Intraspecific and interspecific variation in Setaria revealed by RAPD analysis

Random amplified polymorphic DNA (RAPD) analysis was applied to foxtail millet (Setaria italica) and other Setaria species in order to assess the degree of polymorphism among and within the species and to investigate their genetic relationships. Twenty accessions of foxtail millet, five of green foxtail (S. viridis), five of yellow foxtail (S. glauca), one each of S. germanica, S. verticilliformis, S. pallidifusca, S. macrostachya, S. sphacelata and S. faberi, and one unidentified, were evaluated for variability using a set of 19 random 10-mer primers. A total of 148 markers were scored for all the accessions. Wide variations in banding profiles among species were observed with nearly every primer used. The results showed that foxtail millet and S. glauca had a considerable degree of variation. The geographic differentiation of RAPD patterns in foxtail millet accessions examined seemed to exist. The present study confirmed that foxtail millet is more closely related to green foxtail than to other species in Setaria, providing support for the origin of foxtail millet from S. viridis and the conspecificity of these two species. The results confirmed that S. germanica and S. italica are conspecific and the former can be replaced by the latter. Setaria glauca and S. sphacelata are distinct from foxtail millet, implying that elite traits found in these two species are relatively difficult to be used in foxtail millet improvement. This study demonstrates that RAPD analysis can be used in assessing intraspecific and interspecific variation in foxtail millet and its wild relatives.     

Genetic variation in captive population of chinese alligator, Alligator sinensis, revealed by random amplified polymorphic DNA (RAPD)

Chinese alligator (Alligator sinensis) is an endemic species in China. The likely extinction of it in the wild has been recognised. To prevent this species becoming extinct, the Anhui Research Centre of Chinese Alligator Reproduction (ARCCAR) was established in Xuanzhou, Anhui Province in 1979, where has been established the largest captive population of Chinese alligator (XZSP) in the world. Another farm (CXSP) was established by villagers in Changxin, Zhejiang Province. The results of an investigation of the two captive subpopulation structures by genetic analysis are presented in this paper. We examined the genetic variation in the two captive subpopulations using RAPDs. Thirty-one random primers were selected among 199 random primers screened. A total of 193 reproducible RAPD fragments were scored among 43 individuals, of which 21 (10.88%) were polymorphic. The genetic distances between 43 individuals ranged from 0 to 0.0376 with average of 0.0104±0.0055 S.E. The genetic similarity in CXSP (0.9948±0.0029 S.E.) was higher than that in XZSP (0.9894±0.0055 S.E.). The founder effect is a possible explanation for very low genetic variation in CXSP. Analysis of the RAPD data showed that the mean phenotypic band frequencies of each polymorphic loci was 0.6656±0.3730 S.E. The lowest phenotypic band frequency (0.0233) was found in four of those polymorphic loci. There was no genetic difference between the two subpopulations (D_ij=0.0009). According to the dendrogram and the distribution of polymorphic fragments in two subpopulations, CXSP originated genetically from XZSP. This paper summarises a preliminary research on genetic structure in populations of Chinese alligator. Although there is higher genetic similary (0.9896±0.0055 S.E.) in captive population of A. sinensis, we did not determine whether or not loss of genetic variation had occurred in relation to a wild control population. The data of malformed offspring will be collected carefully, and wild samples be added to set up a control population in future study.     

Characterization of genetic variation and relationships among Choix germplasm accessions using RAPD markers

Choix, a plant in the tribe Maydeae of the grass family, has been cultivated in Asia for several thousand years. It is a potential gene resource for improvement of other cereal crops because of its nutritional value and tolerance to stress. Genetic variation and relationships among 21 Choix lachryma-jobi L. accessions were characterized by random amplified polymorphic DNA (RAPD) markers. A total of 205 DNA fragments across all materials were amplified with 31 random primers, averaging 6.61 per primer. Among amplified fragments, 115 showed polymorphism averaging 3.71 per primer. Of amplified markers, 56.1% were polymorphic, indicating considerable variation at the DNA level among these accessions. Some fragments were accession-specific. Pair-wise genetic similarity (GS) among 21 accessions ranged from 0.809 to 0.301. The 21 accessions clustered into two major groups. Three exotic Choix accessions clustered together. Three other Choix accessions, collected from Guangxi, China, clustered into a cohesive subgroup. Four wild types of Choix clustered into the same subgroup. These results indicated that the classification by RAPD data reflected the differences in geographic origins and evolution in Choix.     

Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers

The present study, using RAPD analysis, was undertaken to characterize genetic variation in domesticated cowpea and its wild progenitor, as well as their relationships. The materials used consisted of 26 domesticated accessions, including accessions from each of the five cultivar-group, and 30 wild/weedy accessions, including accessions from West, East and southern Africa. A total of 28 primers generated 202 RAPD bands. One hundred and eight bands were polymorphic among the domesticated compared to 181 among wild/weedy cowpea accessions. Wild accessions were more diverse in East Africa, which is the likely area of origin of V. unguiculata var. spontanea. Var. spontanea is supposed to have spread westward and southward, with a loss of variability, loss counterbalanceed in southern Africa by introgressions with local perennial subspecies. Although the variabilty of domesticated cowpea was the highest ever recorded, cultivar-groups were poorly resolved, and several results obtained with isozyme data were not confirmed here. However primitive cultivars were more diverse than evolved cultivars, which still suggests two consecutive bottlenecks within domesticated cowpea evolution. As isozymes and AFLP markers, although with a larger number of markers, RAPD data confirmed the single domestication hypothesis, the gap between wild and domesticated cowpea, and the widespread introgression phenomena between wild and domesticated cowpea.     

Genetic variations and interrelationships in Vanilla planifolia and few related species as expressed by RAPD polymorphism

Vanilla is naturally distributed in Mexico and parts of Central America and the history of origin of cultivated vanilla suggests that the entire stock outside Mexico may be from a single genetic source. In the present study, RAPD polymorphism was used to estimate the level of genetic diversity and interrelationships among different collections of Vanilla planifolia Andr., and few related species, including both leafy and leafless types such as V. tahitensis J.W.Moore, V. andamanica, Rolfe, V. pilifera Holtt., and V. aphylla Blume. Studies revealed that there are very limited variation within collections of V. planifolia, indicative of its narrow genetic base, and of the related species we tested, V. tahitensis is nearest to V. planifolia. The species studied are diverse and have a similarity ranging from 1.2 to 57.3 %. Of the sampled taxa, V. andamanica is the most divergent and there is also reasonable variability within its collections, indicating the possibility of natural seed set. A total of 82 polymorphic bands expressed in the RAPD profiles were used to generate a genetic distance matrix, which was then used in cluster analysis. Specific groupings were revealed by the cluster analysis whereby the leafless forms (V. aphylla, V. pilifera and the new species) and V. andamanica formed separate clusters. This is the first report of species interrelationship studies, including both cultivated and wild vanilla species.     

Genetic variation analysis in the genus Lathyrus using RAPD markers

RAPD analysis was applied to five species belonging to the genusLathyrus (Fabaceae): L.sativus, L.cicera, L.ochrus, L.sylvestris and L.latifolius. All the species under study belong to thesection Lathyrus except L.ochrus which is in section Clymenum.Nine populations representing these species were used and ten random10-mer primers were sampled. A total of 129 amplification products,ranging in size from 0.3 to 3 Kb, were generated. Partitioning ofvariation was studied using the AMOVA technique. The genetic variation proved tobe nearly equally distributed among species and among populations withinspecies. A similar approach was carried out to distinguish populations, whichproved to be efficient. The between population dissimilarities were calculatedand a dendrogram of genetic relationships was drawn. The RAPDs obtained weresufficient to distinguish between the two accessions of a species and toseparate these accessions by clustering them according to species. A highgenetic similarity between the populations of L.sylvestris and L.latifolius was established. A similar result is also shownfor the populations of L. sativus andL. cicera.     

Morphophysiological variation in some Mexican species of vegetable Amaranthus: evolutionary tendencies under domestication

Summary Amaranth (Amaranthus spp.) is an important food resource for indigenous peoples of México. Grain-producing species are mostly cultivated plants, while the species used as vegetables are commonly encouraged in maize plots. Notable biological differences exist between these two types of amaranths. This study analyzes the morphophysiological variation in some Mexican species of Amaranthus and its relationship to the use and management of this taxa. A sample of individuals grown from 14 field collections representing 3 species and putative hybrid derivatives were grown in experimental plots and 18 morphological and physiological characters were measured. A statistical multivariate analysis was performed on these data. The results show that the grain-producing plants tend to allocate a high proportion of energy to the production of inflorescences while the plants used as vegetables allocate a higher proportion of biomass to the foliage. This suggests thatdomestication of Mexican species of Amaranthus have taken two different evolutionary paths depending upon the form of use and management by humans.     

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.     

A comprehensive collection and regeneration strategy for ex situ conservation

Because the facilities in genebanks are likely to be quite limited, it will usually be possible to raise only small populations of plants when producing fresh seed. These populations need to be large enough, however, to reducethe effects of drift on the erosion of genetical variation to an acceptable level. Calculations show that a sample size of 12 plants is probably sufficient to meet this objective provided that a biparental mating procedure is used toproduce fresh seed. It is argued that for conservation, there is little point in collecting more seed from the source populations of the species in question than can be handled when regenerating this seed. If the species is regarded asthe unit of conservation, this minimum sample size in the gene bank should determine the size of the sample collected from each population of the species. Provided that the product of this sample size and the number ofpopulations from which material is collected is not less than 172, this strategy should ensure the conservation of all or very nearly all of the polymorphic genes that are segregating in the species. A critical analysis of currentregeneration procedures shows that these are very inefficient and that much genetical variation is lost almost as soon as it is captured. Lastly, it is shown that some recent criticisms of the collection strategy proposed in earlierpapers are misplaced.     

Genetic variation and species relationships in Himalayan buckwheats as revealed by SDS PAGE of endosperm proteins extracted from single seeds and RAPD based DNA fingerprints

SDS PAGE of endosperm proteins and␣RAPD profiles from different accessions of Himalayan buckwheat were studied to determine their genetic variation and phylogenetic relationships. Comparisons based on Jaccard’s coefficient and UPGMA clustering revealed interrelationships broadly in conformity with conventional treatments. Cluster analysis of the endosperm protein profiles of the selected accessions revealed three broad clusters. A moderate level of intraspecific variability was detected in the endosperm protein profile of different accessions of Fagopyrum esculentum, Moench. Three subgroups were detected in cluster 1. Subgroup 1 included varieties designated as Local, Kamroo local, OC-2 and␣VL-7 which were collected from VPKAS, Almora. Local, Kamroo local and OC-2 showed a similarity coefficient of 1.0 inspite of their being identified as different accessions. VL-7 emerged out separately from the rest of the three accessions. Accessions having winged grains and those having striations on the seed coat formed a 2nd and 3rd subgroup, respectively. IC-13145 which been identified as “F. himalianum”, showed 100%␣similarity in endosperm protein profile with IC-13376 (F. esculentum) and 85–90% similarity which other accessions of F. esculentum. Our results indicate that “F. himalianum” belongs to the esculentum group and should not be regarded as a different species. Cluster 2 included all the accessions of F. tataricum (L.) Gaertn. with Sangla 1, 2, 3, 5, 6, 7 and IC-412863 showing 100% similarity. F. cymosum emerged as a separate group distinct from both esculentum and tataricum. Accessions of F. tataricum and F. cymosum did not show significant intraspecific variation in the SDS PAGE profile of endosperm proteins. Out of the 20 primers used, 3 generated robust, easily interpretable amplified products. While a 1490 bp and a 300 bp RAPD was detected only in F. tataricum, a 1154 bp RAPD was detected in all accessions of F. tataricum except in Shimla B-1. This variety is early maturing and has high seed yields.     

Genetic variation of Ethiopian and Eritrean sorghum (Sorghum bicolor (L.) Moench) germplasm assessed by random amplified polymorphic DNA (RAPD)

The extent and patterns of distribution of genetic variation among 80 sorghum (Sorghum bicolor (L.) Moench) germplasm accessions from Ethiopia and Eritrea were investigated using RAPD with 20 oligonucleotide primers. The primers generated a total of 147 polymorphic bands across the 80 accessions with a mean of 7.35 bands per primer. Estimation of the extent of variation by the Shannon-Weaver diversity index revealed an intermediate level of overall variation (H = 53), although the levels varied among regions of origin of the accessions. Partitioning of the total variation revealed considerable variation (77%) within the region of origin of the accessions and the remainder (23%) among regions of origin. Similarly, a large portion (94%) of the total variation was found within the adaptation zones compared to among the adaptation zones (6%). The results suggest a weak differentiation of the sorghum material both on regional and agro-ecological bases, which could be ascribed to the high rate of outcrossing in cultivated sorghum and its free natural hybridization with its wild and weedy relatives, as well as to seed movement by humans. The average genetic dissimilarity was found to be 36% among the 80 accessions and 13% among the 15 regions of origin. Cluster analysis failed to group accessions of the same region or the same adaptation zone, which further confirmed the weak differentiation of the material studied. The clustering pattern of the regions of origin was broadly concordant with previous clustering patterns obtained using morphological characters, in which regions with broad agro-climatic conditions were grouped together.     

Genetic diversity of introduced and local Spanish persimmon cultivars revealed by RAPD markers

Persimmon culture has become an alternative for fruit growers in Italy, Israel and Spain. However, there is some confusion concerning cultivar identification in non-Asian countries were the species was introduced. Authenticating the identity of germplasm resources of persimmon would be a great value for breeding. Due to the floral biology of the persimmon species the expected genetic variability is high. RAPD markers were chosen for this study of persimmon germplasm resources in Spain. Nineteen markers were obtained from 8 primers. The average of 2.4 markers/primer was higher than that obtained in other woody fruit species. The availability of data referenced from isozymes and pomological traits revealed complete agreement among groups identified by RAPDs, isozymes and pomological traits. Results suggest that RAPD technology is adequate for fingerprinting persimmon and the data is consistent with persimmon's hypothetical origins, adaptation history and previous classification by isozymes or pomological traits. Many synonyms have been identified, mostly in cultivars from local surveys, suggesting that a few new genotypes arose in Spain since the species was introduced to Europe. By means of RAPD markers, a better identification of the European persimmon germplasm is available.     

Characterisation of thirteen cowpea landraces from Umbria (Italy). Strategy for their conservation and promotion

Thirteen landraces of cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata cv. gr. Unguiculata) have been morphologically and agronomically characterised as part of a plan for safeguarding and protecting plant biodiversity typical of Lake Trasimeno (Umbria, central Italy). Sixty plants per accession were scored for plant vigour, growth habit, flower colour, days to flowering, days to first mature pod, pod length, total number of pods produced, seed colour pattern, 100 seed weight, total seed yield and virus susceptibility. With the exception of vigour and growth habit, all landraces appeared to be well differentiated from one another for all the characters considered. Strategies and problems related to their in situ conservation are discussed.     

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 diversity and differentiation in Ethiopian populations of Phytolacca dodecandra as revealed by AFLP and RAPD analyses

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analyses were performed on six populations (a total of 89 individuals) of Phytolacca dodecandra (endod) collected in Ethiopia. The populations were selected based on our previous investigation to represent two altitude groups: lowland/central-highland (1600–2500 m) and highland (2501–3000 m). A total of 197 AFLP and 68 RAPD markers were scored from 5 primer pairs and 12 random primers, respectively. The overall patterns obtained for AFLPs and RAPDs from diversity, cluster and principal component analyses were very comparable. However, the moderate correlation (r = 0.56) between AFLP and RAPD similarity matrices as well as the discrepancies in diversity estimates between the two techniques in some populations and in the lowland/central-highland plants could be due to differences in sensitivity of reaction conditions, bias in scoring of bands, number of markers used for analyses, and/or parts of the genome surveyed. For both AFLP and RAPD, the lowland/central-highland populations showed higher polymorphism and Shannon information measure (H) than the highlands. Cluster and principal component analyses performed for both marker types have also clearly demonstrated the differentiation of all the lowland/central highland plants from those of the highlands, in agreement with our previous conclusion. Markers scored from any of the five AFLP primer pairs were sufficient to clearly distinguish the two altitude groups; with RAPD, selection of about 8 informative markers produced by seven random primers was needed for the same purpose.     

Landraces in central Italy: where and why they are conserved and perspectives for their on-farm conservation

Four hundred and twenty-seven landraces belonging to different plant species (forages, cereals, pulses, garden crops and fruit trees) were found on-farm in central Italy during exploration and collecting missions carried out since 1981. Open field crops are mostly grown under modern agricultural techniques by relatively young farmers on quite large farms for Italian standards. Garden crops are mostly grown by elderly farmers, running small farms or home gardens and using traditional farming systems which include the use of mechanical tools for soil preparation and occasionally the use of chemical fertilisers. There is no unique situation in on-farm conservation and management in the investigated area: the main factors involved appear to be a fragmented habitat and the presence of relatively elderly farmers. Most landraces are directly used by farmers' families, but a part is sold at local and wider markets. The main reasons why these landraces have been maintained on-farm are: their resistance/good productivity under difficult or harsh climatic conditions, traditional reasons or organoleptic peculiarities, which make them highly valued and expensive on the local and city markets and/or simply because they are appreciated by the families. Three example cases of effective on-farm conservation are presented. Social problems seem to be the main cause of genetic erosion. Perspectives and constraints to on-farm conservation and management are briefly discussed.     

The genus Amygdalus L. (Rosaceae): Species relationships, distribution and evolution under domestication

Summary The paper reviews the taxonomic relationships, morphological distinction, geographical distribution and ecological specificities of the twenty six species recognized (by us) in Amygdalus L. It also surveys the intra-genetic structure in this genus stressing the fact that they fall into five groups of closely related vicarious species: (i) Communis group (9 species), (ii) Orientalis group (6 species), (iii) Sect. Chamaeamygdalus (4 species), (iv) Sect. Spartioides (2 species), and (v) Subgenus Dodecandara (5 species). Within each group, species are separated from one another geographically (in few cases by altitude). The only major exception to such allopatric distribution is found in A. communis L., and this is interpreted as an outcome of domestication. Interspecific sterility barriers are absent, or only weakly developed in Amygdalus, and numerous inter-specific hybrids (particularly between the crop and various wild almond species) have been detected. Therefore most (may be all) wild almond species constitute the primary gene-pool of the cultivated nut crop.The combined botanical and archaeological evidene points to the Levant countries as the place where the almond was taken into cultivation. Wild forms of A. communis are very likely native only to this area. Also the earliest archaeological signs of almond domestication come from this area.     

Genetic diversity in wild cereals: regional and local studies and their bearing on conservation ex situ and in situ

The current alarming global crisis and extinction of biodiversity affect negatively the planet's biosphere. Conservation of biodiversity is one attempt to alleviate the pending extinction of the biosphere by humans. Genetic diversity, the basis of evolution by natural selection, is gravely threatened in the progenitors of cultivated plants and its exploration, evaluation, conservation in situ and ex situ is imperative to guarantee sustainable development. This is illustrated by the population genetics and ecology of two important progenitors of cereals wild, wheat and barley. The wild cereals are rich in adaptive genetic diversity in the Fertile Crescent, primarily in Israel, which is their center of origin and diversity. The 40–55% intrapopulation diversity level in the wild cereals contrasts sharply with the average of 80% in outbreeders. Genetic diversity in wild wheat and barley is structured, particularly in wild emmer wheat, as an 'archipelago' ecological and genetic structure. These include central, semi-isolated and ecologically peripheral and marginal isolated populations, where specific alleles and allele combinations predominate as coadapted blocks of genes, adaptive to diverse ecological stresses. These involve both physical (climatic and edaphic) and biotic (pathogens and parasites) stresses at macro- and microgeographical scales. Complementary in situ and ex situ conservation is imperative across the geographic range of these species, to safeguard their immensely important genetic resources for crop improvement.     

Results of activities to maintain landraces and other material in some European countries in situ before 1945 and what we may learn from them

All three recommendations to maintain landraces in European countries, given in 1927: 1. maintenance by traditional farmers, 2. maintenance by school personnel and pupils, and 3. maintenance by small agricultural institutions, were disregarded. The present outcome: maintenance by genebanks, which often grow landraces and improved cultivars of one crop next to each other, and which often are part of a large agricultural research institute, was advised against.The above observation may be of value to those who at present advocate maintenance of landraces by traditional farmers in developing countries.It is recommended that landraces should be collected and maintained in genebanks as this will result in a partial loss of the material, whereas on farm maintenance (in situ conservation) would lead to a complete loss.     

Inter-simple sequence repeat (ISSR) and RAPD variation among wild barley (Hordeum. vulgare subsp. spontaneum) populations from west Turkey

Inter-Simple Sequence Repeat (ISSR) and Randomly Amplified Polymorphic DNA (RAPD) markers were used to analyze genetic distance among H. vulgare subsp. spontaneum populations from west Turkey. Fifty-five RAPD and 10 ISSR primers were used to detect variation among sample. A total of 55 polymorphic loci were found using 65 primers. Two distinct cluster groups were clearly established among populations. The minimum variation was detected between Pinarbasi and Bornova (GD = 0.192) populations and the maximum was found between Icmeler and Aydin populations (GD = 0.926). As two dominant markers, RAPD and ISSRs are effective and promising marker systems for detecting genetic variation.