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.     

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.     

Genetic relationships among Hibiscus syriacus, Hibiscus sinosyriacus and Hibiscus paramutabilis revealed by AFLP, morphology and ploidy analysis

The genetic relationships between and within Hibiscus syriacus, Hibiscus sinosyriacus and Hibiscus paramutabilis, three winter hardy Hibiscus species native to China, were analysed by the amplified fragment length polymorphisms (AFLP) technique and by morphological evaluation of flower and leaf characteristics. Both methods clearly discriminated between the three species. H. sinosyriacus was classified as an intermediate form between H. paramutabilis and H. syriacus; however, it showed a higher similarity to H. paramutabilis. The different H. syriacus cultivars could be identified by AFLP analysis, while also leaf indices clustered the different cultivars in small groups. Flow cytometry showed that both triploid and tetraploid cultivars occur in the H. syriacus assortment. In general triploid cultivars had larger flowers compared to diploid cultivars.     

Evaluation of genetic relationships among botanical varieties of cultivated peanut (Arachis hypogaea L.) using AFLP markers

Forty-four accessions of cultivated peanut (Arachis hypogaea L.) representing sixbotanical varieties of two subspecies along with three accessions ofthe wild relative A. monticola Krapov et Rigoni were evaluated for their genetic relationships using theAFLP marker technology. Fifteen AFLP primer pairs (EcoRI/MseI) generated 28distinct polymorphic markers that were employed to develop uniqueprofiles of all accessions and to construct a phenogram. The resultsshowed that the botanical varieties aequatoriana and peruviana werecloser to subspecies hypogaea than subspeciesfastigiata Waldr. to which they belong, and the wildA. monticola was notdistinct from the cultivated A.hypogaea. Although the extent of geneticdiversity in peanut is low compared to many other crops, our studiesshow that by employing the AFLP approach, sufficient DNA variationcan be detected in the cultivated peanut germplasm to conductevolutionary studies.     

Phytotoxic and fungitoxic activities of the essential oil of kenaf (Hibiscus cannabinus L.) leaves and its composition

The chemical composition of the essential oil of kenaf (Hibiscus cannabinus) was examined by GC-MS. Fifty-eight components were characterized from H. cannabinus with (E)-phytol (28.16%), (Z)-phytol (8.02%), n-nonanal (5.70%), benzene acetaldehyde (4.39%), (E)-2-hexenal (3.10%), and 5-methylfurfural (3.00%) as the major constituents. The oil was phytotoxic to lettuce and bentgrass and had antifungal activity against Colletotrichum fragariae, Colletotrichum gloeosporioides, and Colletotrichum accutatum but exhibited little or no algicidal activity.     

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.     

Genetic Diversity of Tunisian Olive Tree (Olea europaea L.) Cultivars Assessed by AFLP Markers

About 29 olive (Olea europaea L.) cultivars including oil and table olive cultivars originating from Tunisia and other Mediterranean countries, were genotyped using amplified fragment length polymorphism (AFLP) DNA markers. This technique is a rapid and efficient method for producing DNA fingerprints. Using nine AFLP primer combinations, we produced a total of 410 AFLP markers, among which 172 revealed polymorphism. The results demonstrated a high degree of polymorphism in the olive germplasm we examined with an average of 39%. These AFLP markers were analyzed to estimate genetic distances between pairs of cultivars using Jaccard’s similarity coefficient. Furthermore, cluster and principal component analyses were performed in order to identify the genetic variation patterns. Two main groups were obtained: one comprising primarily small-fruited cultivars grown mainly for oil production and the other comprising large fruited cultivars (regardless of their end-use). Our results show no evidence of clustering of olive cultivars according to their geographic origin.     

Nutrient content of Kenaf (Hibiscus cannabinus) at five growth stages

Abstract

Kenaf (Hibiscus cannabinus) grown during the wet season in the Ord Irrigation Area of Western Australia was sampled at five growth stages. The samples were separated into bark, wood, tops plus foliage and, where applicable, seed. Each fraction was analysed for zinc, manganese, iron, copper, sodium, potassium, calcium and magnesium by atomic absorption spectroscopy, and for nitrogen and phosphorus by colorimetry. Concentrations of these elements in each plant fraction are presented. Calculation of total above‐ground nutrient content of the crop indicated a high content of potassium throughout the growth cycle (up to .280 kg/ha), an initially high content of nitrogen (150 kg/ha) stabilising at a lower level (about 75 kg/ha) up to maturity, and an increasing content of zinc (150 g/ha to 350 g/ha) and calcium (65 kg/ha to 105 kg/ha) with age. A higher content of iron at maturity was also apparent (up to 1400 g/ha). A comparison with other reported data is made.     

Genetic diversity and systematic relationships in sweetpotato (Ipomoea batatas (L.) Lam.) and related species as revealed by RAPD analysis

Summary Fifteen 10mer primers, in combination with the Stoffel fragment, were used to detect random amplified polymorphic DNA (RAPDs) among 26 accessions of sweetpotato (I. batatas (L.) Lam.) from Oceania, Peru, the Philippines, and the United States and between 8 Ipomoea species from section Batatas. Phenetic and principal coordinate analysis of the 56 polymorphisms detected within the hexaploid I. batatas clearly delineated the South Pacific and the Peruvian sweetpotato lines. The two U.S. cultivars clustered with the Oceanic materials. Cladistic and phenetic analysis of 8 Ipomoea species supports previously published phylogenies based on morphological and RFLP data. Among the species examined, I. tabascana, I. trifida and the tetraploid forms of I. batatas from Mexico and Ecuador, including I. batatas var. apiculata, are the taxa most closely related to the cultivated hexaploid I. batatas. These findings support the utility of RAPD markers for evaluating genetic diversity in sweetpotato and for establishing taxonomic and evolutionary relationships in Ipomoea.     

Exploration of intra- and inter-population genetic diversity in <Emphasis Type="Italic">Hedysarum coronarium</Emphasis> L. by AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to characterize the genetic diversity within and among natural populations and cultivars of Hedysarum coronarium. Twelve populations within Tunisia were evaluated with three AFLP primer combinations. A total of 207 reproducible bands was detected of which 178 (86%) were polymorphic. The great discriminative power of AFLP markers and their ability to represent genetic relationships among Hedysarum plants was demonstrated. Genetic diversity within and among populations was assessed through Principal Component Analysis (PCA) and cluster analysis by using the Neighbor-joining clustering algorithm. AFLP technology has provided evidence of a high degree of intra- and inter-population genetic diversity in H. coronarium. AFLP banding patterns provided molecular markers correlated with the plants’ geotropism. In addition, AFLP markers can differentiate wild accessions from cultivars. Moreover, geographical origins did not correspond to population clustering.     

AFLP Fingerprinting in Pigeonpea (Cajanus cajan (L.) Millsp.) and its Wild Relatives

Detection of DNA polymorphism in cultivated pigeonpea (Cajanus cajan) and two of its wild relatives Cajanus volubilis and Rhynchosia bracteata is reported here for the first time using amplified fragment length polymorphism (AFLP) fingerprinting. For this purpose, two EcoRI (three selective nucleotides) and 14 MseI (three selective nucleotides) primers were used. The two wild species shared only 7.15% bands with the pigeonpea cultivars, whereas 86.71% common bands were seen among cultivars. Similarly, 62.08% bands were polymorphic between C. volubilis and pigeonpea cultivars in comparison to 63.33% polymorphic bands between R. bracteata and pigeonpea cultivars, and 13.28% polymorphic bands among pigeonpea cultivars. The cluster analysis revealed low polymorphism among pigeonpea cultivars and very high polymorphism between cultivated pigeonpea and its wild relatives. The AFLP analysis also indicated that only one primer combination (EcoRI + ACT and MseI + CTG), at the most any four primer pair combinations, are sufficient for obtaining reliable estimation of genetic diversity in closely related cultivars like pigeonpea material analyzed herein. AFLP analysis may prove to be a useful tool for molecular characterization of pigeonpea cultivars and its wild relatives and for possible use in genome mapping.     

RAPD analysis of genetic relationships of seven flax species in the genus Linum L

The wild progenitor of the cultivated flax (Linumusitatissimum L.) has been long hypothesized to beL. angustifolium Huds., largely fromseveral phytogeographic cytogenetic and phenotypic studies, but no molecularstudies on the issue are found. In this study, we genotyped 12 flax accessionsrepresenting seven flax species in the genus Linum with 527RAPD loci from 29 informative RAPD primers and analyzed their geneticrelationships with simple matching, Dice's and Jaccard's similaritycoefficients. Large RAPD variations were found among the flax species.L. usitatissimum andL. angustifolium had a higher RAPDsimilarity than the other pairs of flax species and these two species wereconsistently clustered in the same group with all of the similarity coefficientsused. This molecular finding provides an additional support for the hypothesisof L. angustifolium as the wildprogenitor of cultivated flax.     

Analysis of Genetic Diversity and Relationships in Waxy Rice (Oryza sativa L.) using AFLP and ISSR Markers

Opaque endosperm is the main phenotypic indicator for waxy rice, but other phenotypic and genotypic variation among waxy rice accessions has largely been ignored. Previous studies showed that wide diversity in starch physiochemical properties exists in both indica and japonica waxy rices, especially for starch gelatinization temperature (GT) which could be divided into a high- and a low-GT group. In the present study, amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) molecular markers were employed to examine genetic diversity and relationships of 56 waxy rice accessions. A total of 358 AFLP fragments were amplified with five primer combinations, showing a high level of polymorphism (78.3%). A total of 190 ISSR bands were generated with a single primer and a primer pair, showing a very high level of polymorphism (92.2%). The genetic distance matrices obtained from the two sets of markers were significantly correlated (r = 0.731, P = 0.004). The dendrogram generated with combined AFLP and ISSR markers could clearly differentiate the indica and japonica groups. Newly released varieties and breeding lines within each subspecies tended to be clustered together, whereas landraces were more distantly placed in the dendrogram. Only one AFLP band was found specific to the indica type, while no specific bands were found for starch GT. The implications for the conservation and breeding of waxy rice are discussed.     

Identifying and selecting for genetic diversity in Papua New Guinea sweetpotato Ipomoea batatas (L.) Lam. germplasm collected as botanical seed

A total of 141 Ipomoea batatas (L.) Lam. accessionsderived from botanical seed originally collected from 26 sites in 4 Provinces inPapua New Guinea, a secondary center of genetic diversity for sweetpotato, weregenetically analyzed. Two hundred Amplified Fragment Length Polymorphism (AFLP)markers were identified and utilized in the analysis. Relatedness amongaccessions was estimated by analyzing the AFLP data using the Dice coefficientof similarity and UPGMA methods. The molecular analysis revealed relativelylimited genetic diversity within and between sites. Genotypes collected in agiven region often displayed molecular marker variability similar to thatobserved over the entire sampled area. However, a subset of 14 genotypes derivedfrom seed collected from New Ireland island differed from genotypes collected onNew Guinea island. Estimates of genetic diversity-based similarity valuescalculated from the AFLP data indicated a moderate level of diversity (0.767mean coefficient of similarity) across all plant materials analyzed. Threemethods of selection were evaluated for their efficacy in capturing themolecular marker diversity within the plant materials in the form of a subset.They were random, stratified-random (geographic based), and marker-assistedselection (MAS). MAS was the most efficient. A Maximally Diverse Subset (MDS) of12 genotypes capturing 92% of the molecular marker diversity was identified.     

DNA fingerprinting sheds light on the origin of introduced mulberry (Morus spp.) accessions in Italy

Mulberries are members of the genus Morus L., a taxonomic group showing a great genetic variability and adaptability to different environmental conditions. This study deals with the use of AFLP-based fingerprints as a tool for estimating genetic variability within as well as among three different mulberry species (i.e., M. alba L., M. latifolia Poir. and M. bombycis Koidz.). A high level of polymorphism (72.2) was found over all the 48 accessions analyzed. Genetic similarity (GS) within single Morus species ranged from 0.845 (M. bombycis) to 0.884 (M. alba) being intermediate in M. latifolia (0.869). The between-species mean genetic similarity estimates based on pair-wise AFLP marker fingerprint comparison were very similar ranging from 0.861 to 0.874. The partition of the genetic variation over the three Morus species was unexpected a proportion of the among-species genetic diversity as low as GST= 0.084 pointed out that about 92% of the total genetic diversity found among Morus accessions is due to DNA polymorphisms within a species, while only 8% of the total variation was highlighted among species. Our data indicate that some of the introduced accessions showing distinctive phenotypes, clearly differentiated from those revealed in the original habitat where they have been selected and adapted, hide an identical genotype.     

Identification of sweet cherry cultivars (Prunus avium L.) and analysis of their genetic relationships by chloroplast sequence-characterised amplified regions (cpSCAR)

Ten cpSCAR markers that show polymorphism in Prunus avium were used to fingerprint sweet cherry cultivars. The purpose of the study was also to contribute to identification and to help determine their genetic interrelationships. Samples of ‘0900 Ziraat’, a superior Turkish variety, which were collected in several locations all over Turkey, had identical cpSCAR patterns, and they resembled a common European haplotype, A. ‘Sweetheart’, ‘Summit’ and ‘Canada Giant’ and their haplotype are intermediate between the previously described haplotypes A and B, which were originally found in Central and Eastern European sweet and wild cherries, and those from Northern Turkey, respectively. The data therefore suggests a local maternal descent (within Europe and Asia Minor) of the cultivars analysed. Our results show that chloroplast DNA analysis is a straightforward way to classify cherry cultivars. We compare our results to others previously reported for sweet cherry cultivars, and conclude that cpSCAR diversity data could be considered for phylogenetic studies in this group.     

Multivariate analysis of morphological variation in sorghum (Sorghum bicolor (L.) Moench) germplasm from Ethiopia and Eritrea

Multivariate methods, including principal component, cluster and discriminant analyses, were used to assess the patterns of morphological variation and to group 415 sorghum accessions for 15 quantitative characters. The first five principal components explained 79% of the total variation with plant height and days to 50% flowering being the most important characters in the first principal component. Cluster analysis grouped the accessions into ten clusters. A greater proportion of accessions of similar adaptation zones and accessions from regions of origin with similar agro-climatic conditions were grouped together. Moreover, discrimination of accessions was more pronounced when discriminant analysis was based on zone of adaptation rather than regions of origin. Based on the observed patterns of variation, it is concluded that the morphological variation in the material studied is structured by environmental factors. The implications of the results for plant breeding and germplasm conservation programmes arediscussed.     

Assessment of Genetic Diversity in Upland Cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.) Breeding Lines by using Amplified Fragment Length Polymorphism (AFLP) Markers and Morphological Characteristics

Genetic diversity in 24 advanced breeding lines of cotton was studied by using six amplified fragment length polymorphism (AFLP) primer-pairs and 14 morphological characters. The six selected AFLP primer-pairs generated a total of 535 amplification products, of which 460 were found to be polymorphic resulting in 85.9% polymorphism. The observed genetic distances using AFLP markers ranged from 30% to 87% with an average of 34%. A wide range of variability was observed for all the morphological traits studied. The range in taxonomic distance was from 0.60 to 2.77. Most of the lines could be clustered in two major clusters in both the analyses. But the correlation coefficient between the pair-wise distances estimated from AFLPs and the average taxonomic distances estimated from morphological characters was found to be 0.04. UPGMA cluster analysis revealed inconsistencies in the clustering patterns, as the co-phenetic correlation coefficient between the dendrograms for morphological and AFLP data indicated a poor fit for the two data types. From combined information, genotypes ‘RST-12’, ‘H 1226’, ‘P 348’, ‘KDCAKD’, ‘CISV 24’ and ‘H1222’ were found to be distinct from rest of the material.     

RAPD and AFLP assessment of genetic variation in a landrace of pepper (Capsicum annuum L.), grown in North-West Italy

In several regions of Italy as well as other parts of southern Europe, the heterogeneity of the land, the climate and the soil favour the survival in cultivation of a large number of landraces specifically adapted to local conditions. Knowledge on the level and distribution of their genetic variation can help to develop appropriate strategies, in order to suistainably manage in situ these germplasm resources at risk of genetic erosion. C. annuum is an herbaceous diploid species and is considered to be self-pollinating, although different rates of out-crossing have been recorded. We used random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers to assess genetic diversity within and between five populations of a landrace of Capsicum annuum L., grown in a limited area in north-west Italy and locally known as Cuneo pepper. Partitioning the genetic variation with Shannon's diversity index revealed that 41.6% occurred between and 58.4% within populations. Analogous results were obtained when the analysis was based only on RAPD or AFLP markers. However, AFLP was more reliable, since a lower range of variation was observed among primer combinations in detecting the two components of genetic variation. Notwithstanding the rather high level of within genetic variation detected, the five populations were clearly differentiated and differed in the frequency of alleles exclusive and/or present at very low frequencies. Our results show the need for accurate estimation of allele frequencies, in order to identify populations to which priority should be given for dynamic conservation of landraces.     

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.