AFLP analysis of genetic relationships in the tribe Datureae (Solanaceae)

The AFLP technique was evaluated as a tool for assessing species relationships within the tribe Datureae and genetic distances were estimated for 47 accessions of over 12 species. The phenetic trees from various analyses of the AFLP data gave very high co-phenetic correlation values, and were found to be consistent with previous trees based on the analysis of different data types, in particular ITS-1 sequences, isozymes and morphology, carried out on the same accessions. These results indicated that the AFLP technique is both an efficient and effective tool for determining genetic relationships among taxa in the Solanaceae. A new classification is proposed for the tribe Datureae, which maintains the arborescent species as a separate genus, Brugmansia, and recognises three sections within the genus Datura; Stramonium, Dutra and Ceratocaulis. D. discolor, previously placed in section Dutra, was found to be intermediate between sections Dutra and Stramonium. Received: 11 January 1999 / Accepted: 1 February 1999     

Analysis of eggplant (<Emphasis Type="Italic">Solanum melongena</Emphasis>)-related germplasm: morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilization

A total of 94 Solanum accessions, including eggplants and related species, were morphologically characterized based on greenhouse observations, and molecularly analysed by the AFLP technique. Morphological parameters were helpful in assessing similarities or differences among accessions, and molecular data were used to support morphological conclusions. A dendrogram was computed based on the Dice genetic distances using the neighbour-joining method. The analysis was efficient in the assignment of a species name for eight out of nine accessions that were not previously classified, and revealed that 14 further accessions were misnamed in the collection originally received. The results indicate that the taxonomy of Solanum sections and subgenera including several species should be reconsidered. The AFLP technique was revealed as an efficient tool in determining genetic relationships among species. In general, morphological observations were consistent with molecular data, indicating that both approaches complemented to define the phylogenetic status of a large genus like Solanum. In terms of eggplant breeding, the molecular analysis of the Melongena complex, and of the other sections of the subgenus Leptostemonum, establishes useful germplasm relationships in the gene pool available for the genetic improvement of the cultivated species. The results we have provided highlight an urgent necessity to include molecular parameters in handling and characterizing the genebank-deposited germplasm related to cultivated crops.Communicated by F. Salamini     

What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background  

The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species.     

Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP

Gossypium species (± 49) represent a vast resource of genetic diversity for the improvement of cultivated cotton. To determine intra- and inter-specific genetic relationships within a diverse collection of Gossypium taxa, we employed 16 AFLP primer combinations on three diploid species, Gossypium herbaceum L. (A1), Gossypium arboreum L. (A2) and Gossypium raimondii Ulbrich (D5), and 26 AD allotetraploid accessions (Gossypium barbadense L. and Gossypium hirsutum L.). A total of 1180 major AFLP bands were observed; 368 of these (31%) were polymorphic. Genetic similarities among all taxa ranged from 0.21 (between the diploid species G. arboreum and G. raimondii) up to 0.89 (within G. barbadense). Phenetic trees based on genetic similarities (UPGMA, N-J) were consistent with known taxonomic relationships. In some cases, well-supported phylogenetic relationships, as well as evidence of genetic reticulation, could also be inferred. UPGMA trees and principal coordinate analysis based on genetic similarity matrices were used to identify genetically distinct cultivars that are potentially important sources of germplasm for cotton improvement, particularly of fiber quality traits. We show that AFLP is useful for estimating genetic relationships across a wide range of taxonomic levels, and for analyzing the evolutionary and historical development of cotton cultivars at the genomic level. Received: 17 January 2000 / Accepted: 4 May 2000     

Molecular analysis of introgressive breeding in coffee (Coffea arabica L.)

Nineteen arabica coffee introgression lines (BC₁F₄) and two accessions derived from a spontaneous interspecific cross (i.e. Timor Hybrid) between Coffea arabica (2n=4x=44) and C. canephora (2n=2x=22) were analysed for the introgression of C. canephora genetic material. The Timor Hybrid-derived genotypes were evaluated by AFLP, using 42 different primer combinations, and compared to 23 accessions of C. arabica and 8 accessions of C. canephora. A total of 1062 polymorphic fragments were scored among the 52 accessions analysed. One hundred and seventy-eight markers consisting of 109 additional bands (i.e. introgressed markers) and 69 missing bands distinguished the group composed of the Timor Hybrid-derived genotypes from the accessions of C. arabica. AFLP therefore seemed to be an extremely efficient technique for DNA marker generation in coffee as well as for the detection of introgression in C. arabica. The genetic diversity observed in the Timor Hybrid-derived genotypes appeared to be approximately double that in C. arabica. Although representing only a small proportion of the genetic diversity available in C. canephora, the Timor Hybrid obviously constitutes a considerable source of genetic diversity for arabica breeding. Analysis of genetic relationships among the Timor Hybrid-derived genotypes suggested that introgression was not restricted to chromosome substitution but also involved chromosome recombinations. Furthermore, the Timor Hybrid-derived genotypes varied considerably in the number of AFLP markers attributable to introgression. In this way, the introgressed markers identified in the analysed arabica coffee introgressed genotypes were estimated to represent from 9% to 29% of the C. canephora genome. Nevertheless, the amount of alien genetic material in the introgression arabica lines remains substantial and should justify the development of adapted breeding strategies. Received: 2 February 1999 / Accepted: 12 May 1999     

Genetic relationships among perennial and annual<Emphasis Type="Italic"> Cicer</Emphasis> species growing in Turkey assessed by AFLP fingerprinting

AFLP markers were used to assess genetic relationships among Cicer species with distribution in Turkey. Genetic distances were computed among 47 Cicer accessions representing four perennial and six annual species including chickpea, using 306 positions on AFLP gels. AFLP-based grouping of species revealed two clusters, one of which includes three perennial species, Cicer montbretii, Cicer isauricum and Cicer anatolicum, while the other cluster consists of two subclusters, one including one perennial, Cicer incisum, along with three annuals from the second crossability group (Cicer pinnatifidum, Cicer judaicum and Cicer bijugum) and the other one comprising three annuals from the first crossability group (Cicer echinospermum, Cicer reticulatum and Cicer arietinum). Consistent with previous relationship studies in the same accession set using allozyme and RAPD markers, in AFLP-based relationships, C. incisum was the closest perennial to nearly all annuals, and C. reticulatum was the closest wild species to C. arietinum. Cluster analysis revealed the grouping of all accessions into their distinct species-clusters except for C. reticulatum accessions, ILWC247, ILWC242 and TR54961; the former was found to be closer to the C. arietinum accessions while the latter two clustered with the C. echinospermum group. Small genetic distance values were detected among C. reticulatum accessions (0.282) and between C. reticulatum and C. arietinum (0.301) indicating a close genetic similarity between these two species. Overall, the AFLP-based genetic relationships among accessions and species were congruous with our previous study of genetic relationships using allozymes. The computed level of AFLP variation and its distribution into within and between Cicer species paralleled the previous report based on RAPD analyses. AFLP analysis also confirmed the presence of the closest wild relatives and previous projections of the origin of chickpea in southern Turkey. Results presented in this report indicate that AFLP analysis is an efficient and reliable marker technology in determination of genetic variation and relationships in the genus Cicer. Obviously, the use of AFLP fingerprinting in constructing a detailed genetic map of chickpea and cloning, and characterizing economically important traits would be promising as well.Communicated by P. Langridge     

Amplified fragment length polymorphism (AFLP) in soybean: species diversity, inheritance, and near-isogenic line analysis

Amplified fragment length polymorphism (AFLP) analysis is a PCR-based technique capable of detecting more than 50 independent loci in a single PCR reaction. The objectives of the present study were to: (1) assess the extent of AFLP variation in cultivated (Gycine max L. Merr.) and wild soybean (G. soja Siebold & Zucc.), (2) determine genetic relationships among soybean accessions using AFLP data, and (3) evaluate the usefulness of AFLPs as genetic markers. Fifteen AFLP primer pairs detected a total of 759 AFLP fragments in a sample of 23 accessions of wild and cultivated soybean, with an average of 51 fragments produced per primer pair per accession. Two-hundred and seventy four fragments (36% of the total observed) were polymorphic, among which 127 (17%) were polymorphic in G. max and 237 (31%) were polymorphic in G. soja. F₂ segregation analysis of six AFLP fragments indicated that they segregate as stable Mendelian loci. The number of polymorphic loci detected per AFLP primer pair in a sample of 23 accessions ranged from 9 to 27. The AFLP phenotypic diversity values were greater in wild than in cultivated soybean. Cluster and principal component analyses using AFLP data clearly separated G. max and G. soja accessions. Within the G. max group, adapted soybean cultivars were tightly clustered, illustrating the relatively low genetic diversity present in cultivated soybean. AFLP analysis of four soybean near-isogenic lines (NILs) identified three AFLP markers putatively linked to a virus resistance gene from two sources. The capacity of AFLP analysis to detect thousands of independent genetic loci with minimal cost and time requirements makes them an ideal marker for a wide array of genetic investigations.     

The utility of NBS profiling for plant systematics: a first study in tuber-bearing Solanum species

Systematic relationships are important criteria for researchers and breeders to select materials. We evaluated a novel molecular technique, nucleotide binding site (NBS) profiling, for its potential in phylogeny reconstruction. NBS profiling produces multiple markers in resistance genes and their analogs (RGAs). Potato (Solanum tuberosum L.) is a crop with a large secondary genepool, which contains many important traits that can be exploited in breeding programs. In this study we used a set of over 100 genebank accessions, representing 49 tuber-bearing wild and cultivated Solanum species. NBS profiling was compared to amplified fragment length polymorphism (AFLP). Cladistic and phenetic analyses showed that the two techniques had similar resolving power and delivered trees with a similar topology. However, the different statistical tests used to demonstrate congruency of the trees were inconclusive. Visual inspection of the trees showed that, especially at the lower level, many accessions grouped together in the same way in both trees; at the higher level, when looking at the more basal nodes, only a few groups were well supported. Again this was similar for both techniques. The observation that higher level groups were poorly supported might be due to the nature of the material and the way the species evolved. The similarity of the NBS and AFLP results indicate that the role of disease resistance in speciation is limited.     

Low-Cot DNA sequences for fingerprinting analysis of germplasm diversity and relationships in Amaranthus

We examined genetic diversity and relationships among 24 cultivated and wild Amaranthus accessions using the total low-Cot DNA and five individual repetitive sequences as probes. These low-Cot DNA probes were obtained by the isolation of various classes of repetitive-DNA sequences, including satellites, minisatellites, microsatellites, rDNA, retrotransposon-like sequences, and other unidentified novel repetitive sequences. DNA fingerprints generated by different types of repetitive-DNA probes revealed different levels of polymorphism in the Amaranthus genomes. A repetitive sequence containing microsatellites was found to be a suitable probe for characterizing intraspecific accessions, whereas more conservative sequences (e.g. rDNA) were informative for resolving phylogenetic relationships among distantly related species.Genetic diversity, measured as restriction fragment length polymorphism (RFLP) and the similarity index at the low-Cot DNA level, was equally high among intraspecific accessions between the two species groups: grain amaranths (A. caudatus, A. cruentus, and A. hypochondriacus) and their putative wild progenitors (A. hybridus, A. powellii, and A. quitensis). At the interspecific level, however, the grain amaranth species are less divergent from each other than their wild progenitors. With the rare exceptions of certain A. caudatus accessions, grain amaranths were found to be closely related to A. hybridus. The results based on low-Cot DNA were comparable with previous RAPD and isozyme studies of the same set of species/accessions of Amaranthus, indicating that low-Cot DNA sequences are suitable probes for a fingerprinting analysis of plant germplasm diversity and for determining phylogenetic relationships. Received: 19 October 1998 / Accepted: 8 January 1999     

AFLP markers support separation of Solanum nodiflorum from Solanum americanum sensu stricto (Solanaceae)

This study was aimed at examining the relationships between the African material of Solanum americanum (also designated as S. nodiflorum), accessions of this taxon from other geographical areas, and American S. americanum using AFLP markers. 96 individuals representing 39 accessions of S. americanum sensu lato and related diploid species from the widest possible geographical range, and one accession of S. dulcamara (as outgroup) were used. The AFLP results suggested that American S. americanum differs from S. nodiflorum and that the material investigated in this study can be assigned to three different species: S. americanum sensu stricto, S. nodiflorum and a Solanum species from Brazil. These species can be differentiated based on a combination of floral and fruit characteristics.     

The potential of AFLPs in biosystematics: A first application inSolanum taxonomy(Solanaceae)

Using the AFLP technique highly informative DNA fingerprints were generated from 19 taxa ofSolanum sect.Petota (potatoes) and three taxa ofSolanum sect.Lycopersicum (tomatoes). Both phenetic and cladistic analyses were conducted from the individual genotypic level to the species level. An AFLP fingerprint, using a combination of suitable AFLP primers, generated 12 to 71 scorable fragments per genotype which was sufficient for taxonomic interpretation. The classifications based on the molecular markers were generally in agreement with current taxonomic opinions. Unexpectedly,S. microdontum was associated with ser.Megistacroloba rather than with ser.Tuberosa, andS. demissum (ser.Demissa) and species of ser.Acaulia appeared closely affiliated. AFLP is an efficient and reliable technique to generate biosystematic data and therefore a promising tool for evolutionary studies.     

Musa Genetic Diversity Revealed by SRAP and AFLP

The sequence-related amplified polymorphism (SRAP) technique, aimed for the amplification of open reading frames (ORFs), vis-â-vis that of the amplified fragment length polymorphisms (AFLP) were used to analyze the genetic variation and relationships among forty Musa accessions; which include commercial cultivars and wild species of interest for the genetic enhancement of Musa. A total of 403 SRAP and 837 AFLP amplicons were generated by 10 SRAP and 15 AFLP primer combinations, of which 353 and 787 bands were polymorphic, respectively. Both cluster analysis of unweighted pair-grouping method with arithmetic averages (UPGMA) and principal coordinate (PCO) analysis separated the forty accessions into their recognized sections (Eumusa, Australimusa, Callimusa and Rhodochlamys) and species. The percentage of polymorphism amongst sections and species and the relationships within Eumusa species and subspecies varied between the two marker systems. In addition to its practical simplicity, SRAP exhibited approximately threefold more specific and unique bands than AFLP, 37 and 13%, respectively. SRAP markers are demonstrated here to be proficient tools for discriminating amongst M. acuminata, M. balbisiana and M. schizocarpa in the Eumusa section, as well as between plantains and cooking bananas within triploid cultivars.     

Genetic characterization of Paspalum notatum accessions by AFLP markers

Paspalum notatum Flügge is a warm-season forage grass with sexual diploid and apomictic tetraploid races. Genetic improvement was achieved in out-breeding diploids. The acquisition of artificial sexual tetraploids has raised the possibility of performing crosses and plant improvement at the tetraploid level. The objective of our study was to obtain a genetic and cytoembryological characterization of a germplasm collection of P. notatum, including 31 accessions from seven countries of America and 11 experimentally obtained genotypes. Morphology of mature gametophytes was observed to assess the mode of reproduction of the accessions. A total of 1342 AFLP fragments were generated across the 42 genotypes and from two reference taxa: P. urvillei and P. procurrens. AFLP data were converted into a binary matrix and similarity relationships were established. The genetic distance among all the accessions showed a maximum value of 0.36. In addition, eleven AFLP fragments were observed exclusively in apomictic plants, which could be linked to genomic regions implicated in the control of apospory.     

Characterization of genetic diversity of nuclear and mitochondrial genomes in Daucus varieties by RAPD and AFLP

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     

Assessment of genetic diversity among and within Achillea species using amplified fragment length polymorphism (AFLP)

Amplified fragment length polymorphism (AFLP) markers were used to assess the genetic diversity of 57 Achillea accessions belonging to five species, A. millefolium, A. filipendulina, A. tenuifolia, A. santolina and A. biebersteinii. Nine AFLP primer combinations were used, which produced 301 polymorphic bands. In most species, a high level of genetic variation was detected among the genotypes. The Jaccard's similarity indices (J), based on AFLP profiles, were subjected to UPGMA cluster analysis. Application of Mantel's test for cophenetic correlation to the cluster analysis indicated the high fitness of the accessions to a group (r = 0.918). The dendrogram generated revealed five major groups corresponding to five species. The principle coordinate analysis (PCoA) data confirmed the results of the clustering. Among the species, A. teunifolia and A. santolina showed the greatest and the least genetic diversity, respectively. A. filipendulina accessions were acquired primarily from the same ecological regions of western Iran. Accessions belonging to A. biebersteinii originated from the Isfahan province and were separated from other species at the root of the dendrogram. The results of the clustering method, based on AFLP markers, corresponded closely with the geographical origins of the genotypes. The results of the present study could contribute to a better understanding and management of conservation and exploitation of the Achillea germplasm.     

Genetic relationship in ecotypes of Leymus chinensis revealed by polymorphism of amplified DNA fragment lengths

Leymus chinensis (Trin.) Tzvel is a perennial grass in the tribe Gramineae and important forage in Northern China. Knowledge of its genetic diversity is a prerequisite for using modern breeding techniques. Amplified fragment length polymorphism (AFLP) was first used to evaluate the genetic relationship among and within three ecotypes. Distinct clusters were produced based on AFLP markers. All accessions from the same ecotype were grouped in a cluster except accessions 6. According to AFLP profile ecotype-specific bands differ from each other. The genetic differentiation within the ecotype of the species was much smaller than that among ecotypes. Self-incompatibility in this species contributes to evident genetic differentiation together with environment. These results indicate that ecotypes were distinguished visually similarly to genetic variation. Published in Russian in Fiziologiya Rastenii, 2006, Vol. 53, No. 5, pp. 764–770. The text was submitted by the authors in English.     

AFLP assessment of genetic variability among velvetbean (Mucuna sp.) accessions

Velvetbean (Mucuna sp.) is a self-pollinated crop classified within the Leguminosae. Using AFLP markers, gene diversity and phenetic relationships were estimated in a collection of 40 velvetbean accessions from cultivated species and different eco-geographic regions. Eleven selective primer combinations generated a total of 508 amplification products. The average number of scorable fragments was 23 per primer combination. A total of 251 polymorphic markers was detected. The polymorphisms obtained ranged from 36% to 61% with an average of 49%. The final phenetic trees were constructed using Nei and Li’s coefficient of similarity with UPGMA. Other clustering algorithms were examined and all had high co-phenetic correlations, indicating the goodness of fit for the resulting phylogenetic trees. The phenetic tree as well as principal component analysis (PCA) separated the 40 velvetbean accessions into two main clusters. Bootstrap and Jackknife analyses were completed and their values indicated strong to moderate support for the two main clusters. This grouping confirmed the existing phenological difference with regard to maturity. The high values of the similarity coefficients observed (0.87 to 0.97) imply that the accessions used in this study are similar. The level of genetic variability detected within the velvetbean accessions with AFLP analysis suggests that it is a reliable, efficient, and effective marker technology for determining genetic relationships in velvetbean. Received: 19 June 2000 / Accepted: 1 March 2001     

Assessing changes in the genetic diversity of potato gene banks. 1. Effects of seed increase

 Effects of gene bank seed-increases on the genetic integrity of potato germ plasm is a major concern of gene bank managers. Thus the Association of Potato Inter-gene-bank Collaborators (APIC), a consortium of world potato gene bank leaders, initiated this joint research project using RAPD markers to determine genetic relationships between increased generations within accessions. Solanum jamesii (2n=2x=24) and S. fendleri (2n=4x=48), two wild potato species native to North America, were used as plant material. These species represented two major breeding systems found among Solanum species: outcrossing diploids and inbreeding disomic tetraploids, respectively. Comparisons were made between populations one generation apart and between sister populations generated from a common source. Fourteen such comparisons within S. jamesii accessions had an average similarity of 96.3%, and 21 such comparisons within S. fendleri accessions had an average similarity of 96.0%. No pairs of populations were significantly different, despite the fact that RAPD markers easily separated all of these very similar accessions within their respective species. Only one of six S. jamesii accessions analyzed showed a significant change in gene frequencies among generations. These findings indicate that there has been minimal loss or change of genetic diversity in ex situ germplasm using the gene bank techniques standard at NRSP-6 and other world potato gene banks. Received: 28 October 1996 / Accepted: 7 March 1997     

AFLP analysis of the phenetic organization and genetic diversity of Vigna unguiculataL. Walp. reveals extensive gene flow between wild and domesticated types

Amplified fragment length polymorphisms (AFLPs) were used to evaluate genetic relationships within cowpea [Vigna unguiculata (L.) Walp.] and to assess the organization of its genetic diversity. Nei’s genetic distances were estimated for a total of 117 accessions including 47 domesticated cowpea (ssp. unguiculata var. unguiculata), 52 wild and weedy annuals (ssp. unguiculata var. spontanea), as well as 18 perennial accessions of the wild subspecies pubescens, tenuis and alba. AFLP variation was also used to study genetic variation among and within domesticated and wild accessions based on their geographical origin (western, eastern and southern Africa). Wild annual cowpea (var. spontanea) (H _T =0.175) was more diverse than domesticated cowpea (H _T =0.108). Wild cowpea was more diverse in eastern (H _S =0.168) than in western Africa (H _S =0.129), suggesting an eastern African origin for the wild taxon. The AFLP data were consistent with earlier findings of a unique domestication event in cowpea in the northern part of the continent and suggested that domestication in eastern or southern Africa was unlikely. It did not allow a more precise localization of domestication due to extensive gene flow between wild and domesticated forms that has led to a large crop-weed complex distributed over the entire African continent. In addition, wild materials from northeastern Africa are still lacking. Overall, the superiority of the AFLP technique over isozymes resided in its ability to uncover variation both within domesticated and wild cowpea, and should be a powerful tool once additional wild material becomes available. Received: 11 September 2000 / Accepted: 14 June 2001     

Genetic relationships between Korean Calanthe species and some naturally occurring mutants based on multiple DNA markers

RAPD, ISSR and AFLP were used to assess the genetic relationships among Korean Calanthe (Orchidaceae) species. Sixteen accessions belonging to five native Calanthe species and some spontaneous mutants were studied. The mutants clustered with C. sieboldii, indicating that they are genetically closer to C. sieboldii than to the rest of the species. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is close to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor. Calanthe reflexa and C. aristulifera were the most genetically differentiated of the species studied. We identified 117, 42, 50 putative makers via RAPD, ISSR and AFLP analysis, respectively.