Variation among Spanish faba beans cultivars: taxonomic and evolutionary implications

Summary Univariate and multivariate analysis were used to examine phenotypic variability within a Spanish faba bean germplasm collection maintained at the Centro de Investigación y Desarrollo Agrario, Córdoba, Spain.The analysis of 158 Spanish faba bean accessions and 12 quantitative traits indicated highly significant differences among botanical groups for 8 characters and among geographic regions for 10 characters. An east to west clinal pattern of variation for some characters was detected.In order to identify the main characters which account for the major variation, the same collection was subjected to principal component analysis for 12 quantitative traits. Reproductive and plant height characters appeared to be the major sources of diversity.To determine the importance of both geographic and botanical variation among the Spanish cultivars, discriminant analysis was applied. According to these analyses, plant height, height of the lowest pod-bearing node, pod length and 100 seed weight, were important traits discriminating among different geographic regions. The main character discriminating among botanical groups was the 100 seed weight.Our results fit in a pattern in which both agroecological and anthropological causes could have played a role in the observed variation. This analysis can help plant breeders in choosing the most favorable accessions in plant breeding.     

Geographical variation in rooting ability of stem cuttings of Azadirachta indica and Dalbergia sissoo

Geographical variations are among the least studied factors that control or modify rooting by cuttings. In the present study 1 year old branch cuttings of 12 provenances from Central India of Azadirachta indica and Dalbergia sissoo were examined for variation in rooting ability. Application of 500 mg/l-1 indole butyric acid (IBA) significantly increased (P < 0.05) root numbers, root length, root dry weight, rooting percentage, shoot number and shoot height. The auxin treatment amplified the provenance differences in rooting ability of cuttings. No significant variation in survival was evident with respect to provenance or auxin treatment. Correlation coefficients for root parameters were positive and significant (P < 0.01) and results of principal component analysis identified rooting factor having 52.3 and 46.7% of the total sub-plot mean variance among auxin treated cuttings for A. indica and D. sissoo, respectively. On the basis of overall performance of rooting in cuttings among provenances, the Raipur provenance was adjudged the best. Opportunities to develop genetically diverse clonal production stands are discussed.     

Habitat fragmentation reduces genetic diversity and connectivity among toad populations in the Brazilian Atlantic Coastal Forest

Tropical rainforests are becoming increasingly fragmented and understanding the genetic consequences of fragmentation is crucial for conservation of their flora and fauna. We examined populations of the toad Rhinella ornata, a species endemic to Atlantic Coastal Forest in Brazil, and compared genetic diversity among small and medium forest fragments that were either isolated or connected to large forest areas by corridors. Genetic differentiation, as measured by F_ST, was not related to geographic distance among study sites and the size of the fragments did not significantly alter patterns of genetic connectivity. However, population genetic diversity was positively related to fragment size, thus haplotype diversity was lowest in the smallest fragments, likely due to decreases in population sizes. Spatial analyses of genetic discontinuities among groups of populations showed a higher proportion of barriers to gene flow among small and medium fragments than between populations in continuous forest. Our results underscore that even species with relatively high dispersal capacities may, over time, suffer the negative genetic effects of fragmentation, possibly leading to reduced fitness of population and cases of localized extinction.     

Genetic variation and phylogenetic relationships among Indian Citrus taxa revealed by DAMD-PCR markers

Genetic variation and phylogenetic relationships among 50 wild and cultivated accessions of 19 Indian Citrus genotypes were examined through comparison of Directed Amplification of Minisatellite DNA (DAMD) markers and morphological characters. DAMD-PCR analysis with four primers resulted in amplification of a total of 45 bands, of which 35 (78 %) were polymorphic. Morphometric evaluation using 76 morphological characters showed high level of variability ranging from 0.18 to 1.00 (avg 0.39), whereas the Jaccard’s coefficient values of genetic similarity calculated from DAMD data ranged from 0.41 to 1.00 (avg 0.68), indicating moderate genetic divergence among the accessions studied. UPGMA dendrograms generated separately from morphometric and DAMD data segregated all the accessions of Citrus into four main clusters, each containing a true basic species and their probable hybrids. The grouping of individual accessions/genotypes under respective species or cultivars in DAMD dendrogram was based purely on their genetic relationships rather than geographical origin. There was no absolute congruence between the data and dendrograms generated from morphometric and DAMD analyses. The study demonstrates the resolving power of DAMD markers for discrimination of individual genotypes of Citrus under its respective species, hybrid or cultivar groups and inferring their genetic and phylogenetic relationships as well. This is the first report on application of DAMD markers in Citrus.     

The use of shell morphometrics for the management of the endangered malagasy radiated tortoise (Geochelone radiata)

The radiated tortoise (Geochelone radiata) is an endangered species endemic to the spiny forest of southern Madagascar. The main threat that this species faces is illegal harvesting for both local consumption and foreign markets. Large numbers of live individuals are often confiscated and their population of origin is in most cases unknown. Previous work has identified three genetically distinct units across the current distribution of the species. The objective of the present study was to develop a method of assigning G. radiata individuals to their original population based on the analysis of morphometric characters. We measured 39 variables on the shell of tortoises sampled at seven locations across the species range in order to assess differentiation. We employed a PCA-based method to analyze morphometric data and found three distinct groups of populations based solely on shape variation. Discriminant functions allowed for the correct classification of 83% of individuals among these groups. The abundance of tortoises, a variable strongly linked to the level of human exploitation at each site, was correlated with the morphometric differentiation of populations. Our results thus suggest that humans may have played a role in the recent evolution of radiated tortoises. The outlined methodology could become a useful tool for the management of radiated tortoises, and could theoretically be applied to any chelonian species.     

Assessing genetic diversity of <Emphasis Type="Italic">Pyrus</Emphasis> spp. in the central Zagros mountains based on morphological characters

The morphological diversity and relationship among 138 pear genotypes, including 11 commercial cultivars and 127 wild pear accessions from central Zagros mountains located in the west of Iran, based on 64 morphological characters were studied. The higher coefficient of variation indicated that high level of variation was belonged to the petiole stipule, fruit the relative area of the skin color, fruit relative area periphery rust dents end, fruit relative blight on an area of skin, fruit curved tail, fruit dents end, fruit depth dents end, fruit relative area periphery patina tail connection characters. Pyrus communis L. and Pyrus glabra Boiss. species were the highest and the shortest tree, respectively. According to the cluster analysis, 138 genotypes were clustered into nine main groups. Principal components analysis revealed that the first three components accounted for 68.77 % of the total variation in data. Moreover, 19 factors justified 72.57 % of the total variation based on factor analysis. The research results showed that the Zagros mountains are the centers of diversity of pear. Therefore, it is necessary to use the Iranian genotypes as the genetic resources for improving the morphological characters of pear.     

Morphological characterization of snake melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> var. <Emphasis Type="Italic">flexuosus</Emphasis>) populations from Palestine

Genetic diversity in 50 snake melon accessions collected from Palestine (West Bank) was assessed by examining variation in 17 phenotypic characters. These accessions belonged to four important landraces of Cucumis melo var. flexuosus: Green “Baladi” (GB), white Baladi (WB), green Sahouri (GS), and white Sahouri (WS). Principal component analysis (PCA) and a dendrogram were performed to determine relationships among populations and to obtain information on the usefulness of those characters for the definition of cultivars. PCA revealed that secondary fruit skin color, flesh color, primary fruit skin color, and secondary skin color pattern were the principal characters to discriminate melon accessions examined in the present study. According to the scatter diagram and dendrogram, landraces of C. melo var. flexuosus: GB, WB, GS, and WS formed different clusters. However, based on Euclidean genetic coefficient distances, GB and WB had the least degree of relatedness with GS and WS, indicating distantly related landraces (Baladi and Sahouri). On the other hand, the highest degree of relatedness was detected between WS on one hand, and both GS and WB on the other indicating closely related cultivars. Fruit traits variability among the different snake melon landraces was evaluated and discussed in this study. This evaluation of fruit trait variability can assist geneticists and breeders to identify populations with desirable characteristics for inclusion in cultivars breeding programs.     

Specific assemblages of major capsid genes (g23) of T4-type bacteriophages isolated from upland black soils in Northeast China

We surveyed the major capsid genes (g23) of T4-type bacteriophages using the primers MZIA1bis and MZIA6 and DNA extracted from seven upland black soils in Northeast China. In total, 99 different g23 clones were obtained. Approximately half of the clones fell into paddy groups, whereas the rest belonged to one of several groups containing only clones from upland black soils or remained ungrouped, suggesting that the T4-type phage communities in the upland black soil were relatively similar to those in paddy field soils but that specific communities exclusively inhabit the upland black soil. UniFrac analysis of all of the g23 clones obtained from various environments indicated that the T4-type phage communities varied among marine, lake, paddy field soil and upland soil environments and that the T4-type phage communities in upland black soils varied by sampling location.     

High frequency oligonucleotides: targeting active gene (HFO-TAG) markers revealed wide genetic diversity among Citrullus spp. accessions useful for enhancing disease or pest resistance in watermelon cultivars

There is a continuous need to enhance watermelon cultivars for disease and pest resistance. Different U.S. Plant Introductions (PIs) of Citrullus lanatus subsp. lanatus var. lanatus [also known as C. lanatus (Thunb.) Matsum. et Nakai subsp. lanatus var. citroides (Bailey) Mansf. ex Greb.] (CLC) collected in southern Africa are a useful source for enhancing disease or pest resistance in watermelon cultivars. They are also valuable as rootstocks for grafted watermelon, particularly in fields infested with root-knot nematodes or Fusarium wilt. However, there is little information about genetic relationships among these PIs. In this study, genetic diversity was examined among 74 CLC PIs collected from their center of origin in southern Africa. Also, 15 Citrullus lanatus subsp. lanatus (CLL) PIs and the American heirloom cultivars Charleston Gray and Black Diamond (Citrullus lanatus subsp. vulgaris (Schrader ex Eckl. et Zeyh.) Fursa) (CLV) and five Citrullus colocynthis (L.) Schrader (CC) PIs collected in different locations throughout the world were used as out-groups in the phylogenetic analysis for the CLC PIs. Twenty-three high frequency oligonucleotides—targeting active gene (HFO-TAG) primers were used in polymerase chain reaction (PCR) experiments to produce a total of 562 polymorphic markers among the Citrullus PIs and cultivars. Cluster and multidimensional scaling plot analysis produced distinct groups of CLC, CLL, and CC PIs. Several PIs that were designated as CLC or CLL were in transitional positions, indicating that they are the result of gene flow between the major Citrullus groups or subgroups. Population structure analysis indicated that CLC comprises two subgroups; each containing a set of unique alleles. Also, unique alleles exist in the CLL and the CC genotypes. Overall, broad genetic diversity exists among the Citrullus PIs. The data in this study should be useful for identifying PIs with a wide genetic distance between them that could be used in breeding programs aiming to develop heterotic F₁ hybrid rootstock lines for grafted watermelon.     

Mass spectrometric fingerprints of seed protein for defining Lupinus spp. relationships

The Lupinus genus consists of 200–600 species with diversified morphological and biochemical characteristics that provide scope for increasing the value of protein attributes in commercial lupin species through genetic improvement. This study characterised protein polymorphism among 33 selected lupin genotypes representing 19 species from Old World and New World using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight (MALDI-TOF) mass spectrometry with the aim of developing a high throughput screen for assessing variation among samples within a genetic resource. MALDI-TOF mass spectrometry analysis recognized 630 polymorphic protein mass peaks. A total of 19 protein mass peaks were identified as species specific and 23 were recognized to be generally common (observed in more than 10 species). A set of 111 rare protein mass peaks common to 2–3 species were identified to uniquely distinguish the respective species in combination with the species specific mass peaks. Overall, the seed protein profiles showed extensive diversity among the species analysed. Phylogenic analysis based on the protein mass peaks clustered the Old World smooth and rough-seeded and New World lupin species separately, in broad agreement with clustering based on morphological characters, life history, cytogenetics, DNA polymorphism and electrophoreses of seed proteins. Two New World lupin species, L. mutabilis Lindl. and L. succulentus Douglas ex K. Koch were grouped into the smooth-seeded Old World group.     

The pattern of genetic diversity in faba bean collections from Ethiopia and Afghanistan

Summary The pattern of genetic diversity in 106 faba bean accessions from Ethiopia and Afghanistan was analysed. Eight quantitative characters were observed. Differences among origins were highly significant for plant height and yield characters. Principal component analysis and cluster analysis were performed in order to ascertain phenotypic similarities between accessions, which could be useful for sampling in subsequent studies. A core of 21 accessions based on clusters which are assumed to represent a great diversity was defined.     

Survey of major capsid genes (g23) of T4-type bacteriophages in Japanese paddy field soils

Many studies have shown the ecological importance of viruses as the greatest genomic reservoirs on the planet. As bacteriophages (phages) comprise the majority of viruses in the environment, we surveyed the capsid genes (g23) of T4-type phages, Myoviridae, from DNA extracts of three paddy field soils located in northern, central and southern Japan using the degenerate primers MZIA1bis and MZIA6. Denaturing gradient gel electrophoresis (DGGE) was performed to separate PCR-amplified g23 products, and 56 DGGE bands were identified as g23 fragments. Only nine clones were grouped into T-evens, PseudoT-evens and ExoT-evens, and most of the other clones were classified into Paddy Groups I-VI. No significantly different distribution of g23 clones was observed among the paddy fields at the group level, indicating that phage communities estimated from the g23 composition were common on the nationwide level. Comparison of g23 sequences showed that g23 genes in paddy fields were different from those in marine environments, and more divergence of g23 genes was estimated in the paddy fields compared to the marine environment. Two novel g23 clones with very short amino acid residues were detected, suggesting the existence of uncharacterized, novel groups of g23 genes in paddy field soils.     

Variations in morphological and agronomic traits among Jerusalem artichoke (Helianthus tuberosus L.) accessions

Jerusalem artichoke is a diversely-utilized crop. Selection for high yield, inulin content and other economically important traits are useful for improving this crop. The objectives of the present study were to evaluate genetic variability for qualitative and quantitative traits among Jerusalem artichoke accessions and to identify different groups of accessions using morphological and agronomic traits. Seventy-nine accessions were evaluated in a randomized complete block design with two replications in the late rainy season 2008, the early rainy season 2009 and the late rainy season 2009 at Khon Kaen University agronomy farm, Thailand. Morphological and agronomic characteristics were evaluated for genetic variations. High variations were found among Jerusalem artichoke accessions for qualitative and quantitative characters, and selection for these characters is possible. High variations were observed for tuber width, number of tubers/plant, biomass, fresh tuber yield and tuber size. Correlation coefficient between fresh tuber yield and tuber size was positive and significant (0.58, P ≤ 0.01). Improvement of tuber size is a means to improve yield and tuber quality. Based on morphological and agronomic characteristics, Jerusalem artichoke accessions were clustered into four distinct groups (R² = 0.88). These groups may be used as parental material to generate progenies for further improvement of this crop. This information will enable breeders to make informed decisions about possible heterotic groups for their breeding programs and germplasm conservation.     

Variability for quantitative traits in exotic hybrid germplasm of sugarcane

The foreign hybrid collection of sugarcane germplasm comprising 399 clones representing 10 geographical groups, was evaluated for nine yield and quality characters, in relation to their place of origin. Discriminant function analysis showed that all the nine variables contributed significantly to the discrimination of the groups, the maximum contribution being cane height. The overall percentage of correct classification was only 48%, with a range from 32% to 73% with respect to individual groups. This suggests an underlying genetic similarity among the groups, which stem largely from their common genetic base. The exceptions were the Hawaii and Mauritius groups, which had distinct identities. The Hawaii group was the most productive group, having maximum yield and sucrose potential. The Puerto Rico group was the best source for juice sucrose. Australian varieties bred for high juice quality did not show the expected level of juice sucrose in the present study. The use in breeding programmes of Hawaiian varieties, which have a broader genetic base and high yield and quality potential, might impart better productivity to commercial varieties.     

Variability in leaf and fruit morphology and in fruit composition of chestnuts (<Emphasis Type="Italic">Castanea Sativa</Emphasis> Mill.) in the Nazilli region of Turkey

The aim of this study is to characterize 10 European chestnut (Castanea sativa Mill.) accessions which were selected among 80 accessions at the end of a selection study in Nazilli in Turkey. During the harvest periods in 2001, 2002 and 2003, European chestnut accessions were examined. Nineteen morphological, pomological and biochemical characters were used. Significant genotype×year interaction were found for all traits but one. Multivariate methods, including cluster and principal component analysis were performed to characterize the accessions. The first five principal components account for 86.44% of the total variance of all traits, indicating a high degree of correlation among the characteristics analyzed. High level of phenotypic proximity was found between the accessions N-20-2 and N-5-1 based on pomological, morphological and biochemical characteristics.     

The distribution characteristics of the major capsid gene (g23) of T4-type phages in paddy floodwater in Northeast China

Our previous study revealed the high diversity of the major capsid gene (g23) of T4-type phages that existed in the paddy field soils in Northeast China. In this study, the phylogeny and genetic diversity of the g23 gene in the paddy floodwater samples collected from five sampling sites at three sampling times during the rice (Oryza sativa L.) growth season in Northeast China are reported. In total, 104 different g23 clones were isolated, among which 50% of the clones exhibited the highest identities with the clones retrieved in paddy soils and upland black soils. The remaining clones had the highest identities with lake origins. Phylogenetic analysis revealed that 43% of the g23 clones grouped into three novel subgroups which included the clones unique to paddy floodwater, and no g23 sequences obtained in paddy floodwater fell into the paddy soil groups II, III, IV, V, VI, VII and NPC-A. UniFrac analysis of g23 clone assemblages demonstrated that T4-type phage communities in paddy floodwater were changed spatially and temporally, and the communities were different from those in paddy soils. Further comparison of the g23 clone assemblages from different environments demonstrated that T4-type phages were biogeographically distributed, and the distribution was both affected by geographical separation and ecological processes across the biomes.     

Agro-morphological characterization of chili pepper landraces (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) cultivated in Northern Benin

Variability study of agro-morphological characteristics is important for varietal improvement and plant breeding program. For this, 148 chili pepper landraces (Capsicum annuum L.) collected from Northern Benin were characterized using 39 (21 qualitative and 18 quantitative) morphological characters. The trial was conducted in a Fisher block design with 3 replicates at the experimental station of the Faculty of Science and Technology (FAST) of Dassa based in Central Benin. The results revealed considerable morphological variability between landraces. Twenty nine (16 quantitative and 13 qualitative) variables among the 39 examined were discriminatory and group the landraces into 4 classes when considering the qualitative variables. With quantitative variables, 9 groups were obtained. The correlations between the studied quantitative variables show that the yield parameters are correlated with the variables related to the vegetative part of the plant. This study will help breeders to better select their parents for crossing in order to produce desirable and high yielding varieties.     

Genetic diversity and relationships of wild and cultivated <Emphasis Type="Italic">Zanthoxylum</Emphasis> germplasms based on sequence-related amplified polymorphism (SRAP) markers

The genus Zanthoxylum, belonging to Rutaceae, has a long history of cultivation both for economic and chemical values in China. To effectively conserve and sustainably utilize this genus resource, a study on genetic diversity and relationships of Zanthoxylum germplasms was carried out by employing SRAP markers. We used 16 primer combinations to assess genetic variations and relationships among 175 accessions from eight cultivated provenances, including Shandong, Henan, Shanxi, Shaanxi, Gansu, Sichuan, Guizhou and Yunnan. A total of 145 clear repetitive and intense bands were yielded, and the percentage of polymorphic bands was 100 % for per primer combination, indicating a relatively high diversity among Zanthoxylum germplasms. From a geographic perspective, the highest genetic diversity level was observed within Guizhou provenance (N _a  = 1.97, Ne = 1.52, H = 0.31, I = 0.46) while Henan provenance had the lowest genetic diversity (N _a  = 1.68, Ne = 1.45, H = 0.25, I = 0.37). Based on AMOVA results, the abundant genetic variation was mainly caused by variation of intra-provenances (84.96 %), rather than among provenances (15.038 %). The results indicated low genetic differentiation (G _st  = 0.133) and high gene flow (N _m  = 3.2605) among provenances. The neighbor-joining tree revealed that the 175 accessions could be divided into four groups, and groupings indicated a divergence between the cultivated accessions of Zanthoxylum bungeanum Maxim. and Z. armatum DC. Moreover, three accessions of Z. piperitum DC. var. inerme without prickles introduced from Japan gathered one cluster. Cluster IV is composed of accessions of different geographical origin, including 11 wild species and 10 cultivated accessions of Z. bungeanum. The cluster analysis also reflected a relatively close relationship between the geographical origins and the classification of accessions in cluster I. Structure analysis indicated that collected Zanthoxylum accessions could be divided into two major groups. The information obtained from our research would benefit to make use of Zanthoxylum germplasms and assist the management of a Zanthoxylum germplasms collection.