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Primer Combinations (primer + combination)
Kinds of Primer Combinations Selected AbstractsSequence-related amplified polymorphism, an effective molecular approach for studying genetic variation in Fasciola spp. of human and animal health significanceELECTROPHORESIS, Issue 2 2009Qiao-Yan Li Abstract In the present study, a recently described molecular approach, namely sequence-related amplified polymorphism (SRAP), which preferentially amplifies ORFs, was evaluated for the studies of genetic variation among Fasciola hepatica, Fasciola gigantica and the "intermediate" Fasciola from different host species and geographical locations in mainland China. Five SRAP primer combinations were used to amplify 120 Fasciola samples after ten SRAP primer combinations were evaluated. The number of fragments amplified from Fasciola samples using each primer combination ranged from 12 to 20, with an average of 15 polymorphic bands per primer pair. Fifty-nine main polymorphic bands were observed, ranging in size from 100 to 2000,bp, and SRAP bands specific to F. hepatica or F. gigantica were observed. SRAP fragments common to F. hepatica and the "intermediate" Fasciola, or common to F. gigantica and the "intermediate" Fasciola were identified, excised and confirmed by PCR amplification of genomic DNA using primers designed based on sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair-group method with arithmetic averages clustering algorithm categorized all of the examined representative Fasciola samples into three groups, representing the F. hepatica, the "intermediate" Fasciola, or the F. gigantica. These results demonstrated the usefulness of the SRAP technique for revealing genetic variability between F. hepatica, F. gigantica and the "intermediate" Fasciola, and also provided genomic evidence for the existence of the "intermediate" Fasciola between F. hepatica and F. gigantica. This technique provides an alternative and a useful tool for the genetic characterization and studies of genetic variability in parasites. [source] Nestling sex ratios in a population of Bluethroats Luscinia svecica inferred from AFLPÔ analysisJOURNAL OF AVIAN BIOLOGY, Issue 1 2000S. Questiau We studied the sex ratio of Bluethroat Luscinia svecica broods using AFLPs. Our aim was to test whether there is a bias towards males that could be explained by sexual selection theories, or conversely, a bias towards females that could help explain the female-biased sex ratio among juveniles observed at a wintering site. The AFLP technique was reliable in sexing the nestlings from even small initial DNA quantities. Given the large number of polymorphic markers that can be obtained for each primer combination, the probability of detecting a W-chromosome-linked fragment is reasonably high. As a consequence, this method could be used in other species for sex-ratio studies and for other genetic purposes. Among 246 nestlings, we found an overall proportion of males of 50.8% at hatching and the sex-ratio variation using broods as independent units was not significantly different from expectation under a binomial distribution. None of the parental and environmental variables tested changed significantly the deviance to the model. Thus, sex determination in the Bluethroat seems to match the classical Mendelian model of a 1:1 sex ratio and cannot explain the biased sex ratio towards juvenile females found at the wintering site. [source] Genetic diversity in pollen beetles (Meligethes aeneus) in Sweden: role of spatial, temporal and insecticide resistance factorsAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 4 2007Nadiya Kazachkova Abstract 1,Pollen beetles Meligethes aeneus are pests of oilseed Brassica crops that are subject to intensive chemical control. Resistance to pyrethroids has been reported. Although this insect is of great economic importance, little is known about its genetic properties and population structure. 2,Amplified fragment length polymorphism (AFLP) analysis with the restriction endonuclease combination EcoRI and PstI was performed on 133 samples of groups of three pollen beetles collected during 2001,04 from five different provinces of Sweden. Both susceptible and resistant insects were studied. Using one primer combination, more than 450 polymorphic DNA fragments were obtained and, in total, four primer combinations were used for analysis. A subsample of 59 single beetles was analysed using one primer combination. 3,AFLP profiles were analysed by similarity measures using the Nei and Li coefficient and Neighbour-joining dendrograms were generated. The dendrogram built using 133 samples showed three distinct groups, each containing beetles representing one generation. Statistical analysis using analysis of molecular variance of single beetle samples showed no evidence of significant genetic difference between resistant and susceptible beetles. Instead, a clear difference between samples, depending on time of collection and generation, was observed. 4,The expected regional population structure, although statistically significant, explained little of the variation. The levels of genetic variation within populations were very high. There appears to be a high rate of gene flow between pollen beetle populations. The implications of this in the context of insecticide resistance are discussed. [source] The usefulness of amplified fragment length polymorphism markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizardsMOLECULAR ECOLOGY, Issue 3 2002R. Ogden Abstract Fine-level taxon discrimination is important in biodiversity assessment and ecogeographical research. Genomic markers are often required for studies on closely related taxa, however, most existing mitochondrial and nuclear markers require prior knowledge of the genome and are impractical for use in small conservation projects. This study describes the application of amplified fragment length polymorphism (AFLP) to discriminate at four progressively finer evolutionary levels of Caribbean Anolis lizards from the central Lesser Antilles. AFLP is shown to be a rapid and effective method for discriminating between species. Separation increases with primer pair number and choice of primer combination appears to be noncritical. Initial population-level results show markedly less discriminatory power. A screening technique for the identification of population informative markers combining principal component and principal coordinate analyses is presented and assessed. Subsequent results show selected conspecific AFLP data to be remarkably congruent with those of mitochondrial DNA, microsatellite and morphological markers. The use of AFLP as a low-cost nuclear marker in species-level taxon discrimination is supported, whereas population level application demands further consideration. [source] Integration of AFLP markers into an RFLP-based map of durum wheatPLANT BREEDING, Issue 5 2000C. Lotti Abstract Amplified fragment length polymorphism (AFLP) is a powerful technique which can readily be applied to a wide range of species for mapping purposes. AFLPs were added to a linkage map of durum wheat constructed using restriction fragment length polymorphisms (RFLPs). The mapping population included 65 recombinant inbred lines derived from a cross between the durum wheat cultivar ,Messapia' and accession ,MG4343' of the wild Triticum turgidum ssp. dicoccoides (Körn.). Genomic DNA was digested with MseI (4-cutter) and Sse83871 (8-cutter). Using a silver-staining protocol, 14 primer combinations revealed 421 clearly scorable amplicons including 100 polymorphisms. The presence of nine pairs of bands linked in repulsion phase with each pair generated by one primer combination suggested the presence of codominant alleles; sequence analysis of four band pairs confirmed their codominant nature. The integration of 80 AFLP loci extended the map in several telomeric regions, reduced the size of four large gaps present in the previous map, and eliminated one gap. The new map obtained after the inclusion of the 80 AFLP loci and eight additional RFLP loci spans 2063cM which represent a 52.6% increment compared with the previous map. Compared with the distribution of RFLPs, no significant clustering of AFLP markers was observed. [source] Genetic variability of Old Portuguese bread wheat cultivars assayed by IRAP and REMAP markersANNALS OF APPLIED BIOLOGY, Issue 3 2010A. Carvalho Retrotransposons (RTNs) constitute informative molecular markers for plant species as a result of their ability of integrating into a multitude of loci throughout the genome and thereby generating insertional polymorphisms between individuals. Inter-retrotransposon amplified polymorphisms (IRAPs) and the retrotransposon-microsatellite amplified polymorphisms (REMAPs) are marker systems based on long terminal repeats (LTRs) RTNs, developed for plants, that have been widely used for evolution, genetic diversity, DNA fingerprinting of cultivars and varieties, genetic mapping linkage and for detection of genetic rearrangements induced by polyploidisation. In the present study, we aimed to analyse the genetic variability among 48 Old Portuguese bread wheat cultivars using both IRAP and REMAP markers. Five IRAP and six REMAP primer combinations were used. IRAP produced 103 polymorphic fragments in a total of 113 bands. On average, 22.6 bands were amplified per IRAP primer combination. The bands ranged in size from 250 to 5000 bp. The REMAP primer combinations allowed the amplification of 53 bands, 51 of them polymorphic. An average of 8.8 REMAP bands was scored per primer combination. The REMAP bands ranged from 250 to 3000 bp. Both marker systems presented high percentages of polymorphism. However, IRAP markers were suitable for detecting genetic variability at the individual level and did not differentiate higher taxa. The REMAP maker system allowed the clustering by botanical variety and identified most of the homonym bread wheat cultivars. [source] Sequence-related amplified polymorphism, an effective molecular approach for studying genetic variation in Fasciola spp. of human and animal health significanceELECTROPHORESIS, Issue 2 2009Qiao-Yan Li Abstract In the present study, a recently described molecular approach, namely sequence-related amplified polymorphism (SRAP), which preferentially amplifies ORFs, was evaluated for the studies of genetic variation among Fasciola hepatica, Fasciola gigantica and the "intermediate" Fasciola from different host species and geographical locations in mainland China. Five SRAP primer combinations were used to amplify 120 Fasciola samples after ten SRAP primer combinations were evaluated. The number of fragments amplified from Fasciola samples using each primer combination ranged from 12 to 20, with an average of 15 polymorphic bands per primer pair. Fifty-nine main polymorphic bands were observed, ranging in size from 100 to 2000,bp, and SRAP bands specific to F. hepatica or F. gigantica were observed. SRAP fragments common to F. hepatica and the "intermediate" Fasciola, or common to F. gigantica and the "intermediate" Fasciola were identified, excised and confirmed by PCR amplification of genomic DNA using primers designed based on sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair-group method with arithmetic averages clustering algorithm categorized all of the examined representative Fasciola samples into three groups, representing the F. hepatica, the "intermediate" Fasciola, or the F. gigantica. These results demonstrated the usefulness of the SRAP technique for revealing genetic variability between F. hepatica, F. gigantica and the "intermediate" Fasciola, and also provided genomic evidence for the existence of the "intermediate" Fasciola between F. hepatica and F. gigantica. This technique provides an alternative and a useful tool for the genetic characterization and studies of genetic variability in parasites. [source] Sexual or clonal origin?FEDDES REPERTORIUM, Issue 3-4 2005A morpho-ecological, molecular analysis in a patch of Ajuga reptans L. (Lamiaceae) Spatial clonal structure and patch colonisation in Ajuga reptans L. (Lamiaceae), a common stoloniferous semi-rosette plant, were studied using a combined morpho-ecological and molecular genetic approach. Within a natural patch from a forest near Diedorf (Thuringia, Germany), the spatial clonal structure was analysed, correlating both datasets: Morphologically, characteristics of clonal growth and clonal reproduction were studied, the spatial distribution of modules was mapped and merigenet relationships were reconstructed. Samples from the patch and its surroundings, and an additional sample from Berlin were then analysed by AFLP fingerprinting using four different primer combinations to identify genets. Most divergence in banding patterns was already obtained for samples from the Diedorf forest. Within the patch, however, most samples had very similar fingerprints, indicating their belonging to the same genet and hence a clonal origin, although they are morphologically separated into three "plants". Based on AFLP data, the relationships of one sample remained ambiguous; but the correlation with morphological data helped to interpret the pattern and indicated that the sample is probably a dividual of the clone, too. The relevance of the observed vegetative multiplication (clonal growth and subsequent clonal reproduction) for patch colonisation and maintenance are discussed. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) Generativer (sexueller) oder klonaler Ursprung? Eine morpho-ökologische und molekulare Analyse in einem ,patch' von Ajuga reptans L. (Lamiaceae) Die räumliche klonale Struktur und die ,patch' Besiedlung von Ajuga reptans L. (Lamiaceae), einer häufigen Halbrosettenpflanze mit Ausläufern, wurden mit einem morpho-ökologischen und molekular-genetischen Ansatz kombiniert analysiert. Die Untersuchung wurde in einem ,patch' aus einem Wald bei Diedorf (Thüringen) durchgeführt: Morphologisch wurden Merkmale des klonalen Wachstums und der klonalen Reproduktion untersucht, die räumliche Verteilung der Module kartiert und Merigenet-Beziehungen rekonstruiert. Für Proben aus dem ,patch', aus dessen näherer Umgebung und einer Pflanze aus Berlin wurden AFLP Analysen mit vier verschiedenen Primer-Kombinationen durchgeführt, um genetische Individuen (Genets) zu identifizieren. Die meisten Unterschiede in den Fragmentmustern zeigten sich bereits zwischen Proben aus Diedorf. Die ,patch'-Proben (morphologisch aufgeteilt in drei "Pflanzen") hatten jedoch sehr ähnliche fingerprints, was ihre Zugehörigkeit zum selben Genet und eine klonale Abstammung belegt. Für eine Probe ließen sich die Verwandtschaftsbeziehungen mit den AFLP Daten nicht sicher klären. Der Abgleich mit den morphologischen Ergebnissen ermöglichte jedoch eine Interpretation, und deutet auf die Zugehörigkeit zum Klon. Die Bedeutung der "vegetativen Multiplikation" (durch klonales Wachstum und klonale Reproduktion) für die Besiedlung und dauerhafte Besetzung von ,patches' wird diskutiert. [source] Genetic diversity and migration patterns of the aquatic macrophyte Potamogeton malaianus in a potamo-lacustrine systemFRESHWATER BIOLOGY, Issue 6 2009YUANYUAN CHEN Summary 1.,Previously, the Yangtze River connected thousands of shallow lakes which together formed a potamo-lacustrine system capable of sustaining a rich variety of submerged macrophytes. 2.,Potamogeton malaianus is one of the dominant submerged macrophytes in many lakes of this area. Genetic variation and population structure of P. malaianus populations from ten lakes in the potamo-lacustrine system were assessed using inter-simple sequence repeat markers. 3.,Twelve primer combinations produced a total of 166 unambiguous bands of which 117 (70.5%) were polymorphic. Potamogeton malaianus exhibited a moderate level of population genetic diversity (PP = 70.5%, HE = 0.163 and I = 0.255), as compared with that of plants in the same habitat and range. The main factors responsible for this moderate value were the plant's mixed breeding system (both sexual and asexual) and the hydrological connectivity among habitats. 4.,F statistics, calculated using different approaches, consistently revealed a moderate genetic differentiation among populations, contributing about 20% of total genetic diversity. An estimate of gene flow (using FST) suggested that gene flow played a more important role than genetic drift in the current population genetic structure of P. malaianus (Nm = 1.131). 5.,The genetic diversity of P. malaianus did not increase downstream. A high level of linkage,disequilibrium at the whole population level suggested that metapopulation processes may affect genetic structure. The migration pattern of P. malaianus was best explained by a two-dimensional stepping stone model, indicating that bird-mediated dispersal could greatly influence gene movements among lakes. [source] Tuscany autochthonous cattle breeds: an original genetic resource investigated by AFLP markersJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2006R. Negrini Summary The aim of this study was to assess the genetic diversity of four autochthonous cattle breeds of Tuscany and their relationships in comparison with Italian Friesian and Italian Brown, using amplified fragment length polymorphism markers. A total of 212 individuals were genotyped with three primer combinations generating 102 polymorphic markers. Average expected heterozygosity ranged from 0.23 in Mucca Pisana to 0.26 in Chianina, Italian Friesian, Italian Brown and Maremmana. The differences resulted not significant (Kruskall,Wallis test, p = 0.416). Gst-B index revealed that 86% of the total genetic variance is retained within population and only 14% is accounted by the between populations component. Multivariate analysis at individual and population level indicated that: (i) Calvana and Chianina are quite separate from the other breeds as an effect of the bottleneck experienced or as a signature of different origin; (ii) Podolian, Maremmana and Italian Brown clustered with the double purpose Mucca Pisana, revealing their contribution to its admixed genetic make up; (iii) Italian Friesian behaved always as out group. The ,analysis of molecular variance' recovered a significant subdivision clustering the six populations into three groups: Italian Friesian and Italian Brown versus Maremmana and Mucca Pisana versus Chianina and Calvana (6% of the total variance). [source] Genetic diversity in pollen beetles (Meligethes aeneus) in Sweden: role of spatial, temporal and insecticide resistance factorsAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 4 2007Nadiya Kazachkova Abstract 1,Pollen beetles Meligethes aeneus are pests of oilseed Brassica crops that are subject to intensive chemical control. Resistance to pyrethroids has been reported. Although this insect is of great economic importance, little is known about its genetic properties and population structure. 2,Amplified fragment length polymorphism (AFLP) analysis with the restriction endonuclease combination EcoRI and PstI was performed on 133 samples of groups of three pollen beetles collected during 2001,04 from five different provinces of Sweden. Both susceptible and resistant insects were studied. Using one primer combination, more than 450 polymorphic DNA fragments were obtained and, in total, four primer combinations were used for analysis. A subsample of 59 single beetles was analysed using one primer combination. 3,AFLP profiles were analysed by similarity measures using the Nei and Li coefficient and Neighbour-joining dendrograms were generated. The dendrogram built using 133 samples showed three distinct groups, each containing beetles representing one generation. Statistical analysis using analysis of molecular variance of single beetle samples showed no evidence of significant genetic difference between resistant and susceptible beetles. Instead, a clear difference between samples, depending on time of collection and generation, was observed. 4,The expected regional population structure, although statistically significant, explained little of the variation. The levels of genetic variation within populations were very high. There appears to be a high rate of gene flow between pollen beetle populations. The implications of this in the context of insecticide resistance are discussed. [source] Genetic and chemical assessment of Arbequina olive cultivar grown in Córdoba province, ArgentinaJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 3 2009Mariela M Torres Abstract BACKGROUND: Thirty-eight accessions of olive (Olea europaea L.) originating from Córdoba province (Argentina) and preliminarily identified as belonging to the Arbequina variety were genotyped using AFLP (amplified fragment length polymorphism) DNA markers. Also, the oil chemical composition was studied during three consecutive crop years. The objectives of the work were (a) to investigate genetic intra-cultivar diversity and (b) to evaluate the oil chemical composition and compare it with that of Arbequina oil produced in Spain. RESULTS: The 19 primer combinations employed to perform the AFLP analysis produced 98 polymorphic bands. A reduced genetic heterogeneity was obtained, confirming that (a) the selected accessions belong to the Arbequina variety and (b) the traditional vegetative propagation practice has caused low genetic erosion in this variety cultivated in Córdoba. The main features that characterise the Argentinian Arbequina oils studied are the lower content of oleic acid and higher levels of phenolics and high-molecular-weight volatile compounds compared with those found in Spanish Arbequina oils. CONCLUSION: In spite of the small proportion of intra-cultivar variability, the Arbequina variety grown in Argentina produces oils with different chemical traits from those obtained in the original Spanish growing region. These differences can be attributed mainly to the particular environmental conditions of the olive-growing areas in these countries. Copyright © 2008 Society of Chemical Industry [source] Y chromosome microsatellite isolation from BAC clones in the greater white-toothed shrew (Crocidura russula)MOLECULAR ECOLOGY RESOURCES, Issue 1 2006LORI J. LAWSON HANDLEY Abstract We constructed a microsatellite library from four Crocidura russula Y chromosome-specific bacterial artificial chromosome (BAC) clones. Only one of eight microsatellites was male-specific, despite genome walking to obtain more flanking sequence and testing of 93 primer combinations. Potential reasons for this low success are discussed. The male-specific locus, CRY3, was genotyped in 90 males, including C. russula from across the species range and two related species. The large difference in CRY3 allele size between eastern and western lineages supports earlier reports of high divergence between them. Despite polymorphism of CRY3 in Morocco, only one allele was found throughout the whole of Europe, consistent with previous studies that suggest recent colonization of Europe from a small number of Moroccan founders. [source] Microsatellite primers for the Atlantic coastal killifish, Fundulus heteroclitus, with applicability to related Fundulus speciesMOLECULAR ECOLOGY RESOURCES, Issue 2 2005STEPHANIE M. ADAMS Abstract The mummichog (Fundulus heteroclitus), a common Atlantic coastal killifish, is a model vertebrate species for the study of molecular genetic variation in natural populations and of environmental toxicology. We report the development of a set of 20 microsatellite loci in this species. Average expected heterozygosity across all loci was 0.84 (range: 0.60,0.97), revealing a high level of variability at most loci. A survey of seven additional Fundulus species yielded one or two robust amplification products in over half (63%) of the species,primer combinations tested. Therefore, many of these loci will also prove useful in studies of other members of the genus Fundulus. [source] Genetic linkage map of cassava (Manihot esculenta Crantz) based on AFLP and SSR markersPLANT BREEDING, Issue 1 2010S. Kunkeaw With 1 figure Abstract To generate a genetic linkage map of cassava (Manihot esculenta Crantz), 58 F1 progenies from a cross between Rayong 90 (female) and Rayong 5 (male) were examined in amplification fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. A total of 469 polymorphic markers consisting of 378 AFLPs generated from 76 primer combinations and 91 SSRs were identified. These markers were analyzed using the joinmap®3.0 package program to construct a genetic linkage map. A total of 33 linkage groups of a common map were constructed from 119 AFLPs and 18 SSRs, spanning 1095 cM with an average of 7.99 cM between markers. The genetic linkage map generated in this study will be useful for genetic studies in cassava particularly for the identification of genetic markers linked to traits of interest, although the complex cassava genome suggests that maybe a long term objective. [source] Identification of a SCAR marker linked to a recessive male sterile gene (Tems) and its application in breeding of marigold (Tagetes erecta)PLANT BREEDING, Issue 1 2009Y. H. He Abstract In marigold, an F2 segregation population of 167 plants was constructed from a cross of a line (M525A) carrying the male sterility trait × an inbred line (f53f). In line M525A, the male sterility trait was controlled by the recessive gene, Tems. The intersimple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) techniques combined with bulked segregant analysis were used to develop markers linked to the trait. From a survey of the 38 ISSR primers and 170 SRAP primer combinations, only one SRAP marker that was closely linked to the target trait was identified and successfully converted into sequence characterized amplified region (SCAR) marker that was located within 2.4 cM from Tems locus. The marker was validated with five other two-type lines and in each case the male fertile plants were reliably identified. This SCAR marker therefore permits the efficient marker-assisted selection of male sterile individuals in breeding programmes of marigold and will greatly facilitate the breeding of F1 cultivars. [source] Development of molecular markers linked to the wheat powdery mildew resistance gene Pm4b and marker validation for molecular breedingPLANT BREEDING, Issue 2 2008Y. J. Yi Abstract Powdery mildew, caused by Blumeria graminis (DC.) E.O. Speer f. sp. tritici, is an important disease in wheat (Triticum aestivum L.). Bulk segregant analysis (BSA) was employed to identify SRAP (sequence-related amplified polymorphism), sequence tagged site (STS) and simple sequence repeat (SSR) markers linked to the Pm4b gene, which confers good resistance to powdery mildew in wheat. Out of 240 SRAP primer combinations tested, primer combinations Me8/Em7 and Me12/Em7 yielded 220-bp and 205-bp band, respectively, each of them associated with Pm4b. STS- 241 also linked to Pm4b with a genetic distance of 4.9 cM. Among the eight SSR markers located on wheat chromosome 2AL, Xgwm382 was found to be polymorphic and linked to Pm4b with a genetic distance of 11.8 cM. Further analysis was carried out using the four markers to investigate marker validation for marker-assisted selection (MAS). The results showed that a combination of the linked markers STS,241, Me8/Em7,220 and Xgwm382 could be used for marker-assisted selection of the resistance gene Pm4b in wheat breeding programmes. [source] Estimating Genetic Diversity in Durum and Bread Wheat Cultivars from Turkey using AFLP and SAMPL MarkersPLANT BREEDING, Issue 1 2008S. Alt Abstract Since 1925, more than 100 wheat varieties were developed and released in Turkey, and many more were introduced from abroad, but no systematic analysis of their genetic diversity has been performed yet. In this research, a total of 34 domestic and foreign cultivars (12 durum and 22 bread wheats), released in Turkey between 1936 and 2000, were fingerprinted by means of five amplified fragment length polymorphism and three selective amplification of microsatellite polymorphic loci (SAMPL) primer combinations, to evaluate their genetic variation and to determine the existence of cultivar-specific bands. Among the 344 amplicons scored, 214 were polymorphic. The primer combination EACG/MAGG yielded the highest number and the primer combination SAMPL,6/M AGA produced the lowest number of polymorphic bands. Most cultivars were molecularly very similar, although a few distinct ones (the durum wheat ,Kunduru,1149' and the bread wheat ,,kizce,96') were also identified. Seven cultivar-specific markers for different bread wheat cultivars (,Golia', ,Seri,82', ,Adana,99', ,Pandas' and ,Sertak,52') and six cultivar-specific markers for durum wheat cv ,Kunduru' were observed. Our results show that genetic diversity among old and present,day wheat cultivar commonly grown in Turkey is limited. [source] AFLP analysis of genetic variability among Stylosanthes guianensis accessions resistant and susceptible to the stylo anthracnosePLANT BREEDING, Issue 6 2005C.-S. Jiang Abstract Stylosanthes guianensis, belonging to the genus Stylosanthes, is one of the most important tropical forage legumes and is native to South and Central America and Africa. Anthracnose, caused by the fungus Colletotrichum gloeosporioides (Penz.) Sacc., is a major constraint to the extensive use of Stylosanthes as tropical forage. Forty-two accessions of S. guianensis were assessed with amplified fragment length polymorphism (AFLP) for genetic diversity and for resistance to anthracnose. In AFLP analysis, four selective primer combinations screened from 96 primer combinations were used to analyse these accessions, and a total of 225 clear bands were used for genetic similarity (GS) analysis, showing a 95.5% level of polymorphism on average. GS from 31.0% to 95.0% among the accessions was calculated with ntsys -pc software. The dendrogram was constructed with unweighted pair group method of averages (UPGMA) based on the AFLP data, and five clusters were defined at 48% GS. Two typical strains of C. gloeosporioides from Stylosanthes in China were used for anthracnose resistance screening. Most of the plant accessions showed variation in the reaction to two strains, and the correlation of resistance had a value of 0.904 (P < 0.01), suggesting common resistance to the two strains. The resistance accessions were randomly distributed in different groups of UPGMA clustering. These results demonstrate that AFLP analysis is an efficient method for evaluating the genetic diversity among S. guianensis accessions. [source] Linkage map construction and mapping QTL for cotton fibre quality using SRAP, SSR and RAPDPLANT BREEDING, Issue 2 2005Z. Lin Abstract Tetraploid cotton is one of the most extensively cultivated species. Two tetraploid species, Gossypium hirsutum L. and G. barbadense L., dominate the world's cotton production. To better understand the genetic basis of cotton fibre traits for the improvement of fibre quality, a genetic linkage map of tetraploid cotton was constructed using sequence-related amplified polymorphisms (SRAPs), simple sequence repeats (SSRs) and random amplified polymorphic DNAs (RAPDs). A total of 238 SRAP primer combinations, 368 SSR primer pairs and 600 RAPD primers were used to screen polymorphisms between G. hirsutum cv. Handan208 and G. barbadense cv. Pima90 which revealed 749 polymorphic loci in total (205 SSRs, 107 RAPDs and 437 SRAPs). Sixty-nine F2 progeny from the interspecific cross of ,Handan208'×,Pima90' were genotyped with the 749 polymorphic markers. A total of 566 loci were assembled into 41 linkage groups with at least three loci in each group. Twenty-eight linkage groups were assigned to corresponding chromosomes by SSR markers with known chromosome locations. The map covered 5141.8 cM with a mean interlocus space of 9.08 cM. A × test for significance of deviations from the expected ratio (1: 2: 1 or 3: 1) identified 135 loci (18.0%) with skewed segregation, most of which had an excess of maternal parental alleles. In total, 13 QTL associated with fibre traits were detected, among which two QTL were for fibre strength, four for fibre length and seven for micronaire value. These QTL were on nine linkage groups explaining 16.18-28.92% of the trait variation. Six QTL were located in the A subgenome, six QTL in the D subgenome and one QTL in an unassigned linkage group. There were three QTL for micronaire value clustered on LG1, which would be very useful for improving this trait by molecular marker-assisted selection. [source] Segregation patterns of AFLP markers in F1 hybrids of a cross between tetraploid and diploid species in the genus MalusPLANT BREEDING, Issue 4 2004Y. H. Li Abstract Malus xiaojinensis, one of the most important wild genotypes in the genus Malus, is resistant to a variety of stresses such as Fe deficiency chlorosis, drought and cold. However, lack of knowledge of its genetic background prevents using genetic analysis to study those agronomic traits and corresponding gene functions. Here, as the first step towards construction of the linkage map of M. xiaojinensis, genetic analysis of the F1 triploid hybrids (M. xiaojinensis × M. baccata) was performed with amplified fragment length polymorphism (AFLP) markers. Using 15 EcoRI- MseI primer combinations, 1110 AFLPs were identified, with 31.3% of M. xiaojinensis -, 12.7% of M. baccata-specific markers, 54.9% of common markers, and 1.2% of non-parental markers; 93.3% of the AFLP markers exhibit the expected segregation ratio. Thirty-two M. xiaojinensis -specific markers and 47 common markers display a 5 : 1 and 11:1 segregation ratios, respectively, suggesting that M. xiaojinensis is an autotetraploid, or at least an isosyndetic allotetraploid. [source] Utility of AFLP markers for the assessment of genetic diversity within Brassica nigra germplasmPLANT BREEDING, Issue 1 2004M. S. Negi Abstract Genetic diversity of 18 Brassica nigra accessions was estimated using amplified fragment length polymorphism (AFLP) marker technology. Two B. rapa and two B. juncea accessions were selected as outliers in the study. Eight AFLP primer combinations generated a total of 426 bands, of which 79% were polymorphic. The UPGMA method was employed to construct a dendrogram based on the Jaccard's similarity coefficient. The accessions of B. rapa separated from those of B. nigra at a genetic similarity coefficient of 0.27 while those of B. juncea did so at 0.5. The genetic similarity coefficients within the B. nigra accessions ranged from 0.58 to 0.86. Based on these coefficients it was concluded that the B. nigra accessions show high levels of genetic variation. These results have significant implications in the crop improvement programmes for the agronomically important crop B. juncea, an amphidiploid of B. nigra and B. rapa. Two incorrectly labelled B. nigra accessions were also identified. These accessions were found to cluster with those of B. juncea accessions. This result demonstrates the great value of AFLP markers in the management of genebanks. [source] Molecular characterization of novel resynthesized rapeseed (Brassica napus) lines and analysis of their genetic diversity in comparison with spring rapeseed cultivars,PLANT BREEDING, Issue 6 2003F. Seyis Abstract Resynthesized (RS) rapeseed generated from interspecific hybridization between suitable forms of Brassica rapa L. (syn. campestris; genome AA, 2n = 20) and B. oleracea L. (CC, 2n = 18) represents a potentially important resource to expand genetic diversity in the narrow gene pool of oilseed rape (B. napus L., AACC, 2n = 38). In this study 165 RS rapeseed lines originating from crosses between an Indian Yellow Sarson (B. rapa ssp. trilocularis) and five different cauliflower (B. oleracea convar. botrytis) cultivars were studied using amplified fragment length polymorphism (AFLP) markers and their genetic diversity was compared in relationship to an assortment of 40 diverse spring oilseed and fodder rape varieties. Using three AFLP primer combinations, a total of 467 polymorphic bands were scored. Cluster analysis allowed differentiation among the different RS lines, which, as expected, were genetically highly divergent from the cultivars. The genetic diversity of the material is discussed in relation to its morphological variability with a view to the implementation of RS lines in oilseed rape breeding. [source] Assessment of genetic diversity in clover species from Sardinia, Italy, using AFLP analysisPLANT BREEDING, Issue 4 2003S. J. Bennett Abstract Two species, Trifolium glomeratum and T. nigrescens, from Sardinia, Italy, were analysed for genetic diversity using amplified fragment length polymorphism (AFLP). Variation between and within populations was compared between the inbreeder, T. glomeratum, and the outbreeder, T. nigrescens. Four AFLP primer combinations resulted in a total of 292 loci, of which 75% were polymorphic in T. glomeratum and 85% in Trifolium nigrescens. Variation was highest between populations in both species, but the difference between populations was greater in T. glomeratum (Fst = 0.17), compared with T. nigrescens (Fst = 0.02). Cluster analysis and principal coordinates analysis were used to verify the relationships found. The high level of genetic variation within populations in both species is attributed to the movement of sheep between paddocks, the existence of both species in Sardinia for thousands of years and the persistence of a long-lived seedbank due to the production of large numbers of small seeds with high levels of hard seededness. [source] Intraspecific olive diversity assessed with AFLPPLANT BREEDING, Issue 2 2003F. Sanz-Cortés Abstract Amplified fragment length polymorphism (AFLP) was used to study diversity within and among Spanish olive varieties. A high degree of diversity was found among the varieties present in each growing region. Olive oil production and quality relies on appropriate cultivar selection as well as good orchard management. Production based only on a few superior cultivars would result in improved yield, oil quality, and production management. Amplified fragment length polymorphism were evaluated as a tool to identify the intraspecific and intravarietal diversity of olive. Amplified fragment length polymorphism analysis of 38 accessions belonging to 10 cultivars using six primer combinations produced 106 polymorphic bands. Results were analyzed for similarity among accessions via unweighted pair-group means cluster analysis, resulting in 10 clusters corresponding to named variety designations. Similarity among varieties ranged from 0.60 to 0.72. Diversity within varieties was identified. Similarity within named varieties (accessions with the same varietal name) ranged from 0.75 to 0.96. Differences in several markers were found among 34 accessions. Intravarietal diversity was shown to exist within the Spanish olive varieties grown in the region surrounding Valencia. [source] Clustering of amplified fragment length polymorphism markers in a linkage map of ryePLANT BREEDING, Issue 2 2002B. Saal Abstract Amplified fragment length polymorphisms (AFLPs) are now widely used in DNA fingerprinting and genetic diversity studies, the construction of dense genetic maps and in fine mapping of agronomically important traits. The AFLP markers have been chosen as a source to extend and saturate a linkage map of rye, which has previously been generated by means of restriction fragment length polymorphism, random amplified polymorphic DNA, simple sequence repeat and isozyme markers. Gaps between linkage groups, which were known to be part of chromosome 2R, have been closed, thus allowing the determination of their correct order. Eighteen EcoRI- MseI primer combinations were screened for polymorphism and yielded 148 polymorphic bands out of a total of 1180. The level of polymorphism among the different primer combinations varied from 5.7% to 33.3%. Eight primer combinations, which revealed most polymorphisms, were further analysed in all individuals of the F2 mapping population. Seventy-one out of 80 polymorphic loci could be integrated into the linkage map, thereby increasing the total number of markers to 182. However, 46% of the mapped AFLP markers constituted four major clusters located on chromosomes 2R, 5R and 7R, predominantly in proximity to the centromere. The integration of AFLP markers caused an increase of 215 cM, which resulted in a total map length of almost 1100 cM. [source] A PCR-based DNA marker for detection of mutant and normal alleles of the Wx-D1 gene of wheatPLANT BREEDING, Issue 2 2001M. R. Shariflou Abstract To assist waxy wheat breeding a DNA marker was developed to discriminate mutant and normal alleles at the Wx-D1 locus. This polymerase chain reaction-based marker distinguishes the mutant from the normal allele by targeting the previously reported deletion basis of the mutant. The marker codominantly identifies the normal allele of the Wx-D1 gene from the mutant allele originated from the Chinese landrace ,Baihoumai'. However, attempts with a number of primer combinations targeting this deletion failed to amplify the corresponding fragment from an unrelated wheat line (NP150) that has a mutant null allele at the same locus. This indicates that NP150 has a different mutant allele from that of ,Baihoumai'. This marker is a useful tool to identify wheat cultivars with mutant and normal alleles of the Wx-D1 gene, and is used in marker-assisted selection of the Wx-D1 gene in our waxy wheat breeding programme. [source] Integration of AFLP markers into an RFLP-based map of durum wheatPLANT BREEDING, Issue 5 2000C. Lotti Abstract Amplified fragment length polymorphism (AFLP) is a powerful technique which can readily be applied to a wide range of species for mapping purposes. AFLPs were added to a linkage map of durum wheat constructed using restriction fragment length polymorphisms (RFLPs). The mapping population included 65 recombinant inbred lines derived from a cross between the durum wheat cultivar ,Messapia' and accession ,MG4343' of the wild Triticum turgidum ssp. dicoccoides (Körn.). Genomic DNA was digested with MseI (4-cutter) and Sse83871 (8-cutter). Using a silver-staining protocol, 14 primer combinations revealed 421 clearly scorable amplicons including 100 polymorphisms. The presence of nine pairs of bands linked in repulsion phase with each pair generated by one primer combination suggested the presence of codominant alleles; sequence analysis of four band pairs confirmed their codominant nature. The integration of 80 AFLP loci extended the map in several telomeric regions, reduced the size of four large gaps present in the previous map, and eliminated one gap. The new map obtained after the inclusion of the 80 AFLP loci and eight additional RFLP loci spans 2063cM which represent a 52.6% increment compared with the previous map. Compared with the distribution of RFLPs, no significant clustering of AFLP markers was observed. [source] Genetic characterization by fluorescent AFLP of Pseudomonas savastanoi pv. savastanoi strains isolated from different host speciesPLANT PATHOLOGY, Issue 3 2007A. Sisto The genetic diversity of 71 Pseudomonas savastanoi pv. savastanoi strains isolated from different host species and from diverse geographical regions was determined by fluorescent amplified fragment length polymorphism (f-AFLP) analysis. The study was carried out using three different selective primer combinations. Strains of P. syringae pv. syringae, P. syringae pv. phaseolicola, P. syringae pv. glycinea, P. syringae pv. tagetis and P. amygdali were also included as outgroups. Based on cluster analysis of f-AFLP data, all P. savastanoi pv. savastanoi strains showed a high degree of similarity, grouping in a cluster and forming a taxon clearly separate from outgroup strains. AFLP analyses failed to support placing strains of P. savastanoi pv. savastanoi, P. syringae pv. phaseolicola and P. syringae pv. glycinea in the same species. Strains of P. savastanoi pv. savastanoi formed subclusters that correlated with the host species. Strains identified within these subclusters were related to the geographical region where the strains were isolated. Strains of P. savastanoi pv. savastanoi from olive were divided into two subclusters. Strains from oleander were differentiated from those from ash and were divided into two additional subclusters, distinct from olive strains. Three strains isolated from jasmine showed a high level of similarity among them but, at a lower Dice similarity coefficient, were linked to a subcluster including olive strains. Finally, two strains isolated from privet were similar to strains from olive and were included in the same subcluster. [source] A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markersANIMAL GENETICS, Issue 5 2009Q. Li Summary We present the first genetic maps of the sea cucumber (Apostichopus japonicus), constructed with an F1 pseudo-testcross strategy. The 37 amplified fragment length polymorphism (AFLP) primer combinations chosen identified 484 polymorphic markers. Of the 21 microsatellite primer pairs tested, 16 identified heterozygous loci in one or other parent, and six were fully informative, as they segregated in both parents. The female map comprised 163 loci, spread over 20 linkage groups (which equals the haploid chromosome number), and spanned 1522.0 cM, with a mean marker density of 9.3 cM. The equivalent figures for the male map were 162 loci, 21 linkage groups, 1276.9 and 7.9 cM. About 2.5% of the AFLP markers displayed segregation distortion and were not used for map construction. The estimated coverage of the genome was 84.8% for the female map and 83.4% for the male map. The maps generated will serve as a basis for the construction of a high-resolution genetic map and mapping of the functional genes and quantitative trait loci, which will then open the way for the application of a marker-assisted selection breeding strategy in this species. [source] | |||||||||||||||||||||||||