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Genetic variation and relationships among members of the azuki bean complex (Vigna angularis) including wild (V. angularis var. nipponensis), weedy, and cultivated types (V. angularis var. angularis), V. nakashimae, and rice bean (V. umbellata) from Korea were examined using the Amplified fragment length polymorphism (AFLP) method. AFLP analysis of 50 accessions
revealed 333 (72.1%) polymorphic fragments out of 462 fragments amplified using seven primer combinations. The number of polymorphic
fragments within each species was 70 in the azuki bean complex and 41 in V. nakashimae, but there was no polymorphism in rice bean. The number of shared fragments among species ranges from 142 between the azuki
bean complex and V. nakashimae to 166 between the azuki bean complex and rice bean. Within the azuki bean complex, the range of shared bands was from 231
between cultivated and weedy types to 238 between cultivated and wild types. A dendrogram generated from Jaccard’s similarity
matrix was divided into three groups, which correspond to V. nakashimae, azuki bean complex, and rice bean. The relationship between azuki bean and rice bean is closer than between azuki bean and
V. nakashimae. Phenetic distances averaged 0.502 between the azuki bean complex and V. nakashimae and 0.467 between the azuki bean complex and rice bean. Within the azuki bean complex, the weedy type was more closely related
to wild than cultivated types. But UPGMA dendrogram of the azuki bean complex reveals that each type is not clearly isolated.
These results will help to understand genetic diversity and evolutionary dynamics of Vigna in Korea. 相似文献
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Xiao-Hua Qi Ming-Fang Zhang Jing-Hua Yang 《Genetic Resources and Crop Evolution》2007,54(8):1709-1716
Sequence variation of nuclear internal transcribed spacer regions of ribosomal DNA (ITS1, 5.8S rRNA and ITS2) from Chinese
vegetable mustards (AB-genome) and its putative parents Brassica rapa (the A-genome) and Brassica nigra (the B-genome) were used to investigate the molecular phylogeny and the probable evolutional pattern of this amphidiploid
species that uniquely formed in China. Totally, 16 accessions of Chinese vegetable mustard those covering nearly all the diverse
variations were included in this study, and together with three accessions of B. rapa and one accession of B. nigra. The results disclosed two strongly supported clades, one containing four accessions of vegetable mustard which have closer
relationship with B-genome species “B.nigra” lineage and the other containing 12 accessions of B. juncea and three A-genome accessions. This classification was in disagreement with the evidence from chloroplast DNA, mitochondrial
DNA, nuclear DNA restriction fragment length polymorphism (RFLP), which suggested that B. juncea was closely related to the A-genome type. For the incongruence, we speculated that the B. juncea crops derived from Chinese have evolved through different recombined events of the diploid morphutypes and evolved unidirectional
concerted evolution. The traditional phenotypic classification of B. juncea was not wholly supported by ITS results, and hence the phylogenetic relationships among these subspecies need to be reconsidered
on molecular level. 相似文献
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Genetic variation within and among several Sorghum populations from different agroecological zones in Malawi were investigated using random amplified polymorphic markers (RAPDs). DNA samples from individual plants were analyzed using 35 oligonucleotides of random sequence. Twenty five of these primers allowed amplifications of random polymorphic (RAPD) loci. Overall, 52% of the scored loci were polymorphic. Every accession was genetically distinct. The analysis of molecular variance revealed that the within-region (among accessions) variations accounted for 96.43% of the total molecular variance. Observed variations in allelic frequency was not related to agroecological differences. The degree of band sharing was used to evaluate genetic distance between accessions and to construct a phylogenetic tree. Further analysis revealed that the sorghum accessions analyzed were genetically close despite considerable phenotypic diversity within and among them. It is suggested that all the sorghum landraces currently available in Malawi should be conserved both ex situ and in situ to maintain the current level of genetic diversity. 相似文献
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Yomara Rozo Lorena Quintero Mauricio Parra Carlos Rodríguez Luz Marina Melgarejo 《Genetic Resources and Crop Evolution》2009,56(1):77-83
Couepia is a genus distributed in tropical regions of America. The nut of some Couepia species is used as fresh fruit and oil source for local communities. Despite its critical situation of conservation and its
economic potential, there is a lack of information on the genetic variability of Couepia species. This study examines AFLP variation among 40 accessions of Couepia collected in the Colombian Amazonian region, representing two species: Couepia
dolichopoda and Couepia
subcordata. The individuals were examined for 96 markers generated from four EcoRI/MseI primer pairs, with 80% polymorphism across all accessions studied. According to cluster analysis, 40 accessions were grouped
into two major clusters, corresponding to the two species analyzed, except one case whose situation is discussed. In C. dolichopoda accessions, significant correlation between the clustering pattern and the geographical origin was detected; the extent of
variation within and among its collect sites was examined by AMOVA. The knowledge about the genetic variability of the accessions
examined contributes to development of Couepia conservational efforts. 相似文献
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Total 65 lotus accessions in genus Nelumbo mainly collected from China, were subjected to random amplified polymorphic DNA (RAPD) markers to estimate the genetic diversity
and to test the genetic basis of the relationships between morphotypes and molecular markers. Seventeen primers generated
a total of 195 highly reproducible and discernible loci, among which 173 were polymorphic. Percent polymorphism varied from
66.7 to 100 with an average of 88.72, and five primers out of them, OPC05, OPG10, OPN20, OPP09 and OPS17, showed 100% polymorphism.
A relatively high genetic diversity was detected among all the samples with the similarity coefficient values ranging from
0.45 to 0.85, and Nei’s gene diversity (h) 0.30, and Shannon index (I) 0.46. The UPGMA dendrogram clustered 65 accessions in four clusters and the clustering pattern showed two groups, N. nucifera ssp. nucifera and those accessions related to the American lotus, and some special cultivars, landraces, hybrids and the American lotus.
Principal Coordinate Analysis (PCA) further indicated that the genetic diversity of Nelumbo accessions was not evenly distributed, instead, was presented by a clustered distribution pattern. Similar to the results
revealed by the dendrogram, two main groups representing the two subspecies of N. nucifera, as well as some special landraces, cultivars of Chinese lotus, the Japanese lotus and hybrids out of the two groups were
obtained. Neither the UPGMA dendrogram nor the PCA analysis exhibited strict relationship with geographic distribution and
morphotypes among the accessions. 相似文献
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A polymerase chain reaction (PCR) based approach involving the directed amplification of minisatellite DNA region (DAMD-PCR)
was used to identify accession specific DNA markers and study genetic relationships between and within 15 accessions corresponding
to 11 species in genus Capsicum. A touch down PCR profile and unique chemical concentration of ingredients resulted in reproducible and reliable DNA amplifications.
The number of amplified products varied from 1 to 12 fragments depending on the template DNA and the primers. The DAMD-PCR
technique provided a total of 38 accession specific DNA markers (diagnostic DAMD-PCR) which can be utilized in accession identification,
preservation and genetic studies of Capsicum germplasm. Based on 1,292 polymorphic and monomorphic DNA markers directed with 22 minisatellite specific primers, accessions
were divided into four major groups, three of which corresponded to the three distinct Capsicum complexes. Capsicum chacoense was found to be the most distinct species. 相似文献
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Gerard Allan Amber Williams Pablo D. Rabinowicz Agnes P. Chan Jacques Ravel Paul Keim 《Genetic Resources and Crop Evolution》2008,55(3):365-378
Worldwide genetic diversity in 200 individuals comprising 41 castor bean accessions was assessed using amplified fragment
polymorphisms (AFLPs) and simple sequence repeats (SSRs). We found that, despite surveying five continents and 35 countries,
genetic diversity in castor bean germplasm is relatively low (overall H
e = 0.126 for AFLPs and 0.188 for SSRs) compared to estimates of genetic diversity in other plant species. Our data also show
no geographic structuring of genotypes across continents or countries within continents. An assessment of the congruence between
AFLP and SSRs indicates a low correlation (R
2 = 0.19) between the two data sets, but each marker class nonetheless shows similar patterns of low-genetic diversity and
a lack of geographic structure. Our data do suggest that SSRs yield a higher percentage of polymorphic loci, higher heterozyosity
and a greater range of genetic distances, and are therefore more informative than are AFLPs on a locus-by-locus basis. Based
on comparisons with numerous other plant species, we suggest that the lower genetic variation in this worldwide collection
may be due to one or more factors including: sampling strategies that have not captured the full extent of genetic variation
in the species; artifactual variation due to long-term germplasm storage and seed regeneration; or intense selection followed
by domestic cultivation of a limited number of castor bean genotypes, which are widely propagated for their horticultural
and agro-economic value. 相似文献
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Tobias W. Eschholz Roland Peter Peter Stamp Andreas Hund 《Genetic Resources and Crop Evolution》2008,55(7):971-983
About 65 years ago, more than 150 Swiss maize landraces (Zea mays L. ssp. mays) of the flint type were collected and conserved ex situ. Due to the climatically and culturally diverse environment of the Alps, a considerable genetic diversity of this material
was assumed. To prove this, an efficient method was required to carry out genetic profiling of all the accessions in the Swiss
Gene Bank. Simple sequence repeat marker (SSR) profiling in combination with the visualization of the polymerase chain reaction
(PCR) products on agarose gels was chosen. Here a set of 19 different landrace accessions was analyzed to: (i) investigate
their genetic diversity, (ii) investigate and display the population structure and (iii) determine whether DNA bulks rather
than single plants can be used for such analyses. Four repeated samples of one accession were found to be much closer to one
another than to the rest of accessions. Furthermore, specific alleles were identified for several accessions. The PCR products
of the bulked DNA samples represented only a small part of the variation revealed by the analysis of individuals. Loci with
four base repeat motifs performed better in the analysis of bulks than loci with other repeat motifs. The correlation between
genetic distance matrices, based on the analysis of individuals and bulks, respectively, was significant. Thus, the single
plant approach allowed for sufficient differentiation of accessions, and DNA bulks visualized on agarose gels led to correlated
genetic distances although a limited number of alleles were detected. Although the limited resolution of agarose gels likely
causes some bias, profiling of larger sets with the individual plant approach appears feasible and more informative compared
to the bulk analysis we conducted. 相似文献
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Hironori Katayama Shiho Adachi Toshiya Yamamoto Chiyomi Uematsu 《Genetic Resources and Crop Evolution》2007,54(7):1573-1585
Iwateyamanashi (Pyrus ussuriensis var. aromatica) is one of the Pyrus species which grows wild in Japan. The number of Iwateyamanashi trees has been decreasing, so conservation and evaluation
is urgently needed. Over 500 accessions of Pyrus species collected from Iwate in northern Tohoku region are maintained at Kobe University as an Iwateyamanashi germplasm collection.
In order to investigate the genetic diversity, five SSR (simple sequence repeat) markers, developed from Japanese and European
pear were examined for 86 Pyrus individuals including 58 accessions from Iwate. These SSR loci could discriminate between all the Iwate accessions except
for 10 that bear seedless fruit, as well as determine the genetic diversity in Iwateyamanashi germplasms. High levels of variation
were detected in 41 alleles and the mean observed heterozygosity across 5 loci was 0.50 for the Iwate accessions. Seedless
accessions sharing identical SSR genotype with the local pear variety “Iwatetanenashi” were supposed to have been propagated
vegetatively via grafting. In an UPGMA phenogram, Japanese pear varieties (P. pyrifolia) were clustered into two groups with some Iwate accessions including seedless ones. Another 38 Iwate accessions were not
clustered clearly, and there was no clear relationship between these accessions and geographical distribution or morphological
characters. Allele frequency revealed that the Iwate accessions were genetically more divergent than the Japanese pear varieties.
Most Japanese pears possessed a 219 bp deletion at a spacer region between the accD and psaI genes in the chloroplast DNA (cpDNA), but other Pyrus species and two Iwateyamanashi trees did not. In the Iwate accessions, 79.3% had a deletion type cpDNA and others had a standard
type cpDNA without deletion. These results are indicative of the wide range of genetic diversity in the Iwate accessions which
include Japanese pear varieties. A combination of SSR and cpDNA analyses revealed high heterogeneity in Iwateyamanashi and
coexistence of Iwateyamanashi and hybrid progeny with P. pyrifolia. These could be reasons for the wide range of continuous morphological variation described previously. 相似文献
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Arun Kumar M. K. Kaul M. K. Bhan Punit K. Khanna K. A. Suri 《Genetic Resources and Crop Evolution》2007,54(3):655-660
Six phenotypic characters and three withanolide markers were assessed in 25 accessions of Withania somnifera collected from different states of India for studying genetic variability. The variability ranges observed at phenotypic
and chemotypic levels were polymorphic. Based on D2 values and PCA (Principal Component Analysis) of phenotypic traits like plant height, no. of branches/plant, no. of seeds/berry,
root length, root diameter and root yield, these 25 accessions were grouped in five clusters. The relative contribution of
each character towards genetic divergence was worked out. Five accessions–AGB002 (Rajasthan), AGB003 (J&K), AGB004 (Madhya
Pradesh), AGB006 (J&K) and AGB009 (Punjab) representing clusters 2 and 4 exhibited maximum intra and inter-cluster divergence.
Cluster 5 representing accession AGB053 (Andhra Pradesh) was having mixed traits. Chemically most of the accessions in cluster
3 showed uniformity in presence of three marker withanolides Withaferin A, Withanone and Withanolide A in the leaves. 相似文献
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Fifty six germplasm accessions of the important East African fodder crop Napier grass, Pennisetum purpureum, and its hybrids with P. glaucum, were characterised using 67 random amplified polymorphic DNA (RAPD) fragments. No or very low intra-accession variation was found for 49 of the accessions examined, confirming field observations that this species is predominantly clonally propagated. Comparison of intra and inter-accession variation identified several groups of identical/similar accessions that could be targeted if the collection is to be rationalised, and also highlighted two misplantings of germplasm material during transfer to a field trial site. A neighbour joining dendrogram of Jaccard's similarity estimates, clearly separated 50 accessions of P. purpureum from three P. glaucum individuals, and placed six hybrid accessions in an intermediate position. These groupings were well supported by a nested AMOVA (P<0.001; 29.5% of total variance due to taxonomic delineation). The main group of P. purpureum individuals could be further differentiated into five sub-groups (designated East Africa, Southern Africa, USA1, USA2 and Miscellaneous, to reflect the majority membership of sub-groups) and examination of the within P. purpureum component of the nested AMOVA, found them to be significantly different (P<0.001; 18.8% of variance). Genetic diversity across all accessions was found to be fairly high (Shannon's diversity index 0.306) and thus the collection probably represents a wide genetic base for this species. In addition to germplasm accessions, 25 Kenyan farm clones were also analysed. A principal coordinate analysis found that all but one of the clones clustered with the main P. purpureum group of accessions, indicating that the majority are probably not interspecific hybrids. The origin and pedigree of clones is discussed based on genetic similarity amongst clones and to germplasm accessions. 相似文献
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Genetic diversity and intra-specific phylogeny of Triticum turgidum L. subsp. dicoccon (Schrank) Thell. revealed by RFLPs and SSRs 总被引：2，自引：5，他引：2
Today, emmer wheat, T. turgidum subsp. dicoccon, widely grown in the past is a candidate crop for sustainable agriculture in Italy. As part of a research project aimed at the enhanced use of the hulled wheat germplasm, molecular characterization was carried out to understand the genetic structure of the crop and to identify accessions of interest. A collection of 194 accessions was analyzed with 15 microsatellite loci (SSRs), while only a sample of 38 accessions was tested with 19 RFLP probes. The marker loci were selected on the basis of their independent genomic distribution. Genetic distances and allelic frequencies were calculated for each marker class. The genetic relationships were visualized with dendrograms. RFLP loci were, on average, less polymorphic than SSRs. An average Dice's genetic distance of 0.22 for RFLPs vs 0.38 for SSRs was detected, while an expected average heterozygosity per locus of 0.23 for RFLPs vs 0.26 for SSRs was also estimated. With a least number of 10 loci per marker class it was possible to identify each genotype. The most diverse accessions had different geographic origins. Germplasms from Italy and Ethiopia appear to belong to a more primitive genepool, given that a group of accessions from these countries were genetically differentiated from a Russian-Iranian group. 相似文献
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Engin Ertan 《Genetic Resources and Crop Evolution》2007,54(4):691-699
The aim of this study is to characterize 10 European chestnut (Castanea sativa Mill.) accessions which were selected among 80 accessions at the end of a selection study in Nazilli in Turkey. During the
harvest periods in 2001, 2002 and 2003, European chestnut accessions were examined. Nineteen morphological, pomological and
biochemical characters were used. Significant genotype×year interaction were found for all traits but one. Multivariate methods,
including cluster and principal component analysis were performed to characterize the accessions. The first five principal
components account for 86.44% of the total variance of all traits, indicating a high degree of correlation among the characteristics
analyzed. High level of phenotypic proximity was found between the accessions N-20-2 and N-5-1 based on pomological, morphological
and biochemical characteristics. 相似文献
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The collection, identification and maintenance of genebank accessions of the genus Trifolium is a major task because of the large number of genera and their occasional morphological similarity. We investigated whether
the measurement of nuclear DNA content can serve as an additional criterion for identification of mislabeled accessions. Relative
nuclear DNA content was determined by flow cytometry measurements for a total of 151 genebank accessions of 23 Trifolium species with notable agronomical value. Among 23 species analyzed, 15 were found to possess a uniform relative nuclear DNA
content, with intraspecific variability of the majority of analyzed species lower than 5%. Within six Trifolium species, 1–2 atypical accessions with outstanding differences in relative DNA content, chromosome number and morphological
features were found. In T. hybridum and partially in T. ambiguum these outstanding differences could be ascribed to variations in accession ploidy level. For the remaining atypical accessions,
the determined nuclear DNA content, chromosome number and morphological features were not related to those characteristic
of the species. Additionally taxonomic identity of atypical accessions was determined using ITS region sequencing and morphological
observations. We propose flow cytometric measurements of nuclear DNA content as simple and reliable technique which can be
used at seedling stage to verify identity and genetic stability of Trifolium genebank accessions. 相似文献