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1.
Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species 总被引:25,自引:0,他引:25
C. E. Thormann M. E. Ferreira L. E. A. Camargo J. G. Tivang T. C. Osborn 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1994,88(8):973-980
Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic relationships among 18 accessions from six cultivated Brassica species and one accession from Raphanus sativus. Based on comparisons of genetic-similarity matrices and cophenetic values, RAPD markers were very similar to RFLP markers for estimating intraspecific genetic relationships; however, the two marker types gave different results for interspecific genetic relationships. The presence of amplified mitochondrial and chloroplast DNA fragments in the RAPD data set did not appear to account for differences in RAPD- and RFLP-based dendrograms. However, hybridization tests of RAPD fragments with similar molecular weights demonstrated that some fragments, scored as identical, were not homologous. In all these cases, the differences occurred at the interspecific level. Our results suggest that RAPD data may be less reliable than RFLP data when estimating genetic relationships of accessions from more than one species. 相似文献
2.
Bettina Heider Meike S. Andersson Rainer Schultze-Kraft 《Biodiversity and Conservation》2007,16(6):1617-1631
Flemingia macrophylla (Willd.) Kuntze ex Merr., a multi-purpose legume with potential as dry-season forage crop, mainly occurs in subhumid to humid
environments of tropical and subtropical Asia. Despite increasing interest in conservation of germplasm suitable for low-input
production systems information on the genetic diversity of F. macrophylla is extremely scarce. The creation of baseline data is supposed to contribute to more efficient conservation management and
to identify collecting strategies of novel germplasm. Random amplified polymorphic (RAPD) markers were used to investigate
the genetic variation among 37 F. macrophylla accessions. Germplasm analysed in this study originated from Bac Kan province, Northeast Vietnam. Eight primers generated
a total of 47 amplified RAPD loci of which 38 were polymorphic. Jaccard’s similarity coefficients among accessions ranged
from 0.069 to 1 with a mean of 0.67. The UPGMA dendrogram revealed three clusters along with three outliers. No correspondence
between geographic and genetic distance was found (Mantel test: R = 0.21; P = 0.016). Analysis of molecular variance (AMOVA) revealed significant (P < 0.001) differentiation between accessions collected in lowland and upland regions. Results of UPGMA clustering were confirmed
by the pattern of principle coordinates analysis (PCO) plotting. Future collecting strategies should target populations at
large distances and along the altitudinal range. Ex situ conservation should encompass those accessions that showed genetic
divergence. In situ conservation may consist of establishing a system of interconnected population fragments to guarantee
continuing genetic exchange via corridors and of rehabilitating degraded habitats. 相似文献
3.
M. Tucak S. Popović T. Čupić S. Grljušić V. Meglič Z. Jurković 《Russian Journal of Genetics》2010,46(11):1314-1319
Information on genetic diversity and germplasm characterization is essential for successful crop improvement. Diverse data
sets (pedigree, morphological, biochemical, DNA based-markers) are employed in various aspects of plant analysis. The objective
of this study was to determine the efficiency of phenotypic and RAPD markers in diversity assessment of ten alfalfa (Medicago spp.) accessions from Europe, North America and Australia. Field experiment was designed as a randomised complete block with
three replications over two consecutive years (2004, 2005) at one location. Twelve morpho-agronomic traits were recorded on
50 plants per each accession. Genomic DNA’s from 16–20 randomly selected individual plants per accession were used for RAPD
analysis. Six primers selected in this study generated a total of 93 polymorphic RAPD bands. The number of polymorphic bands
detected per primer ranged from 11 to 20. Genetic distances (GD) among investigated accessions and two-dimensional principal
coordinate analysis (2D PCoA) based on phenotypic and molecular data were obtained. The average GD between (0.283–0.416) and
within (0.247–0.332) accessions based on RAPD data was higher than GD values obtained by morpho-agronomic traits (0.171–0.354
and 0.157–0.261, respectively). 2D PCoA based on GD from RAPD data grouped most of the studied individual plants to four clusters
according to their geographical or taxonomy origin. 2D PCoA based only on morpho-agronomic data did not group plants congruently
to their origin, probably due to a strong environmental influence on studied traits. Our results indicated that the RAPD markers
were effective in assessing genetic diversity within and between studied alfalfa accessions. In addition, the obtained results
suggested that the RAPD markers might be useful for grouping of germplasm with similar genetic background and for pre-screening
of potential heterotic groups in our breeding programme. 相似文献
4.
Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop. 相似文献
5.
Characterization of genetic diversity of nuclear and mitochondrial genomes in Daucus varieties by RAPD and AFLP 总被引:2,自引:0,他引:2
The genetic diversity of nuclear genomes of five Daucus species and seven Daucus carota L. subspecies involving 26 accessions was characterized with random amplified polymorphic DNA (RAPD) and amplified fragment
length polymorphism (AFLP). AFLP produced more than four times as many discrete bands per reaction compared with RAPD analysis,
while both AFLP and RAPD basically led to similar conclusions. The dendrograms constructed with both RAPD and AFLP revealed
that all accessions of D. carota were grouped into a major cluster delimited from other Daucus species, in good agreement with the classification by morphological char-acteristics. All accessions of cultivated carrots
[(D. carota ssp. sativus (Hoffm.) Arcang.] were clustered in the same group while the variation within D. carota was relatively extensive. Genetic diversity of mitochondrial genomes was also documented with RAPD for the same accessions.
The mitochondrial dendrogram differed from that of the nuclear genome, suggesting that nuclear and mitochondrial genomes of
some accessions had separate evolutionary histories.
Received: 20 September 1997 / Revision received: 19 January 1998 / Accepted: 28 March 1998 相似文献
6.
The origin of the crop species Allium fistulosum (bunching onion) and its relation to its wild relative A. altaicum were surveyed with a restriction fragment length polymorphism (RFLP) analysis of five noncoding cpDNA regions and with a random amplified polymorhic DNA (RAPD) analysis of nuclear DNA. Sixteen accessions of A. altaicum, 14 accessions of A. fistulosum, representing the morphological variability of the species, and five additional outgroup species from Allium section Cepa were included in this study. The RFLP analysis detected 14 phylogenetically informative character transformations, whereas RAPD revealed 126 polymorphic fragments. Generalized parsimony, neighbor-joining analysis of genetic distances, and a principal co-ordinate analysis were able to distinguish the two species, but only RAPD data allowed clarification of the interrelationship of the two taxa. The main results of this investigation were: (1) A. fistulosum is of monophyletic origin, and (2) A. fistulosum originated from an A. altaicum progenitor, making A. altaicum a paraphyletic species. Compared with A. altaicum the cultivated accessions of the bunching onion show less genetic variability, a phenomenon that often occurs in crop species due to the severe genetic bottleneck of domestication. Allium altaicum and A. fistulosum easily hybridize when grown together, and most garden-grown material is of recent hybrid origin. 相似文献
7.
J. M. Rodriguez T. Berke L. Engle J. Nienhuis 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(1-2):147-156
Germplasm characterization is an important link between the conservation and utilization of plant genetic resources. A total
of 134 accessions from six Capsicumspecies maintained at the Asian Vegetable Research and Development Center were characterized using 110 randomly amplified
polymorphic DNA (RAPD) markers. Ten pairs of potentially duplicated accessions were identified. Multidimensional scaling analysis
of the genetic distances among accessions resulted in clustering corresponding to a previous species assignment except for
six accessions. Diagnostic RAPDs were identified which discriminate among the Capsicumspecies. The diagnostic markers were employed for improved taxonomic identification of accessions since many morphological
traits used in the identification of Capsicumare difficult to score. Three Capsicumaccessions, misclassified based on morphological traits, were reassigned species status based on diagnostic RAPDs. Three accessions,
not previously classified, were assigned to a species based on diagnostic RAPDs. Definitive conclusions about the species
assignment of three other accessions were not possible. The level of diversity between Capsicum annuumaccessions from the genebank and the breeding program were compared and no differences were observed either for RAPD variation
or diversity. The utilization of genetic resources as a source of variance for useful traits in the breeding program may be
the reason for the similarity of these two groups.
Received: 1 September 1998 / Accepted: 28 December 1998 相似文献
8.
R. K. Varshney M. Baum P. Guo S. Grando S. Ceccarelli A. Graner 《Molecular breeding : new strategies in plant improvement》2010,26(2):229-242
Detection and utilization of genetic variation available in the germplasm collection for crop improvement have been the prime
activities of breeders. Here a set of ICARDA barley germplasm collection comprising of 185 cultivated (Hordeum vulgare L.) and 38 wild (H. spontaneum L.) genotypes originated from 30 countries of four continents was genotyped with 68 single nucleotide polymorphism (SNP)
and 45 microsatellite or simple sequence repeat (SSR) markers derived from genes (expressed sequence tags, ESTs). As two SNP
markers provided 2 and 3 datapoints, a total of 71 SNPs were surveyed that yielded a total of 143 alleles. The number of SSR
alleles per locus ranged from 3 to 22 with an average of 7.9 per marker. Average PIC (polymorphism information content) value
for SSR and SNP markers were recorded as 0.63 and 0.38, respectively. Heterogeneity was recorded at both SNP and SSR loci
in an average of 5.72 and 12.42% accessions, respectively. Genetic similarity matrices for SSR and SNP allelic data were highly
correlated (r = 0.75, P < 0.005) and therefore allelic data for both markers were combined and analyzed for understanding the genetic relationships
among the germplasm surveyed. Majority of clusters/subclusters were found to contain genotypes from the same geographic origins.
While comparing the genetic diversity, the accessions coming from Middle East Asia and North East Asia showed more diversity
as compared to that of other geographic regions. Majority of countries representing Africa, Middle East Asia, North East Asia
and Arabian Peninsula included the genotypes that contained rare alleles. As expected, spontaneum accessions, as compared to vulgare accessions, showed a higher number of total alleles, higher number of alleles per locus, higher effective number of alleles
and higher allelic richness and a higher number of rare alleles were observed. In summary, the examined ICARDA germplasm set
showed ample natural genetic variation that can be harnessed for future breeding of barley as climate change and sustainability
have become important throughout all growing areas of the world, drought/heat tolerance being the most important ones. 相似文献
9.
Origin,diffusion and reproduction of the giant reed (Arundo donax L.): a promising weedy energy crop
C. Mariani R. Cabrini A. Danin P. Piffanelli A. Fricano S. Gomarasca M. Dicandilo F. Grassi C. Soave 《The Annals of applied biology》2010,157(2):191-202
Giant reed (Arundo donax) is a promising energy crop of the Mediterranean areas. It has long been associated with humans and has been cultivated in Asia, southern Europe, North Africa and the Middle East for thousands of years. It is a perennial herbaceous plant (Poaceae) found in grasslands and wetlands throughout a wide range of climatic zones. Amplified fragment length polymorphism (AFLP) analysis was used to assess genetic inter and intrarelationships between A. donax and other Arundo species. Furthermore, the development of the sexual apparatus was analysed to understand the basis of sterility in the accession examined. The dendrograms obtained by phenetic and cladistic analysis support the monophyletic origin of giant reed and suggest that it originated in Asia and began to spread into the Mediterranean without traces of hybridisation with the other Arundo species. In particular, samples from Mediterranean areas are characterisd by a lower gene diversity and incidence of rare AFLP fragments indicating that these populations are recent in origin. Moreover, results indicate the occurrence of post-meiotic alterations in the ovule and pollen developmental pathway. Thus, the success of giant reed can be attributed mainly to its rapid clonal spread by rhizome extension, flood dispersal of rhizome and culm fragments. 相似文献
10.
W. Cao G. Scoles P. Hucl R. N. Chibbar 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(3-4):602-607
Crop germplasm collections contain a considerable percentage of misclassified accessions which may affect the use of germplasm
for agricultural crop improvement. The objective of this study was to determine if random amplified polymorphic DNA (RAPD)
analysis could be used to reclassify misclassified Triticum accessions. Twelve accessions suspected to be misclassified, based on morphological characters, as either macha or vavilovii
wheat were studied using RAPD and cytological analyses. In the RAPD analysis, a dendrogram, based on Jaccard genetic similarity
coefficients, grouped 5 dicoccum-like, 1 timopheevii-like, and 6 monococcum-like accessions with Triticum dicoccum, T. timopheevii, and T. monococcum accessions, respectively. These results were confirmed by the cytological analysis. A RAPD marker specific to the D genome
was also detected. This study suggests that RAPD analysis can be used to classify germplasm and to distinguish some species
in Triticum.
Received: 12 June 1998 / Accepted: 18 August 1998 相似文献
11.
The present study applies RAPD technique and morphometric analysis to study the diversity of some accessions belonging to
section Solanum. A total of 252 products were amplified with 23 12-mer arbitrary primer pairs, among which 210 were found to be polymorphic.
Sixteen morphological characters were measured and used to compile a dendrogram. Both the morphological and RAPD marker analysis
clearly separated the different accessions into similar groups. The results indicate that the analyzed cultivars with unknown
origin could be derived from S. retroflexum. We found morphological differences among the S. scabrum subsp. scabrum accession which were not reflected in the molecular data. Presumably these accessions represent cultivated forms selected
for their habit, fruit quantity and/or quality and leaf size, respectively. 相似文献
12.
Using RAPDs to study phylogenetic relationships in Rosa 总被引:6,自引:0,他引:6
T. Millan F. Osuna S. Cobos A. M. Torres J. I. Cubero 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1996,92(2):273-277
Nineteen species of rose (Rosa sp.) were analysed using Random Amplified Polymorphic DNA markers (RAPD). Each 10-base-long arbitrary primer produced a specific DNA banding pattern that grouped plants belonging to the same species and botanical sections as predicted from their genetic background. One hundred and seventy-five amplification products were examined by cluster analysis to assess the genetic relationships among species and their genetic distances. All of the accessions belonging to 1 species grouped together before branching to other species. Dendrograms constructed for intra- and inter-specific studies showed a good correlation with previous classifications by different authors based on morphological and cariological studies. Our results show that the RAPD technique is a sensitive and precise tool for genomic analysis in rose, being useful in assigning unclassified accessions to specific taxonomic groups or else allowing accessions classified by traditional criteria to be re-classified. 相似文献
13.
Folkertsma RT Rattunde HF Chandra S Raju GS Hash CT 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(3):399-409
The Guinea-race of sorghum [Sorghum bicolor (L.) Moench] is a predominantly inbreeding, diploid cereal crop. It originated from West Africa and appears to have spread throughout Africa and South Asia, where it is now the dominant sorghum race, via ancient trade routes. To elucidate the genetic diversity and differentiation among Guinea-race sorghum landraces, we selected 100 accessions from the ICRISAT sorghum Guinea-race Core Collection and genotyped these using 21 simple sequence repeat (SSR) markers. The 21 SSR markers revealed a total of 123 alleles with an average Dice similarity coefficient of 0.37 across 4,950 pairs of accessions, with nearly 50% of the alleles being rare among the accessions analysed. Stratification of the accessions into 11 countries and five eco-regional groups confirmed earlier reports on the spread of Guinea-race sorghum across Africa and South Asia: most of the variation was found among the accessions from semi-arid and Sahelian Africa and the least among accessions from South Asia. In addition, accessions from South Asia most closely resembled those from southern and eastern Africa, supporting earlier suggestions that sorghum germplasm might have reached South Asia via ancient trade routes along the Arabian Sea coasts of eastern Africa, Arabia and South Asia. Stratification of the accessions according to their Snowden classification indicated clear genetic variation between margeritiferum, conspicuum and Roxburghii accessions, whereas the gambicum and guineënse accessions were genetically similar. The implications of these findings for sorghum Guinea-race plant breeding activities are discussed. 相似文献
14.
辣椒种质遗传多样性的RAPD和ISSR及其表型数据分析 总被引:16,自引:3,他引:13
用RAPDI、SSR分子标记及28个表型性状数据对辣椒属5个栽培种的13份材料进行了分析,结果表明:23条RAPD引物共扩增出209条带,平均每个引物扩增出9.09条,多态性位点比率为83.73%;16条ISSR引物共扩增出94条带,平均每个引物扩增出5.88条,多态性位点比率为79.79%.与RAPD相比,ISSR标记检测到的有效等位基因数(Ne)及Shannon多样性指数(I)、遗传离散度(Ht)和遗传分化系数(Gst)等遗传多样性参数都较大,多态性位点比例在亲缘关系较近的一年生辣椒(Capsicum annuum)种内较高,说明ISSR有更高的多态性检测效率,并且适合亲缘关系较近的种群间遗传多样性分析.基于RAPDI、SSR的聚类与基于表型数据的聚类之间存在极显著正相关,且都能将C.annuum与其它栽培种区分开来. 相似文献
15.
I. V. Bartish N. Jeppsson G. I. Bartish R. Lu H. Nybom 《Plant Systematics and Evolution》2000,225(1-4):85-101
Genetic diversity has been investigated by the application of molecular markers in, for the first time, all the taxa recognised in recent treatises of the genusHippophae. RAPD (random amplified polymorphic DNA) analyses were conducted with 9 decamer primers, which together yielded 219 polymorphic markers. We found 16 fixed RAPD markers, i.e. markers that either occurred in all plants of a population or were absent from all plants. Several of these markers were useful for analysis of interspecific relationships, whereas others can be considered as taxon-specific markers. Clustering of taxa and populations in our neighbour-joining based dendrogram was in good agreement with some recently suggested taxonomic treatises ofHippophae. Amount and distribution of genetic variability varied considerably between species. Partitioning of molecular variance withinH. rhamnoides supported earlier findings that a considerable part of the total variance resides among subspecies (59.6%) Within-population variability also differed considerably. Percentage polymorphic RAPD loci and Lynch and Milligan within-population gene diversity estimates showed relatively high values for some species close to the geographic centre of origin in Central Asia, e.g.H. tibetana and the putatively hybridogenousH. goniocarpa. Spatial autocorrelation analyses performed on 12 populations ofH. rhamnoides revealed positive autocorrelation of allele frequencies when geographic distances ranged from 0 to 700 km, and no or negative autocorrelation at higher distances. At distances between 700 and 1900 km, we observed deviations from the expected values with strongly negative autocorrelation of allele frequencies. A corresponding relationship between geographic and genetic distances could not be found when the analysis instead was based on one population from each of 8 species. 相似文献
16.
G. M. Timmerman T. J. Frew N. F. Weeden A. L. Miller D. S. Goulden 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1994,88(8):1050-1055
Linkage analysis was used to determine the genetic map location of er-1, a recessive gene conditioning resistance to powdery mildew, on the Pisum sativum genome. Genetic linkage was demonstrated between er-1 and linkage group 6 markers after analyzing the progeny of two crosses, an F2 population and a set of recombinant inbred lines. The classes of genetic markers surrounding er-1 include RFLP, RAPD and allozyme markers as well as the morphological marker Gty. A RAPD marker tightly linked to er-1 was identified by bulked segregant analysis. After DNA sequence characterization, specific PCR primers were designed to convert this RAPD marker into a sequence characterized amplified region (SCAR). 相似文献
17.
A set of 30 accessions of five Curcuma species-C. latifolia, C. malabarica, C. manga and C. raktakanta and 13 morphotypes (identified on the basis of morphological markers) of C. longa conserved in the In Vitro Genebank at National Bureau of Plant Genetic Resources, New Delhi, were subjected to RAPD analysis. Of the 200 RAPD primers
screened, 21 polymorphic primers were selected for further study. Mean genetic similarities based on Jaccard’s similarity
coefficient ranged from 0.18 to 0.86 in accessions of cultivated species, i.e., C. longa and from 0.25 to 0.86 in wild species. The dendrogram derived from the RAPD data corroborated the morphological classification
of the morphotypes. The efficiency of individual RAPD primers was also compared; primers OPC-20, OPO-06, OPC-01 and OPL-03
were adjudged highly informative in discriminating the germplasm of Curcuma. 相似文献
18.
C. Orozco-Castillo K. J. Chalmers R. Waugh W. Powell 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1994,87(8):934-940
RAPD (randomly amplified polymorphic DNA) markers generated by arbitary decamers have been successfully employed to detect genetic polymorphisms between coffee species and between Coffea arabica genotypes. The RAPD profiles were used to construct dendrograms and these were consistent with the known history and evolution of Coffea arabica. Material originating from Ethiopia and the arabica sub-groups — C. arabica var. typica and C. arabica var. bourbon — were clearly distinguished. RAPD analysis therefore reflects morphological differences between the sub-groups and the geographical origin of the coffee material. Species-specific amplification products were also identified, but, more importantly, amplification products specific to C. canephora were identified in two C. arabica genotypes, Rume Sudan and Catimor 5175. This diagnostic product is therefore indicative of interspecific gene flow in coffee and has biological implications for selective introgressive hybridisation in coffee. Our study demonstrates the power of the polymerase chain reaction technology for the generation of genetic markers for long-lived perennial tree and bush crops.On study leave from: Universidad de San Carlos de Guatemala, Facultad de Agronomia, Ciudad Universitaria, Zona 12, Apartado Postal No. 1545, Guatemala, Central America 相似文献
19.
Random amplified polymorphic DNA (RAPD) markers were used to assess intraspecific variability and relationships in aerial yam (Dioscorea bulbifera L.). A total of 23 accessions from different geographic locations in Africa, Asia, and Polynesia were analyzed by 10 arbitrarily chosen GC-rich decamer primers. Using cesium chloride purified genomic template DNA, highly reproducible polymorphic fingerprints were generated by all 10 primers, resulting in a total of 375 informative characters. Only eight bands were monomorphic among all investigated accessions. A binary character matrix was generated by scoring for presence/absence of a band at a particular position, transformed into a matrix of pairwise distances using either the Jaccard or a simple matching coefficient, and analyzed by neighbour joining, UPGMA (unweighted pair group method with arithmetic averaging) cluster analysis, or split decomposition. All methods of data evaluation resulted in similar groupings that reflected the geographical origin of the samples. The African accessions formed a distinct isolated group, whereas Asian and Polynesian accessions proved to be more heterogeneous. With two exceptions (var. suavior and var. sativa), the RAPD data supported previous varietal classification based on morphological characters. Stepwise reduction of the number of evaluated characters did not affect branching patterns of the trees above a minimum threshold of 150. Key words : Dioscorea bulbifera, random amplified polymorphic DNA (RAPD), genetic variation, genetic relatedness. 相似文献
20.
Twenty populations of kale (Brassica oleracea var. acephala L.) selected from 127 populations in terms of yield and leaf quality characteristics as superior types using weight-based
ranking method from the Black Sea Region of Turkey were evaluated at the DNA level using randomly amplified polymorphic DNA
(RAPD) markers compared to some morphological characters. The seven primers selected from 100 decamers used generated 110
bands, of which 60 (54.5%) were polymorphic. Jaccard’s genetic distances were calculated and dendrogram was generated using
the UPGMA algorithm. The dendrogram obtained was classified into three main groups and four subgroups. The accessions showed
a limited clustering as compared to morphological characters such as the number of leaves, intentation of the leaf margin,
leaf and midrib color, and thickness of midrib, than geographical characteristics. Leaf color and midrib thickness characters
clustered in the same group as OR49 and G18 accessions; S20, G6, and OR37 accessions, respectively.
The text was submitted by the authors in English. 相似文献