Genetic diversity of the African wild rice (Oryza longistaminata Chev. et Roehr) from Ethiopia as revealed by SSR markers

Data from microsatellite markers have been extensively used for both in situ and ex situ conservation strategies by determining the level of genetic diversity of natural populations that can widen the gene pool of cultivated plants. Such conservation practices are based on understanding of the between and within population genetic variations and partitioning populations on the basis of geographic origin. Therefore, the objective of this study was to assess the genetic diversity of Oryza longistaminata Chev. et Roehr and how this variation is partitioned within and between the eight O. longistaminata populations found in the different geographic regions of Ethiopia using simple sequence repeat markers. Five microsatellite markers in 320 samples generated 64 alleles that revealed the presence of large amount of genetic variability (Ho = 0.225; He = 0.768; Na = 7.375; Ne = 6.565 and P = 0.744). The F-statistics detected by the microsatellite loci showed Fst = 0.064 and Fis = 0.743 and there was no population in Hardy–Weinberg equilibrium. The genetic diversity results obtained from this data indicated that there are high levels of genetic diversity in the populations of O. longistaminata studied and it is higher within than between populations. Among the eight populations sampled, five populations were identified as priorities for conservation strategies. Thus, national collection and conservation strategies need to consider these populations.     

Genetic diversity in West African okra (Abelmoschus caillei) (A. Chev.) Stevels — Multivariate analysis of morphological and agronomic characteristics

Summary Factor, Principal component and canonical analyses were used to study the extent of genetic diversity among 30 accessions of West African okra. Genetic variability among the accessions proved to be large. Pigmentation of various parts of the accessions and fruit characteristics contributed significantly to the total variation observed. Factor analysis and principal component analysis produced similar results which were substantially different from those produced by canonical analysis. The first three canonical variables accounted for 100% of the total variance while the number of pods per plant, and pod weight primarily accounted for the first canonical variable. Whereas the second canonical variable was primarily loaded by number of seeds per pod and fruit colour, the third canonical variable was comprised of a weight of 100 seeds and number of epicalyx segments.The level of variability observed supports the opinion (Stevels, 1988, 1990) that this okra type constitutes a separate species.     

Genetic diversity associated with conservation of endangered Dongxiang wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis>)

The wild progenitor species (Oryza rufipogon) of Asian cultivated rice (O. sativa L.) is located in Dongxiang county, China which is considered its the northernmost range worldwide. Nine ex situ and three in situ populations of the Dongxiang wild rice (DXWR) and four groups of modern cultivars were genotyped using 21 SSR markers for study of population structure, conservation efficiency and genetic relationship. We demonstrated that the ex situ conservation of the DXWR failed to maintain the genetic identity and reduced genetic diversity. Therefore, in situ conservation is absolutely necessary to maintain the genetic identity, diversity and heterozygosity. Also, in situ conservation is urgently needed because natural populations in DXWR have decreased from nine to three at present due to farming activity and urban expansion. In DXWR, the three surviving in situ populations had greater expected heterozygosity than any cultivated rice, and were genetically closer to japonica than either the male-sterile maintainer or restorer lines, or indica. Japonica has the lowest genetic diversity of cultivated rice. As a result, DXWR is a rich gene pool and is especially valuable for genetic improvement of japonica rice because these O. rufipogon accessions are most closely related to the japonica as compared to O. rufipogon collected anywhere else in the world.     

Isozyme diversity and analysis of the mating system of the wild rice Oryza latifolia Desv. in Costa Rica

Oryza latifolia is the most abundant and widespread wild relative of rice in the lowlands of Costa Rica. It also has the most diverse morphology. However, little is known about the genetic diversity and mating system of this allotetraploid species. Genetic analyses of nine populations from different life zones from the Pacific and Atlantic slopes were performed using six isozyme loci. Differences in genetic variability were observed among populations, of which Palo Verde and Santa Rosa were the most diverse. Most Atlantic populations clustered together, and a similar result was obtained with the Pacific populations. High levels of interpopulation diversity were observed while most populations were monomorphic for at least one genotype, suggesting little genetic flow within populations. Even in polymorphic populations no variation was observed within progeny groups, combined with Hardy-Weinberg disequilibria in most populations, commonly observed in autogamous species or in species with clonal reproduction. However, the high frequency of heterozygous-like patterns may suggest that the reproductive system of O. latifolia might be more complex. Future research may explain the genetic patterns as well as the reproductive biology of this species. The knowledge of the genetic diversity and mating system of O. latifolia could contribute to the implementation of genetic resource conservation strategies and gene flow analyses, as well as of breeding programs for rice improvement.     

Genetic diversity in wild Tunisian populations of Mentha pulegium L. (Lamiaceae)

The allozyme variation of 15 Tunisian wild populations of Mentha pulegium L. threatened by human activities (clearing, hard-grazing, ploughing, traditional uses) was surveyed by the analysis of 14 isozyme loci using horizontal gel starch electrophoresis. The species exhibited a high level of genetic variation within populations (the mean Ap = 2.20, P = 72%, Ho = 0.349 and He = 0.229), which indicates a predominately outcrossing mating system and the recruitment of new genotypes via dispersal seeds. The genetic structure analysis of the populations using F statistics indicates no inbreeding, and showed an excess of heterozygosity for few loci. The moderate differentiation of populations (F_ST = 0.110) and the low rate of gene flow between them (Nm = 2.02) might been caused by recent isolation of the populations through biotope disturbances. The value of Nei's genetic identity varied from 0.839 to 0.999 reflecting a relatively low genetic divergence between populations. Cluster analysis using UPGMA method and Nei's genetic identity values, showed that populations geographically close didn't always cluster together. However, populations within the same bioclimatic stage generally subclustered together indicating that differentiation between bioclimatic regions occurred.     

Potential use of rock-phosphate-solubilizing bacteria associated with wild rice as inoculants for improved rice (Oryza sativa)

A study was conducted to isolate P-solubilizing bacteria from the rhizosphere of three wild rice species and to test their ability to mobilize P from rock phosphate (RP). Inoculated seeds or seedlings of eight different strains were grown in soils supplemented with a P fertilizer mixture (PFM) consisting triple super phosphate (TSP) and RP, each providing equal amounts of P₂O₅. Crop growth, NaHCO₃-extractable P, crop P uptake and yield were compared with two uninoculated controls, with either TSP or PFM added. In the pot experiment, P availability varied from 20 to 48 mg P kg^?1 soil. Yields ranged between 4.8 and 6.6 g per pot and were not significantly different between treatments. In the field experiment, shoot P accumulation in inoculated and TSP-control treatments at the heading stage ranged between 79–129 mg and 219 mg per pot, respectively. Dual inoculants comprising Staphylococcus scirui, Bacillus pumilus, Bacillus subtilus and Bacillus cereus increased yield by about 29% over PFM-controls (324 g m^?2) but those yields were 21% lower than TSP-controls (510 g m^?2). Therefore, application of inoculants combined with PFM is not a viable alternative for TSP under the tested conditions because yield was limited by the P availability.     

The taxonomic status of the wild rice species Oryza ridleyi Hook. f. and O. longiglumis Jansen (Ser. Ridleyanae Sharma et Shastry) from Southeast Asia

The taxonomic status of the two species O. ridleyi and O. longiglumis in Oryza series Ridleyanae was resolved using morphological and molecular markers. Cluster analysis using a similarity matrix based on 12 qualitative characters separated the O. ridleyi from the O. longiglumis samples and the O. ridleyi samples from Papua New Guinea (PNG). O. ridleyi and O. longiglumis formed distinct groups upon cluster analysis based on 16 quantitative characters. Canonical discriminant analysis showed significant differences between the two species with anther and ligule length and spikelet and leaf dimensions as the most discriminating characters. Cluster analysis based on RAPD markers showed distinct clusters for O. longiglumis and O. ridleyi samples from different geographic origins. Hybridization studies revealed an F₁ sterility barrier in interspecific hybrids and those obtained from intraspecific crosses between O. ridleyi from Southeast Asia and PNG.     

The fragrance (fgr) gene in natural populations of wild rice (Oryza rufipogon Griff.)

The Asian cultivated rice, Oryza sativa L. (spp. indica or japonica), is assumed to have originated from one or both of the two wild Asian species, O. rufipogon Griff. and O. nivara Sharma and Shastry. They occur throughout the monsoon Asia and west Oceania. Fragrance is the most important trait among the domesticated characters of basmati and jasmine rice of Asia. The gene for fragrance in a scented rice shows the presence of a mutated portion (i.e., an eight base pair deletion in exon 7) that result in its loss of fragrance. In the present study, 229 wild rice O. rufipogon accessions were genotyped for this locus using a PCR assay. The wild rice species contained the mutated allele of the fgr gene at a low frequencies of 0.23. The surveyed populations were in Hardy–Weinberg equilibrium. This observation supports the hypothesis that the allele for fragrance was already present in the wild rice, and that this trait appeared in scented rice cultivars because of selection by the farmers of genotypes possessing this character during the process of domestication.     

Genetic diversity studies and screening for rice stem borer (Chilo Agamemnon) resistance in six Egyptian rice cultivars (Oryza sativa L.) using DNA based-markers

Genetic Resources and Crop Evolution - In order to assess the genetic diversity among six Egyptian rice cultivars and developing cultivars resistant to different rice stem borers, random amplified...     

Genetic diversity in the Red wild einkorn: T. urartu Gandilyan (Poaceae: Triticeae)

Red wild einkorn, Triticum urartu, is increasingly being recognized as a source of genetic material for the improvement of wheat grain quality and for conferring resistance to various diseases such as Powdery Mildew and Leaf Rust resistance including the virulent race Ug99. Two hundred and two samples of T. urartu collected throughout much of its distribution were investigated by amplified restriction length polymorphism, AFLP? to estimate the genetic diversity within and among them. To infer the genetic structure of the populations the data were subjected to analyses of molecular variance, AMOVA. The analyses of the samples enabled us to assess the location(s) of the richest area(s) in genetic diversity of the species. This area is found in north-western Syria and the adjacent South Turkey. It was also found that the similarity among populations did not reflect on their geographic closeness.     

Genetic diversity and geographical peculiarity of Tibetan wild soybean (Glycine soja)

Tibet is the highest Plateau in China and the world, however wild soybean has been found in its southeastern fringe region adjacent to the northwest of Yunnan Province. Tibetan wild soybean was distributed only in the Gongrigabuqu-River Gorge in southeast Tibet. This regional plant species belong to the flora of Himalayan-Hengduan Mountains, which comprises composite elements of ancient arcto-tertiary flora, tropical and semitropical flora. To date, few studies have been carried out on Tibetan wild soybean. Studying Tibetan wild soybean together with other regional ones helps to understand the history of the origin and dissemination of wild soybean species in China. Here we reported the status of genetic diversity in Tibetan wild soybean and the genetic relationship between Tibetan and other regional wild soybeans revealed by nuclear SSR markers. The results showed that the Tibetan wild soybean sample was significantly differentiated from other regional ones, as characterized by the lowest mean allelic richness ( [^(\textr)] {\hat{\text{r}}}  = 1.40) and gene diversity (H _e = 0.130) and the highest ratios of regionally unique alleles (63.26%) and fixed alleles (46.94%). These genetic attributes suggested that Tibetan wild soybean may have undergone severe adaptation selection for the plateau climate and ecogeographical conditions, and had less genetic exchange with inland populations. The regional population south of the Changjiang River (Central and South China) showed higher genetic richness. UPGMA cluster analysis revealed two large geographical groups, Tibetan and inland, and revealed closer relationship among the eastern populations, which suggested that the dissemination of this species in the eastern part of China might be rapider.     

Arsenic mobilization in rice (Oryza sativa) and its accumulation in the grains

Flooded rice (Oryza sativa L.) may contain high arsenic (As) concentrations compared to other grain crops. For the development of measures to reduce the As concentration of rice grains, knowledge about the mobility of As within the rice plant is required. Therefore, to investigate the mobilization of As within the plant, rice was grown in nutrient solution and exposed to As either before flowering, after flowering, or continuously until maturity. Furthermore, rice was grown in four soils under greenhouse and field conditions and the time course of As accumulation in grains during the grain‐filling period was investigated. When grown in nutrient solution, As removal at flowering did not reduce As concentrations in polished rice compared to plants supplied with As continuously or after flowering. Plants that received As only after flowering had the same As concentrations in shoot and bran as plants receiving As only before flowering. However, continuous As supply resulted in doubling of As concentrations in both plant parts. In contrast to grain and shoot, the As concentration in the root decreased after As removal compared to the treatments receiving As only after flowering or continuously. The observations indicate that As was mobilized from root or shoot to the grain and that it was accumulated in the grain, although it was not available in nutrient solution during the grain‐filling period. In soil experiments, the 1000‐grain weight increased up to 2 weeks before harvest in the field as well as in the greenhouse. The As concentration in rice grain was constant during the whole grain‐filling period. It was at a similar level under field and greenhouse conditions, and its variation among soils was in the same order indicating that soil was the decisive factor for As concentration in grains. Our results suggest that temporary cultural measures during the cultivation period, for example drainage, might be ineffective because of the mobilization capacity within the rice plant. Moreover, harvest before final maturity of grains would not reduce the As concentration since it remained constant during the grain‐filling period.     

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 diversity in Japanese aromatic rice (Oryza sativa L.) as revealed by nuclear and organelle DNA markers

Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.     

Genetic diversity of thiamin and folate in primitive cultivated and wild potato (Solanum) species

Biofortification of staple crops like potato via breeding is an attractive strategy to reduce human micronutrient deficiencies. A prerequisite is metabolic phenotyping of genetically diverse material which can potentially be used as parents in breeding programs. Thus, the natural genetic diversity of thiamin and folate contents was investigated in indigenous cultivated potatoes (Solanum tuberosum group Andigenum) and wild potato species (Solanum section Petota). Significant differences were found among clones and species. For about 50% of the clones there were variations in thiamin and folate contents between years. Genotypes which contained over 2-fold the thiamin and 4-fold the folate content compared to the modern variety Russet Burbank were identified and should be useful material to integrate in breeding programs which aim to enhance the nutritional value of potato. Primitive cultivars and wild species with widely different amounts of thiamin and folate will also be valuable tools to explore their respective metabolic regulation.     

Genetic diversity of taro (Colocasia esculenta (L.) Schott) in Vanuatu (Oceania): an appraisal of the distribution of allelic diversity (DAD) with SSR markers

In Vanuatu, an oceanic archipelago located in south-west Pacific, taro (Colocasia esculenta (L.) Schott) is one of the staple crops. An eco-geographical survey of its genetic resources was conducted in ten villages, each located on a different island. A sample of 344 landraces referred as the National Sample (NS) was collected. Its genetic diversity was assessed using nine microsatellites markers and then was compared with an International Core Sample (ICS) that was previously distributed in the ten villages of the study in order to test the geographical distribution of allelic diversity as an effective mean for the on-farm conservation of root crops. The ICS was composed of 41 accessions, including 23 originating from South-East Asia. The molecular dataset revealed in the NS (1) 324 distinct multilocus genotypes, (2) six genetic clusters mainly differentiated by rare alleles, (3) a geographical structure of the genetic resources of taro based, within each village, on the dominance of one or two of these clusters rather that their exclusivity, and (4) an analogy between the patterns of dominant clusters between villages and the past and present social networks. In addition, accessions from the ICS revealed 52 new alleles. Based on these findings, we formulate hypotheses regarding the processes involved in the genetic diversification of taro in Vanuatu. We also discuss the use of this set of microsatellite markers along with the molecular dataset obtained from this study as effective tools to monitor the diversity and evolution of taro in the future.