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1.
Genome constitution and classification using retrotransposon-based markers in the orphan crop banana 总被引:2,自引:0,他引:2
Chee How Teo Siang Hee Tan Chai Ling Ho Qamaruz Zaman Faridah Yasmin Rofina Othman John Seymour Heslop-Harrison Ruslan Kalendar Alan Howard Schulman 《Journal of Plant Biology》2005,48(1):96-105
2.
Two DNA fingerprinting techniques, random amplified polymorphic DNA (RAPD) and inter-retrotransposon amplified polymorphism
(IRAP), were used to characterize somaclonal variants of banana. IRAP primers were designed on the basis of repetitive and
genome-wide dispersed long terminal repeat (LTR) retrotransposon families for assessing the somaclonal variation in 2Musa clones resistant and susceptible toFusarium oxysporum f. sp.cubense race 4. RAPD markers successfully detected genetic variation within and between individuals of the clones. IRAP makers amplified
either by a single primer or a combination of primers based on LTR orientation successfully amplified different retrotransposons
dispersed in theMusa genome and detected new events of insertions. RAPD markers proved more polymorphic than IRAP markers. Somaclonal variation
seems to be the result of numerous indels occurring genome-wide accompanied by the activation of retroelements, as a result
of stress caused by micropropagation. It is concluded that characterization of the somaclonal variants requires more than
one DNA marker system to detect variation in diverse components of the genome. 相似文献
3.
Khanna Harjeet Becker Doug Kleidon Jennifer Dale James 《Molecular breeding : new strategies in plant improvement》2004,14(3):239-252
Centrifugation-assisted Agrobacterium-mediated transformation (CAAT) protocol, developed using banana cultivars from two economically important genomic groups (AAA and AAB) of cultivated Musa, is described. This protocol resulted in 25-65 plants/50mg of settled cell volume of embryogenic suspension cells, depending upon the Agrobacterium strain used, and gave rise to hundreds of morphologically normal, transgenic plants in two banana cultivars from the two genomic groups. Development of a highly efficient Agrobacterium-mediated transformation protocol for a recalcitrant species like banana, especially the Cavendish group (AAA) cultivars, required the identification and optimisation of the factors affecting T-DNA delivery and subsequent plant regeneration. We used male-flower-derived embryogenic cell suspensions of two banana cultivars (Cavendish and Lady Finger) and Agrobacterium strains AGL1 and LBA4404, harbouring binary vectors carrying hpt (hygromycin phosphotransferase) and gusA (-glucuronidase) or nptII (neomycin phosphotransferase) and a modified gfp (green fluorescent protein) gene in the T-DNA, to investigate and optimise T-DNA delivery and tissue culture variables. Factors evaluated included pre-induction of Agrobacterium, conditions and media used for inoculation and co-cultivation, and the presence of acetosyringone and Pluronic F68 in the co-cultivation media. One factor that led to a significant enhancement in transformation frequency was the introduction of a centrifugation step during co-cultivation. Post co-cultivation liquid-media wash and recovery step helped avoid Agrobacterium overgrowth on filters supporting suspension culture cells. Marker-gene expression and molecular analysis demonstrated that transgenes integrated stably into the banana genome. T-DNA:banana DNA boundary sequences were amplified and sequenced in order to study the integration profile. 相似文献
4.
Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs) 总被引:14,自引:0,他引:14
M. R. Thomas N. S. Scott 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1993,86(8):985-990
Microsatellite repeat sequences were investigated as sequenced-tagged site (STS) DNA markers to determine the potential for genetic analysis of the grapevine genome. The PCR-generated markers detect codominant alleles at a single locus or site in the genome. The marker type is very informative detecting high heterozygosity (69%–88%) within individual grapevine cultivars and high genetic variation between cultivars, making it a useful marker type for plant genome mapping and genome typing. For five loci a screening of 26 V. vinifera cultivars found 13, 12, 8, 5, and 4 different length alleles respectively with some alleles more common than others. The genomic DNA sequences surrounding microsatellite sequences were conserved within the genus permitting STS primers to amplify STSs from other Vitis species. These Vitis species were found to have some unique alleles not present in V. vinifera. 相似文献
5.
Tui Ray Indrajit Dutta Prasenjit Saha Sampa Das S.C. Roy 《Plant Cell, Tissue and Organ Culture》2006,85(1):11-21
An efficient micropropagation protocol produced large number of plants of the three elite banana (Musa spp.) cultivars Robusta (AAA), Giant Governor (AAA) and Martaman (AAB) from shoot tip meristem. The genetic relationships
and fidelity among the cultivars and micropropagated plants as assessed by random amplified polymorphic DNA (RAPD) and inter-simple
sequence repeat (ISSR) markers, revealed three somaclonal variants from Robusta and three from Giant Governor. A total of
5330 RAPD and 2741 ISSR fragments were generated with 21 RAPD and 12 ISSR primers in micropropagated plants. The percentage
of polymorphic loci by RAPD and ISSR were found to be 1.75, 5.08 in Robusta and 0.83, 5.0 in Giant Governor respectively.
Among the two marker systems used, ISSR fingerprinting detected more polymorphism than RAPD in Robusta and Giant Governor
with most of the primers showing similar fingerprinting profile, whereas Martaman revealed complete genetic stability. 相似文献
6.
S. K. Chakrabarti D. Pattanayak D. Sarkar V. P. Chimote P. S. Naik 《Biologia Plantarum》2006,50(4):531-536
Variations in random amplified polymorphic DNA (RAPD) profiles from leaf, stem, root, and tuber tissues were observed in case
of two glasshouse grown potato cultivars using 40 decamer primers suggesting possible danger of cultivar misidentification.
Genomic DNA extracted from the above four tissues of four in vitro grown potato cultivars, however, produced more uniform RAPD fingerprints. A significant effect of random primers on fingerprint
uniformity was observed in case of both glasshouse and in vitro grown samples. A new concept of stability index for random primers based on homogeneity of RAPD profiles obtained from different
tissues of a single plant have been introduced. It is concluded that RAPD analysis of genomic DNA extracted from any tissue
of in vitro grown potato plants using 14 selected decamer primers could be used to develop RAPD fingerprints for identification of Indian
potato cultivars. 相似文献
7.
P. Winter T. Pfaff S. M. Udupa B. Hüttel P. C. Sharma S. Sahi R. Arreguin-Espinoza F. Weigand F. J. Muehlbauer G. Kahl 《Molecular & general genetics : MGG》1999,262(1):90-101
A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea genome, was screened for
(GA)n, (GAA)n and (TAA)n microsatellite-containing clones, of which 389 were sequenced. The majority (∼75%) contained perfect repeats; interrupted,
interrupted compound and compound repeats were only present in 6%–9% of cases. (TAA)-microsatellites contained the longest
repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite
length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of
which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS)
markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM.
Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P ≥ 0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome.
The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome.
Received: 14 January 1999 / Accepted: 29 April 1999 相似文献
8.
P. Winter T. Pfaff S. M. Udupa B. Hüttel P. C. Sharma S. Sahi R. Arreguin-Espinoza F. Weigand F. J. Muehlbauer G. Kahl 《Molecular genetics and genomics : MGG》1999,262(1):90-101
A size-selected genomic library comprising 280,000 colonies and representing ≈18% of the chickpea genome, was screened for (GA)n, (GAA)n and (TAA)n microsatellite-containing clones, of which 389 were sequenced. The majority (~75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%–9% of cases. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the detection of microsatellite length polymorphisms in six chickpea breeding cultivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossable relatives of chickpea. A total of 174 primer pairs gave interpretable banding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (STMS) markers were genetically mapped in 90 recombinant inbred lines from an inter-species cross between C. reticulatum and the chickpea cultivar ICC 4958. Markers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613?cM. Clustering as well as random distribution of loci was observed. Segregation of 46 markers (39%) deviated significantly (P?≥?0.05) from the expected 1:1 ratio. The majority of these loci (73%) were located in three distinct regions of the genome. The present STMS marker map represents the most advanced co-dominant DNA marker map of the chickpea genome. 相似文献
9.
Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. cubense race 4 (FOC4) results in vascular tissue damage and ultimately death of banana (Musa spp.) plants. Somaclonal variants of in vitro micropropagated banana can hamper success in propagation of genotypes resistant
to FOC4. Early identification of FOC4 resistance in micropropagated banana plantlets is difficult, however. In this study,
we identified sequence-characterized amplified region (SCAR) markers of banana associated with resistance to FOC4. Using pooled
DNA from resistant or susceptible genotypes and 500 arbitrary 10-mer oligonucleotide primers, 24 random amplified polymorphic
DNA (RAPD) products were identified. Two of these RAPD markers were successfully converted to SCAR markers, called ScaU1001
(GenBank accession number HQ613949) and ScaS0901 (GenBank accession number HQ613950). ScaS0901 and ScaU1001 could be amplified
in FOC4-resistant banana genotypes (“Williams 8818-1” and Goldfinger), but not in five tested banana cultivars susceptible
to FOC4. The two SCAR markers were then used to identify a somaclonal variant of the genotype “Williams 8818-1”, which lost
resistance to FOC4. Hence, the identified SCAR markers can be applied for a rapid quality control of FOC4-resistant banana
plantlets immediately after the in vitro micropropagation stage. Furthermore, ScaU1001 and ScaS0901 will facilitate marker-assisted
selection of new banana cultivars resistant to FOC4. 相似文献
10.
G. Sangeetha A. Anandan S. Usha Rani 《Archives Of Phytopathology And Plant Protection》2013,46(4):475-486
Twelve isolates of Lasiodiplodia theobromae were collected from 12 different commercial banana cultivars belonging to various banana growing regions of Tamil Nadu, India. The results revealed that most of the L. theobromae isolates exhibited significant differences in morphology, colour and spore size. However, all 12 isolates took 3–4 days invariably to cover the 90 mm Petri plates. Among the 12 isolates, the isolates LT3a from Robusta and LT10c from dwarf Cavendish produced abundant pycnidia. These isolates were also analysed through Random amplified polymorphic DNA (RAPD) markers for genetic diversity. Polymerase chain reaction amplification of total genomic DNA of the 12 isolates of L. theobromae with 14 random primers generated numerous polymorphisms among the isolates, while many of the intense bands were shared among majority of the isolates. Cluster analysis also indicated a high degree of genetic variability within L. theobromae isolates from different banana cultivars. The 12 isolates were separated into three clusters namely A, B and C. The maximum similarity index of 80% was recorded between the isolates LT7d from Karpuravalli and LT10c from dwarf Cavendish. The least similarity index of 29.41% was recorded with the isolates LT1f isolated from Poovan and LT5a isolated from Virupakshi. Within the species of L. theobromae the genetic variability was high and it underlines and validates existence of significant intra-specific diversity in isolates of L. theobromae infecting different banana cultivars. 相似文献
11.
The spruce (Picea) species are ecologically and economically important in Canada. Highly informative markers with high multiplex ratios are needed to assist spruce genomics, genetics, and breeding programs. Selectively amplified microsatellite polymorphic loci (SAMPL) markers are highly suitable for these programs. We have developed, optimized, and characterized a set of 10 new SAMPL primers in combination with 16 MseI primers and resolved a large number of polymorphic SAMPL markers in spruce. The SAMPL primers were designed from the compound microsatellite repeats found in Norway spruce (Picea abies) and white spruce (Picea glauca). A total of 6313 polymorphic SAMPL makers were produced by 160 SAMPL–MseI primers combinations in eight progeny of a spruce mapping population. 相似文献
12.
13.
Direct amplification of minisatellite-region DNA with VNTR core sequences in the genus Oryza 总被引:3,自引:0,他引:3
Z. Zhou P. J. Bebeli D. J. Somers J. P. Gustafson 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(5-6):942-949
A polymerase chain reaction (PCR) application, involving the directed amplification of minisatellite-region DNA (DAMD) with
several minisatellite core sequences as primers, was used to detect genetic variation in 17 species of the genus Oryza and several rice cultivars (O. sativa L.). The electrophoretic analysis of DAMD-PCR products showed high levels of variation between different species and little
variation between different cultivars of O. sativa. Polymorphisms were also found between accessions within a species, and between individual plants within an accession of
several wild species. The DAMD-PCR yielded genome-specific banding patterns for the species studied. Several DAMD-PCR-generated
DNA fragments were cloned and characterized. One clone was capable of detecting multiple fragments and revealed individual-specific
hybridization banding patterns using genomic DNA from wild species as well as rice cultivars. A second clone detected only
a single polymorphic locus, while a third clone expressed a strong genome specificity by Southern analysis. The results demonstrated
that DAMD-PCR is potentially useful for species and genome identification in Oryza. The DAMD-PCR technique also allows for the isolation of informative molecular probes to be utilized in DNA fingerprinting
and genome identification in rice.
Received: 1 October 1996 / Accepted: 25 April 1997 相似文献
14.
F.-C. Baurens J.-L. Noyer C. Lanaud P. J. L. Lagoda 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(5-6):922-931
The nuclear genome of wild-type banana accessions was investigated for repetitive elements. We report here the occurrence,
in the banana genome, of a sequence family of species-specific repetitive elements: Brep 1. This sequence family is distributed
throughout the Musaceae with various copy numbers. The two species Musa acuminata and M. schizocarpa carry the highest copy numbers in contrast to M. balbisiana and tested representatives of different other sections. PCR primers were defined in the core consensus sequence for specific
amplifications, which allow representatives of this sequence family to be easily detected in wild and cultivated banana clones.
Sequence data were analysed and hypotheses on the evolution of banana cultivars from the wild-type banana clones are discussed.
Received: 17 January 1997 / Accepted : 7 March 1997 相似文献
15.
16.
Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.) 总被引:8,自引:0,他引:8
A recent approach to detecting genetic polymorphism involves the amplification of genomic DNA using single primers of arbitrary sequence. When separated electrophoretically in agarose gels, the amplification products give banding patterns that can be scored for genetic variation. The objective of this research was to apply these techniques to cultivated peanut (Arachis hypogaea L.) and related wild species to determine whether such an approach would be feasible for the construction of a genetic linkage map in peanut or for systematic studies of the genus. Two peanut cultivars, 25 unadapted germplasm lines of A. hypogaea, the wild allotetraploid progenitor of cultivated peanut (A. monticola), A. glabrata (a tetraploid species from section Rhizomatosae), and 29 diploid wild species of Arachis were evaluated for variability using primers of arbitrary sequence to amplify segments of genomic DNA. No variation in banding pattern was observed among the cultivars and germplasm lines of A. hypogaea, whereas the wild Arachis species were uniquely identified with most primers tested. Bands were scored (+/–) in the wild species and the PAUP computer program for phylogenetic analysis and the HyperRFLP program for genetic distance analysis were used to generate dendrograms showing genetic relationships among the diploid Arachis species evaluated. The two analyses produced nearly identical dendrograms of species relationships. In addition, approximately 100 F2 progeny from each of two interspecific crosses were evaluated for segregation of banding patterns. Although normal segregation was observed among the F2 progeny from both crosses, banding patterns were quite complex and undesirable for use in genetic mapping. The dominant behavior of the markers prevented the differentiation of heterozygotes from homozygotes with certainty, limiting the usefulness of arbitrary primer amplification products as markers in the construction of a genetic linkage map in peanut. 相似文献
17.
The cultivated diploid, Gossypium arboreum L., (A genome) is an invaluable genetic resource for improving modern tetraploid cotton (G. hirsutum L. and G. barbadense L.) cultivars. The objective of this research is to select a set of informative and robust microsatellites for studying genetic
relationships among accessions of geographically diverse G. arboreum cultivars. From more than 1,500 previously developed simple sequence repeat (SSR) markers, 115 genomic (BNL) and EST-derived
(MUCS and MUSS) markers were used to evaluate the allelic diversity of a core panel of G. arboreum accessions. These SSR data enabled advanced genome analyses. A set of 25 SSRs were selected based both upon their high level
of informativeness (PIC ≥ 0.50) and the production of clear PCR bands on agarose gels. Subsequently, 96 accessions representing
a wide spectrum of diversity of G. arboreum cultivars were analyzed with these markers. The 25 SSR loci revealed 75 allelic variants (polymorphisms) ranging from 2 to
4 alleles per locus. The Neighborjoining (NJ) method, based on genetic dissimilarities, revealed that cultivars from geographically
adjacent countries tend to cluster together. Outcomes of this research should be useful in decreasing redundancy of effort
and in constructing a core collection of G. arboreum, important for efficient use of this genetic resource in cotton breeding. 相似文献
18.
DNA amplification fingerprinting (DAF) using a high primer-to-template ratio and single, very short arbitrary primers, was used to generate amplified fragment length polymorphic markers (AFLP) in soybean (Glycine max (L.) Merr.). The inheritance of AFLPs was studied using a cross between the ancestral Glycine soja PI468.397 and Glycine max (L.) Merr. line nts382, F1 and F2 progeny. The amplification reaction was carried out with soybean genomic DNA and 8 base long oligounucleotide primers. Silver-stained 5% polyacrylamide gels containing 7 M urea detected from 11 to 28 DAF products with primers of varying GC content (ranging from 50 to 100% GC). Depending on their intensity, AFLPs were classified into three classes. DAF profiles were reproducible for different DNA extractions and gels. Forty AFLPs were detected by 26 primers when comparing G. soja and G. max. Most AFLPs were inherited as dominant Mendelian markers in F1 and F2 populations. However, abnormal inheritance occured with about 25% of polymorphisms. One marker was inherited as a maternal marker, presumably originating from organelle DNA while another showed apparent paternal inheritance. To confirm the nuclear origin and utility of dominant Mendelian markers, three DAF polymorphisms were mapped using a F11 mapping population of recombinant inbred lines from soybean cultivars Minsoy × Noir 1. The study showed that DAF-generated polymorphic markers occur frequently and reliably, that they are inherited as Mendelian dominant loci and that they can be used in genome mapping. 相似文献
19.
Optimization of primer screening for evaluation of genetic relationship in 34 cultivars of rose through random amplified polymorphic
DNA (RAPD) markers was investigated. Four series of decamer primers were used for screening and optimization of RAPD analysis
between which A and N series performed good amplification of fragments as compared with other series. The primers OPN-07 and
OPN-15 produced maximum number of DNA fragments in Rosa hybrida cv. Anuraag. Some primer either did not produce amplification or produced very poor amplification. Further, ten selected
primers were used for genetic analysis of 34 rose cultivars. The primer OPN-15 amplified 21 fragments in all cultivars tested.
A total of 162 distinct DNA fragments (bands) ranging from 100 to 3400 base pairs were amplified by using 10 selected random
primers. The cluster analysis indicated that these rose cultivars formed nine clusters. 相似文献
20.
Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP),
selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified
polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb
from samples collected from various geographical regions of India. Six assays each of AFLP and SAMPL markers and 21 each of
ISSR and RAPD markers were utilized. AFLP yielded 500 scorable amplified products, of which 82.9% were polymorphic. SAMPL
primers amplified 488 bands, 462 being polymorphic (94.7%). The range of amplified bands was 66 [(TC)8G + M-CAG] to 98 [(CA)6AG + M-CAC] and the percentage polymorphism, 89.9 [from (CT)4C (AC)4A + M-CTG] to 100 [from (GACA)4 + M-CTA]. The ISSR primers amplified 239 bands of 0.4–2.5 kb, 73.6% showed polymorphism. The amplified products ranged from
5 to 16 and the percentage polymorphism 40–100. RAPD assays produced 276 bands, of which 163 were polymorphic (59%). Mantel
test employed for detection of goodness of fit established cophenetic correlation values above 0.9 for all the four marker
systems. The dendrograms and PCA plots derived from the binary data matrices of the four marker systems are highly concordant.
High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. The relative efficiency of the
four molecular marker systems calculated on the basis of multiplex ratio, marker index and average heterozygosity revealed
SAMPL to be the best. Distinct DNA fingerprinting profile, unique to every geographical region could be obtained with all
the four molecular marker systems. Clustering can be a good indicator for clear separation of genotypes from different regions
in well-defined groups that are supported by high bootstrap values. 相似文献