Genetic diversity of the African hexaploid species Solanum scabrum Mill. and Solanum nigrum L. (Solanaceae)

Two hexaploid species of Solanum sect. Solanum are present in Africa: Solanum scabrum and S. nigrum. Solanum scabrum is a widely cultivated species and is used as a leafy vegetable, as a source of medicine and as a source of ink dye. In previous studies a wide range of morphological diversity has been reported in this species and in some studies subspecies have been proposed. Subspecies are also recognized in S. nigrum. However, it has not been established whether or not the morphological differences are reflected at the genomic level. The present study applies AFLPs to study the genetic diversity in S. scabrum and its relationship to geographical provenance, morphological differences and the possible existence of subspecies within S. scabrum and S. nigrum. The data obtained were analyzed with cluster analysis (using UPGMA and NJ). The results indicate that the genetic variation within S. scabrum was higher within accessions than between accessions. Accessions did not cluster according to their geographical provenance, indicating that accessions from different geographical areas were not significantly different genetically. The clustering reflected neither morphological differences nor domestication status (cultivated or wild). The morphological differences exhibited by S. scabrum could be due to selection by farmers for different plant types. The AFLP derived clustering pattern did not segregate the subspecies recognized in S. scabrum and S. nigrum into separate subclusters.     

Genetic relationships among cultivated types of Perilla frutescens and their weedy types in East Asia revealed by AFLP markers

AFLP markers were employed to detect genetic diversity in two cultivated Perilla frutescens (i.e. var. frutescens and var. crispa) and their weedy types and to assess their genetic relationships. Analysis of 60 Perilla accessions from China, Korea and Japan by seven AFLP primer combinations identified a total of 125 fragments, of which 80 (64%) were polymorphic at the species level. The phenotypic diversity meassured by Shannon's index of information for the cultivated type of var. frutescens, the weedy type of var. frutescens, the cultivated type of var. crispa and the weedy type of var. crispa were on average 1.07, 2.23, 1.24 and 1.75, respectively. The weedy types exhibited high within-type variation in spite of a small number of samples. In the neighbor joining tree, two major clusters were recognized: (1) cultivated type of var. frutescens, (2) weedy type of var. frutescens, and cultivated and weedy types of var. crispa. The cultivated types of var. frutescens and of var. crispa were sharply separated by AFLPs. However, there remained ambiguities in regard to the intraspecific relaltionships, due to the clustering of the weedy types which occured in each of the clusters of the cultivated types. Two cultivated types of P. frutescens and their weedy types should be taxonomically considered as a P. frutescens complex. The present AFLP data are consistent with the hypothesis that China is the original place of cultivation of var. frutescens and Korea is a secondary center of diffusion of var. frutescens.     

Identification and genetic relationships of kenaf (Hibiscus cannabinus L.) germplasm revealed by AFLP analysis

Kenaf (Hibiscus cannabinus L.) is one of the world's most economically important fiber crops. In order to identify different varieties, and investigate its diversity and genetic relationships, twenty-three kenaf accessions and two accessions of its relative, roselle (H. sabdariffa var. altissima), were analyzed by morphological characterization and AFLP fingerprinting. It is very difficult to identify kenaf accessions based merely on morphological characters, due to their limited variation. For the AFLP study, a total of 505 polymorphic markers (out of 560) were produced by six selected AFLP primer combinations. The AFLP fingerprinting was effective in identifying all kenaf accessions included in the study. Kenaf and roselle are independent species with close relationships, and great genetic diversity was also detected among the kenaf accessions with different origins, based on the analysis of the AFLP markers. The AFLP analysis strongly supports the opinion that kenaf originated in Africa. It also demonstrated that the dissemination of kenaf was from Africa through Asia to Central and North America.     

Comparison of genetic variation among accessions of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> using AFLP and SSR markers

Genetic diversity of 54 accessions of Aegilops tauschii from five countries was assessed using sequence-tagged microsatellites (or simple sequence repeats, SSRs) and amplified fragment length polymorphisms (AFLPs). In the case of AFLP analysis, a total of 256 amplification products obtained, 234 of them were polymorphic across all the 54 accessions. A total of 224 fragments were obtained from the 24 SSR primers and 219 of fragments were polymorphic across all the genotypes screened. Based on both AFLP and SSR markers, the highest percentage of polymorphisms were obtained in Iranian and accessions of unknown origin. The highest polymorphic information content (PIC) value was observed for SSRs (0.82) while the highest marker index (MI) value was for AFLPs (8.5) reflecting the hyper-variability of the first and the distinctive nature of the second system. Principal co-ordinate analysis (PCO) revealed congruent patterns of genetic relationships for both data sets, but did not group accessions strictly according to their geographical origins. Poor correlation was found between AFLP and SSR marker loci. This low association may be due to low number of AFLP and SSR markers. These results show that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.     

Diversity of Nordic Landrace Potatoes (<Emphasis Type="Italic">Solanum tuberosum</Emphasis> L.) Revealed by AFLPs and Morphological Characters

The management of genebank collections of cultivated potato is costly due to the need for in vitro maintenance and virus eradication. Therefore, it is important to set up conservation strategies, which prevent duplicates entering the collections. In this study, 32 Nordic potato landraces were studied for 57 morphological traits and analysed for amplified fragment length polymorphism (AFLP). Most landraces could be distinguished based on the morphological characters, except five accessions. Using five primer combinations to generate 114 reproducible AFLPs, of which 63 (55%) were polymorphic, the five morphologically indistinguishable accessions were placed into two groups with identical AFLP patterns, suggesting that some of the accessions were redundant for long-term preservation. The AFLP data showed that the Nordic collection of potato landraces is composed of genetically different clones, and morphological analysis revealed a wide range of variability. This variability seems to be distributed randomly over the Nordic region since the cluster analysis based on AFLPs and morphological traits revealed no grouping based on the country of origin. Principal component analysis suggests that fewer morphological traits than used in this study will be sufficient to discriminate between different genotypes of cultivated potato (Solanum tuberosum L.). Future possibilities for rationalising potato collections are discussed.     

AFLP analysis of diploid species in the genus Vigna subgenus Ceratotropis

A representative set of germplasm of genusVigna subgenus Ceratotropis specieswas used to analyze genetic diversity using amplified fragment lengthpolymorphism (AFLP) methodology. The germplasm was selected based onmorphological diversity and geographic origin and includes 18 out of the 21species in the subgenus Ceratotropis. Genetic diversitywithin and between taxa was measured using information generated by AFLP bandpolymorphism from which Jaccard's similarity coefficient and nucleotidediversity were estimated. The data were also used to generate phenograms tovisualize relationships among analyzed accessions. All species in sectionsCeratotropis and Aconitifoliae arewell separated. However, most of the species in sectionAngulares show a high level of similarity suggesting a lowlevel of genetic differentiation. In section Angulares onespecies, V. trinervia, is welldifferentiated from the other species and represents a separate evolutionarybranch between section Ceratotropis and other species insection Angulares. The relationships between the newlydescribed species V. aridicola,V. exilis, V.nepalensis and V.tenuicaulis and other species in the subgenusCeratotropis are described for the first time based on AFLPdata.     

Genetic Variation of Ethiopian Mustard (Brassica carinata A. Braun) Germplasm in Western Canada

Information on genetic diversity and genetic relationships among genotypes of Brassica carinata is currently limited. The objectives of this study were to evaluate patterns and levels of genetic diversity in B. carinata based on amplified fragment length polymorphisms (AFLP) as compared with Brassica juncea and Brassica nigra, and to evaluate agronomic and seed quality data for plants grown in the field in western Canada. A total of 296 AFLP bands were generated from four primer pair combinations and scored for presence/absence in 66, 20 and 7 accessions of B. carinata, B. juncea and B. nigra, respectively. B. carinata was less genetically diverse than the other two species. Differences in diversity were evident in the proportion of polymorphic loci within each species: 23, 35 and 50% for B. carinata, B. nigra and B. juncea, respectively. Pair-wise similarity measures based on the Jaccard coefficient were highest among accessions of B. carinata and showed the narrowest range: 0.911 (0.810–0.981) compared to B. nigra: 0.569 (0.438–0.660) and B. juncea: 0.715 (0.345–0.951). AFLP-based genetic distance information can be used by plant breeders to select diverse genotypes. AFLPs are also useful for fingerprinting cultivars and two primer pair combinations were sufficient to uniquely identify all the accessions of B. carinata. More variation among accessions was identified in the agronomic trial than had previously been described in studies of B. carinata in western Canada, but the data were too limited to draw conclusions regarding specific accessions. Overall, the findings were in agreement with other published work describing the favourable agronomic potential of this species.     

Analysis of genetic diversity in Piper nigrum L. using RAPD markers

RAPD analysis was conducted in 22 cultivars of P. nigrum(black pepper) from South India and one accession each of P. longum and P. colubrinum. Twenty-four primers generated 372 RAPD markers of which 367 were polymorphic. Jaccard's similarity between pairs of accessions ranged between 0.11 and 0.66 with a mean of 0.38. Among P. nigrum cultivars, the similarity ranged between 0.20 and 0.66 and the mean was 0.42. The existence of wide genetic diversity as revealed in the present study is supported by earlier reports of extensive inter- and intrapopulation morphological variability in pepper cultivars from South India. UPGMA dendrogram and PCO plot revealed P. colubrinum to be most distant of the three species. Genetic proximity among P. nigrum cultivars could be related to their phenotypic similarities or geographical distribution. Greater divergence was observed among landraces than among advanced cultivars. Landraces grown in southern parts of coastal India and those grown in more northern parts were grouped in separate clusters of the dendrogram.     

Pattern of genetic variability of <Emphasis Type="Italic">Solanum habrochaites</Emphasis> in its natural area of distribution

The tomato wild relative species Solanum habrochaites (previously known as Lycopersicon hirsutum) is a potential source of novel genes for tomato breeding. It shows resistance to many diseases and pests, cold tolerance and fruit quality traits. This species inhabits the western Andean slopes at high elevations from central Ecuador to central Peru. In this study the genetic variation of S. habrochaites was studied using 91 accessions from the whole range of distribution of this species. To this end, we employed two kinds of markers: 9 SSRs and 6 AFLP combinations. The Principal Coordinate Analysis based on AFLP data showed the existence of clinal genetic variation from north to south. The accessions of the different geographic groups were sequentially arranged in the first axis from north to south and a clear separation between them was found. The groups from the centre of the area of distribution showed the highest variation and heterozygosis. The ones from the margins showed lower variability and presented higher homozygosis. The morphotypes typicum and glabratum considered by Müller constituted the extreme forms of the continuous variation in the pubescence grade. These differences in pubescence were not associated with the homozygosis grade.     

Highly polymorphic AFLP markers as a complementary tool to ITS sequences in assessing genetic diversity and phylogenetic relationships of sweetpotato (Ipomoea batatas (L.) Lam.) and its wild relatives

Comparative analyses of genetic diversity and phylogenetic relationshipsof sweetpotato (Ipomoea batatas (L.) Lam.) and its wildrelatives in Ipomoea series Batataswere conducted using amplified fragment length polymorphism (AFLP) and sequencedata from the internal transcribed spacer (ITS) region of the ribosomal DNA. LowITS divergence among thirteen species of ser. Batatasresulted in poorly resolved relationships. More variable AFLP characters werefound to be more efficient in characterizing genetic diversity and phylogeneticrelationships at both intra- and interspecific levels within ser.Batatas. Highly informative AFLP fingerprints of 36accessions representing 10 species of ser. Batatas weregenerated using only six primer combinations. Of the species examined,I. trifida was found to be the mostclosely related to I. batatas, whileI. ramosissima andI. umbraticola were the most distantlyrelated to I. batatas. The highlypolymorphic AFLP markers are a valuable tool in assessing genetic diversity andphylogenetic relationships of sweetpotato and its wild relatives.     

Isozyme variation in Passiflora subgenera Tacsonia and Manicata. Relationships between cultivated and wild species

Isozyme variation was studied in 87 plants from 32 cultivated and wild accessions of banana passion fruit (P. tripartita var. mollissima, P. tripartita var. tripartita, P. tarminiana, and P. mixta), rosy passion fruit (P. cumbalensis), tin-tin (P. pinnatistipula), gulián (P. ampullacea), P. antioquensis, P. bracteosa, and P. manicata, from the Andes of Venezuela, Colombia, and Ecuador. Six polymorphic enzyme systems (IDH, PGDH, PGM, DIA, PRX, and ACP) revealed 31 zymotypes characterized by the presence or absence of 31 electromorphs. Cluster analysis separated clearly the accessions of P. tarminiana, P. tripartita, P. mixta, and P. cumbalensis from the less typical species of subgenus Tacsonia, which is consistent with morphological evidence. P. mixta showed the highest intraspecific variation and the closest affinity with P. tripartita. The accessions of these two species formed two clusters, one dominated by Colombian genotypes and the other dominated by Ecuadorian genotypes. One of the P. tripartita var. mollissima accessions clustered close to P. tarminiana accessions. The affinity between these three species is particularly interesting for conservation and use of banana passion fruit genetic resources. All the other species formed monospecific clusters.     

Worldwide genotyping of castor bean germplasm (<Emphasis Type="Italic">Ricinus communis</Emphasis> L.) using AFLPs and SSRs

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.     

Genetic Diversity in AA and CC Genome Oryza Species in Southern South Asia

The CC genome of Oryza is found in nine species of Oryza that are distributed on all continents having a tropical climate. Three diploid Oryza species with CC genome are found in Africa and Asia to Papua New Guinea. In southern South Asia these three CC genome diploid species can be found, O. eichingeri and O. rhizomatis in Sri Lanka and O. officinalis in India. AA genome wild relatives of rice are also found in the same geographic region. Germplasm of both diploid CC and AA genome Oryza germplasm has recently been collected from Sri Lanka. AFLP analysis was used to compare the genetic diversity of the two Oryza genomes from a similar geographic region in southern South Asia. In addition, the diploid CC Oryza germplasm was also analyzed by RAPD and SSR methodologies and the combined results were analyzed. The results show that in southern South Asia the diploid CC genome species have a high level of genetic diversity compared to the diploid AA genome species. Molecular marker analysis revealed that populations of O. rhizomatis from northern and southeastern Sri Lanka are genetically differentiated. One accession of O. rhizomatis was aligned with O. eichingeri. This accession was collected from the site of O. rhizomatis that is the closest to a population of O. eichingeri. O. eichingeri showed lower genetic diversity than the other two diploid Oryza CC genome species. O. officinalis accessions from Assam, India, and China were genetically less diverged from O. eichingeri and O. rhizomatis than two accessions of O. officinalis from Kerala state, India. The first two authors contributed equally to this research     

Genetic diversity and population structure of Capsicum baccatum genetic resources

Capsicum baccatum is one of five domesticated pepper species which, despite its morphological and ecological variability, has been underexploited for germplasm improvement. Utilizing a broad spectrum of domesticated and wild C. baccatum germplasm, we utilize AFLP markers to describe the species’ molecular diversity and population structure in the South American gene pool. Analysis of molecular variance (AMOVA) revealed greater genetic diversity in the wild form of C. baccatum (C. baccatum var. baccatum) than in the domesticated form of the species (C. baccatum var. pendulum). Both Bayesian and distance based clustering analysis, as well as principal coordinates analysis (PCA), concordantly demonstrated admixture/shared ancestry between wild and cultivated C. baccatum botanical varieties. Two principal genetic groups were identified in the domesticated C. baccatum accessions largely based on their geographic distribution in South America. One group was predominated by accessions from the western territories of the species’ distribution (Peru, Colombia, Ecuador, Bolivia, Chile and northwestern Argentina) and the second by accessions from the eastern regions, Paraguay and eastern Argentina). The two genetic groups overlapped in the geographic location of present-day Bolivia. The grouping pattern suggested that C. baccatum was domesticated in multiple sites and that its evolution took two lineages followed by lineage differentiation. The wild accessions most closely related to the cultigens were found in the highlands of Peru and Bolivia, which support the early hypothesis that this region is one of the domestication sites of this species. A Bayesian assignment analysis demonstrated that Brazilian wild forms of C. baccatum were genetically distant to all other accessions and made little to no contribution to the domesticated genepool. Moreover, results of clustering analysis suggested that C. baccatum likely originated from present day Paraguay. Analysis of inter-specific relationships across selected Capsicum species supported independent lineages for the two crossability groups within Capsicum, the baccatum species-complex (including C. baccatum) and the annuum species-complex (including C. annuum, C. chinense and C. frutescens). However, the results did not support taxonomic distinction of C. baccatum var. umbilicatum from C. baccatum var. pendulum. The present study provides new insights into the domestication of C. baccatum. The results will be useful for identifying accessions for crop improvement and guiding the development of in situ and ex situ conservation programs.     

Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers

The present study, using RAPD analysis, was undertaken to characterize genetic variation in domesticated cowpea and its wild progenitor, as well as their relationships. The materials used consisted of 26 domesticated accessions, including accessions from each of the five cultivar-group, and 30 wild/weedy accessions, including accessions from West, East and southern Africa. A total of 28 primers generated 202 RAPD bands. One hundred and eight bands were polymorphic among the domesticated compared to 181 among wild/weedy cowpea accessions. Wild accessions were more diverse in East Africa, which is the likely area of origin of V. unguiculata var. spontanea. Var. spontanea is supposed to have spread westward and southward, with a loss of variability, loss counterbalanceed in southern Africa by introgressions with local perennial subspecies. Although the variabilty of domesticated cowpea was the highest ever recorded, cultivar-groups were poorly resolved, and several results obtained with isozyme data were not confirmed here. However primitive cultivars were more diverse than evolved cultivars, which still suggests two consecutive bottlenecks within domesticated cowpea evolution. As isozymes and AFLP markers, although with a larger number of markers, RAPD data confirmed the single domestication hypothesis, the gap between wild and domesticated cowpea, and the widespread introgression phenomena between wild and domesticated cowpea.     

An AFLP diversity study of the genus Passiflora focusing on subgenus Tacsonia

DNA variation was studied at the intra- andinterspecific levels within the genus Passiflora, with particular emphasis on the subgenusTacsonia and its relationship with the subgenusPassiflora. AFLP fingerprints were generated for35 accessions from 21 species, 14 of which belong to subgenusTacsonia, and four to subgenusPassiflora. The morphologically intermediateP. manicata (subgenusManicata) was also included, as wereP. trinervia (subgenusPsylanthus) and P.alnifolia (subgenus Decaloba). The two latter were used as outgroup species. Twoprimer combinations generated 34–80 scorable fragments pergenotype for a total of 260 fragments. Polymorphism analyses spannedthe levels from individual genotype to section. SubgenusTacsonia presented wide genetic variability atboth intra- and interspecific levels, particularly within wildspecies. The classification based on these markers generally agreeswell with current taxonomic definitions of common species, but lesswith definitions of sections. A geographical component was evident inthe intraspecific variation of P.mixta, P.tripartita var. mollissimaand P. tarminiana, withwider variation in Ecuador and Peru than in Colombia and Venezuela.These same three species, plus P.cumbalensis, formed adjacent clusters, showingcloser affinity with each other than with the other species ofsubgenus Tacsonia. As expected, P. manicata clustered at anintermediate position between subgenera Tacsoniaand Passiflora.     

Analysis of genetic variability in <Emphasis Type="Italic">Couepia</Emphasis> accessions using AFLP markers

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.     

Genetic relationships among cultivated and wild <Emphasis Type="Italic">Vigna angularis</Emphasis> (Willd.) Ohwi et Ohashi and relatives from Korea based on AFLP markers

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.