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.     

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 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.     

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 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.     

Phenotypic diversity of the big seed type subcollection of wild soybean (Glycine soja Sieb. et Zucc.) in China

Wild soybean (Glycine soja), the progenitor of soybeans, has become an important germplasm source for soybean breeding. The Chinese G. soja germplasm collection includes two subcollections, one typical wild soybean (G. soja) and the other ‘big seed type’ (semi-wild soybean, G. gracilis). In order to understand the nature of this big seed type subcollection, a considerable number of 1,185 accessions were investigated focusing on phenotypes, compositional structure and genetic diversity of this subcollection. The results showed that there were 617 combined morphotypes formed by six major morphological traits. The morphotype number and diversity gradually decreased among four sections from small to large 100-seed weight sizes. The big seed subcollection accumulated distinctly high frequencies for white flower, grey pubescence, seed non-bloom and four seed coat colours (green, yellow, brown and black), differing from the typical G. soja. Between the two subcollections, only the compositional structures of leaf shapes were almost in agreement. A rare strip-shaped leaf only appeared in typical G. soja and small-seeded grade (100-seed wt) of the big seed type. Seed non-bloom trait showed that the increased frequencies were concomitant with the augmenting of 100-seed weight. The data suggested that white flower accumulated rapidly in the big seed type, followed by seed non-bloom, while the slowest rate of accumulation was grey pubecence, and that the ‘large-seeded type (2.51–3 g 100-seed wt)’ of typical G. soja and the ‘smallest-seeded type (3.01–3.5 g 100-seed wt)’ of the big seed type could have a closer genetic relationship. The morphotype number and genetic diversity showed reduced values with increased 100-seed weights. The geographical distribution of genetic diversity indicated two tendencies: decreased from north to south and also from east to west. Our results suggested that Northeast China was the first centre of morphological diversity for the big seed type, and the North was the secondary centre in China.     

Diversity of native rice (Oryza Poaceae:) species of Costa Rica

We found several populations of wild Oryza species in the lowlands of Costa Rica. The plants showed extensive morphological variation, suggesting the presence of several species. In the morphologic study, 33 traits were scored for plants of all the species. A principal component analysis revealed the significant morphological separation of the different species. The analyses indicated that there are three species, O. grandi­glumis, O. latifolia and O. glumaepatula. Two putative hybrid types were found, both significantly differing in their morphology from the known species and intermediate at several traits. O. grandi­glumis is a new record for Costa Rican flora. Its main population is located in Caño Negro Wildlife Refuge, Los Chiles, Alajuela. O. latifolia is distributed throughout the lowlands of the country and the plants of the Atlantic slope are significantly bigger in general habit than those of the Guanacaste area. During this study a population of O. glumaepatula of hundreds of thousands of plants was discovered in the Medio Queso River wetland, Los Chiles, Alajuela. This population is the most important source of genes for cultivar's improvement from the primary gene pool of rice in Costa Rica. The small ligule and the wide flag leaf characteristic of the two CCDD species separated them from the AA diploid O. glumaepatula. Seed size, ligule size, number of branches in the panicle, plant height and sterile lemma length are all bigger in O. grandi­glumis, and influenced the second factor that separated the CCDD species in two discrete clusters. The species found offer great possibilities for the improvement of rice cultivars and they should be thoroughly studied and appropriately protected.     

Viability and patch occupancy of a swamp rabbit metapopulation at the northern edge of its distribution

Swamp rabbits (Sylvilagus aquaticus) are state-endangered in Indiana, USA, and population decline has been attributed to habitat loss. We conducted pellet surveys as part of a long-term survey effort that has been conducted at approximate 10-year intervals over the last 40 years. We modeled patch occupancy and conducted a spatially-explicit population viability analysis (PVA). Although occupancy of individual patches varied over time, occupancy rate has been constant for the last 30 years, and Indiana swamp rabbits exist as a metapopulation that appears to be stable. Metapopulation dynamics were best characterized as being stationary, but area was an important factor in extinction rates; occupied patches (142 ± 37 ha) were significantly larger (P = 0.01) than unoccupied patches (79 ± 20 ha). We did not find strong support for models with colonization rates as a function of distance to neighboring patches, nor was distance to contiguous patches of habitat significantly different (P = 0.12) for occupied and unoccupied sites. Population viability analysis corroborated our findings based on occupancy modeling, and evaluation of the PVA model using occupancy data for the period 1985–2006 resulted in predictions that nearly matched our field observations (33% observed patch occupancy vs. 25% predicted patch occupancy). Population viability was most sensitive to reductions in survival and fecundity rates, but was otherwise robust to changes in parameters such as initial abundance and carrying capacity. Our findings provide novel insights into a poorly studied member of Sylvilagus and into species metapopulation dynamics at the edge of the range.     

Genetic diversity in wild barley (Hordeum spontaneum C. Koch) in the Near East: a molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers

We analyzed the genetic diversity in 88 genotypes from 20 populations of wild barley (Hordeum spontaneum C. Koch) from Israel, Turkey and Iran, by randomly amplified polymorphic DNA (RAPD). Twenty two of the 33 primers used yielded scorable products with 1–11 polymorphic bands. No duplicate patterns were found except for four haplotypes.When the total genetic diversity was estimated, 75% of the variation detected was partitioned within the 88 genotypes and 25% among the populations. When variation between countries was assessed, no substantial differences were found, because most of the variation detected (97%) was partioned within the 20 populations and the remainder among countries. The results of this limited survey indicate that the extensive genetic diversity is present in natural stands of wild barley throughout the Fertile Crescent.     

Dual origin of the cultivated rice based on molecular markers of newly collected annual and perennial strains of wild rice species, Oryza nivara and O. rufipogon

The direct ancestor of rice (Oryza sativa L.) is believed to be AA genome wild relatives of rice in Asia. However, the AA genome wild relatives involve both annual and perennial forms. The distribution of the retrotransposon p-SINE1-r2, a short interspersed nuclear element (SINE) at the waxy locus was analyzed in diverse accessions of the AA genome wild relatives of rice (O. rufipogon sensu lato). Most annual wild rice accessions had this retrotransposon, while most perennial types lacked this element, contradicting results to the previous studies. Results presented here suggest that O. sativa has dual origin that lead to indica-japonica differentiation. Results suggest the indica line of rice varieties evolved from the annual genepool of AA genome and the japonica varieties from the perennial genepool of AA genome wild rice.     

Genetic diversity of the earthworm Octolasion tyrtaeum (Lumbricidae,Annelida)

Octolasion tyrtaeum (Savigny, 1826), a cosmopolite earthworm species widespread around the world, is known to consist of two morphologically distinct forms, small (4–8 cm long) and large (10–14 cm) ones that sometimes are found in sympatry. It was demonstrated that these forms belong to significantly divergent mtDNA lineages, which suggests that the differences among these forms are caused by genetic factors. However, these results were in contrast to the allozyme analyses, and nobody has demonstrated that differences among these lineages exist on nuclear level as well.We analyzed mitochondrial cox1 and cox2 and nuclear ITS2 sequences of O. tyrtaeum specimens from various regions of Russia, Belarus, and Kazakhstan. Our sample only included individuals belonging to the small form, however, we found both genetic lineages described by earlier studies, and, in addition, discovered a new genetic lineage. Nuclear ribosomal sequences confirmed that the differences between these lineages are deep. We also found one example of incongruence for several individuals whose mitochondrial sequences belonged to the “small” lineage, but nuclear ITS2 fell into a separate branch on the phylogenetic tree. In addition, O. tyrtaeum was found to be paraphyletic with respect to the closely related species O. cyaneum (Rosa, 1884).