain tumors that arise in children have distinct pathogenesis and biology, compared with their adult counterparts, even for those with indistinguishable histopathology. Some of the molecular features are so specific to a particular type of tumors, such as the presence of the KIAA1549-BRAF fusion gene for pilocytic astrocytomas or SMARCB1 mutations for atypical teratoid/rhabdoid tumors, that they could practically serve as a diagnostic marker on their own. Expression profiling has resolved the existence of 4 molecular subgroups in medulloblastomas, which positively translated into improved prognostication for the patients. The currently available molecular markers, however, do not cover all tumors even within a single tumor entity. The molecular pathogenesis of a large number of pediatric brain tumors is still unaccounted for, and the hierarchy of tumors is likely to be more complex and intricate than currently acknowledged. One of the main tasks of future molecular analyses in pediatric neuro-oncology, including the ongoing genome sequencing efforts, is to elucidate the biological basis of those orphan tumors. The ultimate goal of molecular diagnostics is to accurately predict the clinical and biological behavior of any tumor by means of their molecular characteristics, which is hoped to eventually pave the way for individualized treatment.

  15. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  16. [Development and appraisement of functional molecular marker: intron sequence amplified polymorphism (ISAP)].

    Science.gov (United States)

    Lu, Cai-Rui; Yu, Shu-Xun; Yu, Ji-Wen; Fan, Shu-Li; Song, Mei-Zhen; Wang, Wu; Ma, Shu-Juan

    2008-09-01

    Molecular markers are playing an increasingly important role in map construction, QTL analysis, gene mapping and marker-assisted selection. Researchers hope the target gene and locus are as close as possible, one locus can present one gene, or linked with some important trait, then, individuals with useful trait can be selected through molecular markers selecting, and it's the functional molecular marker. PCR-based molecular markers such as RAPD, SSR, AFLP amplified non-coding regions, or the whole genome randomly, the locus is far away from the gene of targeted trait, this limit the ap-plication of these molecular markers. This study established a kind of functional molecular markers based on intron of gene sequence, trying to link loci with gene sequence to achieve the purpose of its function. It used the conservative consistent sequence of intron splicing sites as its core sequence of amplification. ISAP is a PCR-based marker system, it has two kinds of primers: forward primer and reverse primer, both primers are 18 bases. Any of the primers can be used to construct a primer combination with the other kind of primers. Seventeen primers, 9 forward and 8 reverse, were used to construct 72 primer combinations, 67 of them showed polymorphism in a G. hirsutum cv. CCRI36 x G. barbadense cv. H7124 F2 population and a total of 212 loci were obtained. Together with 164 SRAP loci, these 212 loci were used to construct a genetic linkage map. ISAP markers distributed evenly in the entire linkage group, part of the region had a high saturation, might be the coding sequence-rich region. Sequencing results of 20 fragments showed that 85% of the sequences announced homology with published EST sequence stored in the NCBI which indicated that they were amplified adjacent to expressed sequences. These results showed that ISAP marker system was simple, efficient, reliable, and had a relatively high polymorphism, furthermore, it directly targeted gene sequence, was a functional

  17. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

    Directory of Open Access Journals (Sweden)

    Ramina Angelo

    2008-07-01

    Full Text Available Abstract Background After 10-year-use of AFLP (Amplified Fragment Length Polymorphism technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO, consisting in three structured vocabularies (i.e. ontologies describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization

  18. Molecular markers for thyroid cancer diagnosis, prognosis, and targeted therapy.

    Science.gov (United States)

    Yip, Linwah

    2015-01-01

    Molecular markers including gene expression profiles, somatic gene alterations, and circulating peripheral markers have augmented diagnostic, prognostic, and therapeutic options for thyroid cancer patients.

  19. Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers.

    Science.gov (United States)

    Hashimoto, Z; Mori, N; Kawamura, M; Ishii, T; Yoshida, S; Ikegami, M; Takumi, S; Nakamura, C

    2004-11-01

    Japanese rice ( Oryza sativa L.) cultivars that are strictly used for the brewing of sake (Japanese rice wine) represent a unique and traditional group. These cultivars are characterized by common traits such as large grain size with low protein content and a large, central white-core structure. To understand the genetic diversity and phylogenetic characteristics of sake-brewing rice, we performed amplified fragment length polymorphism and simple sequence repeat analyses, using 95 cultivars of local and modern sake-brewing rice together with 76 cultivars of local and modern cooking rice. Our analysis of both nuclear and chloroplast genome polymorphisms showed that the genetic diversity in sake-brewing rice cultivars was much smaller than the diversity found in cooking rice cultivars. Interestingly, the genetic diversity within the modern sake-brewing cultivars was about twofold higher than the diversity within the local sake-brewing cultivars, which was in contrast to the cooking cultivars. This is most likely due to introgression of the modern cooking cultivars into the modern sake-brewing cultivars through breeding practices. Cluster analysis and chloroplast haplotype analysis suggested that the local sake-brewing cultivars originated monophyletically in the western regions of Japan. Analysis of variance tests showed that several markers were significantly associated with sake-brewing traits, particularly with the large white-core structure.

  20. Use of molecular marker techniques in seed testing by Brazilian seed companies

    Directory of Open Access Journals (Sweden)

    Della Vecchia P.T.

    1998-01-01

    Full Text Available Seed market is becoming global and globalization is growing very fast. To compete favourably in this new global seed world, quality and cost are and will be certanly the key issues. High seed quality can only be obtained by a thorough control of the entire seed production process, step by step from planning to final delivery. That requires science, technology, expertise, experience, good management and certanly, the most important, an absolute and unconditional commitment with quality. Seed testing for quality assurance is one important step in the process of production of high quality seed. In the late years a considerable amount of research has been published, particularly on the use of some Polymerase Chain Reaction DNA based new technologies (RAPD, microsatelites, AFLP for genetic purity determinations in seed testing. As far as we know, no Brazilian seed company is using, on regular basis, RAPD or other molecular marker techniques in the determination of genetic purity in seed testing. Most of these are using morphological or physiological traits expressed by seed, seedling or mature plant and/or electrophoresis of seed or seedling proteins/isoenzymes for that purpose. Main reasons for that are: DNA molecular marker techniques are relatively new; lack of specialized personnel to run DNA molecular marker assays on routine basis; higher cost/sample when compared to proteins/isoenzymes electrophoresis.

  1. Molecular and Clinical Markers of Pancreas Cancer

    OpenAIRE

    James L Buxbaum; Eloubeidi, Mohamad A

    2010-01-01

    Pancreas cancer has the worst prognosis of any solid tumor but is potentially treatable if it is diagnosed at an early stage. Thus there is critical interest in delineating clinical and molecular markers of incipient disease. The currently available biomarker, CA 19-9, has an inadequate sensitivity and specificity to achieve this objective. Diabetes mellitus, tobacco use, and chronic pancreatitis are associated with pancreas cancer. However, screening is currently only recommended in those wi...

  2. Fecal Molecular Markers for Colorectal Cancer Screening

    Directory of Open Access Journals (Sweden)

    Rani Kanthan

    2012-01-01

    Full Text Available Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.

  3. Molecular and Clinical Markers of Pancreas Cancer

    Directory of Open Access Journals (Sweden)

    James L Buxbaum

    2010-11-01

    Full Text Available Pancreas cancer has the worst prognosis of any solid tumor but is potentially treatable if it is diagnosed at an early stage. Thus there is critical interest in delineating clinical and molecular markers of incipient disease. The currently available biomarker, CA 19-9, has an inadequate sensitivity and specificity to achieve this objective. Diabetes mellitus, tobacco use, and chronic pancreatitis are associated with pancreas cancer. However, screening is currently only recommended in those with hereditary pancreatitis and genetic syndromes which predispose to cancer. Ongoing work to identify early markers of pancreas cancer consists of high throughput discovery methods including gene arrays and proteomics as well as hypothesis driven methods. While several promising candidates have been identified none has yet been convincingly proven to be better than CA 19-9. New methods including endoscopic ultrasound are improving detection of pancreas cancer and are being used to acquire tissue for biomarker discovery.

  4. Caracterización molecular de introducciones colombianas de caña flecha utilizando la técnica AFLP

    Directory of Open Access Journals (Sweden)

    Hernando Rivera Jiménez

    2008-12-01

    Full Text Available La fibra de la caña flecha Gynerium sagittatum (Aubl. se utiliza como materia prima para fabricar el "sombrero vueltiao", sombrero típico de la costa caribeña colombiana. Se realizó la caracterización molecular con AFLP para estimar variabilidad genética teniendo en cuenta criterios geográficos y morfológicos de 25 introducciones colombianas del banco de germoplasma de la Universidad de Córdoba. El análisis de correspondencia múltiple discriminó las introducciones en cuatro grupos, donde se identificaron características de importancia artesanal (comercial y atributos agronómicos. Se observó escasa correlación entre distancia geográfica y diferenciación genética, lo cual indicó flujos antrópicos por la reproducción asexual del material.

  5. An expanded genetic linkage map of an intervarietal Agaricus bisporus var. bisporusxA. bisporus var. burnettii hybrid based on AFLP, SSR and CAPS markers sheds light on the recombination behaviour of the species.

    Science.gov (United States)

    Foulongne-Oriol, Marie; Spataro, Cathy; Cathalot, Vincent; Monllor, Sarah; Savoie, Jean-Michel

    2010-03-01

    A genetic linkage map for the edible basidiomycete Agaricus bisporus was constructed from 118 haploid homokaryons derived from an intervarietal A. bisporus var. bisporus x A. bisporus var. burnettii hybrid. Two hundred and thirty-one AFLP, 21 SSR, 68 CAPS markers together with the MAT, BSN, PPC1 loci and one allozyme locus (ADH) were evenly spread over 13 linkage groups corresponding to the chromosomes of A. bisporus. The map covers 1156cM, with an average marker spacing of 3.9cM and encompasses nearly the whole genome. The average number of crossovers per chromosome per individual is 0.86. Normal recombination over the entire genome occurs in the heterothallic variety, burnettii, contrary to the homothallic variety, bisporus, which showed adaptive genome-wide suppressed recombination. This first comprehensive genetic linkage map for A. bisporus provides foundations for quantitative trait analyses and breeding programme monitoring, as well as genome organisation studies.

  6. Molecular Identification and Mapping of a Maize Gene (Rf3) in S-type CMS Using AFLP, RFLP and SCAR Techniques%运用近等基因系(NIL)、AFLP、RFLP和SCAR标记对玉米S组育性恢复基因(Rf3)的研究

    Institute of Scientific and Technical Information of China (English)

    王泽立; 王鲁昕; 戴景瑞; 王斌; 李新征

    2001-01-01

    The maize CMS-S near isogenic line (NIL) developed by auther and the backcross progeny (BC1) derived from it were used to identify molecular markers linked to the Rf3 gene and subsequently determine its chromosomal location on the linkage map of maize. Bulk segreant analysis was performed using AFLP technique. From the survey of AFLP primer combination, two AFLP markers, (EcoR-AGG/ Mse-CAC and EcoR-AAC/Mse-CAG), which were named RR6 and RR7 respectively, linked to the Rf3 gene were identified. However, AFLP marker RR6 showed polymorphism between parents, and bulks were used to survey the available 100 individuals of the BC1 population, 2 out of 100 shed recombination. The recombination-rate was 2%. The genetic distance between Rf3 gene and AFLP marker RR6, was approximately 2.0cM. And then, the RR6 was successfully cloned and sequenced, primer synthesized and converted to SCAR marker so that PCR marker can be developed for the marker-assisted selection. In RFLP analysis, marker RR6 linked to Rf3 was found to be located between RFLP loci asg20 and php20581b, and mappedon chromosome 2L.%以1对近等基因系(NIL)及其回交群体(BC1)为材料,采用BSA法,利用AFLP技术,筛选与Rf3基因连锁的分子标记。在筛选的128个AFLP引物组合中,有2个能在NIL及其可育池、不育池间扩增出多态性条带RR6和RR7。100个BC1个体验证结果表明,AFLP标记RR6扩增产物中仅出现2个重组体,重组率2%,由此估测RR6距Rf3基因约2.0cM。并成功地将此标记转化为SCAR标记,进行了NIL和BC1个体的特异性扩增。在来自综3×P138的F23的群体上经RFLP分析后,将RR6定位于第二染色体的长臂上。不仅为辅助育种奠定了基础,而且为克隆Rf3基因提供了有益的信息。

  7. MOLECULAR PROGNOSTIC MARKERS OF URINE BLADDER CANCER

    Directory of Open Access Journals (Sweden)

    V. N. Pavlov

    2012-01-01

    Full Text Available Bladder cancer (BC remains a current problem in oncourology. Despite that bladder cancer risk factors have been studied and described in the literature, new molecular and genetic mechanisms have been identified that predisposes to the disease development. There are numerous cellular processes involve in BC pathogenesis. The less-aggressive, non-invasive slow progressing bladder cancer types are defined by Ras-MAPK system activation. Tumors that are more aggressive and have low cancer-specific survival rate are characterized by changes in retinoblastoma genes and p53. Attempts are made to develop prognostic tests to predict tumor behavior, targeted treatment. perspectively, BC patients will be treated using molecular genetic markers allowing the accurate prediction of the patient’s tumor behavior and fitting the treatment tactics on the individual basis.

  8. Similaridade genética entre cultivares de cebola de diferentes tipos e origens, baseada em marcadores AFLP Genetic similarity among onion cultivars of different types and origins, based on AFLP markers

    Directory of Open Access Journals (Sweden)

    CAF Santos

    2011-03-01

    Full Text Available Foi estimada a similaridade genética entre cultivares de cebola de diferentes tipos e regiões geográficas, de forma a orientar programas de recursos genéticos e melhoramento da espécie no Nordeste brasileiro. Foram analisadas 41 cultivares, adotando-se para a visualização da similaridade genética o fenograma UPGMA gerado da matriz de distâncias genéticas estimadas pelo coeficiente de Jaccard e baseadas em 146 bandas polimórficas de Pst1 e Mse1 de AFLP. A correlação cofenética foi de 0,91, indicando boa confiabilidade da representação gráfica para a interpretação dos resultados. Foram observados dois grupos principais no fenograma, no ponto de corte de 0,55 de similaridade: 1 grupo formado por cultivares predominantemente brasileiras, com algumas inclusões de cultivares estrangeiras; e 2 grupo formado por três cultivares estrangeiras (Mercedes, Perfect e TEG 502 PRR. Rijnsburger Jumbo e IPA 8 apresentaram a maior similaridade (85%, enquanto Madrugada foi a mais divergente em relação às demais cultivares. As cultivares da série IPA se dividiram em subgrupos no grupo das cultivares brasileiras (IPA 8, IPA 10 e IPA 11; IPA 12, IPA 7, IPA 2 e IPA 6; IPA 3, IPA 4 e IPA 9, indicando haver variabilidade genética a ser explorada entre aquelas situadas em subgrupos distintos. Bola Precoce e BRS Cascata apresentaram a maior similaridade entre as cultivares de origem brasileira. Foi observada similaridade superior a 39%, refletindo a alta variabilidade genética da coleção de cebola estudada. A introdução de novos acessos deve considerar procedências outras que não norte americanas, para aumentar a variabilidade de germoplasma de cebola disponível no Nordeste do Brasil.The genetic similarity among onion cultivars of different origins was evaluated, in order to carry out genetic resources and breeding programs for this species on the Brazilian Northeast. Forty-one onion cultivars were analyzed for 146 polymorphic Pst1/Mse1

  9. Construction of a genetic linkage map of black gram, Vigna mungo (L.) Hepper, based on molecular markers and comparative studies.

    Science.gov (United States)

    Gupta, S K; Souframanien, J; Gopalakrishna, T

    2008-08-01

    A genetic linkage map of black gram, Vigna mungo (L.) Hepper, was constructed with 428 molecular markers using an F9 recombinant inbred population of 104 individuals. The population was derived from an inter-subspecific cross between a black gram cultivar, TU94-2, and a wild genotype, V. mungo var. silvestris. The linkage analysis at a LOD score of 5.0 distributed all 428 markers (254 AFLP, 47 SSR, 86 RAPD, and 41 ISSR) into 11 linkage groups. The map spanned a total distance of 865.1 cM with an average marker density of 2 cM. The largest linkage group spanned 115 cM and the smallest linkage group was of 44.9 cM. The number of markers per linkage group ranged from 11 to 86 and the average distance between markers varied from 1.1 to 5.6 cM. Comparison of the map with other published azuki bean and black gram maps showed high colinearity of markers, with some inversions. The current map is the most saturated map for black gram to date and will provide a useful tool for identification of QTLs and for marker-assisted selection of agronomically important characters in black gram.

  10. The role of Molecular Markers in Improvement of Fruit Crops

    Directory of Open Access Journals (Sweden)

    Zahoor Ahmad BHAT

    2010-06-01

    Full Text Available Markers have been used over the years for the classification of plants. Markers are any trait of an organism that can be identified with confidence and relative easy, and can be followed in a mapping population on another hand markers be defined as heritable entities associated with the economically important trait under the control of polygenes. Morphological markers can be detected with naked eye (naked eye polymorphism or as difference in physical or chemical properties of the macromolecules. In other words, there are two types of genetic markers viz. morphological markers or naked eye polymorphism and non-morphological markers or molecular markers. Morphological markers include traits such as plant height, disease response, photoperiod, sensitivity, shape or colour of flowers, fruits or seeds etc. Molecular markers include biochemical constituents. Morphological markers have many limitations for being used as markers particularly in fruit crops because of long generation time and large size of fruit trees besides being influenced by environment. Consequently, molecular markers could be appropriate choice to study and preserve the diversity in any germplasm. Molecular markers have diverse applications in fruit crop improvement, particularly in the areas of genetic diversity and varietal identification studies, gene tagging, disease diagnostics, pedigree analysis, hybrid detection, sex differentiation and marker assisted selection.

  11. Identificação de marcas moleculares associadas à ausência de sementes em videira Identification of molecular markers associated to the absence of seeds in grapevine

    Directory of Open Access Journals (Sweden)

    Ana Veruska Cruz da Silva

    2006-06-01

    Full Text Available A ausência de sementes tem sido uma característica bastante exigida pelos consumidores de uvas de mesa. O objetivo deste trabalho foi identificar marcas moleculares associadas à ausência de sementes, utilizando as técnicas RAPD e fAFLP. Foram utilizadas folhas jovens de 19 cultivares. Na análise RAPD 30, iniciadores possibilitaram amplificação de todas as amostras, produzindo 392 bandas polimórficas. Foi possível encontrar uma marca específica para a ausência de sementes, utilizando o iniciador UBC 443, que poderá futuramente ser utilizado para o desenvolvimento de marcadores SCAR, possibilitando a criação de um teste de identificação rápida e precoce de apirenia em videira. A análise fAFLP proporcionou a visualização de um dendrograma com grupos específicos de cultivares com sementes, sem sementes e porta enxertos.Seedless has been an important characteristic of table grapes required by consumers. The objective was to identify molecular markers associated to seedless, by RAPD and fAFLP techniques with young leaves samples of 19 cultivars. Thirty primers were used for RAPD analysis, producing a total of 337 polymorphic bands. It was also to find a specific mark for seedless, using UBC 443 primer. This mark would be transformed in a scar marker, making possible the early identification of seedless grape possible. The fAFLP analysis provided a visualization of a dendrogram with specific groups, separated in three different cultivars: with seeds, without seeds and the rootstocks.

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

    Science.gov (United States)

    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

  13. Review of the Methods for Developing SSR Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xue; CHANG Wei; HAN Yingpeng; LI Wenbin

    2008-01-01

    Microsatellite marker (or Simple Sequence Repeate,SSR) is a marker technology based on DNA molecular length polymorphism.It is also one of the most commonly used molecular markers.Traditional SSR marker development methods are relatively time-consuming and mostly relying on the known genome sequence information while recently developed methods of SSR marker based on RAPD,ISSR-PCR SSR,the use of hybrid options, sequence tag SSR library access and screening EST-SSR have been widely used.This paper gave an overview of the methods mentioned above for the development of SSR markers.

  14. Determinación del sexo en borojó (Borojoa patinoi, Cuatrecasas mediante marcadores moleculares Determination of borojo sex (Borojoa patinoi, Cuatrecasas through molecular markers

    Directory of Open Access Journals (Sweden)

    Aguilar Enrique

    2004-12-01

    Full Text Available El borojó (Borojoa patinoi, Cuatrecasas una rubiacea endémica de la región Pacífica de Colombia, produce un fruto carnoso con importantes propiedades alimenticias que lo posicionan como un recurso genético promisorio. Se usa para preparar conservas y vino, pero su principal uso es como bebida refrescante. Económicamente representa una fuente de ingresos para algunas poblaciones nativas que comercializan la fruta o sus derivados en el mercado local o en las principales ciudades colombianas. El borojó es una planta dioica y los dos sexos no son fenotípicamente distinguibles antes de la floración (3-4 años después de la siembra, por lo cual la productividad de una plantación no seleccionada es sustancialmente reducida. El objetivo de este estudio fue determinar marcadores moleculares AFLP (Polimorfismo en la Longitud de Fragmentos Amplificados asociados al sexo de borojó. Con base en la secuencia de uno de estos marcadores ligados al sexo, se diseñó una pareja de iniciadores de 20 y 22 pb para diagnosticar el sexo de las plantas vía reacción en cadena de la polimerasa. Se analizaron plantas con sexo molecularmente identificado por PCR, encontrándose resultados congruentes entre éstas y los AFLP. Esto representa para los agricultores una oportunidad para establecer cultivos de borojó diseñados en cuanto a espacio y productividad esperada, en términos de número de árboles femeninos y masculinos plantados. Palabras clave: Borojoa patinoi, plantas dioicas, AFLP, marcadores ligados al sexo, diagnóstico de sexo.Borojó (Borojoa patinoi, Cuatrecasas, a rubiacea indigenous to the Colombian Pacific Region, produces a fleshy fruit having interesting nutritious characteristics making it a promising plant resource. It is used for fresh beverages; preserves and wine can also be obtained. It is an especially important source of income for some of the native population who sell it in local food markets and the main Colombian cities

  15. AFLP variation in 25 Avena species.

    Science.gov (United States)

    Fu, Yong-Bi; Williams, David J

    2008-08-01

    Current molecular characterization of ex situ plant germplasm has placed more emphasis on cultivated gene pools and less on exotic gene pools representing wild relative species. This study attempted to characterize a selected set of germplasm accessions representing various Avena species with the hope to establish a reference set of exotic oat germplasm for oat breeding and research. The amplified fragment length polymorphism (AFLP) technique was applied to screen 163 accessions of 25 Avena species with diverse geographic origins. For each accession, 413 AFLP polymorphic bands detected by five AFLP primer pairs were scored. The frequencies of polymorphic bands ranged from 0.006 to 0.994 and averaged 0.468. Analysis of molecular variance revealed 59.5% of the total AFLP variation resided among 25 oat species, 45.9% among six assessed sections of the genus, 36.1% among three existing ploidy levels, and 50.8% among eight defined genome types. All the species were clustered together according to their ploidy levels. The C genome diploids appeared to be the most distinct, followed by the Ac genome diploid A. canariensis. The Ac genome seemed to be the oldest in all the A genomes, followed by the As, Al and Ad genomes. The AC genome tetraploids were more related to the ACD genome hexaploids than the AB genome tetraploids. Analysis of AFLP similarity suggested that the AC genome tetraploid A. maroccana was likely derived from the Cp genome diploid A. eriantha and the As genome diploid A. wiestii, and might be the progenitor of the ACD genome hexaploids. These AFLP patterns are significant for our understanding of the evolutionary pathways of Avena species and genomes, for establishing reference sets of exotic oat germplasm, and for exploring new exotic sources of genes for oat improvement.

  16. Genetic Structure and Diversity Analysis Revealed by AFLP Markers on Different Glycyrrhiza glabra L. an Endangered Medicinal Species from South of Iran and Implications for Conservation.

    Science.gov (United States)

    Hakimi, Atieh; Zolfaghari, Maryam; Sorkheh, Karim

    2016-09-28

    Glycyrrhiza glabra is an endangered and national-protected medicinal plant species distributed in semi-arid and arid areas of South of Iran. This study addresses the genetic diversity and relationship between populations in different habitats by amplified fragment length polymorphism (AFLP). The plant materials consisted of 90 individuals from nine different populating areas of Dezful, Ramhormoz, Ahvaz, Abadan, Khorramshahr, Behbahan, Haft-tapeh, Andimeshk, and Shushtar. Twenty-three AFLP primer combinations generated a total of 1019 bands with 94.80 % polymorphism. Unweighted pair group method based on arithmetic average (UPGMA) analysis was performed on Jaccard's similarity coefficient matrix. According to results, the genetic resources and diversity in wild populations of G. glabra were rich. The number of polymorphic fragments per primer combination detected ranged from 18 to 65 bands with an average of 41.95 bands. Average polymorphic information content (PIC) was 0.81 in overall primer combinations. M-GTC+P-AGC primer combination showed the highest PIC (0.94) which can be a good candidate primer combination to verify genetic diversity in G. glabra. The UPGMA and principal coordinate analysis showed a clear distinction among the genotypes and the genotypes divided into three clusters in the dendrogram results. A model-based structure analysis revealed the presence of three groups. The study showed that genetic variation and population structure are determined among the accessions of G. glabra collected from different locations. High level of genetic variation in both intra- and inter-species was detected. Conservational efforts have to be strengthened for all populations of the plant species in different habitats.

  17. Characterization of Streptococcus suis through serotyping, SE-AFLP and virulence profile

    Directory of Open Access Journals (Sweden)

    Franco F. Calderaro

    Full Text Available Abstract: Streptococcus suis is one of most important pathogens in the swine industry worldwide. Despite its importance, studies of S. suis characterization in South America are still rare. This study evaluates S. suis isolates from distinct Brazilian states, from 1999 to 2004, and its molecular and serological characterization. A total of 174 isolates were studied. S. suis identification was confirmed by PCR and isolates were further serotyped and genotyped by SE-AFLP and amplification of virulence markers. Serotype 1, 2, 3, 4, 7, 18, 22 and 32 were identified among the studied isolates, and only 4% were characterized as non-typeable. The mrp+/epf+/sly+ genotype was the most frequent. The SE-AFLP analysis resulted in 29 patterns distributed in three main clusters with over 65% of genetic similarity. Isolates presented a slight tendency to cluster according to serotype and origin; however, no further correlation with virulence genotypes was observed.

  18. Análise da diversidade genética por AFLP e identificação de marcadores associados à resistência a doenças em videira Genetic diversity and identification of AFLP markers associated with diseases resistance in grapevine

    Directory of Open Access Journals (Sweden)

    Paulo Ricardo Dias de Oliveira

    2005-12-01

    Full Text Available Com objetivo de estudar diversidade genética e identificar marcadores associados à resistência ao míldio (Plasmopara viticola e ao oídio (Uncinula necator, foram analisadas as cultivares de videira A 1976, CG 87746, CNPUV 154-27, Crimson Seedless, Gota de Ouro, Itália, Seyve Villard 12327 e Seyve Villard 12375. As análises de polimorfismo de comprimento de fragmento amplificado (AFLP seguiram as etapas de digestão, ligação, pré-amplificação e amplificação. Efetuou-se a separação dos fragmentos amplificados em gel de 7% de poliacrilamida desnaturante (uréia 7M e coloração com nitrato de prata. A similaridade foi estimada com base no coeficiente de Jaccard, e a agregação, por UPGMA. Foi gerada uma matriz de similaridade com bom ajustamento da agregação (r = 0,84. Os agrupamentos obtidos corresponderam à origem e classificação botânica das cultivares. Foram identificadas 15 marcas dissimilares associadas à resistência, sendo oito para míldio e sete para oídio.The grapevine cultivars A 1976, CG 87746, CNPUV 154-27, Crimson Seedless, Gota de Ouro, Itália, Seyve Villard 12327 and Seyve Villard 12375 were analyzed to establish the genetic relationship and to identify markers associated with resistance to downy mildew (Plasmopara viticola and powdery mildew (Uncinula necator. The amplified fragment lenght polymorphism (AFLP analysis comprise the steps of digestion, ligation, preamplification and amplification. The amplified fragments were separeted on a 7% denaturing polyacrylamide gel (7M urea and silver stained. The similarity was estimated using Jaccard's coefficient and the clustering was estimated by UPGMA. A similarity matrix was generated with a good fit for aggregation (r = 0,84. The clusters corresponded to origin and botany classification of the cultivars. Fifteen markers were associated with resistance, eight for downy mildew and seven for powdery mildew.

  19. Caracterización molecular de introducciones colombianas de caña flecha utilizando la técnica AFLP

    Directory of Open Access Journals (Sweden)

    suarez Padron Isidro

    2008-12-01

    Full Text Available La fibra de la caña flecha Gynerium sagittatum (Aubl. se utiliza como materia prima para fabricar el "sombrero vueltiao", sombrero típico de la costa caribeña colombiana. Se realizó la caracterización molecular con AFLP para estimar variabilidad genética teniendo en cuenta criterios geográficos y morfológicos de 25 introducciones colombianas del banco de germoplasma de la Universidad de Córdoba. El análisis de correspondencia múltiple discriminó las introducciones en cuatro grupos, donde se identificaron características de importancia artesanal (comercial y atributos agronómicos. Se observó escasa correlación entre distancia geográfica y diferenciación genética, lo cual indicó flujos antrópicos por la reproducción asexual del material.

  20. Using of AFLP to evaluate gamma-irradiated amaranth mutants

    Directory of Open Access Journals (Sweden)

    Labajová Mária

    2013-01-01

    Full Text Available To determine which of several gamma-irradiated mutants of amaranth Ficha cultivar and K-433 hybrid are most genetically similar to their non-irradiated control genotypes, we performed amplified fragment length polymorphism (AFLP based analysis. A total of 40 selective primer combinations were used in reported analyses. First analyses of gamma-irradiated amaranth mutant lines were done used the AFLP. In the study, primers with the differentiation ability for all analysed mutant lines are reported. The very specific changes in the mutant lines´ non-coding regions based on AFLP length polymorphism were analysed. Mutant lines of the Ficha cultivar (C15, C26, C27, C82, C236 shared a genetic dissimilarity of 0,11 and their ISSR profiles are more similar to the Ficha than those of K-433 hybrid mutant lines. The K-433 mutant lines (D54, D279, D282 shared genetic dissimilarity of 0,534 but are more distinct to their control plant as a whole, as those of the Ficha mutant lines. Different AFLP fingerprints patters of the mutant lines when compared to the Ficha cultivar and K-433 hybrid AFLP profiles may be a consequence of the complex response of the intergenic space of mutant lines to the gamma-radiance. Although a genetic polymorphism was detected within accessions, the AFLP markers successfully identified all the accessions. The AFLP results are discussed by a combination of biochemical characteristics of mutant lines and their control genotypes.

  1. 大麻雄性基因连锁AFLP分子标记的筛选及鉴定%Screening and Identification of AFLP Markers Linked to Male Gene in Cannabis sativa L.

    Institute of Scientific and Technical Information of China (English)

    郭丽; 张海军; 王明泽; 车野; 刘德泉; 陈井生; 刘德福; 于吉东; 吴耀坤

    2015-01-01

    为建立一种大麻早期性别筛选及鉴定方法,利用 AFLP 标记技术,筛选了64对EcoRI-NNN/MseI-NNN引物组合,对11个不同大麻品种雌﹑雄植株的混合DNA池进行了性别连锁特异性条带的筛选。结果表明,6对引物组合表现出多态性,其中, EcoRI-ACA/MseI-CTG在雄性DNA池中扩增出1条特异条带,经各品种单株DNA验证,该条带只在雄性单株稳定出现,回收﹑克隆﹑测序后获得1条可用于大麻早期田间性别鉴定的734 bp雄性特异条带。%64 pairs of AFLP primer combinations of 8 pairs of EcoRI-NNN and MseI-NNN prim-ers were used to find the polymorphisms between mixed DNA pools of Cannabis sativa L. varieties. Six pairs of sixty -four primer combinations showed polymorphism between male and female DNA pools. 700 bp specific fragments were amplified in the primer combination of EcoRI-ACA and MseI-CTG in male DNA pool. This marker was testified with individual DNA of 11 varieties, and the fragment could only be amplified in male plants. The male-specific fragment of 734bp was recovered, cloned and se-quenced.

  2. Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers

    Institute of Scientific and Technical Information of China (English)

    CHEN Zhong; ZHAO Ru; GU Senchang; YAN Wen; CHENG Zhou; CHEN Muhong; LU Weifeng; WANG Shuhong; LU Baorong; LU Jun; ZHANG Fan; XIANG Rong; XIAO Shangbin; YAN Pin

    2006-01-01

    Genetic diversity is the basic and most important component of biodiversity. It is essential for the effective conservation and utilization of genetic resources to accurately estimate genetic diversity of the targeted species and populations. This paper reports analyses of genetic diversity of a wild soybean population using three molecular marker technologies (AFLP, ISSR and SSR), and computer simulation studies of randomly selected subsets with different sample size (5-90 individuals) drawn 50 times from a total of 100 wild soybean individuals. The variation patterns of genetic diversity indices, including expected heterozygosity (He), Shannon diversity index (/), and percentage of polymorphic loci (P), were analyzed to evaluate changes of genetic diversity associated with the increase of individuals in each subset. The results demonstrated that (1) values of genetic diversity indices of the same wild soybean population were considerably different when estimated by different molecular marker techniques; (2) genetic diversity indices obtained from subsets with different sample sizes also diverged considerably; (3) P values were relatively more reliable for comparing genetic diversity detected by different molecular marker techniques; and (4) different diversity indices reached 90% of the total genetic diversity of the soybean population quite differently in terms of the sample size (number of individuals) analyzed.When using the P value as a determinator, 30-40individuals could capture over 90% of the total genetic diversity of the wild soybean population. Results from this study provide a strong scientific basis for estimating genetic diversity and for strategic conservation of plant species.

  3. The role of molecular markers and marker assisted selection in breeding for organic agriculture

    DEFF Research Database (Denmark)

    Lammerts van Bueren, E.T.; Backes, G.; de Vriend, H.

    2010-01-01

    Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular...... markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture...... identified, e.g. better knowledge about gene pool of breeding material, more efficient introgression of new resistance genes from wild relatives and testing pyramided genes. There were also common concerns among breeders aiming at breeding for organic and/or conventional agriculture, such as the increasing...

  4. AFLP marker analysis revealing genetic structure of the tree Parapiptadenia rigida (Benth. Brenan (Leguminosae-Mimosoideae in the southern Brazilian Tropical Rainforest

    Directory of Open Access Journals (Sweden)

    Laís Bérgamo de Souza

    2013-01-01

    Full Text Available Parapiptadenia rigida is a tropical early secondary succession tree characteristic of the Tropical Atlantic Rainforest. This species is of great ecological importance in the recovery of degraded areas. In this study we investigated the variability and population genetic structure of eight populations of P. rigida. Five AFLP primer combinations were used in a sample of 159 individuals representing these eight populations, rendering a total of 126 polymorphic fragments. The averages of percentage of polymorphic loci, gene diversity, and Shannon index were 60.45%, 0.217, and 0.322, respectively. A significant correlation between the population genetic variability and the population sizes was observed. The genetic variability within populations (72.20% was higher than between these (22.80%. No perfect correlation was observed between geographic and genetic distances, which might be explained by differences in deforestation intensities that occurred in these areas. A dendrogram constructed by the UPGMA method revealed the formation of two clusters, these also confirmed by Bayesian analysis for the number of K cluster. These results show that it is necessary to develop urgent management strategies for the conservation of certain populations of P. rigida, while other populations still preserve reasonably high levels of genetic variability.

  5. DNA分子标记在果树种质资源遗传多样性研究中的应用%Application of DNA Molecular Markers in Genetic Diversity Study of Fruit Tree Germplasm Resources

    Institute of Scientific and Technical Information of China (English)

    周蓓蓓; 朱海军; 生静雅; 刘广勤

    2011-01-01

    简要介绍了DNA分子标记的主要类型、原理及特点,重点综述了RFLP、RAPD、AFLP、SSR、EST - SSR和SNP标记技术在果树种质资源遗传多样性研究中的应用现状.%This article briefly introduces the main type, principle and characteristics of DNA molecular marker techniques, and emphatically summarizes the application status of RFLP, RAPD, AFLP, SSR, EST -SSR and SNP marker techniques in the genetic diversity study of fruit tree germplasm resources.

  6. Studies on Genomic DNA Extraction and Establishment of AFLP Reaction System in Chinese Cabbage%大白菜基因组DNA的提取及AFLP反应体系的建立

    Institute of Scientific and Technical Information of China (English)

    孟淑春; 张海英; 郑晓鹰; 刘玉梅; 王永健

    2009-01-01

    [Objective] The obtained clear AFLP fingerprint of Chinese cabbage provided basis for studies on the molecular markers of Chinese cabbage cultivars and the phylogenetic relationship among Chinese cabbage cultivars. [Method] With the test materials of leaves of Chinese cabbages, the high-quality total DNA from leaves of Chinese cabbages was extracted by the modified CTAB method. DNA restriction-ligase reaction, pre-amplification and selective amplification were optimized, and the AFLP silver-staining reaction system for Chinese cabbage was established. [Result] The quality of DNA template influenced restriction enzyme digestion and the subsequent ligase amplification reaction, while the modified CTAB extraction method could be used in AFLP analysis of Chinese cabbage to obtain a clear AFLP fingerprint. The optimum conditions for restriction enzyme digestion of genomic DNA from Chinese cabbage were as follows: 150 g DNA template, 12.5 μl reaction volume, 1.25 U Eco R Ⅰ, 1.25 U Mse Ⅰ and 5×Reaction Buffer with 4 h at 37 ℃. The ligation reaction with 2.5 h at 20 ℃ was the optimum condition. Six pairs of primers including E-AAC/M-CAG, E-AAG/M-CAC, E-ACA/M-CTG, E-ACT/M-CAC, E-ACT/M-CTT and E-ACT/M-CTC all had its own stable and clear patterns. [Conclusion] With abundant bands and high polymorphism, AFLP selective amplification is an efficient molecular marker for genomic polymorphism of Chinese cabbage.

  7. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology

    NARCIS (Netherlands)

    Botton, A.; Galla, G.; Conesa, A.; Bachem, C.W.B.; Ramina, A.; Barcaccia, G.

    2008-01-01

    Background: After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and

  8. Diversidad genética intra e inter-específica de ñame (Dioscorea spp. de la región Caribe de Colombia mediante marcadores AFLP Genetic diversity intra and inter-specific yam (Dioscorea spp. from the colombian caribbean region by AFLP markers

    Directory of Open Access Journals (Sweden)

    Hernando Javier Rivera-Jiménez

    2011-12-01

    Full Text Available Conocer la variabilidad genética del ñame, Dioscorea spp., permite apoyar estrategias de mejoramiento y conservación de este recurso fitogenético. El objetivo de este estudio fue la caracterización molecular de 20 accesiones de Dioscorea spp. mediante la técnica molecular de AFLP para determinar cómo se distribuye la variabilidad genética de manera intra e inter-específica. Los datos fueron analizados mediante los métodos de agrupación de correspondencia múltiple y análisis de similaridad de Dice, estableciendo los niveles de confiabilidad de los grupos genéticos mediante remuestreos. En términos de diversidad interespecífica, los valores promedios de similitud variaron entre 41.81% entre D. alata L. y D. rotundata Poir., y 33.51% entre D. trifida L.f. y D. esculenta (Lour. Burkill, lo que sugiere alta diversidad genética entre las accesiones estudiadas, que formaron cuatro grupos genéticos: D. alata, D. rotundata, D. esculenta y D. trifida, confirmando correspondencia entre la caracterización morfológica, clasificación botánica y la caracterización molecular. En términos de diversidad intraespecífica para la especie D. alata, el análisis también reveló una composición heterogénea en la región Caribe colombiana. Estos estudios ayudarán a definir una estrategia adecuada para fines de conservación y apoyar los esfuerzos futuros en los programas de mejoramiento genético.Knowing the genetic variability of yams, Dioscorea spp., is a good tool to support development and conservation strategies of this plant as genetic resource. The aim of this study was to carried out the molecular characterization of 20 accessions of Dioscorea spp. using the AFLP molecular technique to determine how genetic variation is distributed intra-and inter-specifically. Using multiple correspondence analysis and level of reliability of the genetic groups by resampling, the results showed high genetic variability among the accessions studied

  9. Construction of AFLP Molecular Marking System in Mangifera indica L.%芒果AFLP分子标记体系的建立

    Institute of Scientific and Technical Information of China (English)

    王园; 金志强; 陈业渊; 雷新涛

    2009-01-01

    物组合多态性最大,达100%,可用于芒果品种指纹图谱构建.[结论]利用AFLP可以高效检测芒果种质资源分子标记多样性.%[Objective]The study aimed to construct the AFLP molecular marking system in Mangifera indica. [Method] Four varieties of Mangifera indica were used to explore new ways for high-quality DNA, and AFLP analysis of 31 varieties of Mangifera indica was carried out to detect the varietal genetic diversity. [Result] 14 pairs of primers with stronger polymorphism, better banding patterns and higher resolution were screened out from 64 pairs of selective amplification primers. Then they were used to analyse the fingerprint of 31 varieties of Mangifera indica, the results showed that the ratio of polymorphic bands amplificated by the 14 pairs of primers reached 97% in 31 varieties of Mangifera. [Conclusion] It was suggested that AFLP was suitable for detecting the polymorphism of Mangifera indica resources.

  10. Separation of the genera in the subtribe Cassiinae (Leguminosae: Caesalpinioidae using molecular markers Separação dos gêneros na subtribo Cassiinae (Leguminosae: Caesalpinioidae utilizando marcadores moleculares

    Directory of Open Access Journals (Sweden)

    Laxmikanta Acharya

    2011-03-01

    Full Text Available Random amplified polymorphic DNA (RAPD, Inter simple sequence repeat (ISSR and Amplified fragment length polymorphism (AFLP markers were used to verify the segregation of the genus Cassia L. senso lato into three distinct genera namely Chamaecrista Moench., Senna P. Mill. and Cassia L. sensostricto Eighteen representatives of the three taxa were characterized using the molecular markers. 25 RAPD, six ISSR primers and six AFLP primer combinations resulted in the amplification of 612, 115 and 622 bands (loci respectively. Most of the loci are found to be polymorphic, showing high degrees of genetic diversity among the different taxa studied. The dendrogram constructed on the basis of the RAPD, ISSR and AFLP data using SHAN clustering, divided Cassia L. senso lato. into three different clusters as Chamaecrista Moench. Senna P. Mill. and Cassia L. senso stricto High bootstrap value revealed that all the clusters were stable and robust. It was observed from the present investigation that these genera have their identity at molecular level, which supports the elevation of the genus Cassia L. senso lato to the level of subtribe Cassiinae and segregation into three distinct genera instead of intrageneric categories.Técnicas de Random amplified polymorphic DNA (RAPD, Inter simple sequence repeat (ISSR e Amplified Fragment Length Polymorphism markers (AFLP foram utilizadas para verificar a segregação do gênero Cassia L. senso lato em três diferentes gêneros, Chamaecrista Moench., Senna P. Mill. e Cassia L. senso stricto Dezoito representantes dos três táxons foram caracterizados com o uso de marcadores moleculares: 25 RAPD, seis iniciadores ("primers" ISSR e seis AFLP combinações de iniciadores, resultando na amplificação de 612, 115 e 622 bandas (loci, respectivamente. A maioria dos loci apresentou-se como polimórfico, mostrando um alto grau de diversidade genética entre os táxons estudados. O dendrograma construído com base nos dados de

  11. Molecular markers for human placental investigation.

    Science.gov (United States)

    Huppertz, Berthold

    2006-01-01

    The human placenta is a source for a variety of growth factors, hormones, and other proteins. The cellular source of the proteins can be best determined by immunohistochemistry. Furthermore, immunohistochemistry can also be used to identify a specific cell type and to differentiate it from other types of cells. Thus, there is the need for specific markers of those cell types that are present in the placenta. In this chapter, the basic protocols for the identification of proteins in a tissue section are described. This chapter focuses on methods that are available in the majority of laboratories, and therefore concentrates on methods that are used together with light microscopy.

  12. Modified techniques used for microsatellite and AFLP for the population study of divers species at the Sinu river fish, Colombia

    Directory of Open Access Journals (Sweden)

    Lamprea Natalia

    2004-07-01

    Full Text Available Few genetic conservation studies carried out in Colombia have applied molecular biology techniques. Protocols and modifications arising from the genetic study of four fish species from the Sinú river basin are presented as guidelines for future work in this field (and with other species as laboratory standardisation processes are complex. The original commercial kit's DNA extraction protocols were modified as were those for PCR reactions for obtaining micro-satellite markers and AFLPs, as well as allele genotypification. Particular variations were made f or each of the species studied. Key words: DNA extraction; molecular biology; genotypification; ichthyology.

  13. Molecular markers of phase transition in locusts

    Institute of Scientific and Technical Information of China (English)

    ARNOLD DE LOOF; ILSE CLAEYS; GERT SIMONET; PETER VERLEYEN; TIM VANDERSMISSEN; FILIP SAS; JURGEN HUYBRECHTS

    2006-01-01

    The changes accompanying the transition from the gregarious to the solitary phase state in locusts are so drastic that for a long time these phases were considered as distinct species. It was Boris Uvarov who introduced the concept of polyphenism. Decades of research revealed that phase transition implies changes in morphometry, the color of the cuticle, behavior and several aspects of physiology. In particular, in the recent decade, quite a number of molecular studies have been undertaken to uncover phase-related differences.They resulted in novel insights into the role of corazonin, neuroparsins, some protease inhibitors, phenylacetonitrile and so on. The advent of EST-databases of locusts (e.g. Kang et al., 2004) is a most encouraging novel development in physiological and behavioral locust research. Yet, the answer to the most intriguing question, namely whether or not there is a primordial molecular inducer of phase transition, is probably not within reach in the very near future.

  14. Molecular Genetic Markers in Acute Myeloid Leukemia

    Directory of Open Access Journals (Sweden)

    Sophia Yohe

    2015-03-01

    Full Text Available Genetics play an increasingly important role in the risk stratification and management of acute myeloid leukemia (AML patients. Traditionally, AML classification and risk stratification relied on cytogenetic studies; however, molecular detection of gene mutations is playing an increasingly important role in classification, risk stratification, and management of AML. Molecular testing does not take the place of cytogenetic testing results, but plays a complementary role to help refine prognosis, especially within specific AML subgroups. With the exception of acute promyelocytic leukemia, AML therapy is not targeted but the intensity of therapy is driven by the prognostic subgroup. Many prognostic scoring systems classify patients into favorable, poor, or intermediate prognostic subgroups based on clinical and genetic features. Current standard of care combines cytogenetic results with targeted testing for mutations in FLT3, NPM1, CEBPA, and KIT to determine the prognostic subgroup. Other gene mutations have also been demonstrated to predict prognosis and may play a role in future risk stratification, although some of these have not been confirmed in multiple studies or established as standard of care. This paper will review the contribution of cytogenetic results to prognosis in AML and then will focus on molecular mutations that have a prognostic or possible therapeutic impact.

  15. [Application of molecular marker techniques in invasion ecology].

    Science.gov (United States)

    Chu, Dong; Zhang, You-jun; Wan, Fang-hao

    2007-06-01

    Alien invasive species can cause huge economic loss in agricultural and forestry production, and threaten biodiversity and human health. The research of invasion ecology is of significance in understanding the invasion mechanisms of alien invasive species and in developing corresponding sustainable control methods. Molecular marker is regarded as a useful tool in approaching some essential issues in the research of invasion ecology. In this paper, the applications of molecular marker techniques in the studies of identification, geographic distribution, invasive source, spread pattern, genetic variation, hybridization, and gene introgression of alien invasive species were reviewed, and the application prospects were discussed.

  16. Genetic diversity and differentiation of Pinus sylvestris L. from the IUFRO 1982 provenance trial revealed by AFLP analysis

    Directory of Open Access Journals (Sweden)

    Androsiuk Piotr

    2015-01-01

    Full Text Available DNA markers have become effective tools in genetic diversity studies of forest trees. However, molecular marker analyses are associated with laborious and costly effort. One of the possibilities to overcome these constraints is to analyze bulked samples per population, rather than individual plants. We have used bulked DNA-based AFLP analysis to investigate genetic variations in Pinus sylvestris L. (Scots pine from the IUFRO 1982 provenance trial in Kórnik (western Poland. Four AFLP primer combinations yielded a total of 309 bands, of which 208 (67.31% were polymorphic. Thirty-six (11.65% unique alleles were deployed randomly among the populations. Estimated genetic diversity and differentiation was high, as expressed by He = 0.238 and I = 0.356, and by genetic distance values which ranged from 0.154 to 0.363. A geographic pattern of interpopulation differentiation was observed, pointing to the individual character of populations from northeastern Europe. In the light of available data, we discuss the influence of historical migration routes, gene flow and human activity on observed genetic diversity and differentiation of Scots pine in Europe. Our results indicate that the AFLP method applied to DNA templates extracted from bulked leaf samples provides an efficient approach to elucidate genetic diversity and relationships among Scots pine populations.

  17. Molecular Variability Within and Among Verticillium dahliae Vegetative Compatibility Groups Determined by Fluorescent Amplified Fragment Length Polymorphism and Polymerase Chain Reaction Markers.

    Science.gov (United States)

    Collado-Romero, Melania; Mercado-Blanco, Jesús; Olivares-García, Concepción; Valverde-Corredor, Antonio; Jiménez-Díaz, Rafael M

    2006-05-01

    ABSTRACT A degree of genetic diversity may exist among Verticillium dahliae isolates within vegetative compatibility groups (VCGs) that bears phytopathological significance and is worth investigating using molecular tools of a higher resolution than VCG characterization. The molecular variability within and among V. dahliae VCGs was studied using 53 artichoke isolates from eastern-central Spain, 96 isolates from cotton, 7 from cotton soil, and 45 from olive trees in countries of the Mediterranean Basin. Isolates were selected to represent the widest available diversity in cotton- and olive-defoliating (D) and -nondefoliating (ND) pathotypes, as well as for VCG. The VCG of 96 cotton and olive isolates was determined in this present study. Molecular variability among V. dahliae isolates was assessed by fluorescent amplified fragment length polymorphism (AFLP) analysis and by polymerase chain reaction (PCR) assays for DNA fragments associated with the D (462 bp) and ND (824 bp) pathotypes, as well as a 334-bp amplicon associated with D pathotype isolates but also present in some VCG2B isolates. Isolates from cotton were in VCG1A, VCG1B, VCG2A, VCG2B, and VCG4B and those from olive trees were in VCG1A, VCG2A, and VCG4B. Artichoke isolates included representatives of VCG1A, VCG2A, VCG2B (including a newly identified VCG2Ba), and VCG4B. AFLP data were used to generate matrixes of genetic distance among isolates for cluster analysis using the neighbor-joining method and for analysis of molecular variance. Results demonstrated that V. dahliae isolates within a VCG subgroup are molecularly similar, to the extent that clustering of isolates correlated with VCG subgroups regardless of the host source and geographic origin. VCGs differed in molecular variability, with the variability being highest in VCG2B and VCG2A. For some AFLP/VCG subgroup clusterings, V. dahliae isolates from artichoke grouped in subclusters clearly distinct from those comprising isolates from cotton and

  18. MOLECULAR GENETIC MARKERS AS PREDICTORS OF SUPERFICIAL BLADDER CANCER

    Directory of Open Access Journals (Sweden)

    A. Yu. Babayan

    2009-01-01

    Full Text Available A system of clinical and morphological criteria is currently used to determine the pattern of superficial bladder cancer (SBC. However, this system does not completely reflect the clinical potential of SBC and needs additional markers. The purpose of this study was to search for and evaluate molecular genetic disorders as additional markers of the course of SBC. The diagnostic panel included the deletion of the loci 3р14, 9р21, 9q34, 17р13 (ТР53, mutations of exon 7 of the FGFR3 gene, and hypermethylation of the promoter regions of the RASSF1, RARB, p16, p14, CDH1 genes. The study was made on 108 matched samples (tumor/peripheral blood obtained from patients with SBC. The deletions of the loci 3р14, 9р21 and anomalous methylation of the RARb and p16 genes are markers of the worse course of SBC while FGFR3 gene mutation is a marker of better prognosis. In the context of estimation of the relapsing potential of a primary tumor, the 9p21 locus deletion is a marker associated with recurrence within the first year after malignancy resection. The group of molecular genetic markers determined by the authors for poor prognosis in combination with classical clinical and morphological criteria will specify the pattern of the course of the disease and its prognosis.

  19. Molecular markers in studies on fish parasites (Platyhelminthes: Review

    Directory of Open Access Journals (Sweden)

    Rodrigo Junio da Graça

    2016-12-01

    Full Text Available Studies with molecular markers are currently more common for all groups of living organisms. Molecular techniques used in Platyhelminthes parasites of fishes do not merely reveal complex life cycles, but are important for species distinction and the elucidation of the phylogenetic hypothesis. Current research verified which molecular markers were mainly used phylogenetic studies on Platyhelminthes parasites of fish so that subsidies for further phylogenetic studies in Icthyoparasitology could be provided. Data base of CAPES Journals platform was employed for bibliometric analysis comprising the keywords “fish” and “phylogeny” associated with “Cestoda”, “Digenea” or “Monogenea”. Information retrieved was quantified and tabulated. Most studies were on Monogenea (43%, followed by Digenea (37% and Cestoda (18%. Ribosomal molecular markers were the most used in the phylogenetic studies for fish parasites. Due to the advance of molecular biology techniques and of bioinformatics, with more robust phylogenetic analysis, the use of these techniques in other areas such as Ichytioparasitology is on the increase. In fact, molecular phylogenetics and morphological structures analysis have efficiently contributed towards the understanding of phylogenetic relationships among the groups.

  20. Biological (molecular and cellular) markers of toxicity

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Molecular Marker Development in Post-genomic Era:Leveraging Multiple Resources for Marker Development in Cotton and Other Crops

    Institute of Scientific and Technical Information of China (English)

    KUMPATLA Siva P; SHAH Manali R; MUKHOPADHYAY Snehasis; THOMPSON Steven A; GREENE Thomas W

    2008-01-01

    @@ While the importance of molecular marker technology was realized more than two decades ago,high-throughput marker development came into vogue only after the availability of hundreds of thousands of sequences in public databases.Many examples now exist where markers are being used routinely in breeding programs for marker-assisted selection (MAS) of traits of interest or marker assisted recovery of genome of interest.

  2. Molecular Markers with Predictive and Prognostic Relevance in Lung Cancer

    Directory of Open Access Journals (Sweden)

    Alphy Rose-James

    2012-01-01

    Full Text Available Lung cancer accounts for the majority of cancer-related deaths worldwide of which non-small-cell lung carcinoma alone takes a toll of around 85%. Platinum-based therapy is the stronghold for lung cancer at present. The discovery of various molecular alterations that underlie lung cancer has contributed to the development of specifically targeted therapies employing specific mutation inhibitors. Targeted chemotherapy based on molecular profiling has shown great promise in lung cancer treatment. Various molecular markers with predictive and prognostic significance in lung cancer have evolved as a result of advanced research. Testing of EGFR and Kras mutations is now a common practice among community oncologists, and more recently, ALK rearrangements have been added to this group. This paper discusses various predictive and prognostic markers that are being investigated and have shown significant relevance which can be exploited for targeted treatment in lung cancer.

  3. Molecular pathology in adult gliomas: diagnostic, prognostic, and predictive markers.

    LENUS (Irish Health Repository)

    Jansen, Michael

    2010-07-01

    Over the past 10 years, there has been an increasing use of molecular markers in the assessment and management of adult malignant gliomas. Some molecular signatures are used diagnostically to help pathologists classify tumours, whereas others are used to estimate prognosis for patients. Most crucial, however, are those markers that are used to predict response to certain therapies, thereby directing clinicians to a particular treatment while avoiding other potentially deleterious therapies. Recently, large-scale genome-wide surveys have been used to identify new biomarkers that have been rapidly developed as diagnostic and prognostic tools. Given these developments, the pace of discovery of new molecular assays will quicken to facilitate personalised medicine in the setting of malignant glioma.

  4. Applying Molecular Markers in Coriander Populations with Diverse Geographical Origins

    Science.gov (United States)

    Relationships between patterns of genetic diversity and geographical origins were studied in coriander by using amplified fragment length polymorphisms (AFLP) to survey coriander accessions. In 2005, 60 coriander accessions from 28 countries, from the USDA-ARS North Central Regional Plant Introduct...

  5. Genetic structure in cultivated and wild carrots (¤Daucus carota¤ L.) revealed by AFLP analysis

    DEFF Research Database (Denmark)

    Shim, S.I.; Bagger Jørgensen, Rikke

    2000-01-01

    Genetic variation within and among five Danish populations of wild carrot and five cultivated varieties was investigated using amplified fragment length polymorphism (AFLP). Ten AFLP primer combinations produced 116 polymorphic bands. Based on the marker data an UPGMA-cluster analysis and princip...

  6. Identification of Epinephelus malabaricus and Epinephelus coioides using DNA markers

    Institute of Scientific and Technical Information of China (English)

    WANG Shifeng; DU Jiaying; WANG Jun; DING Shaoxiong

    2007-01-01

    Using multi-molecular marker technologies and based on morphological criteria, the genetic relationship between Epinepheelus malabaricus and E.coioides was examined in the hope of resolving the long-standing issue of identifying these two species.Results showed that: (1) E.coioides and E.malabaricus should be identified as two species, the consistency of mitochondrial DNA cytochrome b gene sequence between E.malabaricus and E.coioides is 94.4%, and the genetic similarity by AFLP was 0.753 9; (2) Hybridization exists between E.malabaricus and E.coioides, the specific RAPD and AFLP fragments are found to be useful in the identification of these two species, and the genetic properties (both with exterior and inheritance) of hybrid is significantly biased to the male parents; and (3) AFLP was a potentially powerful tool in constructing the genetic linkage map for these two groupers.

  7. Molecular markers and sentinel organisms for environmental monitoring

    Directory of Open Access Journals (Sweden)

    Graczyk T.K.

    2008-09-01

    Full Text Available Molecular methods are useful for both to monitor anthropogenic viral, bacterial, and protozoan enteropathogens, and to track pathogen specific markers in a complex environment in order to reveal sources of these pathogens. Molecular genetic markers for fecal viruses, bacteria, and protozoans hold promise for monitoring environmental pollution and water quality. The demand for microbiologically safe waters grows exponentially due to the global demographic rise of the human population. Economically important shellfish, such as oysters, which are harvested commercially and preferentially consumed raw can be of public health importance if contaminated with human waterborne pathogens. However, feral molluscan shellfish which do not have an apparent economic value serve as indicators in monitoring aquatic environments for pollution with human waterborne pathogens and for sanitary assessment of water quality. Current technology allows for multiplexed species-specific identification, genotyping, enumeration, viability assessment, and source-tracking of human enteropathogens which considerably enhances the pathogen source-tracking efforts.

  8. Molecular Markers for Breast Cancer: Prediction on Tumor Behavior

    Directory of Open Access Journals (Sweden)

    Bruna Karina Banin Hirata

    2014-01-01

    Full Text Available Breast cancer is one of the most common cancers with greater than 1,300,000 cases and 450,000 deaths each year worldwide. The development of breast cancer involves a progression through intermediate stages until the invasive carcinoma and finally into metastatic disease. Given the variability in clinical progression, the identification of markers that could predict the tumor behavior is particularly important in breast cancer. The determination of tumor markers is a useful tool for clinical management in cancer patients, assisting in diagnostic, staging, evaluation of therapeutic response, detection of recurrence and metastasis, and development of new treatment modalities. In this context, this review aims to discuss the main tumor markers in breast carcinogenesis. The most well-established breast molecular markers with prognostic and/or therapeutic value like hormone receptors, HER-2 oncogene, Ki-67, and p53 proteins, and the genes for hereditary breast cancer will be presented. Furthermore, this review shows the new molecular targets in breast cancer: CXCR4, caveolin, miRNA, and FOXP3, as promising candidates for future development of effective and targeted therapies, also with lower toxicity.

  9. The phylogenetic relationship of the family Lutjanidae based on analyses of AFLP and mitochondrial 12S rRNA sequences

    Institute of Scientific and Technical Information of China (English)

    ZHANG Junbin; LIU Xin

    2006-01-01

    Fishes of the family Lutjanidae are commercially important in South China Sea. However,the phylogeny of Lutjanids is still unclear and there are many controversies over it. Herein, studies about the phylogeny of Lutjanids were performed based on Amplified Fragment Length Polymorphism (AFLP) analysis of genome DNA and sequence analysis of mitochondrial 12S rRNA gene, and 10 Lutjanidae species and 1 Lethrinidae species were employed.The topologies of minimum evolution (ME) trees based on the two analyses respectively were congruent except for positions of genera Pristipomoides and Caesio. The optimal substitution model TrN + G for DNA sequences of 12S rRNA genes in Lutjanids was obtained using MODELTEST 3.6 software and maximum likelihood (ML) analysis supports the topology displayed by the ME tree. The test of log-likelihood suggests that the use of molecular clock calibrations to estimate species divergence time appeared valid. Phylogenetic analyses using AFLP data and DNA sequences of mitochondrial 12S rRNA genes indicated the monophyly of Lutjanus genra. However, further studies are required to reveal the phylogenetic relationship among other genera. In addition, the results demonstrated that AFLP genetic marker was suitable for the phylogenetic analysis of Lutjanids.

  10. Molecular Marker Development in Post-genomic Era:Leveraging Multiple Resources for Marker Development in Cotton and Other Crops

    Institute of Scientific and Technical Information of China (English)

    KUMPATLA; Siva; P; SHAH; Manali; R; MUKHOPADHYAY; Snehasis; THOMPSON; Steven; A; GREENE; Thomas; W

    2008-01-01

    While the importance of molecular marker technology was realized more than two decades ago,high-throughput marker development came into vogue only after the availability of hundreds of thousands of sequences in public databases.Many examples now exist where markers are being used routinely in breeding programs for marker-assisted selection(MAS) of traits of interest or marker assisted recovery of genome of interest.Genetic analysis with thousands to tens of thousands of markers is now possible due to the...

  11. The application of LTR retrotransposons as molecular markers in plants.

    Science.gov (United States)

    Schulman, Alan H; Flavell, Andrew J; Paux, Etienne; Ellis, T H Noel

    2012-01-01

    Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction.

  12. [AFLP Analysis of Genetic Diversity in the Genus Mallus Mill. (Apple)].

    Science.gov (United States)

    Savelyeva, E N; Kudryavtsev, A M

    2015-10-01

    The first molecular genetic analysis of the apple species and varieties from Russian collections with the AFLP marker system was performed in order to study the genetic diversity of the genus Malus, as well as to clarify the phylogeny and solve some systematic issues of the genus. Nienty-one apple accessions, including species from five sections of the genus Malus and hybrid species, were examined. The level of polymorphism constituted 90.2%. It was demonstrated that the classical taxonomy of the genus Malus, which identifies five sections based on differences in their morphological characters, is valid and may be used to classify apple species. The species assignment of the Antonovka landraces was established. All of them belonged to the species M. domestica. It was demonstrated that the Yakutskaya apple variety was a domesticated species of the section Gymnomeles, presumably, M. baccata. AFLP analysis confirmed the hybrid nature of many species. The relationships between apple varieties of the Golden group with American wild species were demonstrated. The data suggest that the species M. sieversii was the ancestor of not only the domestic apple but also of other species of the Malus sections.

  13. 思茅松AFLP分子标记体系的建立%Establishment of AFLP Molecular Mark System of Pinus kesiya var.langbianensis

    Institute of Scientific and Technical Information of China (English)

    姚鹏强; 李培; 王曙光; 普晓兰

    2012-01-01

    采用改进的SDS法,提取思茅松胚乳DNA,获得较高质量的DNA样品,用Eco RI和Pst I2种限制性内切酶完全酶切后,再经过预扩和选扩,从82对引物中筛选出24对带型分布均匀、多态性高且分辨力强的引物.扩增产物经聚丙烯酰胺凝胶电泳后,可获得清晰指纹图谱,重复性较好.建立的思茅松AFLP体系可用于后续研究.%High quality genome DNA of Pinus kesiya var. langbianensis was extracted from endosperm by the improved SDS method. After the DNA samples were completely digested by restriction enzymes of EcoRI and PstI and through pre-amplification and selective amplification, 24 pairs of primers out of 82 pairs with even band distribution , abundant polymorphism and high distinctiveness were selected. The distinct finger-printings of Pinus kesiya var. langbianensis with high reproducibility were obtained through electrophoresis of the amplified product. The establishment of this AFLP mark system will be helpful to further study on Pinus kesiya var. langbianensis.

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

    Science.gov (United States)

    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.

  15. MicroRNAs as molecular markers in lung cancer

    Directory of Open Access Journals (Sweden)

    Javier Silva

    2013-10-01

    Full Text Available Lung cancer is the most common cause of cancer death in the western world for both men and women. Lung cancer appears to be a perfect candidate for a screening program, since it is the number one cancer killer, it has a long preclinical phase, curative treatment for the minority of patients who are diagnosed early and a target population at risk (smokers and it is also a major economic burden. The earliest approaches to identifying cancer markers were based on preliminary clinical or pathological observations, although molecular biology is a strong candidate for occupying a place among the set of methods. In search of markers, several alterations, such as mutations, loss of heterozygosity, microsatellite instability, DNA methylation, mitochondrial DNA mutations, viral DNA, modified expression of mRNA, miRNA and proteins, and structurally altered proteins have all been analysed. MicroRNAs (miRNA are small RNA molecules, about 19-25 nucleotides long and encoded in genomes of plants, animals, fungi and viruses. It has been reported that miRNAs may have multiple functions in lung development and that aberrant expression of miRNAs could induce lung tumorigenesis. We review here the role of miRNAs in lung tumorigenesis and also as a novel type of biomarker.-----------------------------------Cite this article as:Silva J, Garcia V, Lopez-Gonzalez A, Provencio M. MicroRNAs as molecular markers in lung cancer. Int J Cancer Ther Oncol 2013;1(1:010111. DOI: http://dx.doi.org/10.14319/ijcto.0101.11

  16. QTL Analysis for Plant Height with Molecular Markers in Maize

    Institute of Scientific and Technical Information of China (English)

    YAN Jian-bing; TANG Hua; HUANG Yi-qin; SHI Yong-gang; ZHENG Yong-lian; LI Jian-sheng

    2003-01-01

    Plant height has become one of important agronomic traits with the increase of planting densityrecently and the rapid developments of molecular markers have provided powerful tools to localize importantagronomic QTL at the genomic level. The purposes of this investigation are to map plant height QTL with mo-lecular markers and to analyze their genetic effects in maize. An F2:3 population from an elite combination(Zong3 × 87-1) was utilized for evaluating plant height in two locations, Wuhan and Xiangfan, with a ran-domized complete block design. The mapping population included 266 F2:3 family lines. A genetic linkagemap, containing 150 SSR and 24 RFLP markers, was constructed, spanning a total of 2 531.6 cm with an av-erage interval of 14.5 cm. Totally 10 QTL affecting plant height were mapped on six different chromosomeswith the composite interval mapping. Seven of 10 QTL were detected in two locations. The contributions tophenotypic variations for the single QTL varied between 5.3 and 17.1%. Additive, partial dominance, domi-nance, and overdominance actions existed among all detected QTL affecting plant heights. A large number ofdigenic interactions for plant height were detected by two-way analyses of variance. 107 and 98 two-locus com-binations were found to be significant at a 0.01 probability level in two locations respectively. 23 of them weresimultaneously detected in both locations. They accounted for phenotypic variations of 4.5 -11%. It was no-ticed that a locus, umc1122, had digenic interactive effects with other four different loci for plant height,which distributed on three chromosomes. A few of plant height QTL was involved in significant digenic inter-actions, but most significant interactions occurred between markers that are not adjacent to mapped QTL.These results demonstrated that epistatic interactions might play an equal importance role as the single-locuseffects in determining plant height of maize.

  17. Genetic diversity of Chilean and Brazilian alstroemeria species assessed by AFLP analysis.

    Science.gov (United States)

    Han, T H; de Jeu, M; van Eck, H; Jacobsen, E

    2000-05-01

    One to three accessions of 22 Alstroemeria species, an interspecific hybrid (A. aurea x A. inodora), and single accessions of Bomarea salsilla and Leontochir ovallei were evaluated using the AFLP-marker technique to estimate the genetic diversity within the genus Alstroemeria. Three primer combinations generated 716 markers and discriminated all Alstroemeria species. The dendrogram inferred from the AFLP fingerprints supported the conjecture of the generic separation of the Chilean and Brazilian Alstroemeria species. The principal co-ordinate plot showed the separate allocation of the A. ligtu group and the allocation of A. aurea, which has a wide range of geographical distribution and genetic variation, in the middle of other Alstroemeria species. The genetic distances, based on AFLP markers, determined the genomic contribution of the parents to the interspecific hybrid.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Introgression Threatens the Genetic Diversity of Quercus austrocochinchinensis (Fagaceae), an Endangered Oak: A Case Inferred by Molecular Markers

    Science.gov (United States)

    An, Miao; Deng, Min; Zheng, Si-Si; Jiang, Xiao-Long; Song, Yi-Gang

    2017-01-01

    Natural introgression can cause negative effects where rare species experience genetic assimilation and invade by their abundant congeners. Quercus austrocochinchinensis and Q. kerrii (subgenus Cyclobalanopsis) are a pair of closely related species in the Indo-China area. Morphological intermediates of the two species have been reported in this region. In this study, we used AFLP, SSR and two key leaf morphological diagnostic traits to study the two Q. austrocochinchinensis populations, two pure Q. kerrii and two putative hybrid populations in China. Rates of individual admixture were examined using the Bayesian clustering programs STRUCTURE and NewHybrids, with no a priori species assignment. In total, we obtained 151 SSR alleles and 781 polymorphic loci of AFLP markers. Population differentiation inferred by SSR and AFLP was incoherent with recognized species boundaries. Bayesian admixture analyses and principal coordinate analysis identified more hybrids and backcrossed individuals than morphological intermediates in the populations. SSR inferred a wide genetic assimilation in Q. austrocochinchinensis, except for subpopulation D2 in the core area of Xi-Shuang-Ban-Na Nature Reserve (XSBN). However, AFLP recognized more Q. austrocochinchinensis purebreds than SSR. Analysis using NewHybrids on AFLP data indicated that these hybridized individuals were few F2 and predominantly backcrosses with both parental species. All these evidences indicate the formation of a hybrid swarm at XSBN where the two species co-exist. Both AFLP and SSR recognized that the core protected area of XSBN (D2) has a high percentage of Q. austrocochinchinensis purebreds and a unique germplasm. The Hainan population and the other subpopulations of XSBN of the species might have lost their genetic integrity. Our results revealed a clear genetic differentiation in the populations and subpopulations of Q. austrocochinchinensis and ongoing introgression between Q. austrocochinchinensis and Q

  20. [Matrix metalloproteases as molecular markers in gastric cancer].

    Science.gov (United States)

    de la Peña, Sol; Sampieri, Clara L; León-Córdoba, Kenneth

    2010-02-06

    Gastric cancer is the second leading cause of cancer-associated mortality in the world. Prognosis in patients with gastric cancer is difficult to establish because it is commonly diagnosed when gastric wall invasion and metastasis have occurred. Currently, some members of the extracellular matrix metalloproteinases have been identified, whose expression in gastric tumor tissue is significantly elevated compared to healthy gastric tissue. Matrix metalloproteinases are 24 zinc-dependent endopeptidases that catalyze the proteolysis of the extracellular matrix. This degradation allows the cancer cells invade the surrounding stroma and trigger metastasis. Upregulation of certain matrix metalloproteinases in gastric cancer has been associated with a poor prognosis and elevated invasive capacity. This review compiles evidence about the genetic expression of matrix metalloproteinases in gastric cancer and their role in tumour invasion and metastasis, emphasizing their potential as molecular markers of prognosis.

  1. Genetic diversity assessment of summer squash landraces using molecular markers.

    Science.gov (United States)

    Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

    2013-07-01

    Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash.

  2. Epigenetic Markers for Molecular Detection of Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Vera L. Costa

    2007-01-01

    Full Text Available Prostate cancer is a highly prevalent malignancy, which is clinically silent but curable while organ-confined. Because available screening methods show poor sensitivity and specificity, the development of new molecular markers is warranted. Epigenetic alterations, mainly promoter hypermethylation of cancer-related genes, are common events in prostate cancer and might be used as cancer biomarkers. Moreover, the development of quantitative, high-throughput techniques to assess promoter methylation enabled the simultaneous screening of multiple clinical samples. From the numerous cancer-related genes hypermethylated in prostate cancer only a few proved to be strong candidates to become routine biomarkers. This small set of genes includes GSTP1, APC, RARβ2, Cyclin D2, MDR1, and PTGS2. Single and/or multigene analyses demonstrated the feasibility of detecting early prostate cancer, with high sensitivity and specificity, in body fluids (serum, plasma, urine, and ejaculates and tissue samples. In addition, quantitative hypermethylation of several genes has been associated with clinicopathologic features of tumor aggressiveness, and also reported as independent prognostic factor for relapse. The identification of age-related methylation at specific loci and the differential frequency of methylation among ethnical groups, also provided interesting data linking methylation and prostate cancer risk. Although large trials are needed to validate these findings, the clinical use of these markers might be envisaged for the near future.

  3. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida

    OpenAIRE

    Hoolahan, Angelique H.; Blok, Vivian C.; Gibson, Tracey; Dowton, Mark

    2012-01-01

    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), ...

  4. Molecular Imaging Markers to Track Huntington's Disease Pathology.

    Science.gov (United States)

    Wilson, Heather; De Micco, Rosa; Niccolini, Flavia; Politis, Marios

    2017-01-01

    Huntington's disease (HD) is a progressive, monogenic dominant neurodegenerative disorder caused by repeat expansion mutation in the huntingtin gene. The accumulation of mutant huntingtin protein, forming intranuclear inclusions, subsequently leads to degeneration of medium spiny neurons in the striatum and cortical areas. Genetic testing can identify HD gene carriers before individuals develop overt cognitive, psychiatric, and chorea symptoms. Thus, HD gene carriers can be studied in premanifest stages to understand and track the evolution of HD pathology. While advances have been made, the precise pathophysiological mechanisms underlying HD are unclear. Magnetic resonance imaging (MRI) and positron emission tomography (PET) have been employed to understand HD pathology in presymptomatic and symptomatic disease stages. PET imaging uses radioactive tracers to detect specific changes, at a molecular level, which could be used as markers of HD progression and to monitor response to therapeutic treatments for HD gene expansion carriers (HDGECs). This review focuses on available PET techniques, employed in cross-sectional and longitudinal human studies, as biomarkers for HD, and highlights future potential PET targets. PET studies have assessed changes in postsynaptic dopaminergic receptors, brain metabolism, microglial activation, and recently phosphodiesterase 10A (PDE10A) as markers to track HD progression. Alterations in PDE10A expression are the earliest biochemical change identified in HD gene carriers up to 43 years before predicted symptomatic onset. Thus, PDE10A expression could be a promising marker to track HD progression from early premanifest disease stages. Other PET targets which have been less well investigated as biomarkers include cannabinoid, adenosine, and GABA receptors. Future longitudinal studies are required to fully validate these PET biomarkers for use to track disease progression from far-onset premanifest to manifest HD stages. PET imaging

  5. Molecular Imaging Markers to Track Huntington’s Disease Pathology

    Science.gov (United States)

    Wilson, Heather; De Micco, Rosa; Niccolini, Flavia; Politis, Marios

    2017-01-01

    Huntington’s disease (HD) is a progressive, monogenic dominant neurodegenerative disorder caused by repeat expansion mutation in the huntingtin gene. The accumulation of mutant huntingtin protein, forming intranuclear inclusions, subsequently leads to degeneration of medium spiny neurons in the striatum and cortical areas. Genetic testing can identify HD gene carriers before individuals develop overt cognitive, psychiatric, and chorea symptoms. Thus, HD gene carriers can be studied in premanifest stages to understand and track the evolution of HD pathology. While advances have been made, the precise pathophysiological mechanisms underlying HD are unclear. Magnetic resonance imaging (MRI) and positron emission tomography (PET) have been employed to understand HD pathology in presymptomatic and symptomatic disease stages. PET imaging uses radioactive tracers to detect specific changes, at a molecular level, which could be used as markers of HD progression and to monitor response to therapeutic treatments for HD gene expansion carriers (HDGECs). This review focuses on available PET techniques, employed in cross-sectional and longitudinal human studies, as biomarkers for HD, and highlights future potential PET targets. PET studies have assessed changes in postsynaptic dopaminergic receptors, brain metabolism, microglial activation, and recently phosphodiesterase 10A (PDE10A) as markers to track HD progression. Alterations in PDE10A expression are the earliest biochemical change identified in HD gene carriers up to 43 years before predicted symptomatic onset. Thus, PDE10A expression could be a promising marker to track HD progression from early premanifest disease stages. Other PET targets which have been less well investigated as biomarkers include cannabinoid, adenosine, and GABA receptors. Future longitudinal studies are required to fully validate these PET biomarkers for use to track disease progression from far-onset premanifest to manifest HD stages. PET

  6. Evaluación de la variación somaclonal en vitroplantas de caña de azúcar mediante marcadores moleculares Evaluation of somaclonal variation in in vitro produced sugarcane plants through molecular markers

    Directory of Open Access Journals (Sweden)

    María F. Perera

    Full Text Available El cultivo in vitro de tejidos vegetales puede producir variación somaclonal, fenómeno que consiste en modificaciones genéticas en las células y tejidos cultivados. Esto puede limitar la aplicación de dicha técnica para la micropopagación masiva, especialmente si la variación provoca un cambio fenotípico de importancia agronómica. En este trabajo se optimizó una metodología basada en la comparación de perfiles de marcadores moleculares AFLP (del inglés "Amplified Fragment Length Polymorphism", para la detección de la variación somaclonal en vitroplantas de caña de azúcar. Para la optimización de la técnica de AFLP en caña de azúcar, se utilizaron plantas de seis genotipos propagados convencionalmente y dos tipos de muestras: hojas tiernas y meristemas. La variación somaclonal fue evaluada en líneas de vitroplantas de los mismos genotipos al final del cultivo in vitro, luego de seis meses de micropropagación. Con las 19 combinaciones de cebadores utilizadas, se diferenciaron los perfiles moleculares de los seis genotipos. En los plantines micropropagados se detectaron perfiles diferenciales en las variedades LCP85-384 y TUCCP77-42 con 3 de las 19 combinaciones de cebadores utilizadas. Este resultado muestra la validez de la técnica para detectar variantes somaclonales, y deja en evidencia la diferencia de susceptibilidad de los genotipos al cultivo in vitro. Esto permitió ajustar la metodología de micropropagación para cada genotipo multiplicado y asegurar la pureza genética de cada vitroplanta.In vitro culture of plant tissue can produce somaclonal variation, which consists of genetic modifications in cultured cells and tissues. This may constrain the use of this technique in massive micropopagation, especially if such change causes an agronomically relevant phenotypical modification. In this work, a methodology based on the comparison of AFLP (Amplified Fragment Length Polymorphism molecular marker profiles was

  7. Comparison of molecular markers for strain typing of Leishmania infantum.

    Science.gov (United States)

    Botilde, Yanick; Laurent, Thierry; Quispe Tintaya, Wilber; Chicharro, Carmen; Cañavate, Carmen; Cruz, Israel; Kuhls, Katrin; Schönian, Gabriele; Dujardin, Jean-Claude

    2006-11-01

    The epidemiology of Leishmania infantum, the etiological agent of visceral leishmaniasis, is changing rapidly; hence powerful typing tools are required in order to monitor the parasite populations spreading and to adapt adequate control measures. We compared here the resolving power of four molecular methods at the zymodeme level: PCR-RFLP analysis of kDNA minicircles (kDNAPCR-RFLP) and antigen genes (cysteine proteinase b and major surface protease, cpb- and gp63PCR-RFLP), multilocus microsatellite typing (MLMT) and random amplification of polymorphic DNA (RAPD) were applied to samples of 25 L. infantum MON-1 strains obtained from different hosts (HIV+ patients, HIV- patients and dogs) coming from three Spanish foci: Madrid, Mallorca and Ibiza. While RAPD was not sufficiently resolving, the other three methods allowed genotyping within the zymodeme. KDNAPCR-RFLP and MLMT were the most discriminatory and appeared the most adequate for strain fingerprinting. In an eco-geographical context, cpbPCR-RFLP, MLMT and kDNAPCR-RFLP were all informative: they showed here a similar picture, with the existence of cluster(s) of isolates from the islands and other one(s) of mixed composition (Madrid and the islands). None of the markers revealed an association with the host type or the clinical form. In general, there was a significant correlation between each pair of distances calculated from the cpb, microsatellite and kDNA data, respectively, but visual inspection of the trees revealed a better congruence between cpb and microsatellite trees. The methods used here are complementary and each adapted to answer specific epidemiological questions. Their choice should be the result of a compromise between the required resolving power, the genetic features of the respective markers and the technical aspects.

  8. Molecular markers of endocrine disruption in aquatic organisms.

    Science.gov (United States)

    Rotchell, Jeanette M; Ostrander, Gary K

    2003-01-01

    neurohormone. Current molecular-level techniques rely on ligand-binding assays, enzyme-linked immunosorbent assay (ELISA), and, more recently, gene expression. In the future, more reliance will be placed on the development of gene expression assays using reporter systems combined with cross-species PCR-based or polyclonal antibody-based assays. We discuss the use of recombinant receptors as a means of primary screening of environmental samples for estrogenicity and antiestrogenicity, which avoids species and seasonal variation in receptor response to ligand binding, a recognized problem of earlier bioassays. Most exciting is the potential that microarray and proteomics approaches have to offer. Such techniques are now used routinely in medical research to identify specific genes and proteins affected by treatment with endocrine disruptors, including estradiol. The technique has yet to be used to screen aquatic organisms, but it has the potential to implicate previously unsuspected estradiol-sensitive genes that may later become molecular markers of endocrine disruption.

  9. Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers

    DEFF Research Database (Denmark)

    Andersen, Lars Dyrskjøt; Zieger, Karsten; Ørntoft, Torben Falck

    2007-01-01

    individually contributed to the management of the disease. However, the development of high-throughput techniques for simultaneous assessment of a large number of markers has allowed classification of tumors into clinically relevant molecular subgroups beyond those possible by pathological classification. Here......, we review the recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers....

  10. [Progress in researches on molecular markers of Plasmodium falciparum drug resistance].

    Science.gov (United States)

    Zhang, Mei-hua; Lu, Feng; Cao, Jun; Gao, Qi

    2015-06-01

    Effective chemotherapy is the mainstay of malaria control. However, it is undergoing the serious threat by resis- tance of falciparum malaria to antimalarial drugs. In recent years, with the development of molecular biology technology, molec- ular markers have been widely used to monitor antimalarial drug resistance. This paper reviews the researches on the common molecular markers related to Plasmodiumfalciparum drug resistance.

  11. Rat hippocampal GABAergic molecular markers are differentially affected by ageing.

    Science.gov (United States)

    Vela, José; Gutierrez, Antonia; Vitorica, Javier; Ruano, Diego

    2003-04-01

    We previously reported that the pharmacological properties of the hippocampal GABAA receptor and the expression of several subunits are modified during normal ageing. However, correlation between these post-synaptic modifications and pre-synaptic deficits were not determined. To address this issue, we have analysed the mRNA levels of several GABAergic molecular markers in young and old rat hippocampus, including glutamic acid decarboxylase enzymes, parvalbumin, calretinin, somatostatin, neuropeptide Y and vasoactive intestinal peptide (VIP). There was a differential age-related decrease in these interneuronal mRNAs that was inversely correlated with up-regulation of the alpha1 GABA receptor subunit. Somatostatin and neuropeptide Y mRNAs were most frequently affected (75% of the animals), then calretinin and VIP mRNAs (50% of the animals), and parvalbumin mRNA (25% of the animals) in the aged hippocampus. This selective vulnerability was well correlated at the protein/cellular level as analysed by immunocytochemistry. Somatostatin interneurones, which mostly innervate principal cell distal dendrites, were more vulnerable than calretinin interneurones, which target other interneurones. Parvalbumin interneurones, which mostly innervate perisomatic domains of principal cells, were preserved. This age-dependent differential reduction of specific hippocampal inteneuronal subpopulations might produce functional alterations in the GABAergic tone which might be compensated, at the post-synaptic level, by up-regulation of the expression of the alpha1 GABAA receptor subunit.

  12. Towards a transferable and cost-effective plant AFLP protocol.

    Directory of Open Access Journals (Sweden)

    Marguerite Blignaut

    Full Text Available Amplified fragment length polymorphism (AFLP is a powerful fingerprinting technique that is widely applied in ecological and population genetic studies. However, its routine use has been limited by high costs associated with the optimization of fluorescently labelled markers, especially for individual study systems. Here we develop a low-cost AFLP protocol that can be easily transferred between distantly related plant taxa. Three fluorescently labelled EcoRI-primers with anchors that target interspecifically conserved genomic regions were used in combination with a single non-labelled primer in our AFLP protocol. The protocol was used to genotype one gymnosperm, two monocot and three eudicot plant genera representing four invasive and four native angiosperm species (Pinus pinaster (Pinaceae, Pennisetum setaceum and Poa annua (Poaceae, Lantana camara (Verbenaceae, Bassia diffusa (Chenopodiaceae, Salvia lanceolata, Salvia africana-lutea, and Salvia africana-caerulea (Lamiaceae. Highly polymorphic and reproducible genotypic fingerprints (between 37-144 polymorphic loci per species tested were obtained for all taxa tested. Our single protocol was easily transferred between distantly related taxa. Measures of expected heterozygosity ranged from 0.139 to 0.196 for P. annua and from 0.168 to 0.272 for L. camara which compared well with previously published reports. In addition to ease of transferability of a single AFLP protocol, our protocol reduces costs associated with commercial kits by almost half. The use of highly conserved but abundant anchor sequences reduces the need for laborious screening for usable primers that result in polymorphic fingerprints, and appears to be the main reason for ease of transferability of our protocol between distantly related taxa.

  13. Towards a transferable and cost-effective plant AFLP protocol.

    Science.gov (United States)

    Blignaut, Marguerite; Ellis, Allan G; Le Roux, Johannes J

    2013-01-01

    Amplified fragment length polymorphism (AFLP) is a powerful fingerprinting technique that is widely applied in ecological and population genetic studies. However, its routine use has been limited by high costs associated with the optimization of fluorescently labelled markers, especially for individual study systems. Here we develop a low-cost AFLP protocol that can be easily transferred between distantly related plant taxa. Three fluorescently labelled EcoRI-primers with anchors that target interspecifically conserved genomic regions were used in combination with a single non-labelled primer in our AFLP protocol. The protocol was used to genotype one gymnosperm, two monocot and three eudicot plant genera representing four invasive and four native angiosperm species (Pinus pinaster (Pinaceae), Pennisetum setaceum and Poa annua (Poaceae), Lantana camara (Verbenaceae), Bassia diffusa (Chenopodiaceae), Salvia lanceolata, Salvia africana-lutea, and Salvia africana-caerulea (Lamiaceae)). Highly polymorphic and reproducible genotypic fingerprints (between 37-144 polymorphic loci per species tested) were obtained for all taxa tested. Our single protocol was easily transferred between distantly related taxa. Measures of expected heterozygosity ranged from 0.139 to 0.196 for P. annua and from 0.168 to 0.272 for L. camara which compared well with previously published reports. In addition to ease of transferability of a single AFLP protocol, our protocol reduces costs associated with commercial kits by almost half. The use of highly conserved but abundant anchor sequences reduces the need for laborious screening for usable primers that result in polymorphic fingerprints, and appears to be the main reason for ease of transferability of our protocol between distantly related taxa.

  14. Bootsie: estimation of coefficient of variation of AFLP data by bootstrap analysis

    Science.gov (United States)

    Bootsie is an English-native replacement for ASG Coelho’s “DBOOT” utility for estimating coefficient of variation of a population of AFLP marker data using bootstrapping. Bootsie improves on DBOOT by supporting batch processing, time-to-completion estimation, built-in graphs, and a suite of export t...

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

    Science.gov (United States)

    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.

  16. APPLICATION OF MOLECULAR MARKERS IN FARM ANIMAL IMPROVEMENT: PROSPECTS AND CHALLENGES

    Directory of Open Access Journals (Sweden)

    V.N. EBEGBULEM

    2013-05-01

    Full Text Available The discovery of genetic polymorphism at the DNA sequence level has been exploited as markers to explain the observed phenotypic variability in animals. Molecular markers have proven to be more reliable than other forms of genetic markers. The overview of the applications of molecular markers in the areas of genetic diversity conservation, identification of disease carriers, parentage determination, marker-assisted selection, transgenesis, sex-determination; and the enumeration of some challenges to the application of these markers in the developing countries, especially Nigeria, form the crux of this paper. Some of the challenges include economic factors, mechanical and logistics factors, lack of funding/grants for research, IPR issues and lack of adequately trained personnel in areas of molecular genetics.

  17. Molecular evaluations of thirty one clones of poplar based on RAPD and SSR molecular markers

    Directory of Open Access Journals (Sweden)

    Singh M.K.

    2014-01-01

    Full Text Available Poplar is an important tree species valued all over the world for its wood importance. Despite limited knowledge of the levels of genetic diversity and relatedness, their cultivation as a source of plywood is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for selective breeding programme, genetic analysis of 31 genotypes was performed using RAPD and SSR molecular markers. Twenty six RAPD primers and 14 SSR primers amplified a total of 236 and 85 scoreable bands of which 86.44% and 86.02% were polymorphic. The mean coefficient of gene differentiation (Gst was 0.388 and 0.341 indicating that 61.2% and 65.9% of the genetic variation resided within the populations. Analysis of molecular variance (AMOVA indicated that majority of genetic variation (94.6% using RAPD and 89% using SSR occurred among genotypes, while the variation between the three groups (categorized as tall, medium and small plants height was 5.4% (using RAPD and 11% (using SSR. The dendrogram obtained from NJ and STRUCTURE analysis revealed splitting of genotypes into four clusters with clear distinction between short, medium and tall height genotypes, indicated that genetic differentiations measure with respect to RAPD and SSR. However, both the markers were equally useful in providing some understanding about the genetic relationship of different genotypes of poplar that are important in the conservation and exploitation of poplar genetic resources.

  18. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis

    KAUST Repository

    Sudheer Pamidimarri, D. V N

    2014-01-29

    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity. © Springer Science+Business Media 2014.

  19. Indel Group in Genomes (IGG) Molecular Genetic Markers1[OPEN

    Science.gov (United States)

    Burkart-Waco, Diana; Kuppu, Sundaram; Britt, Anne; Chetelat, Roger

    2016-01-01

    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

  20. Genetic confirmation of mungbean (Vigna radiata and mashbean (Vigna mungo interspecific recombinants using molecular markers

    Directory of Open Access Journals (Sweden)

    Ghulam eAbbas

    2015-12-01

    Full Text Available The present study was conducted with the aim to investigate recombination between mungbean (female and mashbean (male interspecific crosses using molecular markers i.e., URP (Universal Rice Primers, RAPD (Random Amplified Polymorphic DNA and SSR (Simple Sequence Repeats. As a first step parental screening was performed and polymorphic markers differentiating parent genotypes were identified. Recombinations were then confirmed through polymorphic DNA markers in many of the hybrids. The NM 2006 × Mash 88 was found to be most successful interspecific cross as many of true recombinants, confirmed by molecular markers, belonged to this cross combination. The SSR markers were more efficient in detecting genetic variability and recombinations with reference to specific chromosomes and particular loci, while SSR (RIS and RAPD identified variability dispersed throughout the genome. The DNA based marker assisted approach provided evidence for genetic confirmation of mungbean and mashbean interspecific recombinants and escalated the authenticity of selection in mungbean improvement programme.

  1. Molecular markers in prostate cancer.Part II:potential roles in management

    Institute of Scientific and Technical Information of China (English)

    Sachin Agrawal; Krishnaji P.Patil; William D.Dunsmuir

    2009-01-01

    Predicting treatment responses in advanced prostate cancer (PCa) currently centres on prostate-specific antigen (PSA) kinetics and on being able to visualize measurable changes in imaging modalities.New molecular markers have emerged as potential diagnostic and prognostic indicators;these were summarized in Part I of this review in the Asian Journal of Andrology.A number of molecular markers are now being used to enhance PCa imaging and staging.However,management options for advanced and hormone-resistant PCa (HRPC) are limited and additional therapeutic options are needed.Molecular markers have been proposed as potential therapeutic targets using gene therapy and immunomodulation.Additionally,markers identified in early PCa and precursor lesions may offer novel targets for chemoprevention and vaccine development.This review summarizes the current advances regarding the roles of these markers in the management of PCa.

  2. Construction of AFLP-based genetic linkase maps for the Chinese shrimp Fenneropaeneus chinensis

    Institute of Scientific and Technical Information of China (English)

    TIAN Yi; KONG Jie; WANG WeiJi

    2008-01-01

    Fenneropaeneus chinensis is an important species in marine fishery resources and aquaculture in China. A genetic linkage map is essential for improving the efficiency of its breeding by marker-as-sisted selection and identifying commercially important genes. Linkage maps of F. Chinensis were constructed with an F2 mapping population (110 progenies) using amplified fragment length polymor-phic (AFLP) marker in this study. Fifty-five AFLP primer combinations produced 532 AFLP markers fitting for map strategy in mapping family. The markers with 3:1 segregating ratios were analyzed using F2 intercross model for the common linkage map, while the markers with 1:1 ratio were analyzed using the pseudo-testcross strategy. The maps of male, female and common were constructed. The female map included 103 markers that formed 28 linkage groups, covering a total length of 1090 cM. All mark-ers were linked with the linkage groups. Segregation distortion was observed for 6 of 103 markers in the female map. The average distance between markers was 14.53 cM and ranged from 4.4 to 24.8 cM. The male map included 144 markers that formed 35 linkage groups. Ten markers remained unlinked in male map. Segregation distortion was observed for 7 of 144 markers in the male map. The total dis-tance of male map covered 1617 cM. The average distance between markers was 16.36 cM. The male map was 32.6% longer than the female map, which may reflect sex-specific recombination rates in Chinese shrimp. The common map was composed of 216 markers, including in 44 linkage groups covering a total distance of 1772.1 cM. Two markers remained unlinked. No distorted markers of 216 markers were shown in the common map. The distance between markers was 10.42 cM. An average estimated genome size for the Chinese shrimp was 2420 cM, which was consistent with the relative size of the Penaeid genome. The distribution of AFLP markers was relatively even in chromosomes of Chi-nese shrimp maps. The linkage analysis

  3. Analysis of Genetic Changes in Newly Synthesized Wheat Amphiploids Using AFLP Markers%人工合成双二倍体小麦过程中遗传变异的AFLP分析

    Institute of Scientific and Technical Information of China (English)

    刘迪; 霍纳新; 张立芳; 贾继增

    2012-01-01

    为了给人工合成双二倍体小麦育种中亲本的选配提供基因表达水平的依据,通过AFLP方法对人工合成双二倍体小麦Am1、Am5、Am6及其亲本基因组DNA 进行了遗传变异分析。结果表明,亲本间遗传差异越小,亲本与子代间DNA片段的遗传比率越高。母本Ps5与父本Y95之间四、二倍体差异带率最小,为 35.2%,它们与后代Am5三者之间公共带率最大,为47.9%;后代双二倍体倾向于缺失二倍体亲本的遗传信息。Am1、Am5和Am6缺失二倍体亲本中DNA扩增片段的比率高,分别为71.0%、82.8%和90.0%,分别是缺失四倍体亲本的2.4、4.8和9.0倍;亲本间的遗传差异与后代中出现特异DNA片段的概率没有直接相关性。Am1中出现特异DNA片段的比率最高(6.2%),但是其亲本间遗传差异介于其他两组试验材料之间。%A total of 178 pairs of AFLP primer combinations were chosen to amplify the DNA of three amphidiploid wheats (AABBDD) and their diploid (DD)/tetraploid (AABB) parents. Rapid genetic changes in Am1, Am5, Am6, and their parents were analysed by DNA AFLP technique. It is the monomorphic bands present in the amphidiploids and their parents, indicating the existence of DD and AABB genomes in the synthesized amphidiploid wheats and the genetic relation of the synthesized amphidiploid wheats and their parents. The genetic difference between parents is the smaller and the percentage of monomorphic bands is the higher. In cross Ps5×Y95, there was the lowest percentage of polymorphic bands (35.2%) between parents compared with the highest percentage of monomorphic bands (47.9%).Sequence deletion occurred in amphiploids, the loci of which were mainly from their diploid male parent. The bands that had disappeared in Am1, Am5 and Am6 originated from their diploid parents and the percentage of bands were 71.0%, 82.8% and 90.0% respectively, which were 2.4 fold, 4.8 fold and 9.0 fold higer than the

  4. Tracking neuronal marker expression inside living differentiating cells using molecular beacons

    DEFF Research Database (Denmark)

    Ilieva, Mirolyuba; Della Vedova, Paolo; Hansen, Ole

    2013-01-01

    Monitoring gene expression is an important tool for elucidating mechanisms of cellular function. In order to monitor gene expression during nerve cell development, molecular beacon (MB) probes targeting markers representing different stages of neuronal differentiation were designed and synthesized...

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

    Science.gov (United States)

    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.

  6. MOLECULAR GENETIC MARKERS AND METHODS OF THEIR IDENTIFICATION IN MODERN FISH-FARMING

    OpenAIRE

    I. Hrytsyniak; O. Zaloilo; I. Zaloilo; N. Borysenko

    2014-01-01

    Purpose. The application of molecular genetic markers has been widely used in modern experimental fish-farming in recent years. This methodology is currently presented by a differentiated approach with individual mechanisms and clearly defined possibilities. Numerous publications in the scientific literature that are dedicated to molecular genetic markers for the most part offer purely practical data. Thus, the synthesis and analysis of existing information on the general principles of action...

  7. Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner

    Directory of Open Access Journals (Sweden)

    Devaraja Achar

    2015-01-01

    Full Text Available 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.

  8. Female-only sex-linked amplified fragment length polymorphism markers support ZW/ZZ sex determination in the giant freshwater prawn Macrobrachium rosenbergii.

    Science.gov (United States)

    Jiang, Xue-Hui; Qiu, Gao-Feng

    2013-12-01

    Sex determination mechanisms in many crustacean species are complex and poorly documented. In the giant freshwater prawn, Macrobrachium rosenbergii, a ZW/ZZ sex determination system was previously proposed based on sex ratio data obtained by crosses of sex-reversed females (neomales). To provide molecular evidence for the proposed system, novel sex-linked molecular markers were isolated in this species. Amplified fragment length polymorphism (AFLP) using 64 primer combinations was employed to screen prawn genomes for DNA markers linked with sex loci. Approximately 8400 legible fragments were produced, 13 of which were uniquely identified in female prawns with no indication of corresponding male-specific markers. These AFLP fragments were reamplified, cloned and sequenced, producing two reliable female-specific sequence characterized amplified region (SCAR) markers. Additional individuals from two unrelated geographic populations were used to verify these findings, confirming female-specific amplification of single bands. Detection of internal polymorphic sites was conducted by designing new primer pairs based on these internal fragments. The internal SCAR fragments also displayed specificity in females, indicating high levels of variation between female and male specimens. The distinctive feature of female-linked SCAR markers can be applied for rapid detection of prawn gender. These sex-specific SCAR markers and sex-associated AFLP candidates unique to female specimens support a sex determination system consistent with female heterogamety (ZW) and male homogamety (ZZ).

  9. Mapping Quantitative Trait Loci Controlling Endosperm Traits with Molecular Marker

    Institute of Scientific and Technical Information of China (English)

    XU Chen-wu; LI Tao; SUN Chang-sen; GU Shi-liang

    2002-01-01

    Based on the genetic models for triploid endosperm traits and on the methods for mapping diploid quantitative traits loci (QTLs), the genetic constitutions, components of means and genetic variances of QTL controlling endosperm traits under flanking marker genotypes of different generations were presented. From these results, a multiple linear regression method for mapping QTL underlying endosperm traits in cereals was proposed, which used the means of endosperm traits under flanking marker genotypes as a dependent variable, the coefficient of additive effect ( d ) and dominance effect ( h 1 and/or h2 ) of a putative QTL in a given interval as independent variables. This method can work at any position in a genome covered by markers and increase the estimation precision of QTL location and their effects by eliminating the interference of other relative QTLs. This method can also be easily used in other uneven data such as markers and quantitative traits detected or measured in plants and tissues different either in generations or at chromosomal ploidy levels, and in endosperm traits controlled by complicated genetic models considering the effects produced by genotypes of both maternal plants and seeds on them.

  10. Molecular markers for granulovacuolar degeneration are present in rimmed vacuoles.

    Directory of Open Access Journals (Sweden)

    Masahiro Nakamori

    Full Text Available BACKGROUND: Rimmed vacuoles (RVs are round-oval cytoplasmic inclusions, detected in muscle cells of patients with myopathies, such as inclusion body myositis (IBM and distal myopathy with RVs (DMRV. Granulovacuolar degeneration (GVD bodies are spherical vacuoles containing argentophilic and hematoxyphilic granules, and are one of the pathological hallmarks commonly found in hippocampal pyramidal neurons of patients with aging-related neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. These diseases are common in the elderly and share some pathological features. Therefore, we hypothesized that mechanisms of vacuolar formation in RVs and GVD bodies are common despite their role in two differing pathologies. We explored the components of RVs by immunohistochemistry, using antibodies for GVD markers. METHODS: Subjects included one AD case, eight cases of sporadic IBM, and three cases of DMRV. We compared immunoreactivity and staining patterns for GVD markers. These markers included: (1 tau-modifying proteins (caspase 3, cyclin-dependent kinase 5 [CDK5], casein kinase 1δ [CK1δ], and c-jun N-terminal kinase [JNK], (2 lipid raft-associated materials (annexin 2, leucine-rich repeat kinase 2 [LRRK2], and flotillin-1, and (3 other markers (charged multi-vesicular body protein 2B [CHMP2B] and phosphorylated transactive response DNA binding protein-43 [pTDP43] in both GVD bodies and RVs. Furthermore, we performed double staining of each GVD marker with pTDP43 to verify the co-localization. RESULTS: GVD markers, including lipid raft-associated proteins and tau kinases, were detected in RVs. CHMP2B, pTDP43, caspase 3, LRRK2, annexin 2 and flotillin-1 were detected on the rim and were diffusely distributed in the cytoplasm of RV-positive fibers. CDK5, CK1δ and JNK were detected only on the rim. In double staining experiments, all GVD markers colocalized with pTDP43 in RVs. CONCLUSIONS: These results suggest that RVs of muscle

  11. A genetic map of cucumber composed of RAPDs, RFLPs, AFLPs, and loci conditioning resistance to papaya ringspot and zucchini yellow mosaic viruses.

    Science.gov (United States)

    Park, Y H; Sensoy, S; Wye, C; Antonise, R; Peleman, J; Havey, M J

    2000-12-01

    The watermelon strain of papaya ringspot virus (PRSV-W) and zucchini yellow mosaic virus (ZYMV) are potyviruses that cause significant disease losses in cucumber. Resistances have been identified primarily in exotic germplasm that require transfer to elite cultivated backgrounds. To select more efficiently for virus resistances, we identified molecular markers tightly linked to PRSV-W and ZYMV resistances in cucumber. We generated F6 recombinant inbred lines (RILs) from a cross between Cucumis sativus L. 'Straight 8' and a line from 'Taichung Mou Gua', TMG1 (susceptible and resistant, respectively, to both viruses), and studied the segregations of amplified fragment length polymorphism (AFLP) markers, randomly amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and resistances to PRSV-W and ZYMV. A 353-point map of cucumber was generated, delineating 12 linkage groups at LOD 3.5. Linkage arrangements among RFLPs were consistent with previously published maps; however linkages among RAPDs in our map did not agree with a previously published map. Resistances to PRSV-W and ZYMV were tightly linked (2.2 cM) and mapped to the end of one linkage group. One AFLP cosegregated with resistance to ZYMV.

  12. Application of AFLP molecular markers to genetic characterisation of duck (Anas platyrhyncos, turkey (Meleagris gallopavo and helmeted guinea fowl (Numida meleagris Veneto breeds

    Directory of Open Access Journals (Sweden)

    M. Cassandro

    2010-01-01

    Full Text Available In the last decade, the conservation of local breeds and of their genetic resources has gained more and more importance (Notter, 1999. In fact, the safeguard of animal genetic variability is determinant to maintain ecosystem equilibriums but it is also essential to guarantee future economic potentials of these animal resources. Moreover, biodiversity has a great cultural value and it can be also used for scientific purposes (FAO, 1992.

  13. Studies on the AFLP Molecular Markers of Kava and Piper nigrum%卡瓦胡椒及胡椒的荧光AFLP分子标记研究

    Institute of Scientific and Technical Information of China (English)

    施江; 辛莉; 杨彦; 郑学勤

    2007-01-01

    对6份卡瓦胡椒材料、23份栽培胡椒和野生胡椒材料、1份不同属的草胡椒材料、1份不同科的普通烟材料,共计31份试验材料,进行荧光AFLP分子标记,研究卡瓦胡椒与胡椒及其他近缘野生种的亲缘关系.结果表明,在相似系数0.52处将31份种质划分为5个类群,第1个类群有普通烟,第2个类群有草胡椒,第3个类群是卡瓦胡椒,第4个类群有胡椒,第5个类群有山胡椒、蒌叶和蒟蒌.说明卡瓦胡椒与胡椒及其他近缘野生种的亲缘关系有一定距离,为卡瓦胡椒真伪性的分子鉴定和构建卡瓦胡椒的指纹图谱提供了基础性的工作.

  14. Molecular characterization of the U.S. Phaseolus acutifolius A. Gray collection using Amplified Fragment Length Polymorphism (AFLP) and Targeted Region Amplification Polymorphism (TRAP) markers.

    Science.gov (United States)

    Tepary bean (Phaseolus acutifolius A. Gray), a truly Native American crop, is a short life-cycle annual desert legume indigenous to northwestern Mexico and the southwestern USA and is considered drought and heat tolerant. The Western Regional Plant Introduction Station currently maintains 211 acce...

  15. Mating type-correlated molecular markers and demonstration of heterokaryosis in the phytopathogenic fungus Thanatephorus cucumeris (Rhizoctonia solani) AG 1-IC by AFLP DNA fingerprinting analysis

    NARCIS (Netherlands)

    Julian, M.C.; Acero, J.; Salazar, O.; Keijer, J.; Rubio, O.

    1999-01-01

    The destructive soil-borne plant pathogenic basidiomycetous fungus Thanatephorus cucumeris (Frank) Donk [anamorph: Rhizoctonia solani Kühn] is not a homogeneous species, but is composed of at least twelve anastomosis groups (AG), which seem to be genetically isolated. The genetics of several T. cucu

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

    Science.gov (United States)

    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.

  17. The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.

    Science.gov (United States)

    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 ...

  18. Genetic relationship of Curcuma species from Northeast India using PCR-based markers.

    Science.gov (United States)

    Das, Archana; Kesari, Vigya; Satyanarayana, Vinod M; Parida, Ajay; Rangan, Latha

    2011-09-01

    Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD), 19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic fragments. ISSR confirmed maximum polymorphism of 98.55% whereas RAPD and AFLP showed 93.22 and 97.27%, respectively. Marker index and polymorphic information content varied in the range of 8.64-48.1, 19.75-48.14, and 25-28 and 0.17-0.48, 0.19-0.48, and 0.25-0.29 for RAPD, ISSR, and AFLP markers, respectively. The average value of number of observed alleles, number of effective alleles, mean Nei's gene diversity, and Shannon's information index were 1.93-1.98, 1.37-1.62, 0.23-0.36, and 0.38-0.50, respectively, for three DNA markers used. Dendrograms based on three molecular data using unweighted pair group method with arithmetic mean (UPGMA) was congruent and classified the Curcuma species into two major clusters. Cophenetic correlation coefficient between dendrogram and original similarity matrix were significant for RAPD (r = 0.96), ISSR (r = 0.94), and AFLP (r = 0.97). Clustering was further supported by principle coordinate analysis. High genetic polymorphism documented is significant for conservation and further improvement of Curcuma species.

  19. Usefulness of molecular markers in the diagnosis of occupational and recreational histoplasmosis outbreaks.

    Science.gov (United States)

    Frías-De-León, María Guadalupe; Ramírez-Bárcenas, José Antonio; Rodríguez-Arellanes, Gabriela; Velasco-Castrejón, Oscar; Taylor, Maria Lucia; Reyes-Montes, María Del Rocío

    2017-03-01

    Histoplasmosis is considered the most important systemic mycosis in Mexico, and its diagnosis requires fast and reliable methodologies. The present study evaluated the usefulness of PCR using Hcp100 and 1281-1283(220) molecular markers in detecting Histoplasma capsulatum in occupational and recreational outbreaks. Seven clinical serum samples of infected individuals from three different histoplasmosis outbreaks were processed by enzyme-linked immunosorbent assay (ELISA) to titre anti-H. capsulatum antibodies and to extract DNA. Fourteen environmental samples were also processed for H. capsulatum isolation and DNA extraction. Both clinical and environmental DNA samples were analysed by PCR with Hcp100 and 1281-1283(220) markers. Antibodies to H. capsulatum were detected by ELISA in all serum samples using specific antigens, and in six of these samples, the PCR products of both molecular markers were amplified. Four environmental samples amplified one of the two markers, but only one sample amplified both markers and an isolate of H. capsulatum was cultured from this sample. All PCR products were sequenced, and the sequences for each marker were analysed using the Basic Local Alignment Search Tool (BLASTn), which revealed 95-98 and 98-100 % similarities with the reference sequences deposited in the GenBank for Hcp100 and 1281-1283(220), respectively. Both molecular markers proved to be useful in studying histoplasmosis outbreaks because they are matched for pathogen detection in either clinical or environmental samples.

  20. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.

    Science.gov (United States)

    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.

  1. Genetic diversity in palmyrah genotypes using morphological and molecular markers

    Directory of Open Access Journals (Sweden)

    V.Ponnuswami

    2010-07-01

    Full Text Available Palms are woody monocotyledons in the family Arecaceae which is placed in the order Arecales. Slow and tall growing,hardy and non branching, dioecious and perennial in nature, palmyrah palm has no distinguishing features to identify sex,stature and high neera yielding types until flowering age of about 12 to 15 years. Under these circumstances molecularmarkers can be effectively utilized to diagnose and select a genotype. Twenty palmyrah accessions were analysed usingRAPD and ISSR markers. In RAPD analysis, a total of 57 bands were obtained, among them 43 were polymorphic and restof them were monomorphic. Amplification size ranged between 250 and 3200 bp. UPGMA based cluster diagram showedthat all 20 different genotypes were grouped into four different clusters based on the stature, sex and high neera yieldingtypes. The distance matrix between genotypes showed an average distance range from 0.54 to 0.91 with a mean of 0.70. Atotal of 130 ISSR markers were scored, of which 65 were polymorphic, equivalent to 47.94% polymorphism. These markerswere used to estimate the genetic similarity among accessions using Jaccard’s similarity coefficient, with similarity valuesranging from 71.6 to 95.7%. The average number of markers produced per primer was 6.11. For each of the 21 ISSRprimers PIC value ranged between 0 and 0.46. Cluster analysis based on ISSR data grouped the 20 palmyrah accessions intotwo major clusters. PCA based on ISSR data clearly distinguished genotypes similar to the results of cluster analysis.

  2. Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers.

    Directory of Open Access Journals (Sweden)

    Ngoot-Chin Ting

    Full Text Available 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.

  3. Molecular and cellular markers of toxicity in the Japanese Medaka @

    Energy Technology Data Exchange (ETDEWEB)

    Shugart, L.R.; McCarthy, J.F.; D' Surney, S.J.; Greeley, M.S. Jr.; Hull, C.G.

    1990-01-01

    The Japanese Medaka (Oryzias latipes) has been recommended for use as a model organism to detect carcinogenic, teratogenic, cytotoxic, and genotoxic compounds in aquatic systems. Because a long latent period often occurs between initial contact with deleterious chemicals and subsequent expression of the pathology, we are investigating early biologically-relevant responses that can be used as genotoxicity markers of exposure and effect. This project focuses on the development of genotoxic bioassays and experimental protocols for exposing Japanese Medaka to genotoxic compounds. 21 refs., 8 figs, 2 tabs.

  4. The Fate of Molecular Markers in Soils and Their Implications for Soil Carbon Cycling

    Science.gov (United States)

    Wiesenberg, G. L.

    2014-12-01

    During the past decades molecular markers were discovered to be of diagnostic character for tracing the origin and fate of organic matter in soils. Molecular proxies themselves and their combination with compound-specific isotope analyses became powerful tools to distinguish between various biogenic and anthropogenic sources of organic matter and to trace carbon turnover at a molecular level. In the meantime various field and laboratory experiments provided deeper insight into soil organic matter dynamics at a molecular scale. We learnt from these experiments that carbon turnover at a molecular scale occurs in a similar time frame like for bulk soil organic matter and that selective preservation is not an issue for most coumpounds in active soils, but e.g. in fossil soils. Nevertheless, e.g. plant wax-derived alkanes and root-derived suberin markers point to a slower turnover of specific compounds. Recently, molecular markers enabled deciphering root-derived processes that occur in the rhizosphere of living and dead roots within the soil or even in the deep subsoil (up to several meters below the soil surface). Thus, the proposed carbon sequestration by roots in subsoils is not necessarily relevant in the long-term on a decadal or centennial scale. Although molecular markers were not determined to be valuable tools to sequester carbon in the soil, they strongly help elucidating processes relevant for cycling of bulk organic matter from the soil surface towards the deep subsoil.

  5. Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar.

    Science.gov (United States)

    Tollenaere, C; Jacquet, S; Ivanova, S; Loiseau, A; Duplantier, J-M; Streiff, R; Brouat, C

    2013-01-01

    Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300 kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection.

  6. Molecular imaging of rheumatoid arthritis: emerging markers, tools, and techniques.

    Science.gov (United States)

    Put, Stéphanie; Westhovens, René; Lahoutte, Tony; Matthys, Patrick

    2014-04-15

    Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor κB and its ligand, chemokine receptors, vascular cell adhesion molecule-1, αVβ₃ integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein.

  7. Molecular markers to study competition and diversity of Rhizobium.

    NARCIS (Netherlands)

    Sessitsch, A.

    1997-01-01

    The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous microbes is a serious problem in

  8. Predictive and prognostic molecular markers for cancer medicine.

    Science.gov (United States)

    Mehta, Sunali; Shelling, Andrew; Muthukaruppan, Anita; Lasham, Annette; Blenkiron, Cherie; Laking, George; Print, Cristin

    2010-03-01

    Over the last 10 years there has been an explosion of information about the molecular biology of cancer. A challenge in oncology is to translate this information into advances in patient care. While there are well-formed routes for translating new molecular information into drug therapy, the routes for translating new information into sensitive and specific diagnostic, prognostic and predictive tests are still being developed. Similarly, the science of using tumor molecular profiles to select clinical trial participants or to optimize therapy for individual patients is still in its infancy. This review will summarize the current technologies for predicting treatment response and prognosis in cancer medicine, and outline what the future may hold. It will also highlight the potential importance of methods that can integrate molecular, histopathological and clinical information into a synergistic understanding of tumor progression. While these possibilities are without doubt exciting, significant challenges remain if we are to implement them with a strong evidence base in a widely available and cost-effective manner.

  9. Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity.

    Science.gov (United States)

    Wahyuni, Yuni; Ballester, Ana-Rosa; Tikunov, Yury; de Vos, Ric C H; Pelgrom, Koen T B; Maharijaya, Awang; Sudarmonowati, Enny; Bino, Raoul J; Bovy, Arnaud G

    2013-02-01

    An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC-MS and headspace GC-MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum-C. chinense-C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0432-6) contains supplementary material, which is available to

  10. Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii.

    Science.gov (United States)

    Gygax, M; Gianfranceschi, L; Liebhard, R; Kellerhals, M; Gessler, C; Patocchi, A

    2004-11-01

    Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes, molecular markers are already available; but until now, none existed for the apple scab resistance gene Vbj originating from the crab apple Malus baccata jackii. Using bulk segregant analysis, three RAPD markers linked to Vbj were first identified. These markers were transformed into more reliable sequence-characterised amplified region (SCAR) markers that proved to be co-dominant. In addition, three SSR markers and one SCAR were identified by comparing homologous linkage groups of existing genetic maps. Discarding plants showing genotype-phenotype incongruence (GPI plants) plants, a linkage map was calculated. Vbj mapped between the markers CH05e03 (SSR) and T6-SCAR, at 0.6 cM from CH05e03 and at 3.9 cM from T6-SCAR. Without the removal of the GPI plants, Vbj was placed 15 cM away from the closest markers. Problems and pitfalls due to GPI plants and the consequences for mapping the resistance gene accurately are discussed. Finally, the usefulness of co-dominant markers for pedigree analysis is also demonstrated.

  11. Molecular markers in the surgical margin of oral carcinomas

    DEFF Research Database (Denmark)

    Bilde, A.; Buchwald, C. von; Dabelsteen, E.;

    2009-01-01

    BACKGROUND: Local or regional lymph node recurrence is the most common pattern of treatment failure in oral squamous cell carcinoma (SCC). The local recurrence rate is 30% even when the surgical resection margin is diagnosed as tumour free. Accumulation of genetic changes in histologically normal...... epithelium in the surgical resection margin may explain the local recurrence rate. The purpose of this study is to investigate the presence of senescence markers, which may represent early malignant changes in the margin that in routine pathological evaluations are classified as histologically normal....... METHODS: Formalin-fixed, paraffin-embedded surgical specimens from 16 consecutive patients with oral SCC and a clear surgical margin were obtained. The margin was analysed by immunohistochemistry for p53, p16, Chk2, Laminin-5 and glycosylated oncofetal fibronectin. RESULTS: Two patterns of p53 expression...

  12. Estimation of the proportion of genetic variance explained by molecular markers

    OpenAIRE

    Bearzoti,Eduardo; Vencovsky, Roland

    1998-01-01

    Estimation of the proportion of genetic variance explained by molecular markers (p) plays an important role in basic studies of quantitative traits, as well as in marker-assisted selection (MAS), if the selection index proposed by Lande and Thompson (Genetics 124: 743-756, 1990) is used. Frequently, the coefficient of determination (R2) is used to account for this proportion. In the present study, a simple estimator of p is presented, which is applicable when a multiple regression approach is...

  13. Genetic diversity in maize dent landraces assessed by morphological and molecular markers

    Directory of Open Access Journals (Sweden)

    Ristić Danijela

    2013-01-01

    Full Text Available Maize Research Institute “Zemun Polje” genebank maintains a collection of landraces grouped into 18 agro-ecological collected from ex-Yugoslavia territories. The application and comparison of different marker systems are important for the characterization and use of maize landraces in breeding program, as potential sources of desirable traits. In this study, 15 morphological traits, 7 RAPD primers and 10 SSR primer pairs were applied to i to determine genetic distance between 21 maize dent landraces and ii compare results obtained on morphological and molecular markers. Phenotypic analysis showed high level of heterogeneity between landraces. Higher level of genetic diversity was obtained with SSR than with RAPD. Genetic distance mean value for RAPD data was 0.35 i.e. for SSR 0.48. Based on the morphological traits and molecular markers, unweighted pairgroup method (UPGMA analysis was applied for cluster analysis, using statistical NTSYSpc program package. Cluster analysis of morphological and molecular markers distances did not show the same population grouping. Better agreement with agro-ecological data was obtained with RAPD markers. Correlations between dissimilarity matrices for different types of markers were low. Data obtained in this work could be useful for further study of a larger number of landraces, and conservation of genetic resources and their genetic diversity. [Projekat Ministarstva nauke Republike Srbije, br. TR31028: Exploitation of maize diversity to improve grain quality and drought tolerance

  14. Estimating Out-Crossing Rate of Bg 379-2 Using Morphological Markers and Confirmation by Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    L. H. M. Y. K. SOMARATNE; A.S.M.T.ABAYAWICKRAMA; I. P. WICKRAMASINGHE; W. L. G. SAMARASINGHE

    2012-01-01

    Rice is largely self-fertilized and accordingly a field population of rice is completely composed of near homozygotes.Due to the emergence of off-types,homozygosity will be affected.With the time,this will cause the reduction of genetic purity in some rice varieties.One of the reasons has been suspected to be the high out-crossing frequencies of such varieties.Studies were conducted at the Rice Research and Development Institute,Batalagoda,Sri Lanka to estimate the out-crossing rote of Bg 379-2,a variety having the problem of maintaining genetic purity.Bg 379-2 was allowed to out-cross with Bg 450 and the number of outcrossed plants were counted using dominant morphological markers such as short-round grain and purple culm of pollen donor.A molecular confirmation of out-crossing was also performed using sequence tagged site (STS) molecular marker pTA248.The variety Bg 379-2 showed a potential out-crossing rate of 3.41% and an average out-crossing rate of 1.29% using dominant morphological markers.Polymorphism was clearly detected between parents and out-crossed plants as well as selfed plants of Bg 379-2 using their banding patterns.A similar study can be performed to determine the out-crossing rates of other varieties which show high percentage of off-types in the population for the better understanding of the breeding behavior of the varieties.

  15. Molecular markers and targets for colorectal cancer prevention

    Institute of Scientific and Technical Information of China (English)

    Naveena B JANAKIRAM; Chinthalapally V RAO

    2008-01-01

    Colorectal cancer is the third most prevalent cancer in the world. If detected at an early stage, treatment often might lead to cure. As prevention is better than cure, epidemiological studies reveal that having a healthy diet often protects from pro-moting/developing cancer. An important consideration in evaluating new drugs and devices is determining whether a product can effectively treat a targeted disease. There are quite a number of biomarkers making their way into clinical trials and few are awaiting the preclinical efficacy and safety results to enter into clinical trials. Researchers are facing challenges in modifying trial design and defining the right control population, validating biomarker assays from the bio-logical and analytical perspective and using biomarker data as a guideline for decision making. In spite of following all guidelines, the results are disappointing from many of the large clinical trials. To avoid these disappointments, selection of biomarkers and its target drug needs to be evaluated in appropriate animal models for its toxicities and efficacies. The focus of this review is on the few of the potential molecular targets and their biomarkers in colorectal cancers. Strengths and limitations of biomarkers/surrogate endpoints are also discussed. Various pathways involved in tumor cells and the specific agents to target the altered molecular biomarkerin biomolecular pathwayare elucidated. Importance of emerging new platforms siRNAs and miRNAs technology for colorectal cancer therapeutics is reviewed.

  16. AFLP and RAPD Analysis of the Boer and Indigenous Breeds of the Goat in Jiangsu

    Institute of Scientific and Technical Information of China (English)

    CAO Shao-xian; YANG Li-guo; JIANG Xun-ping; LIU Hong-lin; LU Wei-zhong; XIANG Yang-hai

    2003-01-01

    Blood and tissue samples were collected from 105 goats including 60 Boer goats (30 for eachsex), 30 Xuhuai goats (15 for each sex) and 15 Haimen goats (7 stud and 8 does). DNA was extracted andDNA pools were constructed on the basis of goat breeds. In 36 selective primer combinations, 29 combinationsamplified totally 3 253 markers including 92 polymorphic markers by amplified fragment length polymor-phism (AFLP). On average, 3.17 polymorphic markers were amplified per combination, with a polymorphicfrequency of 2.8%. The primer combinations amplifying more polymorphic markers (showed in brackets)were involved in E00+ACG/M00+CAA (13), E00+ACG/M00+CAG (10), E00+AAC/M00+CAC (8)and E00+AAC/M00+ACT (7). A total of 183 markers including 60 polymorphic markers were amplified byRAPD from the pooled DNA of three breeds using 22 primers with strong polymorphism and high reproduc-ibility selected from 93 RAPD primers. On average, 2.73 polymorphic markers were amplified per primer,with a polymorphic frequency of 32.8%. The results of AFLP and RAPD coincidently suggested that the ge-netic distance is the closest between Xuhuai and Haimen goat, next between Xuhuai and Boer goat, and the far-thest between Haimen and Boer goat. According to the UPGMA method, Haimen and Xuhuai goats can begathered together as a cluster, then Boer goat. Both methods can be used to implicate the genetic difference ofthese three breeds, in particular AFLP has more polymorphic markers.

  17. Biomedical wellness monitoring system based upon molecular markers

    Science.gov (United States)

    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.

  18. Molecular markers as therapeutic targets in lung cancer

    Institute of Scientific and Technical Information of China (English)

    Hsin-Hui Tseng; Biao He

    2013-01-01

    Lung cancer is responsible for 29% of cancer deaths in the United States and has very low 5-year survival rates of approximately 11% in men and 15% in women.Although the early diagnosis of lung cancer may increase the survival rate with adequate treatment,advanced lung cancers are often metastasized and receive limited benefit from therapeutic regimens.As conventional treatments for lung cancer reach their limitations,researchers have attempted to discover novel drug therapies aimed at specific targets contributing to the progression of tumorigenesis.Recent advances in systems biology have enabled the molecular biology of lung carcinogenesis to be elucidated.Our understanding of the physiologic processes of tumor development provide a means to design more effective and specific drugs with less toxicity,thereby accelerating the delivery of new drug therapies to the patient's bedside.

  19. Molecular Markers of Dental Pulp Tissue during Orthodontic Tooth Movement: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Rohaya Megat Abdul Wahab

    2012-01-01

    Full Text Available Three specific orthodontic tooth movement genes, that is, FCRL1, HSPG2, and LAMB2 were detected at upper first premolar (with appliance dental pulp tissue by using GeneFishing technique as compared to lower first premolar (without appliance. These three differentially expressed genes have the potential as molecular markers during orthodontic tooth movement by looking at molecular changes of pulp tissue.

  20. Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

    Institute of Scientific and Technical Information of China (English)

    Xiaomin Tang; Weidong Bao; Wenli Zhang; Zhukuan Cheng

    2007-01-01

    To develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller-sized chromosomes. An efficient approach using bacterial artificial chromosome (BAG) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm-specific molecular cytological markers derived from the gene-enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza satlva L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm-specific markers.

  1. Identification of RAPD markers and their use for molecular mapping in pea (Pisum sativum L.).

    Science.gov (United States)

    Cheghamirza, Kianoosh; Koveza, Oksana; Konovalov, Fedor; Gostimsky, Sergei

    2002-01-01

    The RAPD method (Random Amplified Polymorphic DNA) was used for identifying and mapping new molecular markers in pea. RAPD analysis of various cultivars and lines of pea was carried out using 10-mer random primers. The presence of multiple polymorphism between cultivars and lines was revealed; at least one fragment for any given primer was present in the DNA of one form of pea and absent in the DNA of another line or cultivar. To detect molecular markers linked to the genes of chi-15, xa-18 and also to the 12 morphological markers of the L-1238 line, the F2 populations (Chi-15 ? L-1238), (Vio ? L-1238), (Xa-18 ? L-1238), (L-111 ? Chi-15) and (L-84 ? Xa-18) were studied via bulked segregant analysis. DNA molecular analysis of F1 hybrids revealed the presence of parental polymorphic fragments in all of the populations. The study of the F2 plants showed that the obtained fragments are inherited as Mendelian factors. 13 RAPD-markers linked to genes of A/a (flower color), I/i (seed color), Gp/gp (pod color), R/r (seed form), S/s (seeds linkage), and also to genes of Chi-15/chi-15 (leaf color) and Xa-18/xa-18 (leaf color) were discovered. The study of individual plant DNA from the F2 populations allowed us to determine the genetic distances between genes and the RAPD markers linked to them.

  2. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers.

    Science.gov (United States)

    Pavan-Kumar, A; Gireesh-Babu, P; Babu, P P Suresh; Jaiswar, A K; Hari Krishna, V; Prasasd, K Pani; Chaudhari, Aparna; Raje, S G; Chakraborty, S K; Krishna, Gopal; Lakra, W S

    2014-01-01

    The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids.

  3. Molecular markers of neuronal progenitors in the embryonic cerebellar anlage.

    Science.gov (United States)

    Morales, Daniver; Hatten, Mary E

    2006-11-22

    The cerebellum, like the cerebrum, includes a nuclear structure and an overlying cortical structure. Experiments in the past decade have expanded knowledge beyond the traditional function of the cerebellum to include critical roles in motor learning and memory and sensory discrimination. The initial steps in cerebellar development depend on inductive signaling involving FGF and Wnt proteins produced at the mesencephalic/metencephalic boundary. To address the issue of how individual cerebellar cell fates within the cerebellar territory are specified, we examined the expression of transcription factors, including mammalian homologues of LIM homeodomain-containing proteins, basic helix-loop-helix proteins, and three amino acid loop-containing proteins. The results of these studies show that combinatorial codes of transcription factors define precursors of the cerebellar nuclei, and both Purkinje cells and granule neurons of the cerebellar cortex. Examination of gene expression patterns in several hundred lines of Egfp-BAC (bacterial artificial chromosome) transgenic mice in the GENSAT Project revealed numerous genes with restricted expression in cerebellar progenitor populations, including genes specific for cerebellar nuclear precursors and Purkinje cell precursors. In addition, we identified patterns of gene expression that link granule and Purkinje cells to their precerebellar nuclei. These results identify molecular pathways that offer new insights on the development of the nuclear and cortical structures of the cerebellum, as well as components of the cerebellar circuitry.

  4. Genetic Comparison of B. Anthracis and its Close Relatives Using AFLP and PCR Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, P.J.; Hill, K.K.; Laker, M.T.; Ticknor, L.O.; Keim, P.S.

    1999-02-01

    Amplified Fragment length Polymorphism (AFLP) analysis allows a rapid, relatively simple analysis of a large portion of a microbial genome, providing information about the species and its phylogenetic relationship to other microbes (Vos, et al., 1995). The method simply surveys the genome for length and sequence polymorphisms. The pattern identified can be used for comparison to the genomes of other species. Unlike other methods, it does not rely on analysis of a single genetic locus that may bias the interpretation of results and it does not require any prior knowledge of the targeted organism. Moreover, a standard set of reagents can be applied to any species without using species-specific information or molecular probes. The authors are using AFLP's to rapidly identify different bacterial species. A comparison of AFLP profiles generated from a large battery of B. anthracis strains shows very little variability among different isolates (Keim, et al., 1997). By contrast, there is a significant difference between AFLP profiles generated for any B. anthracis strain and even the most closely related Bacillus species. Sufficient variability is apparent among all known microbial species to allow phylogenetic analysis based on large numbers of genetically unlinked loci. These striking differences among AFLP profiles allow unambiguous identification of previously identified species and phylogenetic placement of newly characterized isolates relative to known species based on a large number of independent genetic loci. Data generated thus far show that the method provides phylogenetic analyses that are consistent with other widely accepted phylogenetic methods. However, AFLP analysis provides a more detailed analysis of the targets and samples a much larger portion of the genome. Consequently, it provides an inexpensive, rapid means of characterizing microbial isolates to further differentiate among strains and closely related microbial species. Such information

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

    Science.gov (United States)

    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...

  6. A novel molecular marker for the study of Neotropical cichlid phylogeny.

    Science.gov (United States)

    Fabrin, T M C; Gasques, L S; Prioli, S M A P; Prioli, A J

    2015-12-22

    The use of molecular markers has contributed to phylogeny and to the reconstruction of species' evolutionary history. Each region of the genome has different evolution rates, which may or may not identify phylogenetic signal at different levels. Therefore, it is important to assess new molecular markers that can be used for phylogenetic reconstruction. Regions that may be associated with species characteristics and are subject to selective pressure, such as opsin genes, which encode proteins related to the visual system and are widely expressed by Cichlidae family members, are interesting. Our aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system. We used Bayesian inference and maximum likelihood analysis to support the use of the nuclear opsin LWS gene in the phylogeny of eight Neotropical cichlid species. Their use concatenated to the mitochondrial gene COI was also tested. The LWS gene fragment comprised the exon 2-4 region, including the introns. The LWS gene provided good support for both analyses up to the genus level, distinguishing the studied species, and when concatenated to the COI gene, there was a good support up to the species level. Another benefit of utilizing this region, is that some polymorphisms are associated with changes in spectral properties of the LWS opsin protein, which constitutes the visual pigment that absorbs red light. Thus, utilization of this gene as a molecular marker to study the phylogeny of Neotropical cichlids is promising.

  7. MOLECULAR MARKERS OF BLADDER CANCER: FROM THE PARTICULAR TO THE GENERAL

    Directory of Open Access Journals (Sweden)

    A. A. Zabolotneva

    2014-08-01

    Full Text Available Bladder cancer (BC is the second most common urinary tract malignancy. Early diagnosis of BC generally increases the probability of successful treatment in a patient. The paper considers noninvasive diagnosis methods for BC and gives a database of the known molecular markers of this disease.

  8. Proceedings of the second international symposium on molecular markers in horticulture Acta Horticulturae

    Science.gov (United States)

    The second International Symposium on Molecular Markers in Horticulture was held at the CH2M Hill Alumni Center at Oregon State University (OSU), Corvallis (Oregon, US), from July 29 to August 1st, 2009. This symposium was convened by a scientist at the National Clonal Germplasm Repository (NCGR) of...

  9. Assessment of the Genetic Diversity in Forest Tree Populations Using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ilga Porth

    2014-04-01

    Full Text Available Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

  10. Identification of molecular markers linked to rice bacterial blight resistance genes from Oryza meyeriana

    Directory of Open Access Journals (Sweden)

    Jing WANG,Chen CHENG,Yanru ZHOU,Yong YANG,Qiong MEI,Junmin LI,Ye CHENG,Chengqi YAN,Jianping CHEN

    2015-09-01

    Full Text Available Y73 is a progeny of asymmetric somatic hybridization between Oryza sativa cv. Dalixiang and the wild rice species Oryza meyeriana. Inoculation with a range of strains of Xanthomonas oryzae pv. oryzae showed that Y73 had inherited a high level of resistance to rice bacterial blight (BB from its wild parent. An F2 population of 7125 individuals was constructed from the cross between Y73 and a BB-susceptible cultivar IR24. After testing 615 SSR and STS markers covering the 12 rice chromosomes, 186 markers were selected that showed polymorphism between Y73 and IR24. Molecular markers linked to the BB resistance genes in Y73 were scanned using the F2 population and the polymorphic markers. The SSR marker RM128 on chromosome 1, the STS marker R03D159 on chromosome 3 and the STS marker R05D104 on chromosome 5 were found to be linked to the rice BB resistance genes in Y73.

  11. Low Cost DNA Molecular Weight Marker: Primer-Directed Synthesis from pGEM-T Easy Vector

    Directory of Open Access Journals (Sweden)

    Siriporn RIYAJAN

    2011-06-01

    Full Text Available A low cost DNA molecular weight marker was produced by a marker primer-directed synthetic method using pGEM-T Easy vector as the DNA template. Seven primers were used to amplify eight different DNA fragments, which were 150, 300, 375, 500, 700, 1,000, 1,200 and 1,625 bp, from bacterial culture containing pGEM-T Easy vector. Polymerase chain reactions (PCR for all marker loci required the same optimal annealing temperature, which allowed all the PCR to be completed in a single run. To obtain the molecular weight marker, the PCR product of each locus was mixed together and directly used as marker without any further purification. This custom made molecular weight marker was found to be approximately 17 to 49 times less expensive than other commercial 100 bp DNA ladder markers.Graphical abstract

  12. Advances in Applications of Molecular Marker Technique in Invasive Plants%分子标记技术在入侵植物中的应用研究进展

    Institute of Scientific and Technical Information of China (English)

    高翔; 关亚丽

    2012-01-01

    The invasion mechanism and genetic underpinnings of alien invasivc plants have been paid more and more attention to. It will be the binding site of theory and practice in the future to build safe and effective control measures based on figuring out the hereditary variation characteristics by molecular marker technique. To provide references for forecasting and preventing, eradicating and managing, controlling and repairing the invasive plants in their invasion process, the author summarized the molecular marker technique: RFLP (restriction fragment length polymorphism), RAPD (randomly amplified polymorphic DNA) , AFLP ( amplified fragment length polymorphism), SSR ( simple sequence repeat), ISSR(inter-simple sequence repeat) putting into the study of invasive plants use, and proposcd prospects for further studies.%外来入侵植物的入侵机制和成功入侵的遗传学基础越来越被人们所关注,通过分子标记技术明确入侵植物的遗传变异特点,并在此基础上建立起安全有效的控制措施是未来工作中理论与实践的结合点.为了对入侵植物在入侵过程中的预测和预防、根除与管理、生态控制与修复的实践提供参考,综述了限制性片段长度多态性(restriction fragment length polymorphism,简称RFLP)标记技术、随机扩增多态性DNA(randomly amplified polymorphic DNA,简称RAPD)标记技术、扩增片段长度多态性(amplified fragment length polymorphism简称AFLP)标记技术、简单重复序列(simple sequence repeat简称SSR)标记技术和简单序列重复区间(inter-simple sequence repeat简称ISSR)标记技术在入侵植物中的应用研究状况,并对其应用前景进行了展望.

  13. Identification of Molecular Marker Linked to Salt Tolerance Gene in Alfalfa

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    The study has established the F2 offspring obtained by crossing salt-tolerant with salt-sensitive alfalfa, and appraised the salt-tolerant F2 offspring seedling was evaluated in pot culture. With the F2 segregated population, the research has obtained a molecular marker linked with salt-tolerant genes of alfalfa using the improved BSA combined with RAPD. The RAPD PCR products were excised from the agarose gel and purified using a kit, then were mixed with pMD-18T vector and sequenced. Sequencing result indicated the RAPD marker was 1 438 bp in length. Similarity researches using blast in Genbank indicated that the nucleotide sequence of the RAPD marker showed 93% and 91% similarity with mth2-6el8 gene fragment (347 bp) and mth2-33122 gene fragment (334 bp) of Medicago truncatula respectively. Medicago truncatula is a close relative of alfalfa and Mth2-6e18 is a molecular marker of the gene coding for a cysteine protease which was salt inducible in some plants. These results indicated the RAPD marker was possibly related to cysteine protease genes in alfalfa.

  14. Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).

    Science.gov (United States)

    Buonaccorsi, V P; McDowell, J R; Graves, J E

    2001-05-01

    Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.

  15. Intestinal microflora molecular markers of spleen-deficient rats and evaluation of traditional Chinese drugs

    Institute of Scientific and Technical Information of China (English)

    Ying Peng; Zhuo Wang; Yuan Lu; Chun-Fu Wu; Jing-Yu Yang; Xiao-Bo Li

    2009-01-01

    AIM: To find a rapid and efficient analysis method of gastrointestinal microflora in Pi-deficient (spleendeficient) rats and to evaluate traditional Chinese drugs. METHODS: Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) based assay was performed to examine changes of intestinal microflora in two Pi-deficienct animal models and to evaluate the efficacy of four traditional Chinese drugs as well as a probiotic recipe and another therapy in Pi-deficient rats. RESULTS: A molecular marker was identified for Pideficiency in rats. The pharmacodynamic evaluation system, including identified molecular markers (net integral area and abundance of DNA bands), Shannon's index for diversity of intestinal microflora, and Sorenson's pairwise similarity coefficient, was established. The four major clinical recipes of traditional Chinese drugs for Pi-deficiency in rats, especially at their medium dose (equivalence to the clinical dose), produced more pronounced recovery activities in Pi-deficient rats, while higher doses of these recipes did not show a better therapeutic effect but some toxic effects such as perturbation deterioration of intestinal microflora. CONCLUSION: Both fingerprint analysis and identified marker can show Pi-deficiency in rats and its difference after treatment. The identified molecular marker may be applied in screening for the active compounds both in relative traditional Chinese drugs and in pharmacodynamic study of Pi-deficiency in rats.

  16. Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.

    Science.gov (United States)

    Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun

    2014-09-01

    Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny.

  17. Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

    Directory of Open Access Journals (Sweden)

    Allender Charlotte J

    2010-03-01

    Full Text Available Abstract Background The amphiploid species Brassica napus (oilseed rape, Canola is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C found in B. napus would facilitate incorporation of novel alleles from the wider Brassica genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of B. napus would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised B. napus. We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of B. napus. This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome B. rapa L. (both wild and cultivated types, 94 accessions of B. napus and 181 accessions of C genome wild and cultivated B. oleracea L. and related species. Results Three chloroplast haplotypes occurred in B. napus. The most prevalent haplotype (found in 79% of accessions was not present within the C genome accessions but was found at low frequencies in B. rapa. Chloroplast haplotypes characteristic of B. napus were found in a small number of wild and weedy B. rapa populations, and also in two accessions of cultivated B. rapa 'brocoletto'. Whilst introgression of the B. napus chloroplast type in the wild and weedy B. rapa populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained. Conclusions The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the B. napus accessions. The presence of multiple chloroplast

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

    Science.gov (United States)

    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.

  19. Investigation of Combining Plant Genotypic Values and Molecular Marker Information for Constructing Core Subsets

    Institute of Scientific and Technical Information of China (English)

    Jian-Cheng Wang; Jin Hu; Ning-Ning Liu; Hai-Ming Xu; Sheng Zhang

    2006-01-01

    In the present study, a strategy was proposed for constructing plant core subsets by clusters based on the combination of continuous data for genotypic values and discrete data for molecular marker information. A mixed linear model approach was used to predict genotypic values for eliminating the environment effect.The "mixed genetic distance" was designed to solve the difficult problem of combining continuous and discrete data to construct a core subset by cluster. Four commonly used genetic distances for continuous data (Euclidean distance, standardized Euclidean distance, city block distance, and Mahalanobis distance)were used to assess the validity of the continuous data part of the mixed genetic distance; three commonly used genetic distances for discrete data (cosine distance, correlation distance, and Jaccard distance) were used to assess the validity of the discrete data part of the mixed genetic distance. A rice germplasm group with eight quantitative traits and information for 60 molecular markers was used to evaluate the validity of the new strategy. The results suggest that the validity of both parts of the mixed genetic distance are equal to or higher than the common genetic distance. The core subset constructed on the basis of a combination of data for genotypic values and molecular marker information was more representative than that constructed on the basis of data from genotypic values or molecular marker information alone. Moreover, the strategy of using combined data was able to treat dominant marker information and could combine any other continuous data and discrete data together to perform cluster to construct a plant core subset.

  20. Prognostic value of molecular markers of oral pre-malignant and malignant lesions

    Directory of Open Access Journals (Sweden)

    Peter Agus

    2009-06-01

    Full Text Available Background: The representation of oral cancer and precancerous lesions is often undetected until at later stage and the survival rate of oral cancer has remained essentially unchanged over the past three decades. Over 90% of these tumors are squamous cell carcinoma. The American Cancer Society estimates that among 28,900 new cases of oral diagnosis in 2002, nearly 7,400 people will die from this disease. Oral pre-malignant and malignant lesions have multi-step process both at phenotype and genetic levels that influence tumor behavior and genetic mutations. Purpose: The aim of this presentation was to review the current knowledge of prognostic value of tumor marker in order to achieve early detection, prognostic value, proper and accurate treatment of oral cancer. Reviews: Technological advances in molecular biology have greatly increased the number of new molecular markers that can be detected by molecular analysis such as immunohistochemistry (IHC, polymerase chain reaction (PCR and surgical margin analysis that may increase prognosis and treatment of oral cancer. The result of most valuable tumor markers is twenty nine divided into four groups according to their function such as enhancement of tumor growth, tumor suppression and anti tumor defense, including immune response and apoptosis, angiogenesis, tumor invasion and metastatic potential, including adhesion molecules and matrix degradation. Conclusion: In general the conclusion is that the location of markers within the tumor and not the quantitative assessment is as same as emphasized. Especially, the analysis of new molecular markers have been used to be of great importance for early detection, surgical margin analysis, prognostication and treatment of oral pre-malignant and cancerous lesion.

  1. [The application of DNA molecular markers in conservation of the rare and endangered medicinal plants].

    Science.gov (United States)

    Yan, Zhi-Feng; Zhang, Ben-Gang; Zhang, Zhao; Xia, Tian-Rui

    2005-12-01

    In this paper, the advance in DNA molecular markers techniques in recent years was reviewed. The application of DNA markers in conservation of the rare and endangered medicinal plants was explicated, of which included identification of germ-plasm resource, determination of the habitats unite which should be protected in situ, sampling strategies of ex-situ conservation, evaluation of the conservation effects of the rare and endangered medicinal plants, as well as elucidation of their endangered mechanism etc. The information could help drawing up conservation strategies and conservation measures for references.

  2. DEVELOPMENT OF CODOMINANT MARKERS FOR IDENTIFYING SPECIES HYBRIDS

    Science.gov (United States)

    Herein we describe a simple method for developing species-diagnostic markers that would permit the rapid identification of hybrid individuals. Our method relies on amplified length polymorphism (AFLP) and single strand conformation polymorphism (SSCP) technologies, both of which...

  3. A note on the rationale for estimating genealogical coancestry from molecular markers

    Directory of Open Access Journals (Sweden)

    García-Cortés Luis

    2011-07-01

    Full Text Available Abstract Background Genetic relatedness or similarity between individuals is a key concept in population, quantitative and conservation genetics. When the pedigree of a population is available and assuming a founder population from which the genealogical records start, genetic relatedness between individuals can be estimated by the coancestry coefficient. If pedigree data is lacking or incomplete, estimation of the genetic similarity between individuals relies on molecular markers, using either molecular coancestry or molecular covariance. Some relationships between genealogical and molecular coancestries and covariances have already been described in the literature. Methods We show how the expected values of the empirical measures of similarity based on molecular marker data are functions of the genealogical coancestry. From these formulas, it is easy to derive estimators of genealogical coancestry from molecular data. We include variation of allelic frequencies in the estimators. Results The estimators are illustrated with simulated examples and with a real dataset from dairy cattle. In general, estimators are accurate and only slightly biased. From the real data set, estimators based on covariances are more compatible with genealogical coancestries than those based on molecular coancestries. A frequently used estimator based on the average of estimated coancestries produced inflated coancestries and numerical instability. The consequences of unknown gene frequencies in the founder population are briefly discussed, along with alternatives to overcome this limitation. Conclusions Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift.

  4. Analysis of the Relationship between Genome Diversity and Adult Survive Rate of Botryllus Schlosseri by AFLP

    Institute of Scientific and Technical Information of China (English)

    FENG Xiao-rong; ZHU Jian-zhong; DENG Feng-jiao; Jacob Douek; Baruch Rinkevich

    2004-01-01

    Objective: The self-cross colonial prochordate, Botryllus schlosseri ( B. schlosseri) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B.schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods:AFLP markersare extremely sensitive to even smell sequence variation, using PCR and high-resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% poiymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2,F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation-new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southem hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion:The se results suggest that there are high frequency of polymorphic loci and mutation in genome of B.schlosseri. Gene deletion or iow diversity may be the reason for high rate of death of the offspring of inbred laboratory-reared strains.

  5. Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

    Directory of Open Access Journals (Sweden)

    Masahito Yoshihara

    Full Text Available The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro.

  6. Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

    Science.gov (United States)

    Yoshihara, Masahito; Ohmiya, Hiroko; Hara, Susumu; Kawasaki, Satoshi; Hayashizaki, Yoshihide; Itoh, Masayoshi; Kawaji, Hideya; Tsujikawa, Motokazu; Nishida, Kohji

    2015-01-01

    The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro.

  7. 与甜瓜嫁接亲和性连锁分子标记鉴定%Identification of Molecular Marker Linked to Grafting Compatibility in Melon

    Institute of Scientific and Technical Information of China (English)

    陈亚丽; 郭世荣; 朱为民; 刘龙洲; 陈幼源

    2012-01-01

    Two melon varieties (85-1 and B717), being significant differences in grafting affinity with the pumpkin rootstock "a strong man", were used as parents to construct F2:3 populations; molecular markers linked to graft compatibility were identified by PCR technology based on differential DNA pools in grafting affinity prepared by BSA approach. The results showed that 382 pairs of primers with polymorphism in two melon parents were screened from 750 pairs of SSR, SRAP, AFLP primers, which had published in the cucurbitaceae genetic linkage map. There are 9 pairs of primers that can respectively amplified different fragments in differential DNA pools in grafting affinity, and these different markers were further used to amplify F2 population to calculate the genetic linkage distance between the marker and the trait of grafting affinity. The distance of markers of CMN-0616 and M103 both linked to grafting affinity with the genetic were 17.6 cm and 9.3 cm respectively. These two pairs of primers would be expected to be as assist markers to identify grafting affinity of the melon in order to distinguish varieties with different grafting affinity at the level of molecular background which might provide the reference for developing grafted melon scion in breeding program.%使用与南瓜类型砧木(“壮士”)嫁接亲和性差异明显的两个甜瓜自交系(85-1和B717)为亲本,配制F2∶3家系群体;利用BSA法构建亲和性优差池,结合PCR技术筛选与嫁接亲和性有关的分子标记.结果表明:使用葫芦科遗传连锁图谱上发表的750对SSR、SRAP和AFLP等分子标记引物扩增,最终筛选出在两个甜瓜材料之间具有多态性的382对引物,其中9对引物分别在嫁接亲和性优差DNA池中扩增出差异性片段.将这些标记用于F2群体的扩增,计算标记与嫁接亲和性遗传连锁距离,两对SSR引物CMN-0616和M103与嫁接亲和性的遗传距离分别为17.6 cm和9.3 cm.这2对引物有望成为鉴定甜

  8. Plasmodium falciparum kelch 13: a potential molecular marker for tackling artemisinin-resistant malaria parasites.

    Science.gov (United States)

    Mita, Toshihiro; Tachibana, Shin-Ichiro; Hashimoto, Muneaki; Hirai, Makoto

    2016-01-01

    Although artemisinin combination therapies have been deployed as a first-line treatment for uncomplicated malaria in almost all endemic countries, artemisinin-resistant parasites have emerged and have gradually spread across the Greater Mekong subregions. There is growing concern that the resistant parasites may migrate to or emerge indigenously in sub-Saharan Africa, which might provoke a global increase in malaria-associated morbidity and mortality. Therefore, development of molecular markers that enable identification of artemisinin resistance with high sensitivity is urgently required to combat this issue. In 2014, a potential artemisinin-resistance responsible gene, Plasmodium falciparum kelch13, was discovered. Here, we review the genetic features of P. falciparum kelch13 and discuss its related resistant mechanisms and potential as a molecular marker.

  9. Molecular identification of sex in Simarouba glauca by RAPD markers for crop improvement strategies

    Directory of Open Access Journals (Sweden)

    Gayatri Vaidya

    2014-12-01

    Full Text Available Due to lack of morphological methods to identify sex at early stage in the plants with long juvenile period the application of molecular markers is expected to facilitate breeding program. The objective of this study is to identify molecular markers linked to sex determination of the plant Simarouba glauca which assists in crop improvement program. Random amplified polymorphic DNA primers were tested on dioeceious and hermaphrodite plant Simarouba glauca. A set of eighty five RAPD primers were screened out of which only five primers were found to be associated with sex. The primer OPU-10 is male specific and OPD-19 primer is female specific. Another primer OPU-19 produced a unique amplification in only hermaphrodite individuals. Female and hermaphrodite specific primer OPS-05 amplified an amplicon in female and hermaphrodite and was absent in male plant. Primer OPW-03 produced amplicon specific to male and hermaphrodite plants and was absent in female plants.

  10. Assessing diversity among traditional Greek and foreign eggplant cultivars using molecular markers and morphometrical descriptors

    Directory of Open Access Journals (Sweden)

    Antonios A. Augustinos

    2016-12-01

    Full Text Available Eggplant is a widely cultivated vegetable crop of great economic importance. Its long lasting history of domestication, selection and breeding has led to the development of numerous cultivars with variable traits. In the present study, we assessed the diversity levels within and among eleven Greek and foreign cultivars, using 22 morphological descriptors and two different classes of molecular markers (retrotransposon microsatellite amplified polymorphism-REMAP markers and nuclear microsatellites. Our results, in accordance with other studies in the field showed: a the limited levels of genetic polymorphism within the cultivars; b the high morphological and genetic divergence existing among them as indicated by the genetic distance values calculated, which could be attributed to selection, inbreeding and bottleneck effects; and c the lack of concordance among morphological descriptors and molecular markers. Despite these, our analysis showed that the utilization of combinations of markers is an effective method for the characterization of plant material providing also useful diagnostic tools for the identification and authentication of the selected Greek cultivars.

  11. Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers.

    Science.gov (United States)

    Batley, Jacqueline; Jewell, Erica; Edwards, David

    2007-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of genomes. Molecular marker technology has developed rapidly over the last decade, and two forms of sequence-based markers, simple sequence repeats (SSRs), also known as microsatellites, and single nucleotide polymorphisms (SNPs), now predominate applications in modern genetic analysis. The availability of large sequence data sets permits mining for SSRs and SNPs, which may then be applied to genetic trait mapping and marker-assisted selection. Here, we describe Web-based automated methods for the discovery of these SSRs and SNPs from sequence data. SSRPrimer enables the real-time discovery of SSRs within submitted DNA sequences, with the concomitant design of PCR primers for SSR amplification. Alternatively, users may browse the SSR Taxonomy Tree to identify predetermined SSR amplification primers for any species represented within the GenBank database. SNPServer uses a redundancy-based approach to identify SNPs within DNA sequence data. Following submission of a sequence of interest, SNPServer uses BLAST to identify similar sequences, CAP3 to cluster and assemble these sequences, and then the SNP discovery software autoSNP to detect SNPs and insertion/deletion (indel) polymorphisms.

  12. Polymorphisms in microRNA targets: a source of new molecular markers for male reproduction

    Institute of Scientific and Technical Information of China (English)

    Jernej Ogorevc; Peter Dove; Tanja Kunej

    2011-01-01

    @@ Dear Editor, Herein we discuss the impact of microRNA (miRNA) target genetic variability in male infertility genes, which can represent a source of novel molecular-genetic markers that can be used for the diagnosis of male infertility.Male-factor infertility accounts for 30%-40% of infertility cases.The causes of spermatogenetic failure found in most cases of non-obstructive azoospermia or severe oligozoospermia still remain idiopathic.1

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

    Science.gov (United States)

    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.

  14. Molecular markers in prostate cancer.Part I:predicting lethality

    Institute of Scientific and Technical Information of China (English)

    Sachin Agrawal; William D.Dunsmuir

    2009-01-01

    Assessing the lethality of 'early,' potentially organ-confined prostate cancer (PCa) is one of the central controversies in moderu-day urological clinical practice.Such cases are often considered for radical 'curative' treatment,although active surveillance may be equally appropriate for many men.Moreover,the balance between judicious intervention and overtreatment can be difficult to judge.The patient's age,comorbidities,family history and philosophy of self-health care can be weighed against clinical features such as the palpability of disease,the number and percentage of biopsy cores involved with the disease,histological grade,presenting prostate-specific antigen (PSA) and possible previous PSA kinetics.For many years,scientists and physicians have sought additional molecular factors that may be predictive for disease stage,progression and lethality.Usually,claims for a 'new' unique marker fall short of true clinical value.More often than not,such molecular markers are useful only in multivariate models.This review summarizes relevant molecular markers and models reported up to and including 2008.

  15. [Use of genes of carbon metabolism enzymes as molecular markers of Chlorobi Phylum representatives].

    Science.gov (United States)

    Turova, T P; Kovaleva, O L; Gorlenko, V M; Ivanovskiĭ, R N

    2014-01-01

    This work examined the feasibility of using certain genes of carbon metabolism enzymes as molecular markers adequate for studying phylogeny and ecology of green sulfur bacteria (GSB) of the Chlorobi phylum. Primers designed to amplify the genes of ATP citrate lyase (aclB) and citrate synthase (gltA) revealed the respective genes in the genomes of all of the newly studied GSB strains. The phylogenetic trees constructed based on nucleotide sequences of these genes and amino acid sequences of the conceptually translated proteins were on the whole congruent with the 16S rRNA gene tree, with the single exception of GltA of Chloroherpeton thalassium, which formed a separate branch beyond the cluster comprised by other representatives of the Chlorobi phylum. Thus, the aclB genes but not gltA genes proved to be suitable for the design of primers specific to all Chlorobi representatives. Therefore, it was the aclB gene that was further used asa molecular marker to detect GSB in enrichment cultures and environmental samples. AclB phylotypes of GSB were revealed in all of the samples studied, with the exception of environmental samples from soda lakes. The identification of the revealed phylotypes was in agreement with the identification based on the FMO protein gene (fmo), is a well-known Chlorobi-specific molecular marker.

  16. SILVER NANOPARTICLES AND EXPERESSION OF MOLECULAR MARKERS IN LYMPHOCYTE ACTIVATION AND MARKER OF AUTOIMMUNE PROCESSES IN PERIPHERAL BLOOD OF PATIENTS WITH VIRAL CORNEAL PATHOLOGY

    Directory of Open Access Journals (Sweden)

    Ulyanov V.A.

    2015-08-01

    Full Text Available The influence of the nanoparticles of silver on the expression of molecular markers activation of lymphoid cells CD7+, CD25+, CD38+, CD45+, CD54+, CD95+, CD150+ and CD5+ – marker of the autoimmune process, as well as on phagocytic activity of neutrophils in patients with viral pathologies of the cornea was studied in vitro. In the Laboratory of Immunology, SI Institute of Eye Diseases and Tissue Therapy NAMS of Ukraine was developed technique of cultivation of peripheral blood lymphocytes with immunomodulation drugs, followed by determination of changes in the level of expression of molecular markers of lymphocyte activation. Assessment of the level of expression of molecular markers of activation of peripheral blood lymphocytes was performed method using a panel of monoclonal antibodies, CD5+, CD7+, CD25+, CD38+, CD45+, CD54+, CD95+ and CD 150+. The study was conducted in vitro with the peripheral lymphocytes the blood of 23 patients of viral pathology of the cornea. Our studies of the effects of nanosilver particles in vitro on the state of expression of molecular markers of activation of peripheral blood lymphocytes and phagocytic activity of neutrophils in patients with viral corneal pathology, showed a significant increase in the level of expression of the CD7+, CD25+, CD45+ and phagocytic activity of neutrophils after application silver nanoparticles.

  17. A Reductionist Approach to Extract Robust Molecular Markers from Microarray Data Series -Isolating Markers to Track Osseointegration.

    Science.gov (United States)

    Barik, Anwesha; Banerjee, Satarupa; Dhara, Santanu; Chakravorty, Nishant

    2017-03-10

    Complexities in the full genome expression studies hinder the extraction of tracker genes to analyze the course of biological events. In this study, we demonstrate the applications of supervised machine learning methods to reduce the irrelevance in microarray data series and thereby extract robust molecular markers to track biological processes. The methodology has been illustrated by analyzing whole genome expression studies on bone-implant integration (ossointegration). Being a biological process, osseointegration is known to leave a trail of genetic footprint during the course. In spite of existence of enormous amount of raw data in public repositories, researchers still do not have access to a panel of genes that can definitively track osseointegrtion. The results from our study revealed panels comprising of matrix metalloproteinases and collagen genes were able to track osseointegration on implant surfaces (MMP9 and COL1A2 on micro-textured; MMP12 and COL6A3 on superimposed nano-textured surfaces) 100% classification accuracy, specificity and sensitivity. Further, our analysis showed the importance of the progression of the duration in establishment of the mechanical connection at bone-implant surface. The findings from this study are expected to be useful to researchers investigating osseointegration of novel implant materials especially at the early stage. The methodology demonstrated can be easily adapted by scientists in different fields to analyze large databases for other biological processes.

  18. Predictive gene signatures: molecular markers distinguishing colon adenomatous polyp and carcinoma.

    Science.gov (United States)

    Drew, Janice E; Farquharson, Andrew J; Mayer, Claus Dieter; Vase, Hollie F; Coates, Philip J; Steele, Robert J; Carey, Francis A

    2014-01-01

    Cancers exhibit abnormal molecular signatures associated with disease initiation and progression. Molecular signatures could improve cancer screening, detection, drug development and selection of appropriate drug therapies for individual patients. Typically only very small amounts of tissue are available from patients for analysis and biopsy samples exhibit broad heterogeneity that cannot be captured using a single marker. This report details application of an in-house custom designed GenomeLab System multiplex gene expression assay, the hCellMarkerPlex, to assess predictive gene signatures of normal, adenomatous polyp and carcinoma colon tissue using archived tissue bank material. The hCellMarkerPlex incorporates twenty-one gene markers: epithelial (EZR, KRT18, NOX1, SLC9A2), proliferation (PCNA, CCND1, MS4A12), differentiation (B4GANLT2, CDX1, CDX2), apoptotic (CASP3, NOX1, NTN1), fibroblast (FSP1, COL1A1), structural (ACTG2, CNN1, DES), gene transcription (HDAC1), stem cell (LGR5), endothelial (VWF) and mucin production (MUC2). Gene signatures distinguished normal, adenomatous polyp and carcinoma. Individual gene targets significantly contributing to molecular tissue types, classifier genes, were further characterised using real-time PCR, in-situ hybridisation and immunohistochemistry revealing aberrant epithelial expression of MS4A12, LGR5 CDX2, NOX1 and SLC9A2 prior to development of carcinoma. Identified gene signatures identify aberrant epithelial expression of genes prior to cancer development using in-house custom designed gene expression multiplex assays. This approach may be used to assist in objective classification of disease initiation, staging, progression and therapeutic responses using biopsy material.

  19. Predictive gene signatures: molecular markers distinguishing colon adenomatous polyp and carcinoma.

    Directory of Open Access Journals (Sweden)

    Janice E Drew

    Full Text Available Cancers exhibit abnormal molecular signatures associated with disease initiation and progression. Molecular signatures could improve cancer screening, detection, drug development and selection of appropriate drug therapies for individual patients. Typically only very small amounts of tissue are available from patients for analysis and biopsy samples exhibit broad heterogeneity that cannot be captured using a single marker. This report details application of an in-house custom designed GenomeLab System multiplex gene expression assay, the hCellMarkerPlex, to assess predictive gene signatures of normal, adenomatous polyp and carcinoma colon tissue using archived tissue bank material. The hCellMarkerPlex incorporates twenty-one gene markers: epithelial (EZR, KRT18, NOX1, SLC9A2, proliferation (PCNA, CCND1, MS4A12, differentiation (B4GANLT2, CDX1, CDX2, apoptotic (CASP3, NOX1, NTN1, fibroblast (FSP1, COL1A1, structural (ACTG2, CNN1, DES, gene transcription (HDAC1, stem cell (LGR5, endothelial (VWF and mucin production (MUC2. Gene signatures distinguished normal, adenomatous polyp and carcinoma. Individual gene targets significantly contributing to molecular tissue types, classifier genes, were further characterised using real-time PCR, in-situ hybridisation and immunohistochemistry revealing aberrant epithelial expression of MS4A12, LGR5 CDX2, NOX1 and SLC9A2 prior to development of carcinoma. Identified gene signatures identify aberrant epithelial expression of genes prior to cancer development using in-house custom designed gene expression multiplex assays. This approach may be used to assist in objective classification of disease initiation, staging, progression and therapeutic responses using biopsy material.

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

    Directory of Open Access Journals (Sweden)

    Yaling Liu

    Full Text Available 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.

  1. The Search for Molecular Prognostic Markers of Diabetic Nephropathy in Patients with Type 2 Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    V. M. Ibragimov

    2016-03-01

    Full Text Available The purpose of this study was to search for molecular prognostic markers of diabetic nephropathy (DN in patients with type 2 diabetes mellitus (T2DM. The study included 205 patients with T2DM and DN (stages 1 to 4. All patients were stratified by the MDRD equation. The control group included 30 healthy individuals. All T2DM patients were divided into 4 groups depending on the DN stages. Group 1 included 42 patients with DN-Stage 1 (prenephropathy, Group 2 included 48 patients with DN-Stage 2 (incipient nephropathy; Group 3 included 65 patients with DN-Stage 3 (overt nephropathy, and Group 4 included 50 patients with DN-Stage 4 (kidney failure. Molecular phenotyping of urine was processed with methods of proteomics: the prefractionation, the separation of proteins with standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, «Bruker», USA, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS/MS, Ultraflex II, «Bruker», USA. The data of the molecular interactions and functional features of proteins were received with STRING 10.0 database. Potentially new molecular markers of DN development were identified. The research into signaling pathways and the molecules that are involved in ECM formation may help in developing strategies to prevent DN.

  2. Characterization and molecular marker screening of a rice bacteria-resistant gene Xa-min(t)

    Institute of Scientific and Technical Information of China (English)

    CHEN Yan; HU Jun; QIAN Wei; TIAN Yingchuan; HE Chaozu

    2003-01-01

    To test the resistant spectrum of the Xa-min(t) gene introgressed from Oryza minuta, thirty-four isolates of different bacterial blight pathogen, Xanthomonas oryzae pv. oryzae (Xoo), from 11 countries were used to inoculate the Xa-min(t) introgression line 78-15. Four rice cultivars, IR24, C64 (IRBB21), Nipponbare and Zhonghua 11 were used as controls. The results showed that the Xa-min(t) gene was broad-spectrum and highly resistant to diverse Xoo isolates. The methods of bulk segregant analysis (BSA), randomly amplified polymorphic DNA (RAPD) and sequence characterized amplified regions (SCAR) were used to analyze F2 individuals of the hybrid IR24×78-15 and molecular genetic markers linked to Xa-min(t) gene were identified. A total of 800 arbitrary decamer oligonucleotide primers were used for RAPD analysis. Two RAPD markers, BE05300 and BE061400, produced by primers BE05 and BE06 respectively, were closely linked to the Xa-min(t) gene. Based on the sequences of these two markers, sequence specific primers were designed and used to screen all F2 plants. One RAPD marker, BE05300, was converted into a stable SCAR marker (ScBE05300). Linkage analysis was carried out using markers ScBE05300 and BE061400 on 948 and 719 F2 individuals of the hybrid IR24×78-15. Our results indicate that the genetic distances from Xa-min(t) to ScBE05300 and BE061400 are 2.2 cM and 3.7 cM respectively on the same side. This study may facilitate the construction of the fine physical map of the Xa-min(t) gene.

  3. Molecular markers for population genetic analyses in the family Psittacidae (Psittaciformes, Aves

    Directory of Open Access Journals (Sweden)

    Patrícia J. Faria

    2006-01-01

    Full Text Available The selection of molecular markers for population studies is an important tool for biodiversity conservation. The family Psittacidae contains many endangered and vulnerable species and we tested three kinds of molecular markers for their potential use in population studies of five psitacid species: 43 hyacinth macaws (Anodorhynchus hyacinthinus, 42 blue-and-yellow macaws (Ara ararauna, 23 red-and-green macaws (Ara chloroptera, 19 red-spectacled amazons (Amazona pretrei; and 18 red-tailed amazons (Amazona brasiliensis. We tested 21 clones from a genomic library of golden conure (Guarouba guarouba minisatellites and 12 pairs of microsatellite primers developed for the domestic chicken (Gallus gallus and A. hyacinthinus. We also tested seven tetranucleotide repeat primers for their ability to amplify regions between microsatellite loci (inter simple sequence repeats, ISSRs. We were able to select seven markers that were variable in different degrees for three species (A. hyacinthinus, A. chloroptera and A. ararauna. The mini and microsatellites produced more polymorphic patterns than the ISSRs. The genetic variability of the species studied seems to be correlated with their endangered status.

  4. Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers

    Science.gov (United States)

    Crossa, José; Campos, Gustavo de los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P.; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim

    2010-01-01

    The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed. PMID:20813882

  5. Molecular markers validation to drought resistance in wheat meal (Triticum aestivum L. under greenhouse conditions

    Directory of Open Access Journals (Sweden)

    Gabriel Julio

    2013-08-01

    Full Text Available With the aim to study the genetic resistance to drought and validate molecular markers co-localized with genes/QTLs for this factor, 16 varieties were evaluated as well as advanced lines of wheat meal (Triticum aestivum in two stages of crop development. Physiological parameters were considered: amount of chlorophyll (clo, wilting or severity degree (SEV and recovery (reco, morphological parameters: foliage dry matter (FDM and root dry matter (RDM, the integrated resistance mechanisms: water use efficiency (WUE, other parameters: number of grains (Ngrain and grain weight (Wgrain, biochemical parameters: Catalaza (CAT, Ascorbate Peroxidase (APX and Guaiacol Peroxidase (POX and three microsatellite markers (Xwmc603, Xwmc596, Xwmc9. Results showed significant differences for MSR and Ngrain. It was observed that Anzaldo, ERR2V.L-20, EARII2V.L-5, EARIZV.L-11, ERR2V.L-11 and EE2V.L-19 were the most resistant to drough water stress. There was a highly significant negative correlation between the MSR and Ngrain. All other variables showed low and non-significant correlations. In biochemical analyzes, the Anzaldo variety showed an increased enzymatic activity compared to controls in all cases (CAT-APX and POX, being the most resistant to water stress by drought. Finally, it was found that SSR markers (Xwmc596 and Xwmc9 are co-located with the gene / QTL of drought resistance and can be used for marker-assisted selection.

  6. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

    NARCIS (Netherlands)

    Odong, T.L.; Heerwaarden, van J.; Jansen, J.; Hintum, van T.J.L.; Eeuwijk, van F.A.

    2011-01-01

    Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using

  7. Development of SSR Markers for a Phytopathogenic Fungus, Blumeria graminis f.sp. tritici, Using a FIASCO Protocol

    Institute of Scientific and Technical Information of China (English)

    WANG Meng; XUE Fei; YANG Peng; DUAN Xia-yu; ZHOU Yi-lin; SHEN Chong-yao; ZHANG Guo-zhen; WANG Bao-tong

    2014-01-01

    Simple sequence repeats (SSR) have been widely used as molecular markers due to their abundance and high polymorphism. However, up to now, the SSR markers had not been developed in the obligate biotrophic phytopathogenic fungus, Blumeria graminis f.sp. tritici. From (AC)10 and (AG)10 enriched genomic libraries for Bgt, 25 primer pairs were designed using the FIASCO (fast isolation by AFLP of sequences containing repeats) protocol. Five primer pairs exhibited polymorphism with allelic diversity from two to seven alleles and produced 29 alleles in a survey of 90 isolates collected from six provinces (cities) in China, while the others displayed monomorphic. Levels of observed heterozygosity ranged from 0.000-0.044 (mean 0.025) and expected heterozygosity ranged from 0.297-0.816 (mean 0.538). These molecular markers provide a novel source to genetic diversity assays and to genetic and physical mapping of Bgt. SSR markers of Bgt need to be further explored.

  8. Research of Genetic Diversity in Seven Kobresia by AFLP in Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    ZHENG Hong-mei; HU Tian-ming; WANG Quan-zhen; ZHANG Guo-yun; SONG Jiang-hu

    2009-01-01

    This work analyzed the genetic diversity of Kobresia accessions at the molecular level, and further obtained the necessary information for breeding and germplasm evaluation. Genomic DNA of Kobresia was amplified with four E+3 and M+3 primer combinations with AFLP (amplified fragment length polymorphism). AFLP analysis produced 164 scorable bands,of which 154 (93.96%) were polymorphic. The mean Nei's gene diversity index (H) was 0.2430, and the Shannon's information index (I) was 0.4012, indicating the abundant genetic diversity of Kobresia. The 11 Kobresia accessions from Tibetan Plateau, China, can be classified into five groups after cluster analysis based on the UPGMA (unweighted pair group method arithmetic average) method. In general, there was abundant genetic diversity among Kobresia accessions resources, and the genetic coefficient was unrelated to their geographic latitude. Natural habitats influenced genetic differentiation of Kobresia.

  9. Comparative mitochondrial genomics toward exploring molecular markers in the medicinal fungus Cordyceps militaris.

    Science.gov (United States)

    Zhang, Shu; Hao, Ai-Jing; Zhao, Yu-Xiang; Zhang, Xiao-Yu; Zhang, Yong-Jie

    2017-01-10

    Cordyceps militaris is a fungus used for developing health food, but knowledge about its intraspecific differentiation is limited due to lack of efficient markers. Herein, we assembled the mitochondrial genomes of eight C. militaris strains and performed a comparative mitochondrial genomic analysis together with three previously reported mitochondrial genomes of the fungus. Sizes of the 11 mitochondrial genomes varied from 26.5 to 33.9 kb mainly due to variable intron contents (from two to eight introns per strain). Nucleotide variability varied according to different regions with non-coding regions showing higher variation frequency than coding regions. Recombination events were identified between some locus pairs but seemed not to contribute greatly to genetic variations of the fungus. Based on nucleotide diversity fluctuations across the alignment of all mitochondrial genomes, molecular markers with the potential to be used for future typing studies were determined.

  10. Molecular characterization of Prunus mahaleb L. rootstock canditates by ISSR markers

    Directory of Open Access Journals (Sweden)

    Ozyurt Ibrahim Kursat

    2013-01-01

    Full Text Available Prunus mahaleb is widely used as rootstocks particularly on calcareous and dry soils for both sweet and sour cherry cultivars in Turkey. Genetic diversity and relationships among members of Prunus mahaleb including 29 preselected rootstock candidate accessions from Tokat region in Turkey were investigated by using 15 ISSR markers. The study revealed high genetic diversity among accessions, detecting 138 fragments, of which 103 (75% were polymorphic. The number of polymorphic bands per primer was between 3-13, with average of 6.86. The primers 890 and 891 gave the highest polymorphism ratio (100%. The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation among accessions. Reference rootstock, SL-64 clustered separately. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in Prunus mahaleb rootstock candidate accessions and can contribute to efficient identification, conservation, and utilization of germplasm for rootstock improvement through conventional as well as molecular breeding approaches.

  11. Development and Identification of Novel Rice Blast Resistant Sources and Their Characterization Using Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    S J S RAMA DEVI; M. S. MADHAV; Kuldeep SINGH; B UMAKANTH; B VISHALAKSHI; P RENUKA; K. VIJAY SUDHAKAR; M. S. PRASAD3; B. C. VIRAKTAMATH; V. RAVINDRA BABU

    2015-01-01

    To develop and characterize introgression lines for leaf and neck blast resistance, 326 introgression lines were developed using various accessions of six different AA genome wild species in the genetic background of elite Indian varieties like PR114 and Pusa 44 and were screened for blast resistance. Stringent phenotyping coupled with genotyping using gene based markers led to the identification of four resistant introgression lines, which showed promising resistance and do not possess any of the tested genes. Furthermore, multi-location screening confirmed the field resistance of the four introgression lines to both leaf and neck blast. Molecular characterization of these introgression lines using genome-wide simple sequence repeat markers revealed the presence of small percentage of wildOryza genome introgrssion. So these lines can be used for mapping and identification of novel leaf and neck blast resistance genes. Thus, these four introgression lines can be considered as new genetic resources for blast resistance.

  12. Multidrug resistance as a dominant molecular marker in transformation of wine yeast.

    Science.gov (United States)

    Kozovska, Z; Maraz, A; Magyar, I; Subik, J

    2001-12-14

    Pure wine yeast cultures are increasingly used in winemaking to perform controlled fermentations and produce wine of reproducible quality. For the genetic manipulation of natural wine yeast strains dominant selective markers are obviously useful. Here we demonstrate the successful use of the mutated PDR3 gene as a dominant molecular marker for the selection of transformants of prototrophic wine yeast Saccharomyces cerevisiae. The selected transformants displayed a multidrug resistance phenotype that was resistant to strobilurin derivatives and azoles used to control pathogenic fungi in agriculture and medicine, respectively. Random amplification of DNA sequences and electrophoretic karyotyping of the host and transformed strains after microvinification experiments resulted in the same gel electrophoresis patterns. The chemical and sensory analysis of experimental wines proved that the used transformants preserved all their useful winemaking properties indicating that the pdr3-9 allele does not deteriorate the technological properties of the transformed wine yeast strain.

  13. Determination of specific molecular markers of biomass burning in lake sediments

    Science.gov (United States)

    Kirchgeorg, Torben; Schüpbach, Simon; Kehrwald, Natalie; McWethy, David; Barbante, Carlo

    2014-05-01

    Fire influences regional to global atmospheric chemistry and climate. Molecular markers of biomass burning archived in lake sediments are becoming increasingly important in paleoenvironmental reconstruction and may help determine interactions between climate and fire activity. One group of these molecular markers is the monosaccharide anhydrides levoglucosan, mannosan and galactosan. Several aerosol studies and recent ice core research use these compounds as a marker for biomass burning, but studies from lake sediment cores are rare. Previous sediment methods used gas chromatography - mass spectrometry and required derivatization of samples. Here, we present a high performance anion exchange chromatography-mass spectrometry method to allow separation and detection of the three monosaccharide anhydrides in lake sediments with implications for reconstructing past biomass burning events. We validated the method by quantifying levoglucosan, mannosan and galactosan in selected sediment core samples from Lake Kirkpatrick, New Zealand. The freeze-dried, milled and homogenized sediment samples were first extracted with methanol by pressurized solvent extraction, pre-concentrated and finally separated and analyzed by high performance anion exchange chromatography-mass spectrometry. We compared these isomers with macroscopic charcoal concentrations, as charcoal is a well-known proxy for biomass burning. In addition, we applied the method to a sediment core from Lake Petén Itzá, Guatemala to prove the suitability of these markers for reconstructing biomass burning history over the entire Holocene. In the Lake Kirkpatrick samples, levoglucosan, mannosan and galactosan concentrations significantly correlate with macroscopic charcoal concentrations. The three isomers are present in samples without any macroscopic charcoal, and may reflect the presence of microscopic charcoal. Levoglucosan/mannosan and levoglucosan/(mannosan+galactosan) ratios differ between samples with high

  14. Temperature-induced volatility of molecular markers in ambient airborne particulate matter

    Directory of Open Access Journals (Sweden)

    C. R. Ruehl

    2010-08-01

    Full Text Available Molecular markers are organic compounds used to represent known sources of particulate matter (PM in statistical source apportionment studies. The utility of molecular markers depends on, among other things, their ability to represent PM volatility under realistic atmospheric conditions. We measured the particle-phase concentrations and temperature-induced volatility of commonly-used molecular markers in California's heavily polluted San Joaqin Valley. Concentrations of elemental carbon, organic carbon, levoglucosan, and polycyclic aromatic hydrocarbons were not reduced by mild (~10 K heating. In contrast, both hopane/sterane and n-alkane concentrations were reduced, especially during the summer sampling events at the urban site. These results suggest that hopanes and steranes have effective saturation concentrations ~1 μg m−3, and therefore can be considered semi-volatile in realistic ambient conditions. The volatility behavior of n-alkanes during the urban summer is consistent with that predicted for absorption by suberic acid (a C8 diacid using a group contribution modelling method. Observations can also be matched by an absorbent whose composition is based on recently-obtained high-resolution aerosol mass spectrometer factors (approximately 33% "hydrocarbon-like" and 67% oxygenated organic aerosol. The diminished volatility of the n-alkanes, hopanes, and steranes during rural and/or winter experiments could be explained by a more oxygenated absorbing phase along with a non-absorptive partitioning mechanism, such as adsorption to soot. This suggests that the temperature-induced volatility of large hydrocarbons in PM is most important if a relatively non-polar absorbing organic phase exists. While the activity coefficients of most organic aerosol compounds may be close to unity, the assumption of ideality for large hydrocarbons (e.g., hopanes may result in large errors in partitioning calculations.

  15. Use of RAPD molecular markers on differentiation of brazilian and chinese Ganoderma lucidum strains

    Directory of Open Access Journals (Sweden)

    Leonardo do Nascimento Rolim

    2011-04-01

    Full Text Available The aim of this work was to analyze the Brazilian and Chinese strains of Ganoderma lucidum with molecular RAPD markers. A similarity matrix was elaborated and the RAPD profiles of G. lucidum strains were also compared to two other Ganoderma spp: G. applanatum and G. lipsiense in order to produce genetic similarity among the species. Based on the primers used, it was possible to determine that the Brazilian strains and Chinese strain CC-22 are alike. The method and the primers selection showed to be appropriate for the genetic identification of G. lucidum strains, enabling them to be improved and used in research, as well as in the world market.

  16. Appraisal of progenitor markers in the context of molecular classification of breast cancers.

    Science.gov (United States)

    Haviv, Izhak

    2011-01-25

    Clinical management of breast cancer relies on case stratification, which increasingly employs molecular markers. The motivation behind delineating breast epithelial differentiation is to better target cancer cases through innate sensitivities bequeathed to the cancer from its normal progenitor state. A combination of histopathological and molecular classification of breast cancer cases suggests a role for progenitors in particular breast cancer cases. Although a remarkable fraction of the real tissue repertoire is maintained within a population of independent cell line cultures, some steps that are closer to the terminal differentiation state and that form a majority of primary human breast tissues are missing in the cell line cultures. This raises concerns about current breast cancer models.

  17. Introgression of resistance to pathogens in common bean lines with the aid of molecular markers

    Directory of Open Access Journals (Sweden)

    Alisson Campos Pereira

    2013-06-01

    Full Text Available Aiming to incorporate resistance to the anthracnose and angular leaf spot pathogens in the common bean lines BRSMG Talismã, VC8 and VC9, crosses were made between these lines and the line Rudá-R, donor of the alleles Phg1, Co-4, Co-10, which confer resistance to Pseudocercospora griseola and Colletotrichum lindemuthianum. After the crosses, the backcross populations were obtained, and the RC1F1 plants were inoculated with race 65 of C. lindemuthianum. The resistant plants were genotyped with the markers SCARH13, SCARY20 and SCARF10, linked to the alleles Phg1, Co-4 and Co-10, respectively. Based on the molecular data, 44 plants were selected. The progenies originating from multiplication of these plants were evaluated over three seasons for grain yield, plant architecture and grain aspects. Based on these considerations and molecular data, 13 promising progenies were selected for developing inbreds.

  18. Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers.

    Science.gov (United States)

    Das, Sabyasachi; Nikolaidis, Nikolas; Klein, Jan; Nei, Masatoshi

    2008-10-28

    The phylogenetic relationships of Ig light chain (IGL) genes are difficult to resolve, because these genes are short and evolve relatively fast. Here, we classify the IGL sequences from 12 tetrapod species into three distinct groups (kappa, lambda, and sigma isotypes) using conserved amino acid residues, recombination signal sequences, and genomic organization of IGL genes as cladistic markers. From the distribution of the markers we conclude that the earliest extant tetrapods, the amphibians, possess three IGL isotypes: kappa, lambda, and sigma. Of these, two (kappa and lambda) are also found in reptiles and some mammals. The lambda isotype is found in all tetrapods tested to date, whereas the kappa isotype seems to have been lost at least in some birds and in the microbat. Conservation of the cladistic molecular markers suggests that they are associated with functional specialization of the three IGL isotypes. The genomic maps of IGL loci reveal multiple gene rearrangements that occurred in the evolution of tetrapod species. These rearrangements have resulted in interspecific variation of the genomic lengths of the IGL loci and the number and order of IGL constituent genes, but the overall organization of the IGL loci has not changed.

  19. Microevolutionary Patterns and Molecular Markers: The Genetics of Geographic Variation in Ascaris suum

    Science.gov (United States)

    Nadler, S. A.

    1996-01-01

    Molecular markers have been used only rarely to characterize the population genetic structure of nematodes. Published studies have suggested that different taxa may show distinct genetic architectures. Isoenzyme and RAPD markers have been used to investigate geographic variation of Ascaris suum at the level of infrapopulations (nematodes within individual hosts), within localities, and among geographic regions. Independent estimates of genetic differentiation among population samples based on isoenzyme and RAPD data showed similar patterns and substantial correlation. Heterozygote deficiencies within infrapopulations and large values for inbreeding coefficients among infrapopulations suggested that the composition of these populations was not consistent with a model of random recruitment from a large panmictic pool of life-cycle stages. Both isoenzyme and RAPD markers revealed moderate levels of genetic differentiation among samples representing infrapopulations and localities. Of total gene diversity, 9.4% (isoenzyme) and 9.2% (RAPD) was partitioned among infrapopulations. Geographic localities accounted for 7.8% (isoenzyme) and 6.2% (RAPD) of total diversity. Only infrapopulations from the same farm had low levels of differentiation. PMID:19277145

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

    Science.gov (United States)

    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.

  1. Caracterização molecular de butiazeiro por marcadores RAPD Molecular characterization of Pindo palm by RAPD markers

    Directory of Open Access Journals (Sweden)

    Adrise Medeiros Nunes

    2008-09-01

    Full Text Available O grupo botânico Arecaceae é de extremo interesse por compreender plantas em extinção e por apresentar um grande potencial de exploração econômica. O butiazeiro (Butia capitata (Mart. Becc. ocorre naturalmente no Sul do Brasil. Sua caracterização molecular é de extremo interesse para futuros trabalhos de melhoramento genético. Assim sendo, verificou-se a variabilidade genética existente entre vinte e dois genótipos de butiazeiro da espécie (Butia capitata, pertencentes ao BAG (Banco Ativo de Germoplasma de frutíferas nativas do Centro Agropecuário da Palma - UFPel. Esses genótipos foram analisados usando marcadores do tipo RAPD (Random Amplified Polymorphic DNA. Um total de 136 fragmentos foram obtidos, sendo 77 polimórficos. O primer OPA11 apresentou maior polimorfismo, produzindo 9 perfis diferentes. A análise de agrupamento, realizada pelo método UPGMA, produziu um dendrograma que permitiu a clara separação dos genótipos em dois grupos principais. Verificou-se que, com a técnica de marcadores de RAPD, foi possível obter um perfil molecular único e uma estimativa da variabilidade existente entre os genótipos de butiazeiro avaliados.The study of the botanical group Arecaceae is of extreme interest for evolving several endangered species of plants and for presenting a great potential of economical exploration. The Pindo palm (or wine palm, jelly palm (Butia capitata (Mart. Becc. is natural from the south of Brazil. Its molecular characterization is of extreme interest for future researches of genetic improvement. Since little is known about the variability of the species, the existent genetic variability was verified among twenty-two genotypes of Pindo palm (or wine palm, jelly palm, from BAG (Germoplasm Assets Bank of fruit trees native from the Agricultural Center of the Palma - UFPEL, which were analyzed using markers RAPD (Random Amplified Polymorphic DNA with Operon Technologies' decamers primers. With 21 primers

  2. Screening white spot syndrome virus (WSSV)-resistant molecular markers from Fenneropenaeus chinensis

    Science.gov (United States)

    Wu, Yingying; Meng, Xianhong; Kong, Jie; Luan, Sheng; Luo, Kun; Wang, Qingyin; Zheng, Yongyun

    2017-02-01

    White spot syndrome virus (WSSV)-resistant molecular markers were screened from the selectively bred new variety `Huanghai No. 2' of Fenneropenaeus chinensis using unlabeled-probe high-resolution melting (HRM) technique. After the artificial infection with WSSV, the first 96 dead shrimps and the last 96 surviving shrimps were collected, representing WSSV-susceptible and -resistant populations, respectively. The genotypes at well-developed 39 single nucleotide polymorphisms (SNPs) loci were obtained. As revealed in the Chi-square test, 3 SNPs, genotype A/A of contig C364-89AT, genotype A/A of C2635-527CA and genotype C/T of contig C12355-592CT, were positively correlated with disease-resistance traits. Other 2 SNPs, genotype G/G of contig C283-145AG and genotype C/C of contig C12355-592CT, were negatively correlated. Moreover, analysis with BlastX program for disease-resistant SNPs indicated that 3 contigs, Contig283, Contig364 and Contig12355, matched to the functional genes of effector caspase of Penaeus monodon, peptide transporter family 1-like protein, and 40S ribosomal protein S2 of Perca flavescens with high sequence similarity. The results will be helpful to provide theoretical and technical supports for molecular marker-assisted selective breeding of F. chinensis.

  3. Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma

    Directory of Open Access Journals (Sweden)

    David L. Wachter

    2014-01-01

    Full Text Available Background. Carcinomas of the breast with neuroendocrine features are incorporated in the World Health Organization classification since 2003 and include well-differentiated neuroendocrine tumors, poorly differentiated neuroendocrine carcinomas/small cell carcinomas, and invasive breast carcinomas with neuroendocrine differentiation. Neuroendocrine differentiation is known to be more common in certain low-grade histologic special types and has been shown to mainly cluster to the molecular (intrinsic luminal A subtype. Methods. We analyzed the frequency of neuroendocrine differentiation in different molecular subtypes of breast carcinomas of no histologic special type using immunohistochemical stains with specific neuroendocrine markers (chromogranin A and synaptophysin. Results. We found neuroendocrine differentiation in 20% of luminal B-like carcinomas using current WHO criteria (at least 50% of tumor cells positive for synaptophysin or chromogranin A. In contrast, no neuroendocrine differentiation was seen in luminal A-like, HER2 amplified and triple-negative carcinomas. Breast carcinomas with neuroendocrine differentiation presented with advanced stage disease and showed aggressive behavior. Conclusions. We conclude that neuroendocrine differentiation is more common than assumed in poorly differentiated luminal B-like carcinomas. Use of specific neuroendocrine markers is thus encouraged in this subtype to enhance detection of neuroendocrine differentiation and hence characterize the biological and therapeutic relevance of this finding in future studies.

  4. Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma

    Science.gov (United States)

    Wachter, David L.; Hartmann, Arndt; Beckmann, Matthias W.; Fasching, Peter A.; Hein, Alexander; Bayer, Christian M.; Agaimy, Abbas

    2014-01-01

    Background. Carcinomas of the breast with neuroendocrine features are incorporated in the World Health Organization classification since 2003 and include well-differentiated neuroendocrine tumors, poorly differentiated neuroendocrine carcinomas/small cell carcinomas, and invasive breast carcinomas with neuroendocrine differentiation. Neuroendocrine differentiation is known to be more common in certain low-grade histologic special types and has been shown to mainly cluster to the molecular (intrinsic) luminal A subtype. Methods. We analyzed the frequency of neuroendocrine differentiation in different molecular subtypes of breast carcinomas of no histologic special type using immunohistochemical stains with specific neuroendocrine markers (chromogranin A and synaptophysin). Results. We found neuroendocrine differentiation in 20% of luminal B-like carcinomas using current WHO criteria (at least 50% of tumor cells positive for synaptophysin or chromogranin A). In contrast, no neuroendocrine differentiation was seen in luminal A-like, HER2 amplified and triple-negative carcinomas. Breast carcinomas with neuroendocrine differentiation presented with advanced stage disease and showed aggressive behavior. Conclusions. We conclude that neuroendocrine differentiation is more common than assumed in poorly differentiated luminal B-like carcinomas. Use of specific neuroendocrine markers is thus encouraged in this subtype to enhance detection of neuroendocrine differentiation and hence characterize the biological and therapeutic relevance of this finding in future studies. PMID:24701575

  5. Bladder Carcinoma Data with Clinical Risk Factors and Molecular Markers: A Cluster Analysis

    Directory of Open Access Journals (Sweden)

    Enrique Redondo-Gonzalez

    2015-01-01

    Full Text Available Bladder cancer occurs in the epithelial lining of the urinary bladder and is amongst the most common types of cancer in humans, killing thousands of people a year. This paper is based on the hypothesis that the use of clinical and histopathological data together with information about the concentration of various molecular markers in patients is useful for the prediction of outcomes and the design of treatments of nonmuscle invasive bladder carcinoma (NMIBC. A population of 45 patients with a new diagnosis of NMIBC was selected. Patients with benign prostatic hyperplasia (BPH, muscle invasive bladder carcinoma (MIBC, carcinoma in situ (CIS, and NMIBC recurrent tumors were not included due to their different clinical behavior. Clinical history was obtained by means of anamnesis and physical examination, and preoperative imaging and urine cytology were carried out for all patients. Then, patients underwent conventional transurethral resection (TURBT and some proteomic analyses quantified the biomarkers (p53, neu, and EGFR. A postoperative follow-up was performed to detect relapse and progression. Clusterings were performed to find groups with clinical, molecular markers, histopathological prognostic factors, and statistics about recurrence, progression, and overall survival of patients with NMIBC. Four groups were found according to tumor sizes, risk of relapse or progression, and biological behavior. Outlier patients were also detected and categorized according to their clinical characters and biological behavior.

  6. QTL molecular marker location of powdery mildew resistance in cucumber (Cucumis sativus L.)

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The cucumber lines, S94 (Northern China open-field type, powdery mildew (PM) susceptible) and S06 (European greenhouse type, PM resistant), and their F6:7 populations were used to investigate PM re-sistance under seedling spray inoculation in 2005/Autumn and 2006/Spring. QTL analysis was under-taken based on a constructed molecular linkage map of the corresponding F6 population using com-posite interval mapping. A total of four QTLs (pm1.1, pm2.1, pm4.1 and pm6.1) for PM resistance were identified and located on LG 1, 2, 4 and 6, respectively, explaining 5.2%-21.0% of the phenotypic variation. Three consistent QTLs (pm1.1, pm2.1 and pm4.1) were detected under the two test conditions. The QTL pm6.1 was only identified in 2005/Autumn. The total phenotypic variation explained by the QTLs was 52.0% and 42.0% in 2005/Autumn and 2006/Spring, respectively. Anchor markers tightly linked to those loci (<5 cM) could lay a basis for both molecular marker-assisted breeding and map-based gene cloning of the PM-resistance gene in cucumber.

  7. Molecular marker differences relate to developmental position and subsets of mesodiencephalic dopaminergic neurons.

    Directory of Open Access Journals (Sweden)

    Simone M Smits

    Full Text Available The development of mesodiencephalic dopaminergic (mdDA neurons located in the substantia nigra compacta (SNc and ventral tegmental area (VTA follow a number of stages marked by distinct events. After preparation of the region by signals that provide induction and patterning, several transcription factors have been identified, which are involved in specifying the neuronal fate of these cells. The specific vulnerability of SNc neurons is thought to root in these specific developmental programs. The present study examines the positions of young postmitotic mdDA neurons to relate developmental position to mdDA subset specific markers. MdDA neurons were mapped relative to the neuromeric domains (prosomeres 1-3 (P1-3, midbrain, and hindbrain as well as the longitudinal subdivisions (floor plate, basal plate, alar plate, as proposed by the prosomeric model. We found that postmitotic mdDA neurons are located mainly in the floorplate domain and very few in slightly more lateral domains. Moreover, mdDA neurons are present along a large proportion of the anterior/posterior axis extending from the midbrain to P3 in the diencephalon. The specific positions relate to some extent to the presence of specific subset markers as Ahd2. In the adult stage more of such subsets specific expressed genes are present and may represent a molecular map defining molecularly distinct groups of mdDA neurons.

  8. The Analysis of High-Risk Molecular Markers for Cervical Cancer Patients under Thirty-Five

    Institute of Scientific and Technical Information of China (English)

    Yi Luo; Jian Wang; Changyin Zhao

    2006-01-01

    OBJECTIVE To explore molecular markers for cervical cancer in female patients below thirty-five years of age, so that the markers may be used to formulate a prognosis and to provide some useful targets for improving therapy.METHODS Pathological data were collected from 64 cervical cancer patients under the age of 35 from June, 1995 to June, 2000 in our institution.The data were retrospectively analyzed as a study group, and compared to data obtained from 90 cervical cancer cases over the age of 35 as controls who underwent treatment during the same time period. Immunohistochemical and quantified image analyses were conducted to look for differences between the two groups in expression of survivin, p27,CD44v6, MMP-2 and TIMP-2.RESULTS The overall 5-year survival rate (65.6%) of the study group was significantly lower (P<0.05) compared to the control group (84.4%). The expression of survivin, MMP-2 and CD44v6 was much higher in the younger study group compared to the older control group, but TIMP-2 displayed higher expression in the control group (P<0.05). There was no significant difference in p27 expression between the two groups (P>0.05).CONCLUSION Young women patients with cervical cancer have a poorer prognosis compared to old women. Our study reveals that survivin,MMP-2, TIMP-2 and CD44v6 expression have a correlation with shorter 5-year survival. Improvement in the prognosis for young cervical cancer patients can be expected using biomedical therapy which targets these molecular markers.

  9. Status of potential PfATP6 molecular markers for artemisinin resistance in Suriname

    Directory of Open Access Journals (Sweden)

    Adhin Malti R

    2012-09-01

    Full Text Available Abstract Background Polymorphisms within the PfATP6 gene have been indicated as potential molecular markers for artemisinin efficacy. Since 2004, the use of artemisinin combination therapy (ACT was introduced as first-line treatment of the uncomplicated malaria cases in Suriname. The aim of this research was to determine changes in Suriname in the status of the polymorphic markers in the PfATP6 gene before and after the adoption of the ACT-regimen, particularly of the S769N mutation, which was reported to be associated with in vitro Artemether resistance in the neighboring country French Guiana. Methods The PfATP6 gene from Plasmodium falciparum parasites in Suriname was investigated in 28 samples using PCR amplification and restriction enzyme analysis, to assess and determine the prevalence of potentially interesting single nucleotide polymorphisms. The polymorphisms [L263E; A623E; S769N], which may be associated with the artemisinin resistant phenotype were characterized in parasites from three endemic regions before and after the adoption of the ACT-regimen. In addition, the status of these molecular markers was compared in paired P. falciparum isolates from patients with recurring malaria after controlled ACT. Results All the investigated samples exhibit the wild-type genotype at all three positions; L263, A623, S769. Conclusion All investigated isolates before and after the adoption of the ACT-regimen and independent of endemic region harbored the wild-type genotype for the three investigated polymorphisms. The study revealed that decreased artemisinin susceptibility could occur independent from PfATP6 mutations, challenging the assumption that artemisinin resistance is associated with these mutations in the PfATP6 gene.

  10. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Dharmendra Singh

    Full Text Available 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.

  11. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    Science.gov (United States)

    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.

  12. Genetic Diversity of Some Sweet Cherry Cultivars Based on Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ioana Virginia Berindean

    2016-11-01

    Full Text Available Sweet cherry (Prunus avium L., originated around the Caspian and Black Sea, is an important fruit tree species of economic interest, and hence, breeding and conservation are requested (. Genetic analysis at the molecular level can be used effectively to study molecular polymorphism existing between intraspecific and interspecific tree species and phylogenetic relationships between them and their hybrids. The purpose of this study was to characterize and determine genetic relationships among the sweet cherry native genotypes belonging to Fruit Research & Development Station Bistrita, Romania, using RAPD markers. To eliminate the existence of possible synonyms from national romanian collection, we collect four Van cultivars, from four different national collection. For molecular analysis of the 16 varieties of sweet cherry were considered 13 RAPD primers selected from the literature. They were later used to determine the genetic variability at the molecular level using PAST program, and the dendrogram was generated based on Jaccard’s genetic distance. The dendrogram constructed by PAST software. The quantity and quality of the DNA obtained was suitable to achieve PCR amplification step. Only seven out of the 13 RAPD primers have generate polymorphic bands. The rest of seven were monomorphics. The most polymorphic primer was OPB10 which generated 11 bands from which 100% were polymorphic.Seven RAPD primers generated a high level of polymorphism which allowed to divide these cherry varieties into two groups according to their genetic geographical origin and the pedigree.

  13. Molecular Markers of Tubulointerstitial Fibrosis and Tubular Cell Damage in Patients with Chronic Kidney Disease.

    Directory of Open Access Journals (Sweden)

    Shunsaku Nakagawa

    Full Text Available In chronic kidney disease (CKD, progressive nephron loss causes glomerular sclerosis, as well as tubulointerstitial fibrosis and progressive tubular injury. In this study, we aimed to identify molecular changes that reflected the histopathological progression of renal tubulointerstitial fibrosis and tubular cell damage. A discovery set of renal biopsies were obtained from 48 patients with histopathologically confirmed CKD, and gene expression profiles were determined by microarray analysis. The results indicated that hepatitis A virus cellular receptor 1 (also known as Kidney Injury Molecule-1, KIM-1, lipocalin 2 (also known as neutrophil gelatinase-associated lipocalin, NGAL, SRY-box 9, WAP four-disulfide core domain 2, and NK6 homeobox 2 were differentially expressed in CKD. Their expression levels correlated with the extent of tubulointerstitial fibrosis and tubular cell injury, determined by histopathological examination. The expression of these 5 genes was also increased as kidney damage progressed in a rodent unilateral ureteral obstruction model of CKD. We calculated a molecular score using the microarray gene expression profiles of the biopsy specimens. The composite area under the receiver operating characteristics curve plotted using this molecular score showed a high accuracy for diagnosing tubulointerstitial fibrosis and tubular cell damage. The robust sensitivity of this score was confirmed in a validation set of 5 individuals with CKD. These findings identified novel molecular markers with the potential to contribute to the detection of tubular cell damage and tubulointerstitial fibrosis in the kidney.

  14. Thrombophilic molecular markers in young patients (<40 years with coronary artery disease

    Directory of Open Access Journals (Sweden)

    Mingma Sherpa

    2012-01-01

    Full Text Available Background: There has been an alarming rise in the incidence of coronary artery disease (CAD in India especially involving the age group of less than 45 years. In recent past, various studies focused on hemostatic aspects of CAD, but could not determine the significance of thrombophilic molecular marker in combination. The study was undertaken to investigate the association of thrombophilia related molecular markers in young patients with CAD. Materials and Methods: Thirty diagnosed patients with CAD of either sex under 40 years were included. Thirty healthy age and sex matched control subjects without evidence of CAD formed the control group. Detailed history and clinical examination findings were recorded. In addition to routine investigations, polymerase chain reaction (PCR based molecular analysis for Factor V Leiden (FVL, methyltetrahydrofolate reductase (MTHFR gene, tumor necrosis factor receptor 2 (TNFR2 gene, and prothrombin gene mutation were carried out. Results: The mean age (± SD was 36.86 ± 3.90 years in the patients. Smoking was the most prevalent risk factor. FVL, MTHFR and TNFR2 gene mutation were seen in nine (30% patient. Three patients had presence of more than one mutation. FVL, MTHFR and TNFR2 gene mutation was found in 4 (13.3%, 3 (10%, and 5 (16.6% patients respectively. Prothrombin gene mutation was not seen in any of the subjects. There was no significant difference in lipid profile, fibrinogen levels and CRP among the patients with mutation and patients without mutation. Conclusion: Almost one-third of the cases were positive for the various mutations in the study and the presence of at-least one or the other risk factor adds on to the risk of future thrombosis. There is a need to demonstrate or document these mutations in a larger group further based upon ethnicity and geographic distribution.

  15. DNA分子标记在中药鉴定中的应用进展%DNA Molecular Marker in Progress in the Application of Chinese Medicine Identification

    Institute of Scientific and Technical Information of China (English)

    海学忠

    2012-01-01

    DNA molecular markers including molecular hybrid (southern hybridization) as the foundation of DNA molecular markers, PCR-based DNA molecular markers and DNA sequence to the basis of molecular markers and DNA sequencing by technology. This paper summarizes the commonly used DNA molecular markers on the features of DNA molecular markers in recent years Chinese medicine identification in this paper reviewed the application.%DNA分子标记包括以分子杂交(southern杂交)为基础的DNA分子标记技术、以PCR为基础的DNA分子标记技术和以DNA序列为基础的分子标记技术和DNA序列测定技术。本文概述了常用DNA分子标记技术的特点,对近年来DNA分子标记在中药鉴定中的应用进行了综述。

  16. Isolation of Ty1-copia retrotransposon in myrtle genome and development of S-SAP molecular marker.

    Science.gov (United States)

    Woodrow, Pasqualina; Pontecorvo, Giovanni; Ciarmiello, Loredana F

    2012-04-01

    Long terminal repeat (LTR)-retrotransposons are mobile genetic elements that are ubiquitous in plants and constitute a major portion of their nuclear genomes. LTR- retrotransposons possess unique properties that make them appropriate for investigating relationships between populations, varieties and closely related species. Myrtus communis L. is an evergreen shrub growing spontaneously throughout the Mediterranean area. Accessions show significant variations for agriculturally important traits, so the development of specific molecular markers for conservation and characterization of myrtle germplasm is desirable to conserve biodiversity. In this study, we isolated the first retrotransposon Ty1-copia-like element (Tmc1) in Myrtus communis L. genome and used this as a molecular marker. We successfully employed the S-SAP marker system to specifically characterize four myrtle accessions belonging to different areas in the province of Caserta (Italy). The high level of polymorphism detected in isolated LTRs, make Tmc1 a good molecular marker for this species. Our findings confirm that retrotransposon-based molecular markers are particularly valuable tools for plant molecular characterization studies.

  17. Molecular markers of anti-malarial drug resistance in Lahj Governorate, Yemen: baseline data and implications

    Directory of Open Access Journals (Sweden)

    Chance Michael L

    2011-08-01

    Full Text Available Abstract Background This is an investigation of anti-malarial molecular markers coupled with a therapeutic efficacy test of chloroquine (CQ against falciparum malaria in an area of unstable malaria in Lahj Governorate, Yemen. The study was aimed at assessment of therapeutic response to CQ and elucidation of baseline information on molecular markers for Plasmodium falciparum resistance against CQ and sulphadoxine/pyrimethamine (SP. Methods Between 2002 and 2003 the field test was conducted according to the standard WHO protocol to evaluate the therapeutic efficacy of CQ in 124 patients with falciparum malaria in an endemic area in Lahj Governorate in Yemen. Blood samples collected during this study were analysed for P. falciparum chloroquine resistance transporter gene (pfcrt-76 polymorphisms, mutation pfcrt-S163R and the antifolate resistance-associated mutations dihydrofolate reductase (dhfr-C59R and dihydropteroate synthase (dhps-K540E. Direct DNA sequencing of the pfcrt gene from three representative field samples was carried out after DNA amplification of the 13 exons of the pfcrt gene. Results Treatment failure was detected in 61% of the 122 cases that completed the 14-day follow-up. The prevalence of mutant pfcrt T76 was 98% in 112 amplified pre-treatment samples. The presence of pfcrt T76 was poorly predictive of in vivo CQ resistance (PPV = 61.8%, 95% CI = 52.7-70.9. The prevalence of dhfr Arg-59 mutation in 99 amplified samples was 5%, while the dhps Glu-540 was not detected in any of 119 amplified samples. Sequencing the pfcrt gene confirmed that Yemeni CQ resistant P. falciparum carry the old world (Asian and African CQ resistant haplotype CVIETSESI at positions 72,73,74,75,76,220,271, 326 and 371. Conclusion This is the first study to report baseline information on the characteristics and implications of anti-malarial drug resistance markers in Yemen. It is also the first report of the haplotype associated with CQR P. falciparum

  18. AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

    Science.gov (United States)

    Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

    2016-04-01

    Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

  19. Temperature-induced volatility of molecular markers in ambient airborne particulate matter

    Directory of Open Access Journals (Sweden)

    C. R. Ruehl

    2011-01-01

    Full Text Available Molecular markers are organic compounds used to represent known sources of particulate matter (PM in statistical source apportionment studies. The utility of molecular markers depends on, among other things, their ability to represent PM volatility under realistic atmospheric conditions. We measured the particle-phase concentrations and temperature-induced volatility of commonly-used molecular markers in California's heavily polluted San Joaqin Valley. Concentrations of elemental carbon, organic carbon, levoglucosan, and polycyclic aromatic hydrocarbons were not reduced by mild (~10 K heating. In contrast, both hopane/sterane and n-alkane concentrations were reduced, especially during the summer sampling events at the urban site. These results suggest that hopanes and steranes have effective saturation concentrations ~1 μg m−3, and therefore can be considered semi-volatile. The volatility of an individual compound depends both on its inherent properties (primarily vapour pressure and the interactions between itself and any potential absorbing phase. The volatility behavior of n-alkanes during the urban summer is consistent with that predicted for absorption by suberic acid (a C8 diacid using a group contribution modelling method. Observations can also be matched by an absorbent whose composition is based on recently-obtained high-resolution aerosol mass spectrometer factors (approximately 33% "hydrocarbon-like" and 67% oxygenated organic aerosol. The reduced evaporation of the n-alkanes, hopanes, and steranes with mild heating during rural and/or winter experiments could be explained by a more oxygenated absorbing phase along with a non-absorptive partitioning mechanism, such as adsorption to soot. This suggests that the temperature-induced volatility of large hydrocarbons in PM is most important if a relatively non-polar absorbing organic phase exists. While the activity coefficients of most organic

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

    OpenAIRE

    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...

  1. 石家庄市水环境中嗜肺军团菌AFLP分型研究%AFLP Typing of Legionella pneumophila in Water Environment in Shijiazhuang

    Institute of Scientific and Technical Information of China (English)

    秦丽云; 张鑫; 郭玉梅; 徐保红; 陈慧巧; 王苋; 吕国平; 曹春红

    2011-01-01

    Objective To study the molecular genotyping of Legionella pneumophila strains isolated from different water environment in Shijiazhuang and dominant species and species distribution. Methods Amplified fagment length polymorphism (AFLP) made by the European Working Group for Legionella Infections was used for typing Legionella from water environment in Shijiazhuang. Cluster analysis was used to explore the relationships among the strains. Results According to the serum typing methods, Legionella in water were classified into Lp1 ,Lp2-14. The use of AFLP technology for 39 strains of Legionella and serogroup Lpl were classified into 18 types,denoted as AFLP1-AFLP18,AFLP1 type and AFLP11 type as the main type; The 9 strains of serotypes Lp2-\\4 were classified into 7 types,denoted as AFLP I -AFLP VH ,AFLP M as the main type. In the same area of Legionella pneumophila strains,the same serum type similarity coefficient had difference, but there was still the dominant strain; between different regions of some strains of similarity coefficient of 100%, showed that the Legionella strains belonged to the same source of different regions of the water. Conclusion Every genotype isolate presents polymorphic, which can control typing information of Legionella pneumophila molecular.%目的 对石家庄市水环境中分离到的嗜肺军团菌进行分子分型,研究嗜肺军团菌AFLP分型特征,为建立嗜肺军团菌分子型别库提供资料.方法 运用欧洲军团菌感染工作组(European Working Group on Legionella Infection,EWGLI)组织制定的扩增片断长度多态性分型(amplified fragment length polymorphism,AFLP)方法,对石家庄市水环境中分离到的39株嗜肺军团菌进行分子分型,对分型结果进行聚类分析,探讨菌株间的相互关系.结果 按照血清分型方法,将水样中嗜肺军团菌分为Lp1型和Lp2~14型.运用AFLP技术对39株嗜肺军团菌菌株分型,其中,将31株Lp1血清型分为18

  2. Marcadores moleculares na bovinocultura de corte - Molecular Marker for beef cattle production - Marcadores moleculares en la producción

    OpenAIRE

    Dias-Salman, Ana Karina; Polaina-Fernanda Giachetto; Malago, Wilson Jr

    2009-01-01

    ResumenLa producción de ganado de corte en Brasil se encuentra todavía buscando mejores índices productivos y de precocidad del rebaño. La grande esperanza para el mejoramiento genético más eficaz y rápido de las razas cebú, en especial la raza Nelore, está aliada a los resultados obtenidos con la genética molecular, que se ha establecido cada vez más en los centros de pesquisa. El desarrollo de las técnicas moleculares surge como una herramienta adicional para ser utilizada en el análisis ge...

  3. Marcadores moleculares na bovinocultura de corte - Molecular Marker for beef cattle production - Marcadores moleculares en la producción

    Directory of Open Access Journals (Sweden)

    Dias-Salman, Ana Karina

    2009-02-01

    Full Text Available ResumenLa producción de ganado de corte en Brasil se encuentra todavía buscando mejores índices productivos y de precocidad del rebaño. La grande esperanza para el mejoramiento genético más eficaz y rápido de las razas cebú, en especial la raza Nelore, está aliada a los resultados obtenidos con la genética molecular, que se ha establecido cada vez más en los centros de pesquisa. El desarrollo de las técnicas moleculares surge como una herramienta adicional para ser utilizada en el análisis genética buscando lamejora de características de interés económico. Además de la grandenotoriedad, los conceptos sobre marcadores moleculares son todavía poco conocidos por la grande mayoría de los profesionales que se ocupan con la producción de ganado de corte nacional. Esta es una revisión organizada en forma de preguntas y respuestas, que intentan definir marcadores moleculares, esclarecer como ellos son detectados en laboratorio y explicar como los resultados de pesquisa pueden ser aplicados para mejorar el desempeño de los bovinos, con énfasis en aquellos destinados à la producción de carne.ResumoA pecuária de corte no Brasil ainda está em busca de melhores índices em termos de produtividade e precocidade do rebanho. A grande esperança para o melhoramento genético mais eficaz e mais rápido das raças zebuínas, em especial a Nelore, está aliada aos resultados obtidos com a genética molecular, a qual vem se estabelecendo cada vez mais nos centros de pesquisas. O desenvolvimento de técnicas moleculares surge como uma ferramenta a mais a ser utilizada na análise genética visando oaprimoramento de características de interesse econômico. Apesar dagrande notoriedade, os conceitos sobre marcadores moleculares ainda são pouco conhecidos pela grande maioria dos atores envolvidos com apecuária de corte nacional. Esta é uma revisão organizada em forma deperguntas e respostas, as quais visam definir marcadores moleculares

  4. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma.

    Science.gov (United States)

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  5. De novo transcriptome analysis and molecular marker development of two Hemarthria species

    Directory of Open Access Journals (Sweden)

    Xiu eHuang

    2016-04-01

    Full Text Available 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 8,330 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.

  6. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma

    Science.gov (United States)

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  7. Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

    Science.gov (United States)

    Odong, T L; van Heerwaarden, J; Jansen, J; van Hintum, T J L; van Eeuwijk, F A

    2011-07-01

    Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of traditional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correlation coefficient is directly related to subgroup differentiation and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.

  8. Biological (molecular and cellular) markers of toxicity. Final report, September 15, 1988 - September 14, 1991

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  9. Advances in Localization and Molecular Markers of Wheat Leaf Rust Resistance Genes

    Institute of Scientific and Technical Information of China (English)

    YANG Wen-xiang; LIU Da-qun

    2004-01-01

    Genetic resistance is the most economical method of reducing yield losses caused by wheat leaf rust. To identify the leaf rust resistance genes in commonly used parental germplasm and released cultivars become very important for utilizing the genetic resistance tc wheat leaf rust fully. Up to date, about 90 leaf rust resistance genes have been found,of which 51 genes have been located and mapped to special chromosomes, and 56 genes have been designated officially according to the standards set forth in the Catalogue of Gene Symbols for wheat. Twenty-four wheat leaf rust resistance genes have been developed for their molecular markers. It is very important to isolate, characterize, and map leaf rust resistance genes due to the resistance losses of the genes caused by the pathogen continuously.

  10. A molecular marker-based linkage map of diploid bananas (Musa acuminata).

    Science.gov (United States)

    Fauré, S; Noyer, J L; Horry, J P; Bakry, F; Lanaud, C; Gońzalez de León, D

    1993-12-01

    A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F2 population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36% of all loci, mostly favoring the male parent. Chromosome structural rearrangements were believed to be one of the main causes of these distortions. The use of genetic linkage data to further the genetic and evolutionary knowledge of the genus Musa, as well as to help improve the design of breeding strategies, is discussed.

  11. A survey of molecular marker compounds in sediments of San Francisco Bay, California

    Science.gov (United States)

    Hostettler, Frances D.; Rapp, John B.; Geological Survey (U.S.) Pereira, Wilfred E.; Kvenvolden, Keith A.

    1994-01-01

    An areal survey of surficial sediments in San Francisco Bay has been conducted to evaluate the presence of extractable organic compounds. Molecular marker compounds studied include hydrocarbons (PAH's), chlorinated pesticides, and other organic compounds that provide information on sources of organic input into the Bay. Fairly uniform source profiles are seen throughout the Bay. Biomarker profiles contain mature constituents indicating anthropogenic influences and extensive sediment reworking. The dominant input signatures in San Francisco Bay sediment are those of anthropogenic PAH's from combustion and other sources, and long chain n-alkanes and n-aldehydes from terrigenous vascular plants. A comparison of the sums of the combustion PAH's and the terrigenous n-alkanes shows that an anthropogenic influence is dominant in the most urban parts of the Bay close to shore, and in mid-Bay channel areas, and a terrigenous signature is dominant nearshore in San Pablo Bay and at the southernmost station in South Bay.

  12. [Cellular and molecular mechanisms of radiation-induced brain injury: can peripheral markers be detected?].

    Science.gov (United States)

    Piskunov, A K; Nikitin, K V; Potapov, A A

    2015-01-01

    Investigation of the mechanisms of radiation-induced brain injury is a relevant fundamental objective of radiobiology and neuroradiology. Damage to the healthy brain tissue is the key factor limiting the application of radiation therapy in patients with nervous systems neoplasms. Furthermore, postradiation brain injury can be clinically indiscernible from continued tumor growth and requires differential diagnosis. Thus, there exists high demand for biomarkers of radiation effects on the brain in neurosurgery and radiobiology. These markers could be used for better understanding and quantifying the effects of ionizing radiation on brain tissues, as well as for elaborating personalized therapy. Despite the high demand, biomarkers of radiation-induced brain injury have not been identified thus far. The cellular and molecular mechanisms of the effect of ionizing radiation on the brain were analyzed in this review in order to identify potential biomarkers of radiation-induced injury to nervous tissue.

  13. Molecular markers for genetic stability of intergeneric hybrids Fragaria x Potentilla derived from tissue culture

    Directory of Open Access Journals (Sweden)

    Anca Nicoleta SUTAN

    2009-11-01

    Full Text Available The effect of growth regulators, explant source and culture age on genetic stability of plants obtained from tissue culture propagation of ornamental strawberry “Serenata” were examined. Genomic DNAs of in vitro-derived shoots and control plant were extracted and compared by RAPD-PCR analyses. Ten primers (from 48 previously tested were selected and used in RAPD analysis to prove the clonal fidelity (i.e. genetic stability of the tissue culture-derived ornamental strawberry plants. The lack of polymorphisms in micropropagated plants screened through molecular markers was used to suggest genetic fidelity. Identicaly banding patterns of the RAPD profiles obtaining from vitroplants, regenerated via organogenesis or meristems culture, suggested that in the ornamental strawberry, variety “Serenata”, neither explant source, nor callus age or limited number of subcultures, in basal media supplemented with low concentration of growth regulators, were associated with occurence of somaclonal variation.

  14. Assessment on Evaluating Parameters of Rice Core Collections Constructed by Genotypic Values and Molecular Marker Information

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Eleven evaluating parameters for rice core collection were assessed based on genotypic values and molecular marker information. Monte Carlo simulation combined with mixed linear model was used to eliminate the interference from environment in order to draw more reliable results. The coincidence rate of range (CR) was the optimal parameter. Mean Simpson index (MD), mean Shannon-Weaver index of genetic diversity (M1) and mean polymorphism information content (MPIC) were important evaluating parameters. The variable rate of coefficient of variation (VR) could act as an important reference parameter for evaluating the variation degree of core collection. Percentage of polymorphic loci (p) could be used as a determination parameter for the size of core collection. Mean difference percentage (MD) was a determination parameter for the reliability judgment of core collection. The effective evaluating parameters for core collection selected in the research could be used as criteria for sampling percentage in different plant germplasm populations.

  15. CD24 as a Molecular Marker in Ovarian Cancer: A Literature Review

    Directory of Open Access Journals (Sweden)

    Lu Huang

    2016-01-01

    Full Text Available Ovarian cancer is the most lethal gynecologic cancer, with a mortality rate of > 60%. Cancer stem cell (CSC hypothesis offers an attractive explanation of chemoresistance, metastasis, etc., associated with the disease. However, there are still controversy and limitation in defining the CSC markers. CD24 is a mucin-type glycosyl-phosphatidylinositol-linked glycoprotein, expressed on the surface of cells, which serves as a normal receptor for P-selectin and is found involved in molecular adhesion and metastatic tumor spread. Expression rate of CD24 has been associated with progression of various cancers and poor survival rates. In this review, the function of CD24 in ovarian cancer, especially in ovarian CSC system, was discussed in an effort to broaden the interpretation of potential mechanism.

  16. Phylogenetic position of Oryzolejeunea (Lejeuneaceae,Marchantiophyta): Evidence from molecular markers and morphology

    Institute of Scientific and Technical Information of China (English)

    Wen YE; Yu-Mei WEI; Alfons SCH(A)FER-VERWIMP; Rui-Liang ZHU

    2013-01-01

    The systematic position of the small neotropical genus Oryzolejeunea (three spp.) has long been controversial.Phylogenetic analyses of molecular data for the present study using DNA markers (trnL,psbA,and a nuclear ribosomal internal transcribed spacer [nrITS] region) shows that the genus is nested in Lejeunea.The results not only reveal the phylogenetic position of Oryzolejeunea for the first time,but also challenge the taxonomic value of the proximal hyaline papilla as a key feature in Lejeunea.The present study shows the urgent need for a reassessment of the perimeters of the genus Lejeunea and its infrageneric classification.Three new combinations,namely Lejeunea saccatiloba,Lejeunea grolleana,and Lejeunea venezuelana,are proposed.

  17. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer.

    Science.gov (United States)

    Kamel, Azza M; Teama, Salwa; Fawzy, Amal; El Deftar, Mervat

    2016-06-01

    Plasma DNA integrity index is increased in various malignancies including breast cancer, the most common cancer in women worldwide; early detection is crucial for successful treatment. Current screening methods fail to detect many cases of breast cancer at an early stage. In this study, we evaluated the level of plasma DNA integrity index in 260 females (95 with breast cancer, 95 with benign breast lesions, and 70 healthy controls) to verify its potential value in discriminating malignant from benign breast lesions. The criteria of the American Joint Committee on Cancer were used for staging of breast cancer patients. DNA integrity index was measured by real-time PCR. DNA integrity index was significantly higher in breast cancer than in benign breast patients and healthy subjects (P = cancer group was 85.3 % at 0.55 DNA integrity index cutoff. In conclusion, the plasma DNA integrity index may be a promising molecular diagnostic marker of malignancy in breast lesions.

  18. Molecular marker heterozygosities and genetic distances as correlates of production traits in F1 bovine crosses

    Directory of Open Access Journals (Sweden)

    Daniella Tambasco-Talhari

    2005-01-01

    Full Text Available Several studies have investigated the relationship between heterozygosity, genetic distance and production traits. The objective of the present study was to evaluate the influence of the degree of heterozygosity and genetic distance on growth, carcass and reproductive related features in F1 bovine crosses. We tested 10 polymorphic markers in 330 purebred cattle (Nelore, Canchim, Aberdeen Angus and Simental and 256 crossbred cattle belonging to four crossbred groups. Individual heterozygosities (Hi and multilocus genetic similarity (Dm were estimated and used in correlation analysis against individual phenotypic measurements. Significant (p < 0.05 Hi effects occurred for birth weight, 15 to 18 month weight, hot carcass weight and longissimus rib eye area. The extent to which increased heterozygosity (deltaH in F1 crosses can be predicted from the genetic distance of parental breeds was also investigated using Nei's standard genetic distance (Ds and standard heterozygosity (Hs. High correlations were found between deltaHi, deltaHs and the Ds of the parental breeds. Our results suggest that heterozygosity of the ten molecular markers used in this study may affect live weight during at least one growth phase. Parental genetic distance was a suitable predictor of the degree of progeny heterozygosity.

  19. Hypothermic machine preservation reduces molecular markers of ischemia/reperfusion injury in human liver transplantation.

    Science.gov (United States)

    Henry, S D; Nachber, E; Tulipan, J; Stone, J; Bae, C; Reznik, L; Kato, T; Samstein, B; Emond, J C; Guarrera, J V

    2012-09-01

    Hypothermic machine perfusion (HMP) is in its infancy in clinical liver transplantation. Potential benefits include diminished preservation injury (PI) and improved graft function. Molecular data to date has been limited to extrapolation of animal studies. We analyzed liver tissue and serum collected during our Phase 1 trial of liver HMP. Grafts preserved with HMP were compared to static cold stored (SCS) transplant controls. Reverse transcription polymerase chain reaction (RT-PCR), immunohistochemistry and transmission electron microscopy (TEM) were performed on liver biopsies. Expression of inflammatory cytokines, adhesion molecules and chemokines, oxidation markers, apoptosis and acute phase proteins and the levels of CD68 positive macrophages in tissue sections were evaluated. RT-PCR of reperfusion biopsy samples in the SCS group showed high expression of inflammatory cytokines, adhesion molecules and chemokines, oxidative markers and acute phase proteins. This upregulation was significantly attenuated in livers that were preserved by HMP. Immunofluorescence showed larger numbers of CD68 positive macrophages in the SCS group when compared to the HMP group. TEM samples also revealed ultrastructural damage in the SCS group that was not seen in the HMP group. HMP significantly reduced proinflammatory cytokine expression, relieving the downstream activation of adhesion molecules and migration of leukocytes, including neutrophils and macrophages when compared to SCS controls.

  20. Photosynthetic and Molecular Markers of CO2-mediated Photosynthetic Downregulation in Nodulated Alfalfa

    Institute of Scientific and Technical Information of China (English)

    (A)lvaro Sanz-Sáez; Gorka Erice; Iker Aranjuelo; Ricardo Aroca; Juan Manuel Ruíz-Lozano; Jone Aguirreolea; Juan José Irigoyen

    2013-01-01

    Elevated CO2 leads to a decrease in potential net photosynthesis in long-term experiments and thus to a reduction in potential growth.This process is known as photosynthetic downregulation.There is no agreement on the definition of which parameters are the most sensitive for detecting CO2 acclimation.In order to investigate the most sensitive photosynthetic and molecular markers of CO2 acclimation,the effects of elevated CO2,and associated elevated temperature were analyzed in alfalfa plants inoculated with different Sinorhizobium meliloti strains.Plants (Medicago sativa L.cv.Aragón) were grown in summer or autumn in temperature gradient greenhouses (TGG).At the end of the experiment,all plants showed acclimation in both seasons,especially under elevated summer temperatures.This was probably due to the lower nitrogen (N) availability caused by decreased N2-fixation under higher temperatures.Photosynthesis measured at growth CO2 concentration,rubisco in vitro activity and maximum rate of carboxylation were the most sensitive parameters for detecting downregulation.Severe acclimation was also related with decreases in leaf nitrogen content associated with declines in rubisco content (large and small subunits) and activity that resulted in a drop in photosynthesis.Despite the sensitivity of rubisco content as a marker of acclimation,it was not coordinated with gene expression,possibly due to a lag between gene transcription and protein translation.

  1. Molecular diversity of brinjal (Solanum melongena L. and S. aethiopicum L. genotypes revealed by SSR markers

    Directory of Open Access Journals (Sweden)

    Abdul Majid Ansari, and Y. V. Singh

    2014-12-01

    Full Text Available In the present study, simple sequence repeat (SSR markers were used to study the genetic diversity among 14 genotypes of brinjal. A total of 14 polymorphic SSR primer pairs were used. Amplification of genomic DNA of 14 genotypes yielded 50 fragments, of which 43 were polymorphic. A clear cut differentiation was exhibited among the genotypes. The range of similarity coefficient varied from 17.8% [between S. aethiopicum L. (2n=2x=24 and Pant Rituraj (S. melongena L., 2n=2x=24] to 94.1% [between PB-71 and NDB-1] followed by 88.9% [between SMB-115 and KS-331] and 88.6% [between BARI and PB-67]. SAHN cluster analysis using UPGMA method separated the genotypes into six cluster groups. Solanum aethiopicum and PB-67 were positioned as single genotype in separate groups i.e., cluster-I & II, SMB-115 and KS-331 in cluster-III, BARI, PB-66 and Pant Rituraj in cluster-IV, WB-1, PB-4, PB-70 and LC-7 in cluster-V and PB-71, Pant Samrat and NDB-1 in cluster-VI. Morphological characters viz., shape, size and peel colour of brinjal fruits and plant type showed a positive relationship with the DNA based molecular analysis through SSR markers.

  2. Transcriptome analysis in Concholepas concholepas (Gastropoda, Muricidae): mining and characterization of new genomic and molecular markers.

    Science.gov (United States)

    Cárdenas, Leyla; Sánchez, Roland; Gomez, Daniela; Fuenzalida, Gonzalo; Gallardo-Escárate, Cristián; Tanguy, Arnaud

    2011-09-01

    The marine gastropod Concholepas concholepas, locally known as the "loco", is the main target species of the benthonic Chilean fisheries. Genetic and genomic tools are necessary to study the genome of this species in order to understand the molecular basis of its development, growth, and other key traits to improve the management strategies and to identify local adaptation to prevent loss of biodiversity. Here, we use pyrosequencing technologies to generate the first transcriptomic database from adult specimens of the loco. After trimming, a total of 140,756 Expressed Sequence Tag sequences were achieved. Clustering and assembly analysis identified 19,219 contigs and 105,435 singleton sequences. BlastN analysis showed a significant identity with Expressed Sequence Tags of different gastropod species available in public databases. Similarly, BlastX results showed that only 895 out of the total 124,654 had significant hits and may represent novel genes for marine gastropods. From this database, simple sequence repeat motifs were also identified and a total of 38 primer pairs were designed and tested to assess their potential as informative markers and to investigate their cross-species amplification in different related gastropod species. This dataset represents the first publicly available 454 data for a marine gastropod endemic to the southeastern Pacific coast, providing a valuable transcriptomic resource for future efforts of gene discovery and development of functional markers in other marine gastropods.

  3. Detection and source identification of faecal pollution in non-sewered catchment by means of host-specific molecular markers.

    Science.gov (United States)

    Ahmed, W; Powell, D; Goonetilleke, A; Gardner, T

    2008-01-01

    Multiple host-specific molecular markers were used to detect the sources of faecal pollution in a mixed land use non-sewered catchment in Southeast Queensland, Australia. These markers included human-specific Bacteroides (HF183 and HF134), cattle-specific Bacteroides (CF128), dog-specific Bacteroides (BacCan) and human-specific enterococci surface protein (esp) markers. The sensitivity and specificity of these markers were determined by testing 197 faecal samples from 13 host groups. The overall sensitivity and specificity of these markers was high (sensitivity>/=85% and specificity>/=93%) indicating their suitability for detecting the sources of faecal pollution. Of the 16 samples collected from the study area, 14 (87%) were positive for at least one of the molecular marker tested. Amongst all the markers, cattle-specific CF128 was more prevalent than others, followed by human-specific HF183 which was consistently detected in samples collected from sites within close proximity to urban development. Significant correlations were found between E. coli and enterococci concentrations with the positive/negative results of human-specific Bacteroides HF183 (psources of human faecal pollution in surface waters in Southeast Queensland, Australia.

  4. Calretinin expression as a reliable prognostic marker in different molecular subtypes of breast carcinoma

    Directory of Open Access Journals (Sweden)

    Mayada Saad Farrag

    2017-01-01

    Full Text Available Background: Calretinin (CR, a known mesothelial marker, is expressed in both epithelial and mesenchymal malignancies including breast cancer. Aims: We aimed to measure the frequency of CR expression in correlation with other clinicopathological parameters of different molecular subtypes of invasive breast carcinoma and to study its prognostic implications in this common cancer.Study Design: Tissue microarrays were constructed from 225 tissue samples of breast carcinoma cases. Subjects and Methods: Immunostaining for CR in addition to estrogen receptors, progesterone receptors, human epidermal growth factor receptor 2 (HER2, epidermal growth factor receptor, CK5/6, and Ki-67 for molecular subtyping. Statistical Analysis Used: Chi-square and Fisher's exact tests were done using SPSS 18.0 software (IBM Inc.. Survival data were analyzed using Kaplan–Meier test, Log-rank test, and Cox proportional hazard models. Results: Cases of invasive breast carcinomas with different grades were classified into 84 luminal A, 45 luminal B, 27 HER2 positive, 40 basal-like, and 29 unclassified. High CR expression was associated with tumors of high grade (P < 0.0001, high locoregional recurrence (P = 0.005, hormonal receptors negative, and high Ki-67 indices. They frequently display a basal-like phenotype (70%, P < 0.0001, HER2 (59.3%, and luminal B (33.3% tumors compared to luminal A (9.5% and unclassified subtypes (17.2%. Moreover, it is associated with poor overall patient survival (P = 0.034, but it does not affect disease-free survival. Conclusions: Calretinin could be a reliable predictor marker of adverse prognosis in breast cancer.

  5. Chromosome composition and AFLP analysis of Pagrosomus major, Spraus macrocephalus and the hybirds%真鲷、黑鲷及其杂交子代的染色体构成与 AFLP 分析

    Institute of Scientific and Technical Information of China (English)

    林勉; 苗亮; 李明云; 俞寅寅; 徐万土

    2014-01-01

    In this paper,the karyotyping analysis and AFLP molecular marker technique were used to analyze the ge-netic differences among Pagrosomus major ,Sparus macrocephalus and the hybrids.The karyotype analysis showed that they all contained 48 chromosomes and the karyotypes were respectively:2n=2st+46t,NF=48;2n=4m+4sm+38t+2st,NF=56;2n=2st+8t+8sm+30m=48,NF=86.The karyotype of the hybrids was different from maternal and paternal species.AFLP analysis of P.major,S.macrocephalus and the hybrids showed that a total of 278 bands were obtained by 2 primer combinations,including 93 paternal species (S.macrocephalus)specific bands and 108 maternal species (P .major)specific bands.Among these parent specific bands,21 male parent specific bands and 67 female parent specific bands were detected in the hybrids.In addition,there were 15 nonparental bands appeared in the hybrids.Analysis of molecular variance revealed that the Nei's unbiased measures of genetic identity were 0.113 between the hybrids and S.macrocephalus and 0.350 between the hybrids and P .major,respectively. The Nei's unbiased measures of genetic distance were 2.180 between the hybrids and S.macrocephalus and 1.050 between the hybrids and P .major,respectively.This study indicated that the hybrids of P .major♀ and S.macro-cephalus♂ were heterologous diploid containing 48 chromosomes and the genetic material of maternal and paternal species was partly reorganized during the hybridization and showed a partially maternal hereditary characteristics.%采用核型分析和 AFLP 技术对真鲷、黑鲷及其杂交子代进行遗传差异分析。结果显示真鲷、黑鲷和杂交子代均含有48条染色体,核型分别为2n=2st+46t,NF=48、2n=4m+4sm+2st+38t,NF=56和2n=30m+8sm+2st+8t=48,NF=86,杂交子代核型与其父、母本种均不一致。两对 AFLP 选扩引物组合在真鲷、黑鲷和杂交子代中共扩增到278个条带,其中黑鲷特异性条带93

  6. Detection of inter-species contaminations in a cell line collection using isoenzymes and molecular markers

    Directory of Open Access Journals (Sweden)

    M. Ferarri

    2011-03-01

    Full Text Available As in human research, also in livestock species the use of continuous cell cultures is an important tool for the study of physiological and tissue developmental processes, as well as for immunological, virological and toxicological assays. This widespread use of animal cell cultures needs that quality control tests are systematically performed in order to evaluate the authenticity of the cells used. Cell cross-contamination (CCC can occur with cells from other species (interspecies contamination or with unrelated cells from the same species (intraspecies contamination. Several methods have been used to identify inter- and intraspecies CCC: isoenzyme profile (Nims, 1998, cytogenetic analysis (Macville et al., 1996, DNA fingerprinting (Stacey et al., 1992, and, more recently, PCR-based methods (Matsuo et al., 1999. Amplified Fragment Length Polymorphism (AFLP technology is a PCR-based technique (Vos et al., 1995 able to reveal polymorphism, with no need of prior sequence information or probe isolation..........

  7. Molecular characterization of arabica and Conilon coffee plants genotypes by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Ludymila Brandão Motta

    2014-10-01

    Full Text Available The molecular characterization of ten genotypes of the Coffea arabica plants and of seven genotypes of C. canephora having interesting features for coffee breeding programs was carried to select the parents for breeding. A total of 40 SSR and 29 ISSR primers were used. The primers generated a total of 331 (307 polymorphic and 24 monomorphic bands. Analysis of genetic diversity presented dissimilarity intervals ranging from 0.22 to 0.44 between the Conilon genotypes, from 0.02 to 0.28 between the Arabica genotypes, and from 0.49 to 0.60 between the genotypes of the two species in the joint analysis. Four groups were formed: I = genotypes of C. arabica, II = four progenies of C. canephora, Conilon group, and one non defined C. canephora (Conilon or Robusta, III = one progeny of un-defined C. canephora (Conilon or Robusta and IV = one progeny of C. canephora of Robusta group. The grouping formed was consistent with the origins of each group. High stabilities of the bifurcations were found by bootstrap analysis. The use of molecular markers of the SSR and ISSR types in the diversity study was efficient in distinguishing genotypes between and within C. arabica and C. canephora.

  8. Linkage mapping in tetraploid willows: segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba x Salix fragilis interspecific hybrids.

    Science.gov (United States)

    Barcaccia, G; Meneghetti, S; Albertini, E; Triest, L; Lucchin, M

    2003-02-01

    Salix alba-Salix fragilis complex includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of these willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Since nothing is known about their genomic constitution, tetraploidy (2n=4x=76) in willow species makes basic and applied genetic studies difficult. We have used a two-way pseudotestcross strategy and single-dose markers (SDMs) to construct the first linkage maps for both pistillate and staminate willows. A total of 242 amplified fragment length polymorphisms (AFLPs) and 50 selective amplifications of microsatellite polymorphic loci (SAMPL) markers, which showed 1:1 segregation in the F(1) mapping populations, were used in linkage analysis. In S. alba, 73 maternal and 48 paternal SDMs were mapped to 19 and 16 linkage groups covering 708 and 339 cM, respectively. In S. fragilis, 13 maternal and 33 paternal SDMs were mapped in six and 14 linkage groups covering 98 and 321 cM, respectively. For most cosegregation groups, a comparable number of markers linked in coupling and repulsion was identified. This finding suggests that most of chromosomes pair preferentially as occurs in allotetraploid species exhibiting disomic inheritance. The detection of 10 pairs of marker alleles from single parents showing codominant inheritance strengthens this hypothesis. The fact that, of the 1122 marker loci identified in the two male and female parents, the vast majority (77.5%) were polymorphic and as few as 22.5% were shared between parental species highlight that S. alba and S. fragilis genotypes are differentiated. The highly difference between S. alba- and S. fragilis-specific markers found in both parental combinations (on average, 65.3 vs 34.7%, respectively) supports the (phylogenetic) hypothesis that S. fragilis is derived from S. alba-like progenitors.

  9. Molecular markers from three organellar genomes unravel complex taxonomic relationships within the coralline algal genus Chiharaea (Corallinales, Rhodophyta).

    Science.gov (United States)

    Hind, Katharine R; Saunders, Gary W

    2013-05-01

    The use of molecular markers in taxonomic studies has become a standard practice in biology. However, consensus on which markers to use at the species level is lacking because evolutionary lineages show differences in divergence rates between organellar genomes. Ideally, researchers use multiple lines of evidence when first describing a species, such as the incorporation of several molecular markers from varied genomes (mitochondrion, plastid and nucleus). This study examined species boundaries in the red algal genus Chiharaea. We used five molecular markers, with at least one marker from each genome, coupled with thorough morphological analyses. We recognized three species in Chiharaea (C.americana, C. rhododactyla sp. nov., C. silvae) and two forms (C. americana f. americana and C. americana f. bodegensis (H.W. Johansen) stat. nov.). For C. americana f. americana and C. americana f. bodegensis differentiation based on morphological data was reflected in the plastid-encoded large subunit of RuBisCO (rbcL), but was not concordant with either the mitochondrial cytochrome c oxidase subunit 1 (COI-5P) or nuclear internal transcribed spacer (ITS) sequence data. We suggest that this discordance is indicative of ongoing hybridization and introgression between populations of C. americana f. americana and C. americana f. bodegensis. In addition, we used a PCR assay with ITS specific primers to amplify multiple ITS variants for collections assignable to C. americana indicating that there is genetic variability within ITS copies most likely due to introgression, crossing over and/or the retention of ancestral variants.

  10. Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland Cotton

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Using 219 F2 individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 in Gossypium hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat (SSR) markers. Compared with our tetraploid backboned molecular genetic map from a (TM-1xHai 7124)xTM-1 BC1 population, 17 of the 19 linkage groups were combined and anchored to 12 chromosomes (sub-genomes). Of these groups, four morphological marker genes in T586 had been mapped into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.

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

    Science.gov (United States)

    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.

  12. Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.

    Science.gov (United States)

    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.

  13. Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.

    Directory of Open Access Journals (Sweden)

    Haiming Han

    Full Text Available 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.

  14. Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridization between Betula pubescens and B. nana.

    Science.gov (United States)

    Eidesen, Pernille Bronken; Alsos, Inger Greve; Brochmann, Christian

    2015-08-01

    Birches (Betula spp.) hybridize readily, confounding genetic signatures of refugial isolation and postglacial migration. We aimed to distinguish hybridization from range-shift processes in the two widespread and cold-adapted species B. nana and B. pubescens, previously shown to share a similarly east-west-structured variation in plastid DNA (pDNA). We sampled the two species throughout their ranges and included reference samples of five other Betula species and putative hybrids. We analysed 901 individual plants using mainly nuclear high-resolution markers (amplified fragment length polymorphisms; AFLPs); a subset of 64 plants was also sequenced for two pDNA regions. Whereas the pDNA variation as expected was largely shared between B. nana and B. pubescens, the two species were distinctly differentiated at AFLP loci. In B. nana, both the AFLP and pDNA results corroborated the former pDNA-based hypothesis that it expanded from at least two major refugia in Eurasia, one south of and one east of the North European ice sheets. In contrast, B. pubescens showed a striking lack of geographic structuring of its AFLP variation. We identified a weak but significant increase in nuclear (AFLP) gene flow from B. nana into B. pubescens with increasing latitude, suggesting hybridization has been most frequent at the postglacial expansion front of B. pubescens and that hybrids mainly backcrossed to B. pubescens. Incongruence between pDNA and AFLP variation in B. pubescens can be explained by efficient expansion from a single large refugium combined with leading-edge hybridization and plastid capture from B. nana during colonization of new territory already occupied by this more cold-tolerant species.

  15. The development of 7E chromosome-specific molecular markers for Thinopyrum elongatum based on SLAF-seq technology.

    Directory of Open Access Journals (Sweden)

    Shiqiang Chen

    Full Text Available Thinopyrum elongatum is an important relative of wheat, it is favored by many researchers for the disease resistant genes that exist in its E genome. Some studies have showed that the 7E chromosome of Th. elongatum contains resistance genes related to Fusarium head blight and wheat rust. Therefore, developing 7E chromosome-specific molecular markers linked to resistance genes will provide an important tool for exploring and using the resistant genes of Th. elongatum. In addition, it would greatly contribute in the effort to cultivate disease-resistant wheat varieties. Featured in high throughput, high-accuracy and low-cost, SLAF-seq technology has been widely used in molecular breeding, system evolution, and germplasm resource detection. Based on SLAF-seq, 518 specific fragments on the 7E chromosome of Th. elongatum were successfully amplified. A total of 135 primers were designed according to 135 randomly selected fragments, and 89 specific molecular markers of Th. elongatum were developed, with efficiencies up to 65.9%. These markers were all detected in a variety of materials, and they are all proved to be specific and stable. These markers can be used not only for detecting the 7E chromosome of Th. elongatum but also for providing an important theoretical and practical basis for wheat breeding by marker-assisted selection (MAS. This paper reports the first application of SLAF-seq technology with a high success rate in developing specific molecular markers for Th. elongatum, providing a strong case for the application of this new technology.

  16. IDENTIFICATION OF PARAMECIUM BURSARIA SYNGENS THROUGH MOLECULAR MARKERS – COMPARATIVE ANALYSIS OF MITOCHONDRIAL CYTOCHROME C OXIDASE SUBUNIT I (COI

    Directory of Open Access Journals (Sweden)

    Patrycja Zagata

    2014-08-01

    Full Text Available The aim of this study is an identification of Paramecium bursaria syngens originating from different geographical locations and proving the correlation between distributions and belonging to any of five syngens. Ten strains of Paramecium bursaria belonging to five different syngens and strain of Paramecium multimicronucleatum were investigated using molecular marker — mitochondrial cytochrome c oxidase subunit I (COI. According to results, obtained in this study, using phylogenetic methods like Neighbor Joining (NJ and Maximum Likelihood (ML, relationship between analyzing strains through their clustering in clusters and correlation between strains belonging to any syngen and syngen’s distribution was confirmed. Phylograms constructed using NJ and ML methods revealed strains’ grouping in five clusters. Results which were obtained revealed usefulness of COI as a biomarker, which is important in identification of Paramecium bursaria syngens. This reports to a great potential of COI as a molecular marker and obtaining dependable results through combination of molecular methods with classical ones.

  17. Use of molecular markers for the study of wild fungus basidiomycetes

    Directory of Open Access Journals (Sweden)

    Blanca Estela Gómez Luna

    2012-09-01

    Full Text Available Molecular marker techniques in the study of wild basidiomycete, are increasingly applied to ecology projects, with special focus on analysis of genetic diversity. Often require specialized methods for extracting the DNA of organisms of natural environments, because of the complex compounds that are (carbohydrate polymers and contaminants from the environment (soil particles. Biological materials used were basidiocarps collected in the forest of Santa Rosa, Guanajuato. And mycelium isolated from these basidiocarps. In this work we used a DNA extraction method that allowed the PCR amplification, restriction enzyme digestion and Southern hybridization by non-radioactive method. The results were obtained: Amplification of the ITS1 region of ribosomal unit of the different species of Basidiomycetes. It was possible to observe the genetic diversity among different species of basidiomycetes and the mycelia. Furthermore, the results also suggest differences in DNA methylation between the vegetative mycelium and mycelium of basidiocarp. Finally it is noteworthy that there were no previous work on the application of methods of non-radioactive Southern hybridization for analysis of wild Basidiomycetes and this pioneering work in applying this technique.

  18. Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation

    Directory of Open Access Journals (Sweden)

    Wiid Ian JF

    2009-02-01

    Full Text Available Abstract Background Although the gene encoding for glutamine synthetase (glnA is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1 is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4 are not. Results In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved. Conclusion Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria.

  19. Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei

    Science.gov (United States)

    Yu, Yang; Zhang, Xiaojun; Liu, Jingwen; Li, Fuhua; Huang, Hao; Li, Yijun; Liu, Xiaolin; Xiang, Jianhai

    2015-01-01

    Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However, the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety, Kehai No. 1 (KH-1), from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province, which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group, five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group, four haplotypes were observed in the KH-1 group, whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis, the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.

  20. Molecular markers and imaging tools to identify malignant potential in Barrett’s esophagus

    Institute of Scientific and Technical Information of China (English)

    Michael; Bennett; Hiroshi; Mashimo

    2014-01-01

    Due to its rapidly rising incidence and high mortality, esophageal adenocarcinoma is a major public health concern, particularly in Western countries. The steps involved in the progression from its predisposing condition, gastroesophageal reflux disease, to its premalignant disorder, Barrett’s esophagus, and to cancer, are incompletely understood. Current screening and surveillance methods are limited by the lack of population-wide utility, incomplete sampling of standard biopsies, and subjectivity of evaluation. Advances in endoscopic ablation have raised the hope of effective therapy for eradication of high-risk Barrett’s lesions, but improvements are needed in determining when to apply this treatment and how to follow patients clinically. Researchers have evaluated numerous potential molecular biomarkers with the goal of detecting dysplasia, with varying degrees of success. The combination of biomarker panels with epidemiologic risk factors to yield clinical risk scoring systems is promising. New approaches to sample tissue may also be combined with these biomarkers for less invasive screening and sur-veillance. The development of novel endoscopic imaging tools in recent years has the potential to markedly improve detection of small foci of dysplasia in vivo. Current and future efforts will aim to determine the combination of markers and imaging modalities that will most effectively improve the rate of early detection of highrisk lesions in Barrett’s esophagus.

  1. Method of Constructing Core Collection for Malus sieversii in Xinjiang, China Using Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    ZHANG Chun-yu; CHEN Xue-sen; ZHANG Yan-min; YUAN Zhao-he; LIU Zun-chun; WANG Yan-ling; LIN Qun

    2009-01-01

    The method for constructing core collection of Malus sieversii based on molecular marker data was proposed. According to 128 SSR allele of 109 M. sieversii, an allele preferred sampling strategy was used to construct M. sieversii core collection, using the UPGMA (unweighted pair-group average method) cluster method according to Nei & Li, SM, and Jaccard genetic distances, by stepwise clustering, and compared with the random sampling strategy. The number of lost allele and t-test of Nei's gene diversity and Shannon's information index were used to evaluate the representative core collections. The results showed that compared with the random sampling strategy, allele preferred sampling strategy could construct more representative core collections. SM, Jaccard, and Nei & Li genetic distances had no significant difference for construction of M. sieversii core collection. SRAP (sequence-related amplified polymorphism) data and morphological data showed that allele preferred sampling strategy was a good sampling strategy for constructing core collection of M. sieversii. Allele preferred sampling strategy combined with SM, Jaccard, and Nei & Li genetic distances using stepwise clustering was the suitable method for constructing M. sieversii core collection.

  2. Pink berry grape (Vitis vinifera L.) characterization: Reflectance spectroscopy, HPLC and molecular markers.

    Science.gov (United States)

    Rustioni, Laura; De Lorenzis, Gabriella; Hârţa, Monica; Failla, Osvaldo

    2016-01-01

    Color has a fundamental role for the qualitative evaluation and cultivar characterization of fruits. In grape, a normally functional pigment biosynthesis leads to the accumulation of a high quantity of anthocyanins. In this work, 28 Vitis vinifera L. cultivars accumulating low anthocyanins in berries were studied to characterize the biosynthetic dysfunctions in both a phenotypic and genotypic point of view. Reflectance spectroscopy, HPLC profiles and molecular markers related to VvMybA1 and VvMybA2 genes allowed a detailed description of the pigment-related characteristics of these cultivars. Data were consistent concerning the heterozygosity of the non-functional allele in both investigated genes, resulting in a low colored phenotype as described by reflectance. However, the variability in berry colour among our samples was not fully explained by MybA locus, probably due to specific interferences among the biosynthetic pathways, as suggested by the anthocyanin profile variations detected among our samples. The results presented in this work confirmed the importance of the genetic background: grapes accumulating high levels of cyanidin-3-O-glucosides (di-substituted anthocyanin) are generally originated by white cultivar retro-mutations and they seem to preserve the anomalies in the flavonoid hydroxylases enzymes which negatively affect the synthesis of tri-substituted anthocyanins.

  3. Comparison of algorithms to infer genetic population structure from unlinked molecular markers.

    Science.gov (United States)

    Peña-Malavera, Andrea; Bruno, Cecilia; Fernandez, Elmer; Balzarini, Monica

    2014-08-01

    Identifying population genetic structure (PGS) is crucial for breeding and conservation. Several clustering algorithms are available to identify the underlying PGS to be used with genetic data of maize genotypes. In this work, six methods to identify PGS from unlinked molecular marker data were compared using simulated and experimental data consisting of multilocus-biallelic genotypes. Datasets were delineated under different biological scenarios characterized by three levels of genetic divergence among populations (low, medium, and high FST) and two numbers of sub-populations (K=3 and K=5). The relative performance of hierarchical and non-hierarchical clustering, as well as model-based clustering (STRUCTURE) and clustering from neural networks (SOM-RP-Q). We use the clustering error rate of genotypes into discrete sub-populations as comparison criterion. In scenarios with great level of divergence among genotype groups all methods performed well. With moderate level of genetic divergence (FST=0.2), the algorithms SOM-RP-Q and STRUCTURE performed better than hierarchical and non-hierarchical clustering. In all simulated scenarios with low genetic divergence and in the experimental SNP maize panel (largely unlinked), SOM-RP-Q achieved the lowest clustering error rate. The SOM algorithm used here is more effective than other evaluated methods for sparse unlinked genetic data.

  4. Confirmation of cross-fertilization using molecular markers in ornamental passion flower hybrids.

    Science.gov (United States)

    Conceição, L D H C S; Belo, G O; Souza, M M; Santos, S F; Cerqueira-Silva, C B M; Corrêa, R X

    2011-01-11

    Several interspecific Passiflora hybrids are produced in the northern hemisphere for the ornamental plant market. In Brazil, production of passion flower hybrids is limited to the introgression of genes into the main cultivated species, yellow passion fruit, to be used as rootstocks. Confirmation of hybridization in the initial developmental stage is important for breeding perennial and sub-perennial plants, such as passion flowers, reducing time and costs in plant stock maintenance. In order to obtain F₁ hybrids with ornamental potential, four species of Passiflora (P. alata, P. gardneri, P. gibertii, and P. watsoniana) from the Active Germplasm Bank at UESC were hybridized. Flower buds, in pre-anthesis, of the genitors were previously protected, and the female buds were emasculated. To confirm hybridization, the genomic DNA of the genitor species and the supposed hybrids was extracted and RAPD primers were used to obtain molecular markers and select passion flower interspecific hybrids. Eight primers were used to confirm hybrids derived from P. gardneri with P. alata, P. watsoniana with P. alata, P. watsoniana with P. gardneri, and P. gardneri with P. gibertii; 75, 50, 45, and 46% of the informative bands, respectively, confirmed the hybrid nature of these plants. The RAPD technique was effective in the early identification of hybrids; this will be useful for development of hybrid Passiflora progeny.

  5. Identification and Assessing the Cultivars of Laminaria Lamx.(Phaeophyceae) with Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    Cui-Juan SHI; Zi-Min HU; Ying-Jun HE; Yu-Ping ZOU; Da-Ming ZHANG; De-Lin DUAN

    2005-01-01

    Molecular markers were used to identify and assess cultivars ofLaminaria Lamx. and to delineate their phylogenetic relationships. Random amplified polymorphic DNA (RAPD) analysis was used for detection. After screening, 11 primers were selected and they yielded 133 bands in all, of which approximately 99.2% were polymorphic. The genetic distances between gametophytes ranged from 0.412 to 0.956.Two clusters were formed with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the simple matching coefficient. All cultivars of Laminaria japonica Aresch. used for breed ing in China fell into one cluster. L. japonica from Japan, L. saccharina (L.) Lam., and L. angustata Kjellm.formed the other cluster and showed higher genetic variation than L. japonica from China. Nuclear ribosomal DNA (rDNA) sequences, including internal transcribed spacers (ITS1 and ITS2) were studied and aligned. The nucleotides of the sequences ranged from 634 to 668, with a total of 692 positions including ITS1, ITS2, and the 5.8S coding region. The phylogenetic tree obtained by the neighbor-joining method favored, to some extent, the results revealed by RAPD analysis. The present study indicates that RAPD and ITS analyses could be used to identify and assess Laminaria germplasm and to distinguish some species and, even intraspecies, in Laminaria.

  6. Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

    Directory of Open Access Journals (Sweden)

    Matos Margarida

    2009-06-01

    Full Text Available Abstract Here we present a correction to our article "Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura". We have recently detected an error concerning the application of the Ln RH formula – a test to detect positive selection – to our microsatellite data. Here we provide the corrected data and discuss its implications for our overall findings. The corrections presented here have produced some changes relative to our previous results, namely in a locus (dsub14 that presents indications of being affected by positive selection. In general, our populations present less consistent indications of positive selection for this particular locus in both periods studied – between generations 3 and 14 and between generation 14 and 40 of laboratory adaptation. Despite this, the main findings of our study regarding the possibility of positive selection acting on that particular microsatellite still hold. As previously concluded in our article, further studies should be performed on this specific microsatellite locus (and neighboring areas to elucidate in greater detail the evolutionary forces acting on this specific region of the O chromosome of Drosophila subobscura.

  7. A comparison of molecular markers to detect Lutzomyia longipalpis naturally infected with Leishmania (Leishmania infantum

    Directory of Open Access Journals (Sweden)

    Kárita Cláudia Freitas-Lidani

    2014-07-01

    Full Text Available The aim of the present study was to detect natural infection by Leishmania (Leishmania infantum in Lutzomyia longipalpis captured in Barcarena, state of Pará, Brazil, through the use of three primer sets. With this approach, it is unnecessary to previously dissect the sandfly specimens. DNA of 280 Lu. longipalpis female specimens were extracted from the whole insects. PCR primers for kinetoplast minicircle DNA (kDNA, the mini-exon gene and the small subunit ribosomal RNA (SSU-rRNA gene of Leishmania were used, generating fragments of 400 bp, 780 bp and 603 bp, respectively. Infection by the parasite was found with the kDNA primer in 8.6% of the cases, with the mini-exon gene primer in 7.1% of the cases and with the SSU-rRNA gene primer in 5.3% of the cases. These data show the importance of polymerase chain reaction as a tool for investigating the molecular epidemiology of visceral leishmaniasis by estimating the risk of disease transmission in endemic areas, with the kDNA primer representing the most reliable marker for the parasite.

  8. Matrix metalloproteinases and their tissue inhibitors in gastric cancer as molecular markers

    Directory of Open Access Journals (Sweden)

    Clara L Sampieri

    2013-01-01

    Full Text Available Gastric cancer is a complex disease that involves a range of biological individuals and tumors with histopathological features. The pathogenesis of this disease is multi-factorial and includes the interaction of genetic predisposition with environmental factors. Gastric cancer is normally diagnosed in advanced stages where there are few alternatives to offer and the prognosis is difficult to establish. Metastasis is the leading cause of cancer deaths. Identification of key genes and signaling pathways involved in metastasis and recurrence could predict these events and thereby identify therapeutic targets. In this context, the extracellular matrix metalloproteinases (MMPs and their inhibitors (TIMPs represent a potential prognostic tool, because both genetic families regulate growth, angiogenesis, invasion, immune response, epithelial mesenchymal transition and cellular survival. Proteolytic parameters based on MMP/TIMP expression could be useful in the identification of patients with a high probability of developing distant metastases or peritoneal dissemination for each degree of histological malignancy. It is also probable that these parameters can allow improvement in the extent of surgery and dictate the most suitable therapy. We reviewed papers focused on human gastric epithelial cancer as a model and focus on the potential use of MMPs and TIMPs as molecular markers; also we include literature regarding gastric cancer risk factors, classification systems and MMP/TIMP regulation.

  9. Matrix metalloproteinases and their tissue inhibitors in gastric cancer as molecular markers.

    Science.gov (United States)

    Sampieri, Clara L; León-Córdoba, Kenneth; Remes-Troche, Jos Maria

    2013-01-01

    Gastric cancer is a complex disease that involves a range of biological individuals and tumors with histopathological features. The pathogenesis of this disease is multi-factorial and includes the interaction of genetic predisposition with environmental factors. Gastric cancer is normally diagnosed in advanced stages where there are few alternatives to offer and the prognosis is difficult to establish. Metastasis is the leading cause of cancer deaths. Identification of key genes and signaling pathways involved in metastasis and recurrence could predict these events and thereby identify therapeutic targets. In this context, the extracellular matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) represent a potential prognostic tool, because both genetic families regulate growth, angiogenesis, invasion, immune response, epithelial mesenchymal transition and cellular survival. Proteolytic parameters based on MMP/TIMP expression could be useful in the identification of patients with a high probability of developing distant metastases or peritoneal dissemination for each degree of histological malignancy. It is also probable that these parameters can allow improvement in the extent of surgery and dictate the most suitable therapy. We reviewed papers focused on human gastric epithelial cancer as a model and focus on the potential use of MMPs and TIMPs as molecular markers; also we include literature regarding gastric cancer risk factors, classification systems and MMP/TIMP regulation.

  10. Adverse biological effects of Milan urban PM looking for suitable molecular markers of exposure

    Directory of Open Access Journals (Sweden)

    Mantecca Paride

    2012-01-01

    Full Text Available The results presented summarise the ones obtained in the coordinated research project Tosca, which extensively analysed the impact of Milan urban PM on human health. The molecular markers of exposure and effects of seasonally and size-fractionated PMs (summer and winter PM10, PM2.5 were investigated in in vitro (human lung cell lines and in vivo (mice systems. The results obtained by the analyses of cytotoxic, pro-inflammatory and genotoxic parameters demonstrate that the biological responses are strongly dependent upon the PM samples seasonal and dimensional variability, that ultimately reflect their chemical composition and source. In fact summer PM10, enriched in crustal elements and endotoxins, was the most cytotoxic and pro-inflammatory fraction, while fine winter PMs induced genotoxic effects and xenobiotic metabolizing enzymes (like CYP1B1 production, likely as a consequence of the higher content in combustion derived particles reach in PAHs and heavy toxic metals. These outcomes outline the need of a detailed knowledge of the PMs physico-chemical composition on a local scale, coupled with the biological hazard directly associated to PM exposure. Apparently this is the only way allowing scientists and police-makers to establish the proper relationships between the respirable PM quantity/quality and the health outcomes described by clinicians and epidemiologists.

  11. Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers

    Indian Academy of Sciences (India)

    Alexandra V. Amosova; Lyudmila V. Zemtsova; Zoya E. Grushetskaya; Tatiana E. Samatadze; Galina V. Mozgova; Yadviga E. Pilyuk; Valentina T. Volovik; Natalia V. Melnikova; Alexandr V. Zelenin; Valentina A. Lemesh; Olga V. Muravenko

    2014-04-01

    The application of DNA intercalator 9-aminoacridine allowed us to increase the resolution of chromosome C-banding and DAPI-banding patterns and to investigate chromosomal polymorphism in karyotypes of seven spring and six winter rape varieties. It was shown that the pericentromeric and intercalary C-bands of most of the chromosomes in spring rape were smaller in size and less polymorphic than those of winter rape. More 26S and 5S rDNA sites were found in the winter rape karyotypes than the spring varieties. Separate or colocalized 26S and 5S rDNA sites were revealed on chromosomes 4, 5, 6, 8, 10, 14, 15, 16 and 18. Intervarietal and intravarietal polymorphism of the number and chromosomal localization of rDNA sites were detected. The generalized idiogram of chromosomes of 13 Brassica napus varieties with account of all possibilities of C-banding patterns as well as localization of 26S and 5S rDNA sites were constructed. Polymorphism of the examined molecular and cytogenetic markers as well as the heterozygosis level of FAE1.1 gene controlling erucic acid synthesis in rapeseed was higher in the winter varieties than in the spring ones. The obtained data were in a satisfactory agreement with increased tolerance to environmental stress conditions of winter rape.

  12. Screening of Molecular Virulence Markers in Staphylococcus aureus and Pseudomonas aeruginosa Strains Isolated from Clinical Infections

    Science.gov (United States)

    Cotar, Ani-Ioana; Chifiriuc, Mariana-Carmen; Dinu, Sorin; Bucur, Marcela; Iordache, Carmen; Banu, Otilia; Dracea, Olguta; Larion, Cristina; Lazar, Veronica

    2010-01-01

    Staphylococcus (S.) aureus and Pseudomonas (Ps.) aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new strategies in order to elucidate the different mechanisms used by these bacteria at different stages of the infectious process, providing the scientists with new procedures for preventing, or at least improving, the control of S. aureus and Ps. aeruginosa infections. The purpose of this study was to characterize the molecular markers of virulence in S. aureus and Ps. aeruginosa strains isolated from different clinical specimens. We used multiplex and uniplex PCR assays to detect the genes encoding different cell-wall associated and extracellular virulence factors, in order to evaluate potential associations between the presence of putative virulence genes and the outcome of infections caused by these bacteria. Our results demonstrate that all the studied S. aureus and Ps. aeruginosa strains synthesize the majority of the investigated virulence determinants, probably responsible for different types of infections. PMID:21614207

  13. Screening of Molecular Virulence Markers in Staphylococcus aureus and Pseudomonas aeruginosa Strains Isolated from Clinical Infections

    Directory of Open Access Journals (Sweden)

    Veronica Lazar

    2010-12-01

    Full Text Available Staphylococcus (S. aureus and Pseudomonas (Ps. aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new strategies in order to elucidate the different mechanisms used by these bacteria at different stages of the infectious process, providing the scientists with new procedures for preventing, or at least improving, the control of S. aureus and Ps. aeruginosa infections. The purpose of this study was to characterize the molecular markers of virulence in S. aureus and Ps. aeruginosa strains isolated from different clinical specimens. We used multiplex and uniplex PCR assays to detect the genes encoding different cell-wall associated and extracellular virulence factors, in order to evaluate potential associations between the presence of putative virulence genes and the outcome of infections caused by these bacteria. Our results demonstrate that all the studied S. aureus and Ps. aeruginosa strains synthesize the majority of the investigated virulence determinants, probably responsible for different types of infections.

  14. Characterizing the transcriptome and molecular markers information for roach, Rutilus rutilus

    Indian Academy of Sciences (India)

    Wei Chi; Xufa Ma; Jiangong Niu; Ming Zou

    2016-03-01

    Rutilus rutilus (roach) is native to most of Europe and western Asia, and the Irtysh River basin in Sinkiang, northwest Chinais the marginal area of their natural distribution. The wide distribution and unique characteristic of this species makes it anideal model for analysing ecological and comparative genomics. However, the limited genome sequences available for thisspecies have hindered these investigations. Transcriptomes from the brains and livers of five individuals collected from theIrtysh River basin were sequenced using Illumina paired-end sequencing technology. A collection of 132,289 unigenes for thisspecies were obtained using a de novo assembly method based on nearly 120 million clean reads encompassing more than 14Gb data. Approximately 37.5% (49,656), 27.1% (35,867) and 21.2% (27,987) of the transcriptome had homologues depositedin Nt, Nr and Swiss-Prot, respectively; 12.3% (16,328) were assigned to eukaryotic orthologous groups of proteins classifications,and 21.5% (28,429) harboured Interpro domains. On the basis of the assembled transcriptome, we detected 177,493single-nucleotide variation resident in 39.3% (52,029) of the sequences and 20.8% (27,497) of the sequences harbouring 36,639simple sequence repeats. The identified molecular markers are a basis for further ecological analysis, and the transcriptome reportedhere allows for more extensive evolutionary analyses of the Cyprinidae, the most species-rich family of freshwater fishes.

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

    Directory of Open Access Journals (Sweden)

    Salvador J. Diaz-Cano

    2012-02-01

    Full Text Available 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.

  16. Planarian (Platyhelminthes, Tricladida Diversity and Molecular Markers: A New View of an Old Group

    Directory of Open Access Journals (Sweden)

    Marta Álvarez-Presas

    2014-04-01

    Full Text Available Planarians are a group of free-living platyhelminths (triclads best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms.

  17. AFLP analysis of genetic diversity and relationship among some Chinese domestic ducks and wild ducks

    Institute of Scientific and Technical Information of China (English)

    YAN Feihuan; ZUO Zhenghong; CHEN Mei; SONG Yueqiang; L(U) Liangju; CHEN Yixin

    2006-01-01

    The amplified fragment length polymorphic(AFLP)technique was used to analyze the genome DNA polymorphism among 8 breeds of domestic ducks and 2 species of wild ducks.Nine of the 17 selected primers pairs gave reproducible polymorphic DNA amplification bands.The amplified bands ranged from 44 to 83 per primer pair.Of the 513 AFLP markers obtained.498 were polymorphic.The proportion of polymorphic loci was 97.1%.The genetic distance(D)and similarity coefficients(GS)were calculated based on the polymorphic data.Between domestic ducks D ranged from 0.331 to 0.589,while between domestic ducks and the wild ducks,it ranged from 0.298 to 0.520(vs.Anas Platyrhynchos)and from 0.316 to 0.522(vs.A.Poecilorhyncha),respectively.The variance analysis showed no significant difference between the two groups of data,which indicated that both mallard and spot-billed ducks made contributions to domestic duck evolution.A dendrogram was constructed according to the D value.

  18. Genetic variation of Porphyra yezoensis by using AFLP1

    Institute of Scientific and Technical Information of China (English)

    Rui Yang; Biqian Liu; Qijun Luo; Yajun Wang; Jiamei Bao

    2003-01-01

    Genetic variation of 11 lines of Porphyra yezoensis from the coastline of Kagoshima ofJapan, Qingdao, Nantong, Putuo and Nanji Islands of China were studied by using amplified fragmentlength polymorphism (AFLP). 778 bands were obtained with AFLP analysis of 16 primer combina-tions, among which 15 were unique, about 98.07% were polymorphic. The AFLP data showed thatthe closest genetic distance was 0.180 between two Kagoshima samples, and the farthest one was 0.397between Kagoshima No. 1 and Nantong No. 9 line. The genetic distance showed that the variation waswithin the inner species scope. Neighbor-joining cluster and UPGMA cluster indicated that samples fromKagoshima and Qingdao were with high similarity and either with the samples of Nantong, Putuo andNanji Islands. P. yezoensis in China shared high genetic diversity, and the genetic distance showed posi-tive correlation with the geographic distance.

  19. AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota

    Directory of Open Access Journals (Sweden)

    Vleeshouwers Vivianne GAA

    2008-05-01

    Full Text Available Abstract Background The secondary genepool of our modern cultivated potato (Solanum tuberosum L. consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date. The aim of the present study is to describe the structure present in section Petota. When possible, at least 5 accessions from each available species and 5 individual plants per accession (totally approx. 5000 plants were genotyped using over 200 AFLP markers. This resulted in the largest dataset ever constructed for Solanum section Petota. The data obtained are used to evaluate the 21 series hypothesis put forward by Hawkes and the 4 clade hypothesis of Spooner and co-workers. Results We constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with >69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana. Conclusion Most of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also

  20. [Development of a sex-specific molecular marker for Japanese hop Humulus japonicus Siebold & Zucc].

    Science.gov (United States)

    Aleksandrov, O S; Divashuk, M G; Karlov, G I

    2011-08-01

    Japanese hop (Humulus japonicus Siebold & Zucc.) is a dioecious plant and a suitable model for studying the XX/XY1Y2 system of sex chromosomes. To develop a sex-specific marker, 12 RAPD and 36 ISSR markers were analyzed on the basis of pools of male and female plants identified after flowering. We were the first to identify ISSR marker K-16, which manifested stable amplification of an approximately 300-bp fragment in male plants and the absence of amplification in female plants in the populations examined. Marker effectiveness was confirmed in several Japanese hop populations of different origin.

  1. Identification of Molecular Markers Linked to TuMV Resistant Gene in Cabbage

    Institute of Scientific and Technical Information of China (English)

    GAO Jinping; WANG Chao; LIU Ying

    2008-01-01

    A total of 144 F2 individuals were obtained from the crossing between 1047 (susceptible) and A21 (resistant).Two RAPD markers were screened out in 200 random primers using BSA(Bulked Segregant Analysis). Two RAPD markers, designated as AG13/2000 and U16/660,were 7.7 cM and 8.38 cM apart from the TuMV resistant gene,respectively. The two RAPD fragments were converted to SCAR markers.SCAR markers were confined in germplasm.

  2. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    Science.gov (United States)

    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.

  3. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L. A. Rich.

    Directory of Open Access Journals (Sweden)

    Rusama Marubodee

    Full Text Available 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.

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

    Science.gov (United States)

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

    2016-04-04

    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.

  5. Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.

    Directory of Open Access Journals (Sweden)

    Alexandra Olarte

    Full Text Available Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea.

  6. Molecular markers in management of ex situ PGR - A case study

    Indian Academy of Sciences (India)

    Andreas Börner; Elena K Khlestkina; Sabina Chebotar; Manuela Nagel; Mian Abdur Rehman Arif; Kerstin Neumann; Borislav Kobiljski; Ulrike Lohwasser; Marion S Röder

    2012-11-01

    Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of longterm-stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50 years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement.

  7. Molecular markers indicate different dynamics of leaves and roots during litter decomposition

    Science.gov (United States)

    Altmann, Jens; Jansen, Boris; Palviainen, Marjo; Kalbitz, Karsten

    2010-05-01

    lignin degradation. Preliminary results show, that we were able to distinguish the different species and plant parts using various approaches, e.g., abundance and patterns of different substances and different ratios of compounds. The polyesters suberin and cutin were particularly useful to differentiate between roots and leaves. We conclude that knowledge of the decomposition patterns of molecular markers will largely improve the identification power of organic matter sources in soils.

  8. The asphericity of the metabolic tumour volume in NSCLC: correlation with histopathology and molecular markers

    Energy Technology Data Exchange (ETDEWEB)

    Apostolova, Ivayla; Ego, Kilian; Steffen, Ingo G. [University Hospital, Otto-von-Guericke University Magdeburg, Clinic of Radiology and Nuclear Medicine, Magdeburg (Germany); Buchert, Ralph [University Medicine Charite, Clinic of Nuclear Medicine, Berlin (Germany); Wertzel, Heinz; Achenbach, H.J. [Lung Clinic Lostau GmbH, Lostau (Germany); Riedel, Sandra; Schreiber, Jens [University Hospital, Otto-von-Guericke University Magdeburg, Clinic of Pneumology, Magdeburg (Germany); Schultz, Meinald [Institute of Pathology Stendal, Stendal (Germany); Furth, Christian; Amthauer, Holger [University Hospital, Otto-von-Guericke University Magdeburg, Clinic of Radiology and Nuclear Medicine, Magdeburg (Germany); University Medicine Charite, Clinic of Nuclear Medicine, Berlin (Germany); Derlin, Thorsten [Hannover Medical School, Department of Nuclear Medicine, Hannover (Germany); Hofheinz, Frank [Helmholtz-Center Dresden-Rossendorf, Dresden (Germany); Kalinski, Thomas [University Hospital Magdeburg, Otto-von-Guericke University Magdeburg, Institute for Pathology, Magdeburg (Germany); Institute for Pathology Lademannbogen, Hamburg (Germany)

    2016-12-15

    overall survival. The ASP of primary NSCLCs on FDG PET images is associated with tumour dimensions and molecular markers of proliferation and angiogenesis. (orig.)

  9. Review of the molecular profile and modern prognostic markers for gastric lymphoma: how do they affect clinical practice?

    Science.gov (United States)

    Alevizos, Leonidas; Gomatos, Ilias P; Smparounis, Spyridon; Konstadoulakis, Manousos M; Zografos, Georgios

    2012-04-01

    Primary gastric lymphoma is a rare cancer of the stomach with an indeterminate prognosis. Recently, a series of molecular prognostic markers has been introduced to better describe this clinical entity. This review describes the clinical importance of several oncogenes, apoptotic genes and chromosomal mutations in the initiation and progress of primary non-Hodgkin gastric lymphoma and their effect on patient survival. We also outline the prognostic clinical importance of certain cellular adhesion molecules, such as ICAM and PECAM-1, in patients with gastric lymphoma, and we analyze the correlation of these molecules with apoptosis, angiogenesis, tumour growth and metastatic potential. We also focus on the host-immune response and the impact of Helicobacter pylori infection on gastric lymphoma development and progression. Finally, we explore the therapeutic methods currently available for gastric lymphoma, comparing the traditional invasive approach with more recent conservative options, and we stress the importance of the application of novel molecular markers in clinical practice.

  10. [Detection of an NA gene molecular marker in H7N9 subtype avian influenza viruses by pyrosequencing].

    Science.gov (United States)

    Zhao, Yong-Gang; Liu, Hua-Lei; Wang, Jing-Jing; Zheng, Dong-Xia; Zhao, Yun-Ling; Ge, Sheng-Qiang; Wang, Zhi-Liang

    2014-07-01

    This study aimed to establish a method for the detection and identification of H7N9 avian influenza viruses based on the NA gene by pyrosequencing. According to the published NA gene sequences of the avian influenza A (H7N9) virus, a 15-nt deletion was found in the NA gene of H7N9 avian influenza viruses. The 15-nt deletion of the NA gene was targeted as the molecular marker for the rapid detection and identification of H7N9 avian influenza viruses by pyrosequencing. Three H7N9 avian influenza virus isolates underwent pyrosequencing using the same assay, and were proven to have the same 15-nt deletion. Pyrosequencing technology based on the NA gene molecular marker can be used to identify H7N9 avian influenza viruses.

  11. Transmission of the Chromosome 1 R in Winter Wheat Germplasm Aimengniu and Its Derivatives Revealed by Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    ZHAO Chunhua; CUI Fa; ZONG Hao; WANG Yu-hai; BAO Yin-guang; HAO Yuan-feng; DU Bin; WANG Hong-gang

    2009-01-01

    In order to clarify the transmission of the rye chromosome 1R in winter wheat germplasm Aimengniu and its derivatives,17 derivatives and 7 types of Aimengniu were examined through molecular-marker technology.The results showed that the chromosome arm 1RS of Neuzucht was transmitted to 5 of the 7 types of Aimengniu,i.e.,Aimengniu II and Aimengniu Ⅳ-Aimengniu Ⅶ,no segment of 1RS was identified in Aimengniu Ⅰ or Aimengniu Ⅲ.As for the 17 derivatives,the 1RS chromosome arm of Aimengniu was transmitted to 11 derivatives,part segments of 1RS were found in 1 derivative,while no segment was found in the remaining 5 ones.The results provided the evidence that molecular-marker technology was an efficient approach and suitable for analysis of the transmission of chromosome 1R.

  12. Breeding Rice Restorer Lines with High Resistance to Bacterial Blight by Using Molecular Marker-Assisted Selection

    Institute of Scientific and Technical Information of China (English)

    DENG Qi-ming; WANG Shi-quan; ZHENG Ai-ping; ZHANG Hong-yu; LI Ping

    2006-01-01

    Two bacterial blight (BB) resistance genes, Xa21 and Xa4, from IRBB24 were introduced into hybrid rice restorer line Mianhui 725, which is highly susceptible to BB, by using hybridization and molecular marker-assisted selection technology. Four homologous restorer lines were obtained through testing the R target genes with molecular markers and analyzing parental genetic background. Inoculation of the four lines and their hybrids with the specific strains of Xanthomonas oryzae pv. oryzae, P1, P6 and seven representative strains of Chinese pathotype, C Ⅰ -CⅦ, showed that all of the four lines and their hybrids were highly resistant and presented broad resistance-spectrum to BB. The hybrids of G46A / R207-2 displayed good agronomic characters and high yield potential, and R207-2 was named Shuhui 207.

  13. Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

    Science.gov (United States)

    Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

    2015-05-25

    The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

  14. Molecular markers as a tool for breeding for flower longevity in Asiatic hybrid lilies.

    NARCIS (Netherlands)

    Meulen, van der J.J.M.; Oeveren, van J.C.; Sandbrink, J.M.; Tuyl, van J.M.

    1996-01-01

    Segregation of flower longevity in two lily populations was studied and the genetic linkage of morphological markers and RAPD markers with loci involved in flower longevity was investigated. A large variation in flower longevity was found within the two populations tested at individual plant level.

  15. 应用FISH-AFLP技术分析平欧杂种榛主栽品种的遗传关系%Analysis of the Genetic Relationship of the Main Cultivars of Ping’ou Hybrid Hazelnut (C. heterophylla×C. avellana) by FISH-AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    马庆华; 陈新; 赵天田; 刘庆忠; 王贵禧

    2013-01-01

    [目的]建立平欧杂种榛FISH-AFLP技术体系,并应用该技术分析平欧杂种榛主栽品种的遗传关系。[方法]以达维等10个主栽品种为试材,经 DNA 提取、PstⅠ/MseⅠ双酶切,进行 FISH-AFLP 反应,数据转换为“0-1”矩阵后,使用NTSYS pc 2.11F和Popgene 1.32软件进行数据分析并作图。[结果]从64对引物中,筛选出15对多态性强的PstⅠ/MseⅠ引物,共获得1739条谱带,引物平均多态带比率97.94%;平欧杂种榛主栽品种的相似性系数为0.7556-0.8543,当阈值为0.8398时,可分成4个AFLP群,其中,玉坠(84-310)、辽榛4号(85-41)和平欧69号(84-69)单独为1群,其他品种为1群;平欧杂种榛主栽品种的有效等位基因数、基因多样度、Shannon信息指数分别为1.3921、0.2482和0.3957,具有较高的遗传多样性;研究获得的特征条带可用于平欧杂种榛主栽品种的快速鉴别。[结论]由于平欧杂种榛的实生选优群体是多亲本组合的混合后代,因此,该群体是一个具有高度遗传多样性的群体,主栽品种间存在复杂的亲缘关系;研究构建的FISH-AFLP技术流程、筛选得到的引物以及分析得到的各项遗传参数,可为其他榛属植物的相关研究提供参考。%[Objective]The objective of this study is to establish FISH-AFLP analysis system for Ping’ou hybrid hazelnut and analyze the genetic relationship of the main cultivars.[Method]Ten main cultivars, such as Dawei, were selected as materials. High-quality genomic DNA was extracted with improved CTAB method, and the purified DNA samples were digested with PstⅠ/MseⅠ. After ligation reaction, the samples were used to perform FISH-AFLP detection. The information of all bands was converted into“0-1”matrix. NTSYS pc 2.11F and Popgene 1.32 software were used to conduct the data analysis and plotting.[Result]The results showed that:15 PstⅠ/MseⅠ primer pairs were selected from 64

  16. A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance

    Science.gov (United States)

    Sotero-Martins, Adriana; de Jesus, Michele Silva; Lacerda, Michele; Moreira, Josino Costa; Filgueiras, Ana Luzia Lauria; Barrocas, Paulo Rubens Guimarães

    2008-01-01

    The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains. PMID:24031221

  17. Rice seed identification by computerized AFLP-DNA fingerprinting

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ We developed a computerized seed identification system. Fifteen rice varieties that were widely used in China were analyzed by AFLP fingerprinting. 12 primer pairs were screened. In order to simplify the procedure and cut down the cost in seed identification, the least number of primer pairs for practical seed identification should be selected. In this study, 3 primer pairs were selected.

  18. Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

    NARCIS (Netherlands)

    Stölting, K.N.; Gort, G.; Wüst, C.; Wilson, A.B.

    2009-01-01

    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on th

  19. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers

    Indian Academy of Sciences (India)

    Mamta Gupta; Bhawna Verma; Naresh Kumar; Rakesh K. Chahota; Rajeev Rathour; Shyam K. Sharma; Sabhyata Bhatia; Tilak R. Sharma

    2012-12-01

    Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid ($2n = 2x = 14$), cool-season legume crop and is consumed worldwide as a rich source of protein (∼24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F2 plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.

  20. Genetic diversity analyses of Lasiodiplodia theobromae on Morus alba and Agave sisalana based on RAPD and ISSR molecular markers

    Directory of Open Access Journals (Sweden)

    Hong-hui Xie

    2016-10-01

    Full Text Available Genetic diversity of 23 Lasiodiplodia theobromae isolates on Morus alba and 6 isolates on Agave sisalana in Guangxi province, China, was studied by using random amplified polymorphic DNA and inter-simple sequence repeat molecular markers. Results of two molecular markers showed that the average percentage of polymorphic loci of all isolates was more than 93%. Both dendrograms of two molecular markers showed obvious relationship between groups and the geographical locations where those strains were collected, among which, the 23 isolates on M. alba were divided into 4 populations and the 6 isolates on A. sisalana were separated as a independent population. The average genetic identity and genetic distance of 5 populations were 0.7215, 0.3284 and 0.7915, 0.2347, respectively, which indicated that the genetic identity was high and the genetic distance was short in the 5 populations. Average value of the gene diversity index (H and the Shannon’s information index (I of 29 isolates were significantly higher than 5 populations which showed that genetic diversity of those isolates was richer than the populations and the degree of genetic differentiation of the isolates was higher. The Gst and Nm of 29 isolates were 0.4411, 0.6335 and 0.4756, 0.5513, respectively, which showed that the genetic diversity was rich in those isolates.

  1. Sex determination in 58 bird species and evaluation of CHD gene as a universal molecular marker in bird sexing.

    Science.gov (United States)

    Vucicevic, Milos; Stevanov-Pavlovic, Marija; Stevanovic, Jevrosima; Bosnjak, Jasna; Gajic, Bojan; Aleksic, Nevenka; Stanimirovic, Zoran

    2013-01-01

    The aim of this research was to test the CHD gene (Chromo Helicase DNA-binding gene) as a universal molecular marker for sexing birds of relatively distant species. The CHD gene corresponds to the aim because of its high degree of conservation and different lengths in Z and W chromosomes due to different intron sizes. DNA was isolated from feathers and the amplification of the CHD gene was performed with the following sets of polymerase chain reaction (PCR) primers: 2550F/2718R and P2/P8. Sex determination was attempted in 284 samples of 58 bird species. It was successful in 50 bird species; in 16 of those (Alopochen aegyptiacus, Ara severus, Aratinga acuticaudata, Bucorvus leadbeateri, Cereopsis novaehollandiae, Columba arquatrix, Corvus corax, C. frugilegus, Cyanoliseus patagonus, Guttera plumifera, Lamprotornis superbus, Milvus milvus, Neophron percnopterus, Ocyphaps lophotes, Podiceps cristatus, and Poicephalus senegalus), it was carried out for the first time using molecular markers and PCR. It is reasonable to assume that extensive research is necessary to define the CHD gene as a universal molecular marker for successful sex determination in all bird species (with exception of ratites). The results of this study may largely contribute to the aim.

  2. AFLP and single-strand conformation polymorphism studies of recombination in the entomopathogenic fungus Nomuraea rileyi.

    Science.gov (United States)

    Devi, Uma K; Reineke, Annette; Rao, Uma C Maheswara; Reddy, Nageswara Rao N; Khan, Akbar P Ali

    2007-06-01

    In most putative asexual fungi analysed through population genetic studies, recombination has been detected. However, the mechanism by which it is achieved is still not known. A parasexual cycle is known to occur in asexual fungi but there is no evidence, as yet, of its prevalence in natural populations. This study was undertaken to investigate the possibility of a parasexual cycle mediating recombination in the mitosporic fungus Nomuraea rileyi. The genotypic diversity in isolates sampled from an epizootic population from South India was studied through AFLP. The AFLP data were subjected to analysis of molecular variance (AMOVA) and cluster analysis. Great genetic variation was observed in the population including the isolates from a single insect. To assess the occurrence of recombination in the population, single-strand conformation polymorphism (SSCP) of partial regions of two mitochondrial (mt) genes (rRNA genes of LSU and SSU) and a nuclear gene (beta tubulin) was performed. The SSCP data were analysed using MP, the tree length permutation test, and multilocus analysis. Recombination was inferred from the SSCP analysis. The occurrence of isolates with diverse genotypes in a single insect; the fact that fungi multiply as hyphal bodies (cell wall-less) in the insect haemolymph; and the inference of recombination in mitochondrial genes (suggesting cytomixis), all indicate that recombination is accomplished by fusion of hyphal bodies of different isolates infecting the insect.

  3. Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences.

    Science.gov (United States)

    Lee, Heung-Ryul; Bae, Ik-Hyun; Park, Soung-Woo; Kim, Hyoun-Joung; Min, Woong-Ki; Han, Jung-Heon; Kim, Ki-Taek; Kim, Byung-Dong

    2009-01-31

    Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

  4. Sequence based polymorphic (SBP marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Sahu Binod B

    2012-01-01

    Full Text Available Abstract Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs for any genomic regions. Here a sequence based polymorphic (SBP marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0 was obtained by applying Illumina's sequencing by synthesis (Solexa technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0 genome sequence identified putative single nucleotide polymorphisms (SNPs throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for

  5. Status of biotechnology with emphasis on molecular techniques for mutation breeding in the Philippines

    Energy Technology Data Exchange (ETDEWEB)

    Lapade, A.G.; Nazarea, T.Y.; Veluz, A.M.S.; Marbella, L.J.; Nato, A.Q.; Coloma, C.B. Jr.; Asencion, A.B. [Philippine Nuclear Research Institute, Commonwealth Avenue, Quezon (Philippines)

    2002-02-01

    This paper summarizes the status of biotechnology with emphasis on molecular techniques for plant breeding in the Philippines. Several molecular and in-vitro culture techniques are integrated in plant breeding for crop improvement at PNRI, UPLB, IRRI and PhilRice. At IRRI, PCR techniques, RFLP and RAPD, PCR techniques, RFLP and RAPD were developed to establish high density molecular maps, determine breadth and diversity of germplasm and characterize alien introgression. The molecular maps have identified DNA sequence of resistance genes of HYVs and NPTs to abiotic and biotic stresses, the major achievement is the development of high density molecular maps in rice with at least 2000 markers. The biotechnology program at PhilRice for varietal improvement includes: (1) utilization of molecular marker technology such gene mapping of desired traits in rice, analysis of genetic relationships of germplasm materials and breeding lines through DNA fingerprinting and genetic diversity studies and development and application of marker aided selection for disease resistance (RTD and BLB); (2) application of in-vitro techniques in the development of lines with tolerance to adverse conditions; (3) molecular cloning of important genes for RTD resistance; (4) genetic transformation for male sterility and resistance to sheath blight and stem borers; and (5) transfer of disease resistance from wild species to cultivated varieties. In IPB, molecular markers:microsatellites or SSR, AFLP and RGA are being used for mapping and diversity studies in coconut, mango, banana, mungbean, corn and tomato. Mutation breeding at PNRI using gamma radiation has resulted in the development of crop varieties with desirable traits. The use of AFLP coupled to PCR is being used to study polymorphism in plant variants of radiation-induced mutants of rice, pineapple and ornamentals. (author)

  6. Identification of AFLP and SCAR Molecular Markers Linked to Bolting Trait in Radish%萝卜抽薹基因连锁的AFLP和SCAR分子标记鉴定

    Institute of Scientific and Technical Information of China (English)

    徐文玲; 王淑芬; 牟晋华; 王翠花; 刘贤娴

    2009-01-01

    本文运用AFLP分子标记技术,结合BSA法,对萝卜抽薹基因相连锁的AFLP分子标记进行研究,获得两个与萝卜耐抽薹基因相连锁的AFLP标记,遗传距离分别为14.6 cM和9.1 cM.序列测定和Blast分析表明,标记ACG-CAG(123 bp)与拟南芥中锌指蛋白3(zinc finger protein 3,ZFP3)的cDNA同源性为89%,期望值为6e-23;标记ACT-CTG(175 bp)与拟南芥中的Copia类反转录转座子AtRE1基因的同源性为83%,期望值为4e-42.并将其中一个标记转化为简单易行的SCAR标记,遗传距离为7.5 cM.

  7. An AFLP-based linkage map of Japanese red pine (Pinus densiflora) using haploid DNA samples of megagametophytes from a single maternal tree.

    Science.gov (United States)

    Kim, Yong-Yul; Choi, Hyung-Soon; Kang, Bum-Yong

    2005-10-31

    We have constructed an AFLP-based linkage map of Japanese red pine (Pinus densiflora Siebold et Zucc.) using haploid DNA samples of 96 megagametophytes from a single maternal tree, selection clone Kyungbuk 4. Twenty-eight primer pairs generated a total of 5,780 AFLP fragments. Five hundreds and thirteen fragments were verified as genetic markers with two alleles by their Mendelian segregation. At the linkage criteria LOD 4.0 and maximum recombination fraction 0.25(theta), a total of 152 markers constituted 25 framework maps for 19 major linkage groups. The maps spanned a total length of 2,341 cM with an average framework marker spacing of 18.4 cM. The estimated genome size was 2,662 cM. With an assumption of equal marker density, 82.2% of the estimated genome would be within 10 cM of one of the 230 linked markers, and 68.1% would be within 10 cM of one of the 152 framework markers. We evaluated map completeness in terms of LOD value, marker density, genome length, and map coverage. The resulting map will provide crucial information for future genomic studies of the Japanese red pine, in particular for QTL mapping of economically important breeding target traits.

  8. Use of molecular markers for predicting therapy response in cancer patients.

    LENUS (Irish Health Repository)

    Duffy, Michael J

    2012-02-01

    Predictive markers are factors that are associated with upfront response or resistance to a particular therapy. Predictive markers are important in oncology as tumors of the same tissue of origin vary widely in their response to most available systemic therapies. Currently recommended oncological predictive markers include both estrogen and progesterone receptors for identifying patients with breast cancers likely to benefit from hormone therapy, HER-2 for the identification of breast cancer patients likely to benefit from trastuzumab, specific K-RAS mutations for the identification of patients with advanced colorectal cancer unlikely to benefit from either cetuximab or panitumumab and specific EGFR mutations for selecting patients with advanced non-small-cell lung cancer for treatment with tyrosine kinase inhibitors such as gefitinib and erlotinib. The availability of predictive markers should increase drug efficacy and decrease toxicity, thus leading to a more personalized approach to cancer treatment.

  9. Genetic Diversity Assessment Across Different Genotypes Of Mungbean And Urdbean Using Molecular Markers

    Directory of Open Access Journals (Sweden)

    Ashwini Narasimhan , B.R.Patil and S. Datta, M. Kaashyap

    2010-07-01

    Full Text Available Pulses compliment the daily diet of Indians along with cereals. They are rich in proteins with satisfactory proportion ofcarbohydrates. Mungbean, Vigna radiata and Urd bean, Vigna mungo are the important grain legume crops in agriculture,particularly in India. MYMV (Mungbean Yellow vein Mosaic Virus is a virus transmitted by whitefly, Bemesia tabaci, themost serious disease of Mungbean and Urdbean. In this study, six each of MYMV resistant and susceptible genotypes inMungbean and Urbean respectively were selected for the diversity analysis using molecular markers. Twenty four RGAprimers from cowpea were used to screen the twenty four genotypes. Dendrogram generated clearly indicated two bigclusters at 15% similarity. All mungbean genotypes made one cluster (cluster A except PS16, which was included in othercluster made by Urdbean genotypes (cluster B. Cluster A contained eleven genotypes while cluster B contained thirteengenotypes. Cluster A and B were further classified into two sub clusters namely A1 and A2, B1 and B2 respectively. A1consisted of seven genotypes of which five were resistant (PANT MUNG 1, PANT MUNG 5, HUM 12, PUSA 9531, HUM1 and two were susceptible (TARM 2, KOPERGAON 3, while A2 comprised of remaining four genotypes in which threewere susceptible (TAP 7, SML 134 and SML 668, and one (AKM 8803 was resistant. Further, it was found that fourmungbean resistant genotypes of A1 namely Pant Mung1, Pant Mung5, HUM 12, and PUSA 9531 made one cluster at 55%similarity. Cluster B, again was subdivided into B1 and B2. B1 consisted a single genotype which was a cross between IPU99-25* SPS5 while, B2 consisted of the rest of the twelve genotypes. It was interesting to see that two resistant (IPU 02-33and IPU 6-02 and two susceptible (LBG 20 and T9 genotypes of Urd bean made separate cluster with a similarity of 99 percent and which indicated that though genotypes are differing at resistant locus, they are highly similar at all other loci.

  10. Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

    Directory of Open Access Journals (Sweden)

    Rivoltini Licia

    2009-06-01

    Full Text Available Abstract Supported by the Office of International Affairs, National Cancer Institute (NCI, the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc and the United States Food and Drug Administration (FDA to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers

  11. Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology.

    Science.gov (United States)

    Tahara, Hideaki; Sato, Marimo; Thurin, Magdalena; Wang, Ena; Butterfield, Lisa H; Disis, Mary L; Fox, Bernard A; Lee, Peter P; Khleif, Samir N; Wigginton, Jon M; Ambs, Stefan; Akutsu, Yasunori; Chaussabel, Damien; Doki, Yuichiro; Eremin, Oleg; Fridman, Wolf Hervé; Hirohashi, Yoshihiko; Imai, Kohzoh; Jacobson, James; Jinushi, Masahisa; Kanamoto, Akira; Kashani-Sabet, Mohammed; Kato, Kazunori; Kawakami, Yutaka; Kirkwood, John M; Kleen, Thomas O; Lehmann, Paul V; Liotta, Lance; Lotze, Michael T; Maio, Michele; Malyguine, Anatoli; Masucci, Giuseppe; Matsubara, Hisahiro; Mayrand-Chung, Shawmarie; Nakamura, Kiminori; Nishikawa, Hiroyoshi; Palucka, A Karolina; Petricoin, Emanuel F; Pos, Zoltan; Ribas, Antoni; Rivoltini, Licia; Sato, Noriyuki; Shiku, Hiroshi; Slingluff, Craig L; Streicher, Howard; Stroncek, David F; Takeuchi, Hiroya; Toyota, Minoru; Wada, Hisashi; Wu, Xifeng; Wulfkuhle, Julia; Yaguchi, Tomonori; Zeskind, Benjamin; Zhao, Yingdong; Zocca, Mai-Britt; Marincola, Francesco M

    2009-06-17

    Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that

  12. Evolutionary redefinition of immunoglobulin light chain isotypes in tetrapods using molecular markers

    OpenAIRE

    Das, Sabyasachi; Nikolaidis, Nikolas; Klein, Jan; Nei, Masatoshi

    2008-01-01

    The phylogenetic relationships of Ig light chain (IGL) genes are difficult to resolve, because these genes are short and evolve relatively fast. Here, we classify the IGL sequences from 12 tetrapod species into three distinct groups (κ, λ, and σ isotypes) using conserved amino acid residues, recombination signal sequences, and genomic organization of IGL genes as cladistic markers. From the distribution of the markers we conclude that the earliest extant tetrapods, the amphibians, possess thr...

  13. Applications of the green fluorescent protein as a molecular marker in environmental microorganisms.

    Science.gov (United States)

    Errampalli, D; Leung, K; Cassidy, M B; Kostrzynska, M; Blears, M; Lee, H; Trevors, J T

    1999-04-01

    In this review, we examine numerous applications of the green fluorescent protein (GFP) marker gene in environmental microbiology research. The GFP and its variants are reviewed and applications in plant-microbe interactions, biofilms, biodegradation, bacterial-protozoan interactions, gene transfer, and biosensors are discussed. Methods for detecting GFP-marked cells are also examined. The GFP is a useful marker in environmental microorganisms, allowing new research that will increase our understanding of microorganisms in the environment.

  14. Predictive molecular markers for EGFR-TKI in non-small cell lung cancer patients: new insights and critical aspects

    Directory of Open Access Journals (Sweden)

    Paola Ulivi

    2010-07-01

    Full Text Available In recent years, a number of novel agents have been investigated that target specific molecular pathways in non-small cell lung cancer (NSCLC. A great deal of effort has been focused on identifying specific markers that predict treatment response, given that a tailored approach would maximize both the therapeutic index and the cost-effectiveness. The epidermal growth factor receptor (EGFR pathway has emerged as a key regulator of cancer cell proliferation and invasion, and several specific EGFR inhibitors have been examined. Gefitinib and erlotinib are selective EGFR tyrosine kinase inhibitors (EGFR-TKIs, demonstrating good results in selected cases both in terms of objective response rate and of overall survival. At present, EGFR gene mutations are the best positive predictive factors for TKI therapy, and a number of other potential biomarkers are being investigated as additional positive or negative predictors of response. The correct selection of patients that could benefit from these innovative therapies, based on an accurate molecular characterization, is mandatory to provide the best clinical management. Currently, the main factor limiting the characterization of metastatic NSCLC patients is the small quantity of tumor cells available for molecular analysis. In this paper we provide an overview of the most important molecular predictive markers for EGFR-TKIs therapy in NSCLC patients, and focus attention on biological samples suitable for analysis and alternative sampling approaches such as plasma- or serum-derived DNA.

  15. Genetic Diversity of Tropical Hybrid Rice Germplasm Measured by Molecular Markers

    Institute of Scientific and Technical Information of China (English)

    HE Zhi-zhou; XIE Fang-ming; CHEN Li-yun; Madonna Angelita DELA PAZ

    2012-01-01

    Investigation of genetic diversity and relationships among breeding lines is of great importance to facilitate parent selection in hybrid rice breeding programs.In this study,we characterized 168 hybrid rice parents from International Rice Research Institute with 207 simple sequence repeat (SSR) and 353 single nucleotide polymorphism (SNP) markers.A total of 1 267 SSR and 706 SNP alleles were detected with the averages of 6.1 (SSR) and 2.0 (SNP) alleles per locus respectively across all lines.Based on the genetic distances estimated from the SSR and SNP markers separately and combined,the unrooted neighbor-joining cluster and STRUCTURE analyses consistently separated the 168 hybrid rice parents into two major groups:B-line and R-line,which is consistent with known parent pedigree information.The genetic distance matrices derived from the SSR and SNP genotyping were highly correlated (r=0.81,P 0.001),indicating that both of the SSR and SNP markers have distinguishable power to detect polymorphism and are appropriate for genetic diversity analysis among tropical hybrid rice parents.A subset of 60 SSR markers were also chosen by the Core Hunter with 368 alleles,and the cluster analysis based on the total and subset of SSR markers highly corresponded at r =0.91 (P < 0.001 ),suggesting that fewer SSR markers can be used to classify and evaluate genetic diversity among parental lines.

  16. Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers

    Directory of Open Access Journals (Sweden)

    Moradkhani Hoda

    2015-12-01

    Full Text Available The aim of this study is investigation the applicability of SSR and ISSR markers in evaluating the genetic relationships in twenty accessions of Aegilops and Triticum species with D genome in different ploidy levels. Totally, 119 bands and 46 alleles were detected using ten primers for ISSR and SSR markers, respectively. Polymorphism Information Content values for all primers ranged from 0.345 to 0.375 with an average of 0.367 for SSR, and varied from 0.29 to 0.44 with the average 0.37 for ISSR marker. Analysis of molecular variance (AMOVA revealed that 81% (ISSR and 84% (SSR of variability was partitioned among individuals within populations. Comparing the genetic diversity of Aegilops and Triticum accessions, based on genetic parameters, shows that genetic variation of Ae. crassa and Ae. tauschii species are higher than other species, especially in terms of Nei’s gene diversity. Cluster analysis, based on both markers, separated total accessions in three groups. However, classification based on SSR marker data was not conformed to classification according to ISSR marker data. Principal co-ordinate analysis (PCoA for SSR and ISSR data showed that, the first two components clarified 53.48% and 49.91% of the total variation, respectively. This analysis (PCoA, also, indicated consistent patterns of genetic relationships for ISSR data sets, however, the grouping of accessions was not completely accorded to their own geographical origins. Consequently, a high level of genetic diversity was revealed from the accessions sampled from different eco-geographical regions of Iran.

  17. Characterization of the miiuy croaker (Miichthys miiuy transcriptome and development of immune-relevant genes and molecular markers.

    Directory of Open Access Journals (Sweden)

    Rongbo Che

    Full Text Available BACKGROUND: The miiuy croaker (Miichthys miiuy is an important species of marine fish that supports capture fisheries and aquaculture. At present commercial scale aquaculture of this species is limited due to diseases caused by pathogens and parasites which restrict production and limit commercial value. The lack of transcriptomic and genomic information for the miiuy croaker limits the ability of researchers to study the pathogenesis and immune system of this species. In this study we constructed a cDNA library from liver, spleen and kidney which was sequenced using Illumina paired-end sequencing to enable gene discovery and molecular marker development. PRINCIPAL FINDINGS: In our study, a total of 69,071 unigenes with an average length of 572 bp were obtained. Of these, 45,676 (66.13% were successfully annotated in public databases. The unigenes were also annotated with Gene Ontology, Clusters of Orthologous Groups and KEGG pathways. Additionally, 498 immune-relevant genes were identified and classified. Furthermore, 14,885 putative simple sequence repeats (cSSRs and 8,510 putative single nucleotide polymorphisms (SNPs were identified from the 69,071 unigenes. CONCLUSION: The miiuy croaker (Miichthys miiuy transcriptome data provides a large resource to identify new genes involved in many processes including those involved in the response to pathogens and diseases. Furthermore, the thousands of potential cSSR and SNP markers found in this study are important resources with respect to future development of molecular marker assisted breeding programs for the miiuy croaker.

  18. Towards the Development of a Molecular Map in Switchgrass: I. Microsatellite Marker Development

    Energy Technology Data Exchange (ETDEWEB)

    Gunter, L.E.

    2001-08-23

    The long-term goal of the switchgrass breeding program is to improve regionally adapted varieties and increase biomass yield and feedstock quality. Although, to some extent, biomass yields are dependent on environmental constraints, increased yield can be achieved through the development of genotypes with improved seasonal adaptation, tolerance to unfavorable environmental conditions, and improved resistance to pest and disease. To date, improvement in switchgrass has relied on recurrent breeding strategies based on phenotypic or genotypic selection. Yield improvements have been modest by this method. If we expect to make significant increase in yields, we need tools that will allow us to map complex traits and uncover the genes that influence them. A genetic linkage map could be a powerful tool for accelerating switchgrass development through marker-assisted selection, breeding and recombination. This type of mapping requires the development of markers that can be associated with phenotypic traits in a population of known pedigree. The most commonly used markers for mapping include restriction fragment length polymorphisms (RFLP) and simple sequence repeats (SSR). At ORNL, we have been concentrating on the development of SSR markers, while our colleagues at the University of Georgia are developing RFLP markers in order to select parents to produce a mapping population and from there to create a framework map from {approx}100 F1 progeny.

  19. Dominant character of the molecular marker of a Biomphalaria tenagophila strain (Mollusca: Planorbidae resistant to Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Rosa Florence Mara

    2004-01-01

    Full Text Available Biomphalaria tenagophila population from Taim (state of Rio Grande do Sul, Brazil is totally resistant toSchistosoma mansoni, and presents a molecular marker of 350 bp by polymerase chain reaction and restriction fragment length polymorphism of the entire rDNA internal transcriber spacer. The scope of this work was to determine the heritage pattern of this marker. A series of cross-breedings between B. tenagophila from Taim (resistant and B. tenagophila from Joinville, state of Santa Catarina (susceptible was carried out, and their descendants F1 and F2 were submitted to this technique. It was possible to demonstrate that the specific fragment from Taim is endowed with dominant character, since the obtained segregation was typically mendelian.

  20. Genetic Variation Analyses of Apple Triploid Hybrid Progenies from‘Hanfu’ב4xGala’by ISSR and AFLP%‘寒富’ב四倍体嘎拉’苹果的三倍性杂交后代ISSR和AFLP分析

    Institute of Scientific and Technical Information of China (English)

    王玉霞; 李林光; 何平; 张丽杰; 董文轩

    2013-01-01

    Genetic variation of 7 triploid hybrid progenies of‘Hanfu’ב4xGala’ were investigated based on ISSR and AFLP molecular markers in this paper. The results showed that the percentage of polymorphic bands (PPB) of ISSR was 60.00%, observed number of alleles (Na) was 1.600, effective number of alleles (Ne) was 1.420, Nei's gene diversity (H) was 0.236 and Shannon's Information index (I) was 0.346. And these were lower than that of AFLP, which were 66.54%, 1.665, 1.421, 0.240 and 0.357. The UPMGA cluster showed that most of 7 triploid hybrid progenies were tend to the female parent‘Hanfu’ based on ISSR and AFLP. Compared with ISSR, AFLP is more useful to analyze the genetic diversity of apple triploid hybrid progenies, and these triploid hybrid progenies were maternal inheritance. And these results can provide a basis for parent selecting in triploid apple breeding.%  利用ISSR及AFLP分子标记技术研究了‘寒富’ב四倍体嘎拉’苹果的7份三倍性后代及其亲本的遗传变异。结果表明ISSR扩增得到的遗传多样性指数中扩增多态性比率(PPB)为60.00%,观察等位基因数(Na)为1.600,有效等位基因数(Ne)为1.420,Nei's基因多样性指数(H)为0.236,Shannon信息指数(I)为0.346;均小于AFLP扩增的遗传多样性指数66.54%、1.665、1.421、0.240和0.357。根据ISSR和AFLP得到的UPGMA聚类图显示这7份三倍性杂交后代倾向于母本‘寒富’。在三倍性苹果遗传多样性检测上AFLP优于ISSR,且这7份三倍性新种质在遗传上倾向于母本遗传。为三倍性苹果育种的亲本选择提供依据。

  1. Molecular markers of nuclear restoration gene Rf1 in sunflower using bulked segregant analysis-RAPD

    Institute of Scientific and Technical Information of China (English)

    季静; 王罡; E.Belhassen; H.Serieys; A.Berville

    1996-01-01

    Restoration of cytoplasmic male sterility (CMS) in sunflower was demonstrated to be controlled by polygenes by analysing 982 effective crosses among 109 self-crossed lines and 16 CMS lines. Two self-crossed lines and one CMS line with distinct genotypes were applied to creation of segregating populations for DNA bulks of the target gene Rfl. Bulked DNA was prepared in order to investigate single gene Rfl and its gene marker among polygenic characters at the same genetic background. Using 80 10-mer operon primers, 620 RAPD reactions were carried out between fertile and sterile DNA bulks. In about 800 loci, primary results showed that 8 were related to the restoration genes. Furthermore. 2 were confirmed as RAPD markers for gene Rfl by examining 9 maintenance and 7 restoration lines. This method is the improvement for bulked segregant analysis[1] with which markers of single gene of target can be identified rapidly among polygenic characters.

  2. Development of ITS sequence based molecular marker to distinguish, Tribulus terrestris L. (Zygophyllaceae) from its adulterants.

    Science.gov (United States)

    Balasubramani, Subramani Paranthaman; Murugan, Ramar; Ravikumar, Kaliamoorthy; Venkatasubramanian, Padma

    2010-09-01

    Tribulus terrestris L. (Zygophyllaceae) is one of the highly traded raw drugs and also used as a stimulative food additive in Europe and USA. While, Ayurvedic Pharmacopoeia of India recognizes T. terrestris as Goksura, Tribulus lanuginosus and T. subramanyamii are also traded by the same name raising issues of quality control. The nuclear ribosomal RNA genes and ITS (internal transcribed spacer) sequence were used to develop species-specific DNA markers. The species-specific markers efficiently amplified 295bp for T. terrestris (TT1F and TT1R), 300bp for T. lanuginosus (TL1F and TL1R) and 214bp for T. subramanyamii (TS1F and TS1R). These DNA markers can be used to distinguish T. terrestris from its adulterants.

  3. Agrobiodiversity in Cucurbita spp. landraces collected in Rio de Janeiro assessed by molecular markers

    Directory of Open Access Journals (Sweden)

    Marilene Hilma dos Santos

    2012-01-01

    Full Text Available Diversity and genetic relationship in forty landraces of Cucurbita spp. collected at small farms in Rio de Janeiro, Brazil, were analyzed by RAPD and ISSR markers, using 20 and 15 primers, respectively. Both markers were efficient to cluster the accessions separating among species, but not so much to the detection of intra-specific variability, considering the event of different pairs of accessions comprising null genetic distances observed for both markers in C. moschata. Low values observed for genetic distance among the C. moschata landraces showed that most likely genetic losses is in progress in that region of cultivation due to anthropic and market pressure, which are stimulating the small farmers to abandon their local varieties in order to use commercial seeds, including hybrids, which is causing risk of genetic erosion.

  4. Inheritance and molecular markers for the seed coat color in Brassica juncea

    Institute of Scientific and Technical Information of China (English)

    Mingli YAN; Zhongsong LIU; Chunyun GUAN; Sheyuan CHEN; Mouzhi YUAN; Xianjun LIU

    2009-01-01

    To elucidate the inheritance of seed coat color in Brassica juncea, Sichuan Yellow inbred (PY) was crossed with the Ziyejie inbred, and their F1 F2 and BC1 and BC2 progenies, derived from backcrossing to PY, were phenotyped for seed coat color. Results showed that the yellow seed coat was controlled by two independent recessive loci. Seven brown-seeded near-isogenic lines were developed by successive backcrosses to PY and by selfing. One of the BC6>F2 populations segregated for a single locus controlling seed coat color was used for mapping. Using the 88 primer pairs from sequence-related amplified polymorphism and the 500 random primers, two markers were found to be linked to the gene for brown seed coat, which were designated as SCM57 and SCM1078. The crossover between these markers and the brown seed coat loci was 2.35% and 7.06%, respectively. A sequence characterized amplified region (SCAR) marker according to Negi et al. (2000), designated as SZ1-331, was found to be linked to the gene for brown seed coat, with a cross-over estimate of 2.35%. The markers were located on the same side of the brown seed coat loci and 2.41, 7.51 and 2.41 cM away from the brown seed coat locus. The seven brown-seeded near-isogenic lines were classified into two groups by three DNA markers. They were located at the same linkage group of the marker RA2-All previously published by Padmaja et al. (2005).

  5. Investigating the KLF4 Gene Expression as a New Molecular Marker in Breast Tumors

    Directory of Open Access Journals (Sweden)

    MA Hosseinpour Feizi

    2013-12-01

    Results: The results showed that: 1 KLF4 is over expressed in Breast tumors rather than adjacent normal tissues. 2 KLF4 is an oncogene in breast tumors (at least in IDC type. 3 The KLF4 expression levels are related significantly with nature of malignant breast tumors. Conclusion: Findings do not confirm KLF4 as a diagnostic marker in classification and identification of tumoral tissues from non-tumoral ones in breast, but we can use this marker to identify at least 50% of invasive Ductal Carcinoma in breast and utilize it as a potential predictive factor to demonstrate severity degree in various tumors.

  6. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics

    DEFF Research Database (Denmark)

    Harper, Andrea L.; McKinney, Lea Vig; Nielsen, Lene Rostgaard;

    2016-01-01

    is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity...... panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co...

  7. Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

    Science.gov (United States)

    Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

    2014-09-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

  8. Small renal masses: The molecular markers associated with outcome of patients with kidney tumors 7 cm or less

    Science.gov (United States)

    Spirina, L. V.; Usynin, Y. A.; Kondakova, I. V.; Yurmazov, Z. A.; Slonimskaya, E. M.; Pikalova, L. V.

    2016-08-01

    The investigation of molecular mechanisms of tumor cell behavior in small renal masses is required to achieve the better cancer survival. The aim of the study is to find molecular markers associated with outcome of patients with kidney tumors 7 cm or less. A homogenous group of 20 patients T1N0M0-1 (mean age 57.6 ± 2.2 years) with kidney cancer was selected for the present analysis. The content of transcription and growth factors was determined by ELISA. The levels of AKT-mTOR signaling pathway components were measured by Western blotting analysis. The molecular markers associated with unfavorable outcome of patients with kidney tumors 7 cm or less were high levels of NF-kB p50, NF-kB p65, HIF-1, HIF-2, VEGF and CAIX. AKT activation with PTEN loss also correlated with the unfavorable outcome of kidney cancer patients with tumor size 7 cm or less. It is observed that the biological features of kidney cancer could predict the outcome of patients.

  9. Association Mapping in Turkish Olive Cultivars Revealed Significant Markers Related to Some Important Agronomic Traits.

    Science.gov (United States)

    Kaya, Hilal Betul; Cetin, Oznur; Kaya, Hulya Sozer; Sahin, Mustafa; Sefer, Filiz; Tanyolac, Bahattin

    2016-08-01

    Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree.

  10. Genetic Differentiation between Natural and Hatchery Stocks of Japanese Scallop (Mizuhopecten yessoensis as Revealed by AFLP Analysis

    Directory of Open Access Journals (Sweden)

    Zhan-Jiang Liu

    2010-10-01

    Full Text Available Japanese scallop (Mizuhopecten yessoensis is a cold-tolerant bivalve that was introduced to China for aquaculture in 1982. In this study, amplified fragment length polymorphism (AFLP markers were used to investigate levels of genetic diversity within M. yessoensis cultured stocks and compare them with wild populations. Six pairs of primer combinations generated 368 loci among 332 individuals, in four cultured and three wild populations. High polymorphism at AFLP markers was found within both cultured and wild M. yessoensis populations. The percentage of polymorphic loci ranged from 61.04% to 72.08%, while the mean heterozygosity ranged from 0.2116 to 0.2596. Compared with wild populations, the four hatchery populations showed significant genetic changes, such as lower expected heterozygosity and percentage of polymorphic loci, and smaller frequency of private alleles, all indicative of a reduction in genetic diversity. Some genetic structures were associated with the geographical distribution of samples; with all samples from Dalian and Japan being closely related, while the population from Russia fell into a distinct clade in the phylogenetic analysis. The genetic information derived from this study indicated that intentional or accidental release of selected Japanese scallops into natural sea areas might result in disturbance of local gene pools and loss of genetic variability. We recommend monitoring the genetic variability of selected hatchery populations to enhance conservation of natural Japanese scallop resources.

  11. Prevalence of molecular markers of Plasmodium falciparum drug resistance in Dakar, Senegal

    Directory of Open Access Journals (Sweden)

    Wurtz Nathalie

    2012-06-01

    Full Text Available Abstract Background As a result of the widespread resistance to chloroquine and sulphadoxine-pyrimethamine, artemisinin-based combination therapy (ACT (including artemether-lumefantrine and artesunate-amodiaquine has been recommended as a first-line anti-malarial regimen in Senegal since 2006. Intermittent preventive treatments with anti-malarial drugs based on sulphadoxine-pyrimethamine are also given to children or pregnant women once per month during the transmission season. Since 2006, there have been very few reports on the susceptibility of Plasmodium falciparum to anti-malarial drugs. To estimate the prevalence of resistance to several anti-malarial drugs since the introduction of the widespread use of ACT, the presence of molecular markers associated with resistance to chloroquine and sulphadoxine-pyrimethamine was assessed in local isolates at the military hospital of Dakar. Methods The prevalence of genetic polymorphisms in genes associated with anti-malarial drug resistance, i.e., Pfcrt, Pfdhfr, Pfdhps and Pfmdr1, and the copy number of Pfmdr1 were evaluated for a panel of 174 isolates collected from patients recruited at the military hospital of Dakar from 14 October 2009 to 19 January 2010. Results The Pfcrt 76T mutation was identified in 37.2% of the samples. The Pfmdr1 86Y and 184F mutations were found in 16.6% and 67.6% of the tested samples, respectively. Twenty-eight of the 29 isolates with the 86Y mutation were also mutated at codon 184. Only one isolate (0.6% had two copies of Pfmdr1. The Pfdhfr 108N/T, 51I and 59R mutations were identified in 82.4%, 83.5% and 74.1% of the samples, respectively. The double mutant (108N and 51I was detected in 83.5% of the isolates, and the triple mutant (108N, 51I and 59R was detected in 75.3%. The Pfdhps 437G, 436F/A and 613S mutations were found in 40.2%, 35.1% and 1.8% of the samples, respectively. There was no double mutant (437G and 540E or no quintuple mutant (Pfdhfr 108N, 51I and 59R

  12. Marcadores moleculares na predição do sexo em plantas de mamoeiro Molecular markers for sex identification in papaya

    Directory of Open Access Journals (Sweden)

    Eder Jorge de Oliveira

    2007-12-01

    Full Text Available O objetivo deste trabalho foi validar marcadores moleculares, previamente identificados como ligados ao sexo do mamoeiro, para utilização na seleção indireta em genótipos comerciais. Foram analisadas duas variedades do grupo Solo e dois híbridos do grupo Formosa, com utilização de 20 plantas por genótipo, quatro marcadores do tipo SCAR (Sequence Characterized Amplified Region e um RAPD (Random Amplified Polymorphic DNA. O RAPD BC210 permitiu a identificação de todas as plantas femininas e hermafroditas, o que revela grande potencial para ser usado na seleção assistida em alguns dos genótipos mais cultivados no Brasil. Os marcadores do tipo SCAR não permitiram a identificação correta do sexo dos genótipos, pois detectou-se a presença de falso-positivos e falso-negativos nas análises.The objective of this work was the validation of previous discovered sex related molecular markers of papaya, aiming at the indirect selection of Brazilian commercial genotypes. Two varieties of the Solo group and two hybrids of the Formosa group (20 plants for genotype, four SCAR (Sequence Characterized Amplified Region and one RAPD (Random Amplified Polymorphic DNA markers were used. All hermaphrodite and female plants were correctly predicted by RAPD BC210, showing its high potential for marker assisted selection in important commercial genotypes used in Brazil. The SCAR markers did not show the true sex identification of these genotypes, revealing the presence of false positives and negatives in the analyses.

  13. Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers

    NARCIS (Netherlands)

    Kijewski, T.; Zmietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.

    2011-01-01

    The genetic constitution of mussels (Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction b

  14. A clinical, cytogenetic, FISH and molecular study of supernumerary marker 15 chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Dennis, N.R. [Princess Anne Hospital, Southampton (United Kingdom); Crolla, J.A.; Harvey, J.F. [Salisbury District Hospital (United Kingdom)

    1994-09-01

    We studied 17 patients with supernumerary marker chromosomes shown by fluorescent in situ hybridization (FISH) with the 15-centromere specific probe pTRA-25 to be 15-derived. Genetic constitution of the marker chromosomes was investigated using FISH, Southern blot analysis and PCR for proximal and distal loci on 15q as well as conventional cytogenetics. Eight of the 17 patients were mentally retarded. Six of the eight carried a de novo marker 15 containing one or two doses of loci known to be in or near the Prader-Willi/Angelman (PWS/AS) region, whereas none of the nine non-retarded patients had duplications of this region, and only two of the eight whose parents were available had a de novo marker. None of the mentally retarded patients had PWS or AS. In two retarded patients (one de novo, one familial) there was no duplication of the PWS/AS region. Uniparental disomy affecting the normal 15 homologs was excluded in 10 of the patients, including all eight with mental retardation.

  15. Molecular markers in circulating tumour cells from metastatic colorectal cancer patients.

    Science.gov (United States)

    Gazzaniga, Paola; Gradilone, Angela; Petracca, Arianna; Nicolazzo, Chiara; Raimondi, Cristina; Iacovelli, Roberto; Naso, Giuseppe; Cortesi, Enrico

    2010-08-01

    The prognosis of metastatic cancer patients is still largely affected by treatment failure, mainly due to drug resistance. The hypothesis that chemotherapy might miss circulating tumour cells (CTCs) and particularly a subpopulation of more aggressive, stem-like CTCs, characterized by multidrug resistance, has been recently raised. We investigated the prognostic value of drug resistance and stemness markers in CTCs from metastatic colorectal cancer patients treated with oxaliplatin (L-OHP) and 5-fluoruracil (5-FU) based regimens. Forty patients with metastatic colorectal cancer were enrolled. CTCs were isolated from peripheral blood and analysed for the expression of aldheyde dehydrogenase 1 (ALDH1), CD44, CD133 (used as markers of stemness), multidrug resistance related protein 5 (MRP5 used as marker of resistance to 5-FU and L-OHP) and survivin (used as a marker of apoptosis resistance). CTCs were found in 27/40 (67%) patients. No correlation was found between the expression of either CD44 and CD133 in CTCs and the outcome of patients, while a statistically significant shorter progression-free survival was found in patients with CTCs positive for the expression of ALDH1, survivin and MRP5. These results support the idea that isolating survivin and MRP5+ CTCs may help in the selection of metastatic colorectal cancer patients resistant to standard 5-FU and L-OHP based chemotherapy, for which alternative regimens may be appropriate.

  16. Identification of differentiation-stage specific molecular markers for the osteoblastic phenotype

    DEFF Research Database (Denmark)

    Twine, Natalie; Chen, Li; Wilkins, Marc;

    The phenotype of osteoblastic (OB) cells in culture is currently defined using a limited number of markers of low sensitivity and specificity which belong mostly to extracellular matrix proteins. Also, for clinical use of human skeletal (mesenchymal) stem cells (hMSC) in bone regeneration, there ...

  17. 18F-FDG PET Imaging of Murine Atherosclerosis: Association with Gene Expression of Key Molecular Markers

    OpenAIRE

    2012-01-01

    AIM: To study whether (18)F-FDG can be used for in vivo imaging of atherogenesis by examining the correlation between (18)F-FDG uptake and gene expression of key molecular markers of atherosclerosis in apoE(-/-) mice. METHODS: Nine groups of apoE(-/-) mice were given normal chow or high-fat diet. At different time-points, (18)F-FDG PET/contrast-enhanced CT scans were performed on dedicated animal scanners. After scans, animals were euthanized, aortas removed, gamma counted, RNA extracted from...

  18. Molecular Markers of Diabetic Retinopathy: Potential Screening Tool of the Future?

    Science.gov (United States)

    Pusparajah, Priyia; Lee, Learn-Han; Abdul Kadir, Khalid

    2016-01-01

    Diabetic retinopathy (DR) is among the leading causes of new onset blindness in adults. Effective treatment may delay the onset and progression of this disease provided it is diagnosed early. At present retinopathy can only be diagnosed via formal examination of the eye by a trained specialist, which limits the population that can be effectively screened. An easily accessible, reliable screening biomarker of diabetic retinopathy would be of tremendous benefit in detecting the population in need of further assessment and treatment. This review highlights specific biomarkers that show promise as screening markers to detect early diabetic retinopathy or even to detect patients at increased risk of DR at the time of diagnosis of diabetes. The pathobiology of DR is complex and multifactorial giving rise to a wide array of potential biomarkers. This review provides an overview of these pathways and looks at older markers such as advanced glycation end products (AGEs), inflammatory markers, vascular endothelial growth factor (VEGF) as well as other newer proteins with a role in the pathogenesis of DR including neuroprotective factors such as brain derived neurotrophic factor (BDNF) and Pigment Epithelium Derived Factor (PEDF); SA100A12, pentraxin 3, brain natriuretic peptide, apelin 3, and chemerin as well as various metabolites such as lipoprotein A, folate, and homocysteine. We also consider the possible role of proteins identified through proteomics work whose levels are altered in the sera of patients with DR as screening markers though their role in pathophysiology remains to be characterized. The role of microRNA as a promising new screening marker is also discussed. PMID:27313539

  19. Linkage mapping of the Mediterranean cypress, Cupressus sempervirens, based on molecular and morphological markers.

    Science.gov (United States)

    Manescu, C; Hamamouch, N; Maios, C; Harfouche, A; Doulis, A G; Aravanopoulos, F A

    2011-08-30

    Gene mapping for a Cupressus species is presented for the first time. Two linkage maps for the Mediterranean cypress (Cupressus sempervirens) varieties, C. sempervirens var. horizontalis and C. sempervirens var. pyramidalis, were constructed following the pseudo-testcross mapping strategy and employing RAPD, SCAR and morphological markers. A total of 427 loci (425 RAPDs, two SCARs) representing parents and F(1) progeny were screened for polymorphism with 32 random decamer and two SCAR primers. A morphological marker defined as "crown form" was also included. Of 274 polymorphic loci, the 188 that presented Mendelian inheritance formed the mapping dataset. Of these loci, 30% were mapped into seven linkage groups for the horizontalis (maternal) and four linkage groups for the pyramidalis (paternal) map. The putative "crown form" locus was included in a linkage group of both maps. The horizontalis and the pyramidalis maps covered 160.1 and 144.5 cM, respectively, while genome length was estimated to be 1696 cM for the former variety and 1373 cM for the latter. The four RAPD markers most tightly linked to crown form were cloned and converted to SCARs. Each of the cloned RAPD markers yielded two to three different sequences behaving as co-migrating fragments. Two SCAR markers, SC-D05(432) and SC-D09(667), produced amplified bands of the expected sizes and maintained linkage with the appropriate phenotype, but to a lesser extent compared to their original RAPD counterparts. These linkage maps represent a first step towards the localization of QTLs and genes controlling crown form and other polygenic traits in cypress.

  20. Molecular Markers of Diabetic Retinopathy: Potential Screening Tool of the Future?

    Directory of Open Access Journals (Sweden)

    Priyia ePusparajah

    2016-06-01

    Full Text Available Diabetic retinopathy (DR is among the leading causes of new onset blindness in adults. Effective treatment may delay the onset and progression of this disease provided it is diagnosed early. At present retinopathy can only be diagnosed via formal examination of the eye by a trained specialist, which limits the population that can be effectively screened. An easily accessible, reliable screening biomarker of diabetic retinopathy would be of tremendous benefit in detecting the population in need of further assessment and treatment. This review highlights specific biomarkers that show promise as screening markers to detect early diabetic retinopathy or even to detect patients at increased risk of DR at the time of diagnosis of diabetes. The pathobiology of DR is complex and multifactorial giving rise to a wide array of potential biomarkers. This review provides an overview of these pathways and looks at older markers such as advanced glycation end products(AGEs, inflammatory markers, vascular endothelial growth factor (VEGF as well as other newer proteins with a role in the pathogenesis of DR including neuroprotective factors such as brain derived neurotrophic factor (BDNF and Pigment Epithelium Derived Factor (PEDF; SA100A12, pentraxin 3, brain natriuretic peptide, apelin 3 and chemerin as well as various metabolites such as lipoprotein A, folate and homocysteine. We also consider the possible role of proteins identified through proteomics work whose levels are altered in the sera of patients with DR as screening markers though their role in pathophysiology remains to be characterized. The role of microRNA as a promising new screening marker is also discussed.

  1. AFLP analysis of nephthytis (Syngonium podophyllum Schott) selected from somaclonal variants.

    Science.gov (United States)

    Chen, J; Henny, R J; Devanand, P S; Chao, C T

    2006-01-01

    This study analyzed genetic differences of 19 cultivars selected from somaclonal variants of Syngonium podophyllum Schott along with their parents as well as seven additional Syngonium species and six other aroids using amplified fragment length polymorphism (AFLP) markers generated by 12 primer sets. Among the 19 somaclonal cultivars, 'Pink Allusion' was selected from 'White Butterfly'. Tissue culture of 'Pink Allusion' through organogenesis resulted in the development of 13 additional cultivars. Self-pollination of 'Pink Allusion' obtained a cultivar, 'Regina Red Allusion', and tissue culture propagation of 'Regina Red Allusion' led to the release of five other cultivars. The 12 primer sets generated a total of 1,583 scorable fragments from all accessions, of which 1,284 were polymorphic (81.9%). The percentages of polymorphic fragments within 'White Butterfly' and 'Regina Red Allusion' groups, however, were only 1.2% and 0.4%, respectively. Jaccard's similarity coefficients among somaclonal cultivars derived from 'White Butterfly' and 'Regina Red Allusion', on average, were 0.98 and 0.99, respectively. Seven out of the 15 cultivars from the 'White Butterfly' group and three out of six from the 'Regina Red Allusion' group were clearly distinguished by AFLP analysis as unique fragments were associated with respective cultivars. The unsuccessful attempt to distinguish the remaining eight cultivars from the 'White Butterfly' group and three from the 'Regina Red Allusion' group was not attributed to experimental errors or the number of primer sets used; rather it is hypothesized to be caused by DNA methylation and/or some rare mutations. This study also calls for increased genetic diversity of cultivated Syngonium as they are largely derived from somaclonal variants.

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

    Directory of Open Access Journals (Sweden)

    Jingli Wei

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  4. Extracción de ADN y una prueba inical de primers en Pinus pseudostrobus Lindl. Para marcadores AFLP

    OpenAIRE

    2010-01-01

    Se desarrollo un método de extracción de ADN simple, rápido y de alto rendimiento para Pinus pseudostrobus Lindl. del área semillera establecida en Jerahuaro, Michoacán para la producción de semilla de calidad. Se implementaron herramientas moleculares (AFLP) para identificar su relación genética inter-especie. Es muy importante contar con el protocolo de extracción y purificación de ADN estandarizado para la especie de interés, debido a que este proceso constituye una etapa clave en todos lo...

  5. Lowering Grain Amylose Content in Backcross Offsprings of indica Rice Variety 057 by Molecular Marker-Assisted Selection

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shi-lu; NI Da-hu; YI Cheng-xin; LI Li; WANG Xiu-feng; WANG Zong-yang; YANG Jian-bo

    2005-01-01

    To lower the amylose content (AC) of the indica rice restorer line 057 with high AC, backcrosses were made respectively by using four indica varieties (R367, 91499, Yanhui 559, Hui 527) as low AC donor parents and 057 as the recurrent parent. A molecular marker (PCR-Acc I) was used to identify the genotypes (GG, TT and GT) of the waxy (Wx) gene. Plants with GT genotype were selected and used as female parent and crossed with 057 to advance generation. The ACs of rice grains harvested from plants with different Wx genotypes were measured and compared to analyze the efficiency of marker-assisted selection. The ACs of the rice grain, harvested from the plants of Wx genotypes GG, GT and TT, were higher than 20%, in the range of 17.7-28.5%, and less than 18%, respectively. The PCR-Acc I marker could be used for efficiently lowering the AC of 057 through backcrossing, and there were some influence of parental genetic background on the AC of rice grains with the same Wx genotype.

  6. Molecular marker for screening yellow mosaic disease resistance in blackgram [Vigna mungo (L. Hepper

    Directory of Open Access Journals (Sweden)

    L.Prasanthi, B.V.Bhaskara Reddy, B.Geetha, Ramya Jyothi and Abhishek

    2013-06-01

    Full Text Available Yellow mosaic disease is a serious disease in blackgram which causes severe yield losses. Screening of 45 lines along with PU-31 and PU-19 resistant checks for YMD under field conditions with artificial inoculation, identified 19 lines having 1 score with no disease symptoms. PCR reactions using SCAR marker for screening the disease reaction with genomic DNA of these lines resulted in identification of 19 resistant sources with specific amplification for resistance to YMV at 532bp with SCAR 20F/20R developed from OPQ1 RARD primer linked to YMV disease. Considering the YMV reaction and resistance linked SCAR marker, it is possible to identify the new resistance sources in a short time and they can be utilized in breeding programme or for direct release.

  7. Analysis and identification of SCAR molecular markers associated with birch fiber length trait

    Institute of Scientific and Technical Information of China (English)

    WANG Dan; WEI Zhi-gang; YANG Chuan-ping; LIU Guan-jun

    2008-01-01

    The fiber length trait (FLT) of 538 individuals from nature birch population in Maorshan region,Heilongjang,China were measured,of which 100 individuals were selected as representative variety of correlated fragments screening with random amplified polymorphism DNA (RAPD) technique.In total of 20 RAPD primers were tested through multiple regression analysis between amplified strip and the character behaviors,and a correlative segment BFLR-16 was obtained.The correlation coefficient between BFLI-16 and FLT was 0.6144,with the significant level of 1%.BFLI-16 was then cloned,sequenced and transformed into SCAR marker.The percentage of identifying long fiber birches by this SCAR was more than 92.The result indicates that the SCAR markers has high specificity for the long fiber individuals and is highly linked with the gene controlling the character of fiber length,and its existence is significantly correlative with the increase in the fiber length.

  8. Molecular markers detect stable genomic regions underlying tomato fruit shelf life and weight

    Directory of Open Access Journals (Sweden)

    Guillermo Raúl Pratta

    2011-01-01

    Full Text Available Incorporating wild germplasm such as S. pimpinellifolium is an alternative strategy to prolong tomato fruit shelf life(SL without reducing fruit quality. A set of recombinant inbred lines with discrepant values of SL and weight (FW were derived byantagonistic-divergent selection from an interspecific cross. The general objective of this research was to evaluate Genotype x Year(GY and Marker x Year (MY interaction in these new genetic materials for both traits. Genotype and year principal effects and GYinteraction were statistically significant for SL. Genotype and year principal effects were significant for FW but GY interaction wasnot. The marker principal effect was significant for SL and FW but both year principal effect and MY interaction were not significant.Though SL was highly influenced by year conditions, some genome regions appeared to maintain a stable effect across years ofevaluation. Fruit weight, instead, was more independent of year effect.

  9. Application of molecular markers for variety protection of ryegrass (Lolium perenne L.)

    DEFF Research Database (Denmark)

    Jensen, Louise Bach; Deneken, Gerhard; Roulund, N

    2008-01-01

    legislation complies with the Convention of the International Union for the Protection of New Varieties of Plants (UPOV 1991). The corner stone of the UPOV system is that in order to qualify for protection, a newly bred plant variety has to be shown to be distinct (D), uniform (U) and stable (S...... data and the morphological data, indicating that SSR markers can be used for variety identification in ryegrass....

  10. Molecular Markers in Peripheral Blood of Iranian Women with Breast Cancer

    OpenAIRE

    Oloomi, Mana; Bouzari, Saeid; Mohagheghi, Mohammad-Ali; Khodayaran-Tehrani, Hamideh

    2012-01-01

    A biomarker is a quantifiable laboratory measure of a disease specific biologically relevant molecule that can act as an indicator of a current or future disease state. The purpose of this study is to detect the expression of RNA biomarkers using Cytokeratin 19 (CK-19), Mammaglobin (MAM), Carcinoembryonic antigen (CEA), Mucin (MUC), C-Myc, erb-B2, a proliferation marker (Ki-67), Epidermal growth factor receptor (Her2/neu) and Estrogen receptor (ER) in Iranian women who were diagnosed with bre...

  11. Supernumerary marker chromosomes derived from chromosome 6: cytogenetic, molecular cytogenetic, and array CGH characterization.

    Science.gov (United States)

    Huang, Bing; Pearle, Phyllis; Rauen, Katherine A; Cotter, Philip D

    2012-07-01

    Supernumerary marker chromosomes (SMC) are relatively common in prenatal diagnosis. As the clinical outcomes vary greatly, a better understanding of the karyotype-phenotype correlation for different SMCs will be important for genetic counseling. We present two cases of prenatally detected de novo, small SMCs. The markers were present in 80% of amniocyte colonies in Case 1 and 38% of the colonies in Case 2. The SMCs were determined to be derived from chromosome 6 during postnatal confirmation studies. Although the sizes and the chromosomal origin of the SMCs in these two cases appeared to be similar, the clinical outcomes varied. The clinical manifestations observed in Case 1 included small for gestational age, feeding difficulty at birth, hydronephrosis, deviated septum and dysmorphic features, while the phenotype is apparently normal in Case 2. Array comparative genomic hybridization (CGH) was performed and showed increase in dosage for approx