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Pedigree, RAPD and simplified AFLP-based assessment of genetic relationships among Avena sativa L. cultivars 总被引：1，自引：1，他引：1
Edyta Paczos-Grzeda 《Euphytica》2004,138(1):13-22
Two molecular marker techniques: RAPD and simplified PstIAFLP have been compared in order to decide on, which technique is better suited to genetic characterization of oat (Avena sativa L.) cultivars. It was investigated, if the same pattern of variability is revealed by two approaches and whether the observed
molecular variability reflects pedigree-based relationships. Polymorphic RAPD and PstIAFLP markers were sufficient to distinguish all analysed cultivars, demonstrating the usefulness of both methods for cultivar
identification. Genetic similarity estimates derived from RAPD, simplified PstIAFLP and combined RAPD and PstIAFLP data were compared with coefficients of parentage (COP). Molecular markers-based mean genetic similarities were considerably
greater than mean COP value. Correlation coefficients between COP and genetic similarities calculated from RAPD, PstIAFLP and combined molecular data were very low and not significant. A better correlation (0.50) was found between similarity
estimates derived from RAPD and PstIAFLP markers. Four separate dendrograms were constructed based on pedigree and molecular analyses using a neighbor-joining
algorithm (NJ). The dendrograms were compared and found to be topologically different. The results of this study showed, that
both molecular techniques can be conveniently used for genetic characterization of oat cultivars, however PstIAFLP would be the method of choice due to the higher efficiency and reproducibility.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
3.
M.J. Corazza-Nunes M.A. Machado W.M.C. Nunes M. Cristofani M.L.P.N. Targon 《Euphytica》2002,126(2):169-176
The genetic variability of 38 grapefruit (Citrus paradisi Macf.) and three pummelos (C. maxima (Burm.) Merr..) accessions was evaluated using RAPD, and single sequence repeat (SSR) analyses. Approximately49% of the 198 RAPD were polymorphic,
and 4.6 alleles per SSR loci were identified. PIC values changed from 0.093 to 0.450. A UPGMA phenetic tree was constructed
and two main grapefruit groups were identified. The grapefruit accessions `do Cabo' and `Siamesa-Filipinas'clustered very close to the pummelos in Group A. The Group B consisted of three sub-groups, which comprised all of the other
grapefruit accessions. The majority of grapefruit accessions showed a narrow genetic base suggesting that the observed morphological
polymorphism within the group must be associated with somatic mutations, which were not detected by these molecular markers.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
4.
Jorge Luis Fuentes Fabio Escobar Alba Alvarez Geraldo Gallego Miriam Cristina Duque Mirle Ferrer Juan Enrrique Deus Joe M. Tohme 《Euphytica》1999,109(2):107-115
A survey of the genetic diversity among the major cuban rice cultivars was conducted using isozyme, RAPD and AFLP markers.
Polymorphisms were detected for esterases, peroxidases, alcohol dehydrogenases and polyphenoloxidases systems; 21 RAPD primers
and four AFLP primer combinations. Heterozygosity arithmetic mean value (Hav(p)), the effective multiplex ratio (EMR) and the marker index (MI), were calculated for isozyme, RAPD and AFLP markers. The
mean value of genetic similarity among the different varieties was 0.92 for isozyme, 0.73 for RAPD and 0.58 for AFLP analyses.
Thus, AFLP were able to detect polymorphisms with higher efficiency than RAPD (+15%) and isozyme (+34%). Data from the isozyme,
RAPD and AFLP analyses were used to compute matrices of genetic similarities. The efficiency of the UPGMA for the estimation
of genetic relatedness among varieties was supported by cophenetic correlation coefficients. The resulting values indicated
that the distortion level for the estimated similarities was minimal. The correlation coefficients obtained by the Mantel
matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated
values of genetic relationship given for isozyme and RAPD markers (r = 0.89), as well as for AFLP and RAPD markers (r = 0.82)
were properly related. However, AFLP and isozyme data showed only moderate correlation (r = 0.63). Although the genetic variability
found among the different cultivars was low, both RAPD and AFLP markers proved to be efficient tools in assessing the genetic
diversity of rice genotypes.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
5.
Summary Random amplified polymorphic DNA (RAPD) analysis was carried out to evaluate polymorphism and genetic similarity between 39 Mediterranean mandarin genotypes. One hundred eleven amplification products were identified using 21 random primers. An average of 2.2 RAPD markers was obtained for each primer, corresponding to 42% of the amplification products. Genotype-specific RAPD markers were also found, mainly in known hybrids. UPGMA cluster analysis revealed the low level of genetic variation between accessions of Mediterranean mandarins, whereas their hybrids with other Citrus species showed greater genetic dissimilarity. Twenty accessions yielded very similar patterns, suggesting either that they could be a single clone, or that the technique was not able to detect genomic variation. However, for the other specimens genetic polymorphism can easily be detected by RAPD, although the genetic variation between accessions was quite low. The large number of hybrids and the low polymorphism between accessions support the hypothesis that Mediterranean mandarins are all true hybrid of Common mandarins (Citrus reticulata Blanco). 相似文献
6.
Genetic relationships among 18 accessions, including 16 of Ananas and two of Pseudananas, were investigated using RAPD molecular markers. The procedure for DNA extraction was adapted from the method of Dellaporta
et al. (1983) where an incubation in proteinase K and a purification step were included. From the total of 148 markers scored,132
(89.2%) were polymorphic. The similarity matrix was used for cluster analysis. The phenogram developed from the RAPD bands
showed that for most of the cases, the accessions within a species grouped together. Nevertheless, a moderate infraspecific
genetic variation was observed. For example, DNA data grouped all A. comosus accessions with a mean similarity coefficient of 0.85. Comparable results were obtained with all other species investigated.
The highest genetic divergence was found withinA. lucidus where the mean similarity coefficient among accessions was0.75. A similar level of genetic polymorphism was observed among
species,therefore, a definition about which species were involved in the constitution of A. comosus genotypes was not possible. These results agree with the breeders standpoint suggesting that all Ananas species belong to the primary gene pool of pineapple.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
7.
Comparison of molecular markers and coefficients of parentage for the analysis of genetic diversity among spring bread wheat accessions 总被引：8，自引：0，他引：8
The comparison of different methods of estimating genetic diversity could define their usefulness in plant breeding and genetic
improvement programs. This study evaluates and compares the genetic diversity of 70 spring wheat accessions representing a
broad genetic pool based on molecular markers and parentage relationships. The sample was composed of 32 accessions from the
International Maize and Wheat Improvement Center (CIMMYT) and 38 from other breeding programs worldwide. Eight AFLP-primer
combinations and 37 pairs of SSR primers were used to characterize the accessions and the Coefficients of Parentage (COP)
were calculated from registered pedigrees. The average genealogical (COP) similarity (0.09 with a range of 0.0–1.0) was low
in comparison to similarity calculated using SSR markers (0.41 with a range of 0.15–0.88) and AFLP markers (0.70 with a range
of 0.33–0.98). Correlation between the genealogical similarity matrix (excluding accessions with COPs = 0) and the matrices
of genetic similarity based on molecular markers was 0.34≤r≤0.46 (p <0.05). It is concluded that AFLP and SSR markers are generally in agreement with estimates of diversity measured using COPs,
especially when complete pedigree data are available. However, markers may provide a more correct estimate due to some unrealistic
assumptions made when calculating COPs, such as absence of selection. Furthermore, both COP and marker distances indicate
that CIMMYT accessions are different from the worldwide group of accessions.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
8.
Punit Kumar Khanna Ratna Chandra Arun Kumar Nidhi Dogra Heena Gupta Gourav Gupta Vijeshwar Verma 《Journal of Crop Science and Biotechnology》2014,17(1):27-34
Genetic diversity among 14 Withania accessions were studied using morphological, chemical, and RAPD (Rapid Amplification of Polymorphic DNA) markers. On the basis of morphological variation and maximum assimilation of chemical constituents, wild accessions were considered elite as compared to cultivated. The molecular study showed that a total of 12 DNA fragments were amplified with five random decamer primers 75% of which were polymorphic. Genetic similarity matrix based on the Dice index detected coefficients ranging from 0.556 to 0.941. These coefficients were used to construct a dendrogram using unweighted pair group method with arithmetic mean (UPGMA). These accessions were clustered into two major groups; the first group included AGB-009, AGB-012, AGB-042, AGB-030, AGB-053, AGB-019, AGB-017, AGB-002, and AGB-003; the second included AGB-025, AGB-001, AGB-036, AGB-015, and AGB-055. The highest similarity among the Ashwagandha accessions was observed between AGB-009 and AGB-030, AGB-009 and AGB-012, AGB-042 and AGB-030, AGB-025 and AGB-001, AGB-036 and AGB-015, AGB-015 and AGB-055 and between AGB-015 and AGB-055. The most distant populations in the dendrogram were AGB-053 and AGB-055. The combination of morphological, chemical, and molecular markers assessment will be useful in studying the genetic diversity of Withania for identification, conservation, breeding, improvement activities, and in order to achieve elite type in terms of bioactive metabolites. 相似文献
9.
The taxonomic characterisation of annual Beta germplasm in a genetic resources collection using RAPD markers 总被引：1，自引：0，他引：1
Summary Annual beets in the genus Beta section Beta represent an important genetic resource. Representative accessions of annual beets from a beet germplasm collection were analysed using RAPD to assess the patterns of variation and relationships among them. Using arbitrary primers, markers showing variation across accessions were identified. A dendrogram of similarity was produced using these molecular markers. All the accessions analysed were classified into three major groups corresponding to species or subspecies macrocarpa, adanensis and maritima. Macrocarpa was shown to be the most divergent group in this section. Using RAPD molecular markers, it was possible to ascribe an accession to one of three taxonomic groups and overcome much of the confusion encountered when morphological traits are used for identification. The group of maritima was found to be more polymorphic than either the group of macrocarpa or adanensis at both accession and subspecies levels. 相似文献
10.
In order to determine genetically diverse parents for the generation of mapping populations segregating for resistance to
ascochyta blight in wild Cicer species, the genetic diversity between a selection of resistant and susceptible accessions was assessed using molecular markers.
Twenty Cicer accessions — comprising eight C. reticulatum accessions, six C. echinospermum accessions, five C. bijugum accessions, and one C. arietinum accession — were compared using a combination of seven RAPD primers and seven ISSR primers. A total of 231 polymorphic bands
were scored and used to determine the genetic distances between accessions using Jaccard similarity coefficients. The most
genetically diverse parents for the generation of intraspecific and interspecific populations segregating for resistance to
ascochyta blight are reported.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
11.
P.S. Virk J. Zhu H.J. Newbury G.J. Bryan M.T. Jackson B.V. Ford-Lloyd 《Euphytica》2000,112(3):275-284
We have examined the effectiveness of similar numbers of markers from four molecular marker systems (AFLP, isozymes, ISSR
and RAPD) for revealing genetic diversity and discriminating between infraspecific groups of Oryza sativa germplasm. Each marker system classifies the germplasm into three major groups (most effectively with isozymes and AFLPs),
but with differences (primarily with ISSR) between the precise classifications generated. However, at the highest levels of
genetic similarity there was only partial agreement as to relationships between individual accessions when different markers
were used. When variance was partitioned among and within the three subspecific groups, although the differences were not
significant, greater variation was found among than within groups using AFLP and isozymes, with the reverse for RAPD and ISSR.
Measurement of polymorphism using average heterozygosity and effective number of alleles gave similar results for each marker
system. These results are discussed in relation to various genetic resources conservation activities, and the advisability
of extrapolating to other sets of germplasm particularly of other crop species.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
12.
The use of bulked leaf samples from individual plants for amplified fragment length polymorphism (AFLP) analysis was evaluated
as a tool for assessment of genetic diversity in white clover (Trifolium repens L.). Bulking of leaf samples produced slightly simpler AFLP profiles compared to the combined profiles of individual plants
from the same cultivar. Approximately 90% of bands which were present in individual plants were present in bulked samples
of the same cultivar. The majority of those absent were rare bands, shared by less than 25% of individual plants. Replicate
bulk samples gave almost identical banding patterns, demonstrating the robustness of the bulked AFLP technique. Cluster analysis
of AFLP data derived from individual plants resulted in a phenogram similar to that produced from data derived from bulked
samples of the same plants. AFLP analysis of bulked samples detected significant amounts of genetic variability among 52 cultivars
and accessions with genetic similarity values ranging from 0.42 to 0.92. However, cluster analysis of AFLP data only partially
reflected the geographic origin of cultivars and accessions and was not congruent with cluster analysis based on variation
for morphophysiological characters. Bulked AFLP analysis provides a powerful tool for rapid assessment of genetic variability
in white clover and may also be used for cultivar identification.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
13.
Genetic diversity in mustard (Brassica juncea L.) germplasm from Pakistan as determined by RAPDs 总被引：6，自引：0，他引：6
Malik Ashiq Rabbani Aki Iwabuchi Yoshie Murakami Tohru Suzuki Kenji Takayanagi 《Euphytica》1998,103(2):235-242
The genetic diversity and the relationships among a collection of mustard (B. juncea) germplasm, including 41 accessions collected
from Pakistan, 6 oilseed cultivars/ lines and 5 Japanese vegetable cultivars, were evaluated using random amplified polymorphic
DNA (RAPD) markers. A total of 198 polymorphic amplified products were obtained from 30 decamer primers. Of these, 14 were
unique to the accession PAK-85835 and 37 were specific to PAK-85839. Based on pair-wise comparisons of RAPD amplification
products, genetic similarity was estimated using similarity coefficients of Nei & Li (1979) and a dendrogram was constructed
using the unweighted pair-group method with arithmetic averages (UPGMA). Cluster analysis based on these genetic similarities
placed most of the collected germplasm and oilseed cultivars/lines close to each other, showing a low level of polymorphism
between the oilseed accessions collected in Pakistan. However, the clusters formed by the oilseed collections and cultivars
were distinct from those formed by the vegetable cultivars. A low level of genetic variability of oilseed mustard in Pakistan
was attributed to the selection for similar traits and horticultural uses. The farmers' preference for more remunerative crops
and perhaps the close parentage of these accessions further contributed towards their little diversity. The study demonstrated
that the RAPD is a simple and fast technique to compare the genetic relationships and the patterns of variation among accessions
of this crop.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
14.
DNA分子标记广泛用于生物研究的许多方面。本文简要介绍了RFLP、RAPD、AFLP、SSR及ISSR等几种目前常用分子标记的原理,归纳总结了分子标记在银杏中的应用研究进展。(1)获得了2个雄性特有的RAPD标记和2个雌性特有的AFLP标记,为银杏的早期性别鉴定及相关基因克隆奠定了基础;(2)采用RAPD标记和ISSR标记对我国部分栽培品种进行了分子鉴别和分类的研究,编制了一些品种的DNA指纹检索表;(3)利用RAPD和ISSR标记对一些群体、个体及栽培品种或变异类型进行了遗传分化和遗传多样性研究,结果发现银杏具有较高的遗传多样性,群体间、个体间、栽培品种及类型间都存在不同程度的遗传分化;(4)利用ISSR标记对一些个体的遗传杂合性进行了研究,结果显示个体的平均杂合率为43.53%;(5)构建了包含62个RAPD标记、19个连锁群的银杏分子遗传图谱;(6)探索了银杏优先保护种群的确定。分子标记在银杏其它方面的应用还很少。今后,除了继续对上述方面进行深入系统的研究外,还应充分运用DNA分子标记技术,开展银杏的分子标记辅助选择育种、种质评价与鉴别及保育生物学等方面的研究。 相似文献
15.
16.
M. I. Siri G. A. Galván L. Quirici E. Silvera P. Villanueva F. Ferreira L. Franco Fraguas M. J. Pianzzola 《Euphytica》2009,165(2):371-382
Solanum commersonii is a wild tuber-bearing species native to Uruguay with high potential for use in potato breeding programs. Little is known
about the genetic diversity within this wild species and the relationship with the resistance to the bacterial pathogen Ralstonia solanacearum. We studied 30 S. commersonii clonal accessions, 20 of which were collected from geographically different areas across the country, while the other ten
were grown from seeds from a single plant. Resistance against R. solanacearum was tested and different levels of resistance were found, ranging from delayed wilting to asymptomatic reactions. The genetic
variation and the relationships among individuals in this germplasm collection were studied by different molecular markers:
Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP) and Microsatellites or Simple Sequence
Repeats (SSR). AFLP markers generated the largest number of total and polymorphic fragments per assay unit while SSR revealed
the highest frequency of polymorphic bands (100%), followed by AFLP (96.2%) and RAPD (89.4%). In contrast, when comparing
the number of different genetic profiles generated, the SSR markers exhibited the lowest discriminatory power. The clustering
pattern obtained with the three marker systems showed a similar distribution of the S. commersonii germplasm revealing a high correlation between the three methods employed. All three dendrograms grouped most of the accessions
into two main clusters, containing the same accessions regardless of the marker type. Bacterial wilt resistant accessions
were present in both clusters. Accessions originated from different seeds of the same plant were grouped within one of the
major clusters, and differed in the response to R. solanacearum revealing segregation of resistance. Furthermore, the distribution in two main clusters showed high correspondence with the
geographical origin of the accessions, from the north and south of the country, and with the subspecies malmeanum and commersonii morphologically identified. 相似文献
17.
Molecular tools for clone identification: the case of the grapevine cultivar 'Traminer' 总被引：5，自引：0，他引：5
In viticulture, biotype identification problems have traditionally been solved using ampelography, ampelometry and chemical traits analysis. However, these tools have resulted in several false attributions, in particular when used at the clonal level. The availability of relatively cheap, reliable and reproducible tools to identify genetic differences at the clonal level would greatly facilitate the work of clonal patenting. In this work, 24 accessions of ‘Traminer’ cultivars were characterized using molecular markers. Three different approaches were applied: simple sequence repeats (SSR), amplified fragment length polymorphism (AFLP) and methyl‐sensitive amplified length polymorphism (MSAP). Results showed that SSRs were not a powerful tool for clonal distinction. In contrast, the AFLP technique was able to distinguish 16 out of the 24 cultivars, even though the average similarity was high (97.1%). The MSAP technique was used to evaluate qualitative differences in the degree of DNA methylation among clones. Results suggest that morphological differences among clones are probably due to the synergetic effect of genetic and epigenetic modifications, and that clonal identification could be greatly improved using molecular tools such as AFLP and MSAP. 相似文献
18.
Genetic diversity in a crop species is basic to improvement of the species and can be estimated at the molecular level. The
objective of this study was to estimate genetic diversity within and between spelta and macha wheats. Random amplified polymorphic
DNA (RAPD) analysis was conducted on 69 spelta and 32 macha wheat accessions. The classification of spelta and macha accessions,
based on Jaccard genetic similarity coefficients for RAPD markers, was consistent with their geographic origin. The results
indicated that the germplasm of macha wheat was more diverse than that of spelta wheat. In the dendrogram of macha wheat,
four spelta-like accessions grouped together, separate from the remaining macha accessions, suggesting that these accessions
were misclassified. In addition, accessions with identical RAPD patterns were found, indicating that these accessions were
probably duplicated. Thus RAPD analysis can be used to estimate genetic diversity and identify duplicate accessions in wheat
germplasm collections.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
19.
Evaluating genetic variation and relationships among two bromegrass species and their hybrid using RAPD and AFLP markers 总被引：2，自引：0，他引：2
The two most widely grown bromegrass species in North America are smooth bromegrass (Bromus inermis Leyss.), a hay type grass, and meadow bromegrass (Bromus riparius Rehmann), a pasture type grass. Recently a hybrid bromegrass population between the two species has been produced as a dual-purpose
hay-pasture grass. Molecular markers have the potential to improve selection procedures to enhance bromegrass breeding. The
objective of this study was to use RAPD and AFLP markers to determine genetic relationships and variations among bromegrass
populations. Forty-three RAPD markers from 21 primers and 83 AFLP markers from seven primer combinations were used. Both marker
types were able to group the individuals into their respective populations. The relationships among the individuals within
each of the populations were not similar between the two marker types. Analysis of molecular variance (AMOVA) detected greater
within-population variation than among-population variation for both marker types. The highest variation was observed in the
hybrid population followed by meadow and then smooth bromegrass. The inter-population distance from both markers indicated
that the highest genetic distance was between meadow and smooth bromegrass and lowest between smooth and hybrid bromegrass,
which reflect the breeding history of the hybrid population. This study showed that both markers are capable of differentiating
bromegrass genotypes into their respective populations, detecting genetic variation and relationships of the populations.
Results of this study suggest that these two markers can be used in the future to enhance the current breeding practices in
bromegrass, however, AFLP markers would be the marker of choice due to the high number of polymorphic markers.
This revised version was published online in July 2006 with corrections to the Cover Date. 相似文献
20.
Ajay Pratap Singh Samresh Dwivedi Sudhakar Bharti Archana Srivastava Vandana Singh S.P.S. Khanuja 《Euphytica》2004,136(1):11-20
Genetic relationships were examined among thirty germplasm accessions belonging to five Ocimum species using RAPD markers. A very high degree of polymorphism (98.20%) was observed. UPGMA cluster analysis of genetic similarity
indices grouped all the accessions into two major clusters corresponding to previously reported botanical sections. Intra-clustering
within the two clusters precisely grouped the accessions belonging to one species in one sub-cluster as expected from their
genetic background. Our results show that RAPD technique is a sensitive, precise and efficient tool for genomic analysis in
Ocimum species, that may be useful in future studies, by assigning new unclassified germplasm accessions to specific taxonomic groups
and reclassifying previously classified accessions of other Ocimum species by traditional criteria on a more objective basis.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献