Genetic relationships and diversity among Brazilian cultivars and landraces of common beans (Phaseolus vulgaris L.) revealed by AFLP markers

The genetic variation and relationships among 31 accessions of Phaseolus vulgaris L., and two representatives of Vigna unguiculata L., were evaluated by AFLP analysis. A total of 263 DNA fragments across all materials were scored using nine primer combinations, averaging 32 per primer. More than 95% of the amplification products showed polymorphism, indicating high variation at the DNA level among these accessions. Pair-wise genetic similarity (Jaccard's coefficient) ranged from 0.553 to 0.840, with a mean of 0.765. Twenty-three accessions (70%) clustered into three groups. A majority of the commercial cultivars (91%) clustered within a single group, whereas the landraces were distributed along all the variation. An apparent correlation with phaseolin types was detected. Results of this study suggest that Brazilian landraces truly represent the overall genetic variability of Phaseolus vulgaris, confirming the multiple origins of these materials, and their potential as a source of variation for breeding programs.     

Genetic Diversity and Relationships of Japanese Peach (<Emphasis Type="Italic">Prunus persica</Emphasis> L.) Cultivars Revealed by AFLP and Pedigree Tracing

To evaluate the genetic diversity and to clarify the genetic relationships of Japanese peach cultivars, we analyzed the amplified fragment length polymorphism (AFLP) and traced the pedigree of 17 Japanese commercial peach cultivars and six traditional accessions. Sixteen AFLP primer combinations produced a total of 837 fragments and 146 polymorphic bands with a polymorphism percentage of 17.5%. All of the peach accessions could be identified from differences in at least 10 polymorphic bands. A cluster analysis showed that all the Japanese commercial peach cultivars, except ‘Kiyomi’ and ‘Jichigetsuto’, formed a major group consisting of three sub-groups. Of the six traditional accessions, four were genetically distant from the Japanese commercial peach cultivars while two accessions from China were classified into the Japanese commercial peach cultivars group. Both the AFLP analysis and pedigree tracing suggested that Japanese commercial peach cultivars are mainly derived from ‘Shanhai Suimitsuto’, one of the traditional accessions from China. Although the genetic relationships revealed by AFLP were generally in agreement with those shown by the pedigree information, some contradictions were found. Combining the AFLP results and pedigree information can provide a better understanding of the genetic relationships of Japanese peach cultivars.     

Aluminum resistance and cell‐wall characteristics of pineapple root apices

Pineapple (Ananas comosus [L.] Merrill) is one of the economically cultivated crops in Taiwan, which is grown mostly on acid soil. Aluminum (Al) is phytotoxic and sometimes inhibits root growth of crops in strongly acid soils. This study was conducted to evaluate the role in Al resistance of root‐apex cell walls of four important pineapple cultivars (Cayenne, Tainung No. 6, Tainung No. 13, and Tainung No. 17). The cell‐wall characteristics of root apices were determined using Fourier transform infrared spectroscopy (FTIR) and solid‐state ¹³C‐nuclear–magnetic resonance spectroscopy (¹³C‐NMR). The results show that the carboxylic and phenolic groups were highest in the cell wall of Tainung No.17 and lowest in that of Cayenne. Aluminum adsorption by cell wall could be described by Freundlich equation. The adsorption of Al by the cell wall of root apices was highest in Tainung No.17 and lowest in Cayenne. Tainung No.17 contained more carboxylic and phenolic groups in its cell wall of the root apices, causing more Al adsorption and so more damage to its root apices than that of the other three pineapple cultivars.     

AFLP fingerprinting of sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) cultivars: identification,genetic relationship and comparison of AFLP informativeness parameters

Amplified fragments length polymorphism (AFLP) was used to distinguish 20 cultivars of sesame (Sesamum indicum L.) and to elucidate the genetic relationship among these genotypes. The data were also used to estimate the usefulness of parameters currently used to assess the informativeness of molecular markers. A total of 339 markers were obtained using 8 primer combinations. Of the bands, 91% were polymorphic. Five primer combinations were able to distinguish all 20 cultivars used. None of the remaining three primer combinations could distinguish all accessions if used alone, but using all three combinations reduced the probability of a random match to 5 × 10⁻⁵. Polymorphic information content (PIC), resolving power (Rp) and marker index (MI) of each primer combination failed to correlate significantly with the number of genotypes resolved. Jaccard’s similarity coefficients ranged from 0.31 to 0.78. Fifteen cultivars were grouped by four UPGMA-clusters supported by bootstrapping values larger than 0.70. The grouping pattern was similar to the grouping generated by principal coordinate analysis. The results demonstrated that AFLP-based fingerprints can be used to identify unequivocally sesame genotypes, which is needed for cultivar identification and for the assessment of the genetic variability of breeding stocks. We recommend to use the number of cultivars identified by a primer combination instead of PIC, Rp and MI; and to calculate the maximal, instead of average probability of identical match by chance in the assessment of the informativeness of a marker for cultivar identification.     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

AFLP analysis of genetic diversity in leafy kale (<Emphasis Type="Italic">Brassica oleracea</Emphasis> L. convar. <Emphasis Type="Italic">acephala</Emphasis> (DC.) Alef.) landraces,cultivars and wild populations in Europe

AFLP markers were used to characterize diversity and asses the genetic structure among 17 accessions of kale landraces, cultivars and wild populations from Europe. The range of average gene diversity in accessions was 0.11–0.27. Several landraces showed higher levels of diversity than the wild populations and one cultivar had the lowest diversity measures. The landraces that were most genetically diverse were from areas where kales are known to be extensively grown, suggesting in situ conservation in these areas as a supplement to storage of seeds in gene banks. An analysis of molecular variance (AMOVA) showed that 62% of the total variation was found within accessions. For most accessions, genetic distance was not related to geographic distance. Similarities among accessions were probably not caused by recent gene flow since they were widely separated geographically; more likely the relationship among them is due to seed dispersal through human interactions. Our results indicate that a kale population found in a natural habitat in Denmark was probably not truly wild but most likely an escape from a cultivated Danish kale that had subsequently become naturalized.     

Assessment of genetic diversity in cultivars and wild accessions of Luohanguo (<Emphasis Type="Italic">Siraitia grosvenorii</Emphasis> [Swingle] A. M. Lu et Z. Y. Zhang), a species with edible and medicinal sweet fruits endemic to southern China,using RAPD and AFLP markers

Genetic variation of wild populations and cultivars of Luohanguo (Siraitia grosvenorii), a plant species endemic to southern China, was assessed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Based on the results for 130 individuals from seven populations, a high level of genetic diversity of Luohanguo was observed at the species level. The percentage of polymorphic loci (P) was 89.4%, Nei’s gene diversity (H _e) was 0.239, and Shannon’s information index (H _o) was 0.373 based on the combined AFLP and RAPD data. There was a high degree of genetic differentiation, with 45.1% of the genetic variation attributed to differences between the populations. The genetic diversity of the Luohanguo cultivars is much lower than that of wild populations (P = 41.8%, H _e = 0.141, H _o = 0.211), and a distinct genetic differentiation is observed between the cultivars and wild accessions. The pool of genetic variation in the wild populations provides an excellent gene resource for Luohanguo breeding.     

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.     

AFLP similarities among historic Danish cultivars of fodder beet (<Emphasis Type="Italic">Beta vulgaris</Emphasis> L. subsp. <Emphasis Type="Italic">vulgaris</Emphasis>var. <Emphasis Type="Italic">rapacea</Emphasis> Koch)

Dead seeds of a fodder beet cultivar ‘Elvetham’ stored under ambient conditions since 1880 were compared to a homonymous sample preserved in an on-farm situation in Denmark. DNA was isolated from single seeds and successfully applied to Amplified Fragment Length Polymorphism (AFLP) analysis of the accessions. Six primer pairs were used to determine the similarity between the two accessions based on 112 polymorphic bands. Furthermore, similarity among seven cultivars of fodder beets representing the main types used in Scandinavia at the end of the 19th century was determined. This analysis was based on 152 polymorphic bands. Differentiation among the seven cultivars was determined to a mean G _ST value of 0.438, while G _ST between the two ‘Elvetham’ accessions was 0.266. A principal coordinate analysis based on jaccards similarity index illustrates that the two ‘Elvetham’ accessions are different from each other. The differentiation is higher than the value found between two separate ‘Eckerndorfer’ accessions. The results indicate that the cultivated accession has changed. Additionally, the value of applying old dead seed material for documentation in gene banks is demonstrated. During the analysis it was found that DNA isolated from seeds and leaves behaved differently in the AFLP process, however, the two fractions assigned to their common accession.     

Genetic Diversity of the Greater Yam (<Emphasis Type="Italic">Dioscorea alata</Emphasis> L.) and Relatedness to <Emphasis Type="Italic">D. nummularia</Emphasis> Lam. and <Emphasis Type="Italic">D. transversa</Emphasis> Br. as Revealed with AFLP Markers

Amplified fragment length polymorphism markers were used to assess the genetic relatedness between Dioscorea alata and nine other edible Dioscorea. These species include D. abyssinica Hoch., D. bulbifera L., D. cayenensis-rotundata Lamk. et Poir., D. esculenta Burk., D. nummularia Lam., D. pentaphylla L., D. persimilis Prain. et Burk., D. transversa Br. and D. trifida L. Four successive studies were conducted with emphasis on the genetic relationship within D. alata and among species of the Enantiophyllum section from Vanuatu. Study 1 was carried out to select a set of polymorphic primer pairs using 11 combinations and eight species belonging to five distinct sections. The four most polymorphic primer pairs were used in study 2 among six species of the Enantiophyllum section. Study 3 focussed mainly on the genetic relationship among 83 accessions of D. alata, mostly from Vanuatu (78 acc.) but also from Benin, Guadeloupe, New Caledonia and Vietnam. The ploidy level of 53 accessions was determined and results indicated the presence of tetraploid, hexaploid and octoploid cultivars. Study 4, included 35 accessions of D. alata, D. nummularia and D. transversa and was conducted using two primer pairs to verify the taxonomical identity of the cultivars `langlang', `maro' and `netsar' from Vanuatu. The overall results indicated that each accession can be fingerprinted uniquely with AFLP. D. alata is an heterogeneous species which shares a common genetic background with D. nummularia and `langlang', `maro' and `netsar'. UPGMA cluster analysis revealed the existence of three major groups of genotypes within D. alata, each assembling accessions from distant geographical origins and different ploidy levels. The analysis also revealed that `langlang', `maro' and `netsar' clustered together with the cultivar `wael' (D. transversa) from New Caledonia. Results are discussed in the paper.     

Assessing genetic diversity of sweet potato (Ipomoea batatas (L.) Lam.) cultivars from tropical America using AFLP

The sweet potato genebank at the International Potato Center (CIP) maintains 5,526 cultivated I. batatas accessions from 57 countries. Knowledge of the genetic structure in this collection is essential for rational germplasm conservation and utilization. Sixty-nine sweet potato cultivars from 4 geographical regions (including 13 countries) of Latin America were randomly sampled and fingerprinted using AFLP markers. A total of 210 polymorphic and clearly scorable fragments were generated. A geographic pattern of diversity distribution was revealed by mean similarity, multidimensional scaling (MDS), and analysis of molecular variance (AMOVA). The highest genetic diversity was found in Central America, whereas the lowest was in Peru-Ecuador. The within-region variation was the major source of molecular variance. The between-regions variation, although it only explains 10.0% of the total diversity, is statistically significant. Cultivars from Peru-Ecuador, with the lowest level of within region diversity, made the most significant contribution to the between region differentiation. These results support the hypothesis that Central America is the primary center of diversity and most likely the center of origin of sweet potato. Peru-Ecuador should be considered as a secondary center of sweet potato diversity.     

AFLP-based genetic diversity assessment among Chinese vegetable mustards (<Emphasis Type="Italic">Brassica juncea</Emphasis> (L.) Czern.)

Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic relationships and diversities of Chinese vegetable mustards. Fourteen pairs of primers generated a total of 366 scorable fragments among 16 accessions of Brassica juncea studied, of which 296 bands were polymorphic with an average of 21.1% polymorphic bands per primer combination. Genetic similarities were obtained using Nei and Li similarity coefficients, and a dendrogram of the 16 accessions was made by UPGMA clustering method. The Nei and Li Similarity coefficient value ranged from 0.63 to 0.88. This result indicated that the 16 accessions of B. juncea possessed high level genetic variations. The cluster analysis showed that the vegetable mustards could be grouped into two main groups and some minor rami, which was partially in accordance with the traditional classification that based on different edible organs of vegetable mustards. The incongruity between morphological and molecular classification might be attributed to the high selection pressure during domestication of Chinese vegetable mustards, producing some accessions with similar genetic backgrounds evolving into abundant morphological variations. The great diversification among Chinese vegetable mustards not only provides an excellent object for molecular evolution research of B. juncea but also is of great value for widening the genetic basis of breeding programs and breeding materials selection. Besides, our study also indicates that AFLP are informative and can provide significant insights for genetic diversity research in B. juncea.     

Geographic variation for isozymes in cherimoya (<Emphasis Type="Italic">Annona cherimola</Emphasis> Mill.)

Cherimoya (Anonna cherimola Mill.) is a fruit tree which originated in Peru and Ecuador and is now cultivated in several subtropical areas of the world. The characterization of cherimoya cultivars at allozyme level has been previously reported, but the geographic distribution and organization of this variation have not been fully characterized. In this study, we assessed the relationships among 206 cherimoya and four atemoya (A. cherimola ×A. squamosa) cultivars based on allozyme polymorphism. We have confirmed the genetic differences between atemoya and cherimoya cultivars, and showed that cherimoya accessions from Madeira, Bolivia and Spain form homogeneous groups of cultivars. Accessions from Chile and California form heterogeneous groups, probably due to their mixed origins. Cultivars from Peru and Ecuador showed a wide range of allelic variation, as is expected for accessions from the center of origin of this species.     

Genetic Variation and Relationships of Pedigree-Known Oat, Wheat, and Barley Cultivars Releaved by Bulking and Single-Plant Sampling

Applications of bulking procedures have played an increasingly important role in molecular characterization of plant germplasm, but little attention has been made to address the effectiveness of detecting genetic variation and inferring genetic relationships via bulking. An analysis was performed here to compare the genetic variation detected and genetic relationships inferred via bulking and single-plant sampling of five oat (Avena sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.) cultivars with known pedigrees using amplified fragment length polymorphism (AFLP) markers. Three AFLP primer pairs were applied to screen one bulk and eight single-plant samples of each cultivar and up to 140 AFLP bands were scored for each sample. Analyses of these AFLP data showed bulking revealed AFLP variation up to 21.4% less than corresponding single-plant sampling for these crop species and also introduced up to 2.2% upward and 5.1% downward biases in detecting AFLP variations for each cultivar. The genetic relationships inferred by bulking using the Dice's coefficient, the simple matching coefficient, and the Jaccard's coefficient were largely the same, but differed from those in single-plant samples employing average Dice's coefficient, average simple matching coefficient, and AMOVA-based distance method. All of the inferred genetic relationships were not congruent to the known pedigrees. Clearly, substantial biases could exist in detection of AFLP variation and in inference of genetic relationships from bulk samples, even for closely related germplasm, and more efforts to assess the effectiveness of bulking in inferring genetic variation and relationships are needed for more informative molecular characterization of plant germplasm.     

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.     

Genetic Relationship and Diversity of Four MangiferaSpecies Revealed through AFLP Analysis

We used AFLP analysis to explore the genetic relationship and diversity between and within 4 Mangifera species. We analyzed 35 accessions comprising 8 cultivars and 3 landraces of M. indica L., 11 landraces of M. odorata Griff., 7 landraces of M. foetida Lour., and 6 landraces of M. caesia Jack. Using 8 primer combinations produced a total of 518 bands, 499 (96.3%) of which were polymorphic among the 35 accessions. Clustering analysis showed that all 35 accessions were basically classified into 4 groups corresponding to the 4 Mangifera species. Our results indicate that the genetic relationship of these 4 Mangifera species based on AFLP analysis is in good agreement with their classification by classic methods. In addition, it was clearly revealed the genetic diversity between and within 4 Mangifera species. The findings obtained in this study are useful for the breeding in Mangifera species.     

Determining genetic diversity between lines of <Emphasis Type="Italic">Vigna unguiculata</Emphasis> subspecies by AFLP and SSR markers

AFLP (Amplified Fragment Length Polymorphisms) and SSR (Simple Sequence Repeat) markers were utilized to assess genetic diversity and relatedness between Vigna unguiculata subspecies. Three AFLP primer combinations and 10 SSR primer sets successfully identified closely related accessions, and the presence of heterogeneity in some accessions. AFLP methodology was successful in separating different species of Vigna. However, the level of intra-subspecies variation was as great as was the interspecies variation with both marker methods. The number of markers employed was insufficient to successfully group the subspecies into distinct clades.