Genetic diversity of wheat wild relatives in the Near East detected by AFLP

In order to reveal the molecular genetic diversity of wheat wild relatives, an AFLP analysis was conducted with 16 accessions of five Triticum andAegilops species originating from the Near East. Variation within population was studied with at least seven individuals per accession. Four primer combinations were used for selective amplification. Based on the scored bands, we estimated percentage of polymorphic bands, 1 – proportion of shared bands (1-psb) and nucleotide diversity (π). Of the five species used in this study, Ae. speltoides had the highest level of `within population' variation. This species had also the highest value of the variation among populations. As for Triticum species, the level of variation within population was low in diploid species (T. urartu and T. boeoticum),whereas two tetraploid species (T. dicoccoides and T. araraticum) had relatively high levels of variation within population. While the two diploid Triticum indicated a clear interspecific divergence, the two tetraploid wild wheats were not clearly divergent in this study. The variance portioning analysis indicated that the variation detected for diploid Triticum species was mainly composed of `between species' variation, on the other hand that for tetraploid Triticum was mostly composed of `within population' variation. In conclusion, AFLP analysis reveals molecular variation in all accessions used in this study, suggesting a potential genetic diversity of the wheat wild relatives in natural populations. These results have implications for the design of strategies to maintain genetic diversity within genebank collections. This revised version was published online in August 2006 with corrections to the Cover Date.     

Evaluation of amplified fragment length polymorphism markers in tef, Eragrostis tef (Zucc.) Trotter, and related species

Tef is an important cereal crop in Ethiopia. This study was conducted to investigate (1) genetic diversity within and among three Eragrostis species (E. tef, E. pilosa and E. curvula), and (2) the relationship between E. tef, E. pilosa and E. curvula. A total of 529 AFLP markers were obtained, out of which 58% (368) were polymorphic, using 10 primer, combinations. The three species were separated distinctly using amplified fragment length polymorphism (AFLP), However, diversity revealed at the morphological trait level was not commensurate with that observed for AFLP. This was due to the small number of morphological traits available and their interaction with the environment. Within tef, ‘Rubicunda’ and DZ‐01‐1093 were found to be distantly related to the rest of the tef accessions. The diversity within species was such that E. pilosa was the most diverse followed by E. curvula and E. tef. Moreover, E. pilosa was more closely related to E. tef than E. curvula. Therefore, further study is needed of E. pilosa accessions and of ‘Rubicunda’ and DZ‐01‐1093 in a crossing programme to generate a population for selection and/or genetic mapping. A total of 19 cultivars or accessions had one or more unique fragments using one or more AFLP primers, indicating the potential of the technology in fingerprinting tef in a breeding or seed multiplication programme.     

Genetic variability measures among Bromus catharticus Vahl. populations and cultivars with RAPD and AFLP markers

The objectives of this study were to optimize RAPD and AFLP techniques in B. catharticus, and to determine the genetic variability of populations and commercial prairie grass cultivars with the aforementioned molecular markers. Two populations with contrasting morphological characteristics were evaluated from individual and bulked DNA samples using RAPD markers. Both analyses showed a similar information about inter population variability. Each accession was sampled by a single leaf bulk of 10 plants. Accession similarities were established with 276 RAPD and 714 AFLP bands using Jaccard similarity coefficient. The dendrogram of the accessions using RAPD markers showed that they shared high similarity values (>94%). A similar result was obtained with AFLP markers (similarity values >98%), revealing a narrow genetic basis in the analyzed accessions. Consequently, molecular characterization of germplasm should be considered in addition to morphological criteria, to choose the parental genotypes for breeding programs of this forage crop. The AFLP technique was more efficient to detect DNA polymorphism in our experiments and unique fingerprints were detected for all the accessions. RAPD is a simple and non expensive technique, suitable to estimate genetic similarity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity in tef [Eragrostis tef (Zucc) Trotter] and its relatives as revealed by Random Amplified Polymorphic DNAs

Tef is one of the staple cereal crops in Ethiopia. To evaluate genetic diversity of tef and its relatives, 47 accessions of tef, three accessions of E. pilosa, and six accessions of E. curvulawere analyzed using random amplified polymorphic DNA (RAPD) markers. The level of polymorphism among the wild species was extremely high, while low polymorphism was detected among tef accessions. All cultivars and wild species under study could be distinguished with the help of different primers, thereby indicating the potential of RAPD in the genetic fingerprinting of tef. Accessions from E. curvula and E. pilosa can be differentiated by a single selected primer. In spite of low polymorphism within tef, accessions under study could be distinguished by a combination of selected primers. Cluster analysis indicated that tef is a very closely related species to E. pilosa with 45%similarity, supporting the hypothesis that tef originated from E. pilosa based on morphological data. Given that RAPD are relatively quick, simple to use, and are not subjected to environmental influences, they provide a valuable new approach for the genetic fingerprinting and study of genetic diversity in tef. This revised version was published online in July 2006 with corrections to the Cover Date.     

Morphological and molecular characterization of melon accessions resistant to Fusarium wilts

Fusarium wilt incited by Fusarium oxysporum f. sp. melonis (F.o.m) is one of the most widespread and devastating melon diseases. While resistance to physiological races 0, 1, and 2 is relatively frequent in different botanical varieties, sources of resistance to race 1,2 are restricted to a few Far-Eastern accessions. In this work, the results of a screening for resistance to F.o.m. race 1,2 among 32 accessions are presented. Three Japanese accessions (‘Kogane Nashi Makuwa’, ‘C-211’, and ‘C-40’) showed the highest resistance levels, but useful levels of resistance were also detected in one Russian ‘C-160’ and two Spanish (‘C-300’ and ‘Mollerusa-7’) accessions. These resistant materials, together with other accessions previously described as resistant to F.o.m. races 0, 1, and/or 2 have been morphologically and molecularly characterized. Based on cluster analysis, these accessions have been grouped according to the botanical subspecies they belong to. Assessment of genetic diversity indicated that the resistant accessions to races 0, 1 and 2, are scattered along the established clusters. On the other hand, high levels of resistance to the race 1,2 could be found only among accessions belonging to Cucumis melo subsp. agrestis, nevertheless, a certain degree of resistance to this race could also be found within some accessions belonging to subsp. melo. As far as we know, this is the first report of resistance to F.o.m race 1,2 found out from the Far-Eastern melon material. Based on fruits characteristics, it appears that several inodurus and cantalupensis accessions could be exploited in breeding programs as resistance sources to F.o.m races 0, 1 and/or 2 for the improvement of these melon types. The accessions with the highest levels of resistance to the race 1,2 appeared to be very distant both molecularly and morphologically from the commercial types. Nevertheless ‘C-160’, ‘C-300’, and ‘Mollerusa-7’ classified as var. inodorus are morphologically very similar to the Spanish commercial types and might be used as resistant sources in breeding these melon types.     

The nabicol: A horticultural crop in northwestern Spain

Nabicol (B. napus L. var. pabularia) is a traditional crop in the Northwest of Iberian Peninsula (South of Galicia and North of Portugal) where it is grown during the winter season on small farms and gardens using traditional varieties. A collection of 36 populations of nabicol from Galicia (northwestern Spain) was evaluated during 2002 and 2003 in two locations and two growing seasons (spring/summer and autumn/spring) for 28 agronomic and morphological traits. The objectives of this study were to: (i) evaluate a collection of nabicol landraces from northwestern Spain, (ii) determine the suitability of this germplasm as a summer crop and (iii) study the genetic diversity among local populations. Significant differences were observed among populations for most traits. Genotype × environment interaction was significant for most of them. Spring/summer growing season could be recommended for growing nabicol but resistance to Lepidoptera pests attacking Brassica crops should be improved. Most populations had an agronomic value similar to the commercial variety. The most promising variety for horticultural use was MBG-BRS0063, which showed the highest yield. Morphological and agronomic data were subjected to cluster analysis and four groups were defined with a group clustering most populations. The low genetic diversity could be explained because populations were collected in close geographical areas and the selection made by farmers was always for a horticultural use. These results give information about the diversity and breeding value of the nabicol Spanish germplasm, which could be useful in breeding programs.     

Inter and intra-species Inter Simple Sequence Repeat (ISSR) variations in the genus Cicer

Intra and inter-species ISSR variation and use of ISSR markers in determination of genetic relationship were investigated in an accession collection representing twoperennial and six annual Cicerspecies. Screening of Ciceraccessions with SSR primers revealed highly reproducible amplicon profiles with relatively high multiplex ratios. Many of the primers generated amplicon profiles with which not only the differences among species can readily be identified, but also polymorphisms within species could be detected more efficiently. PCR products at 150 gel positions detected using six SSR primers in Cicer accessions were treated as dominant DNA markers and utilized to compute the distances among accessions and species. Cluster analysis of accessions and species revealed groupings that corroborate our previous studies of relationships based on allozyme and AFLP analysis. Consistent with the AFLP analysis carried out in the same accession collection, ISSR-based groupings indicated that perennial C. incisumis genetically close to the annuals of the second crossability group (C. pinnatifidum,C. bijugum, C. judaicum) while C. reticulatum is the closest wild species to the cultivated chickpea. ISSR-based variation estimates were relatively higher when compared to previous estimates computed from RAPD and AFLP data. Technically, ISSR analysis combines the PCR-based targeting of microsatellite-associated polymorphisms with no prior sequence requirement and stringent PCR conditions. Similarly, when compared to AFLP analysis, it is less technically demanding allowing to survey polymorphic loci in the genome. Thus, ISSR-PCR technology is a reliable, fast, and cost-effective marker system that can be used to study genetic variation and genetic relationships in the genusCicer. This revised version was published online in July 2006 with corrections to the Cover Date.     

AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid

S.288 an offspring of a putative spontaneous interspecific hybrid between tetraploid Coffea Arabica (2n = 4x = 44) and diploid C. liberica(2n = 2x = 22) and 17 arabica coffee introgression lines (representing F₂ and F₄) derived from the cross S.288 x Kent arabica were evaluated for introgression of C. liberica genetic material. In all, 36 AFLP primer combinations were used in the analysis. The AFLP profiles of introgressed lines were compared to five accessions each of C. arabica and C. liberica. A total of 137 polymorphic bands were scored among the 29 accessions analysed. The introgressed genotypes exhibited 102 marker bands consisting of 65 additional bands and 37missing bands associated with introgression of C. liberica genetic material. C. liberica accessions of EA group (C. liberica var liberica of Guinean origin) seemed to be the likely progenitor in the origin of natural hybrid. Analysis of genetic relationships in the introgressed lines suggested that introgression was limited to few fragments. Segregation and wide variation in number of marker fragments in the F₂ and F₄progenies were attributed to chromosome recombinations. The differences in the level of introgression between introgressed parent, F₂ and F₄ groups was not pronounced. Therefore the alien genetic material appeared to be fixed and there was no elimination or counter-selection over generations, from introgressed parent to F₄.In C. arabica accessions, only 35 polymorphic bands were seen confirming the low genetic diversity. On the contrary, although representing a small amount of alien genome introgression, the Liberica-introgressed genotypes provided notable genetic diversity. Considering the fact that the diploid species of Coffea constitute a valuable source of genetic diversity, the potential implications of variability generated by Liberica-introgressed genotypes in C. arabica breeding are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.)

The use of bulked leaf samples from individual plants for amplified fragment length polymorphism (AFLP) analysis was evaluated as a tool for assessment of genetic diversity in white clover (Trifolium repens L.). Bulking of leaf samples produced slightly simpler AFLP profiles compared to the combined profiles of individual plants from the same cultivar. Approximately 90% of bands which were present in individual plants were present in bulked samples of the same cultivar. The majority of those absent were rare bands, shared by less than 25% of individual plants. Replicate bulk samples gave almost identical banding patterns, demonstrating the robustness of the bulked AFLP technique. Cluster analysis of AFLP data derived from individual plants resulted in a phenogram similar to that produced from data derived from bulked samples of the same plants. AFLP analysis of bulked samples detected significant amounts of genetic variability among 52 cultivars and accessions with genetic similarity values ranging from 0.42 to 0.92. However, cluster analysis of AFLP data only partially reflected the geographic origin of cultivars and accessions and was not congruent with cluster analysis based on variation for morphophysiological characters. Bulked AFLP analysis provides a powerful tool for rapid assessment of genetic variability in white clover and may also be used for cultivar identification. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity assessment in cultivated cardoon by AFLP (amplified fragment length polymorphism) and microsatellite markers

Cultivated cardoon (Cynara cardunculus L. var. altilis DC) belongs, together with globe artichoke (C. (cardunculus L. var. sylvestris L.) and wild cardoon (C. cardunculus L. var., sylvestris (Lamk) Fiori). to the family Asteraceae (Compositae). Cultivated cardoon is of regional importance in Italy. Spain and southern France, where it is used for the preparation of traditional dishes. It has been shown to have potential as a source of oil from its seeds, inulin from its roots and various biopharmaceuticals from its leaves. Levels of genetic diversity and relatedness between eleven Italian and 10 Spanish accessions were assessed by DNA profiling with eight AFLP primer combinations and at five microsatellite loci. The AFLP analysis of genetic similarities showed that the Spanish and Italian accessions represent two distinct gene pools; substantial variation was present within each accession. On the other hand a limited variation was detectable by applying SSR markers.     

Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond,and its relationships with agronomic traits

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.     

Random amplified polymorphic DNA (RAPD) variation in Fagopyrum tataricum Gaertn. accessions from China and the Himalayan region

The diversity among 52 landraces and cultivars of tartary buckwheat (Fagopyrum tataricum Gaertn.) and one accession of its wild ancestor, F. tataricum ssp. potanini Batalin, from diverse geographic origins was examined using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) markers. Eighteen primers produced a total of 240 fragments, of which 153 (63.75%) were monomorphic and 87 (36.25%) polymorphic bands. UPGMA-based pairwise Jaccard’s coefficient of similarity was used to deduce the relationships among 53 genetically diverse accessions. The similarity between cultivated tartary buckwheat accessions ranged from 0.61 to 1.00. Four distinct clusters were formed which corresponded well with the geographic distribution of the tartary buckwheat. Nepalese accessions showed maximum diversity followed by Chinese accessions. Tartary buckwheat accessions from the Himalayan region of northwestern India revealed a narrow gene pool. The wild buckwheat accession did not group with any of the three cultivated tartary buckwheat groups, and formed its own single-entry group. Genetic similarity (0.59) of Chinese buckwheat accessions with the wild ancestor reaffirmed that cultivated tartary buckwheat originated in the Yunnan province of northwestern China. Consistent with some earlier reports, our study demonstrated the usefulness of the RAPD technique for the characterization of plant genetic resources and assessment of diversity between species. This revised version was published online in August 2006 with corrections to the Cover Date.     

Diversity in the wild potato species Solanum chacoense Bitt.

Summary The morphological and isozyme variation was studied in 22 accessions of Solanum chacoense from Paraguay and Argentina. Clear geographic groups were identified through the use of multivariate analyses. S. chacoense from mountain sites in Argentina could be readily distinguished from plains forms from Paraguay, on the basis of several correlated morphological characters. Three isozyme systems, namely phosphoglucose isomerase (PGI), glutamate-oxaloacetate transaminase (GOT) and peroxidase (PRX) were studied using starch gel electrophoresis. The banding patterns indicated that for each isozyme there were several loci, which were polymorphic. A genetic interpretation of one of the PGI loci was made, and indices of genetic diversity and genetic identity calculated. Principal components analysis, cluster analysis and genetic diversity indicated a close relationship between the geographical groups. These results are discussed in the context of in situ genetic conservation.     

Germplasm diversity and estimate of genetic advance of four morpho-physiological traits in a world collection of jute

Summary To improve jute productivity, locating of sources of suitable quantitative-trait genes in the recently acquired world jute collection was needed. Two hundred sixteen accessions of Corchorus capsularis and 192 accessions of C. olitorius were evaluated at a jute seed research station (87°60\s'E, 23°80\s'N) for four yield and quality linked morpho-physiological traits. The objectives were to estimate the germplasm diversity, phenotypic (PCV) and genetic (GCV) coefficients of variation, broad sense heritability (h²) and genetic advance (GA) with respect to origins and traits. Irrespective of origins all the traits showed more than 60–80% diversity in both species. Trait means of diversity were significant but not the origin means. Generally, only slightly higher PCV values than GCV were obtained for all the traits in both the species. High h² values ranging from 50% to more than 98% were also found. All the traits can be simultaneously utilized for genetic gain. Most of the C. olitorius accessions with two times higher GA estimates than those of the C. capsularis are likely to be more successful for that matter. Maximum genetic gain is expected from Mutants > China > Brazil > India > Thailand > Nepal > Burma in C. capsularis while from Thailand > Tanzania > Mutants > Kenya > Other countries in C. olitorius. C. capsularis mutants with high heterogenity for most of the traits should be useful for finding many rare alleles.     

Allozyme differentiation of European populations and cultivars of Lolium perenne L., and the relation to ecogeographical factors

Summary Sixty Lolium perenne populations were screened for allozyme diversity at five loci. Objective was to determine whether allozyme diversity could be used as selection criterion for genebank accessions of L. perenne. Subsampling of locations was tested with allozyme analysis to determine whether genetically different populations could be collected at one location. Correlations between allelic frequencies and environmental factors and morphological data were established, to find ecogeographical patterns in the observed variation. Results indicated that with few examples each allelic variant could be observed in each population screened; very few unique alleles were found. Differences between populations were largely due to differences in allelic frequencies. Few correlations were found with environmental factors and morphological data. For some allele frequencies a north-south cline was observed. Generally, allozymic data of the five screened loci did not appear to be useful for the selection of accessions for genebank storage. Significant genotypic differences between populations collected at one location could be established. In general these results agreed with earlier results concerning phenotypic variation in the same populations.     

Distribution,ecology and reproductive biology of wild tomatoes and related nightshades from the Atacama Desert region of northern Chile

Over the past 20 years, several expeditions were made to northern Chile to collect populations of wild tomatoes (Solanum chilense, S. peruvianum) and allied nightshades (S. lycopersicoides, S. sitiens), and obtain information about their geographic distribution, ecology and reproductive biology. Restricted mainly to drainages of the Andean and the coastal cordillera, populations are geographically fragmented. The two nightshade species are rare and threatened by human activities. Adaptation to extreme aridity and soil salinity are evident in S. chilense and S. sitiens (the latter exhibits several xerophytic traits not seen in the tomatoes) and to low temperatures in S. lycopersicoides and S. chilense. All tested accessions are self-incompatible, with the exception of one S. peruvianum population collected at the southern limit of its distribution. Several distinguishing reproductive traits—anther color, attachment, and dehiscence, pollen size, and flower scent—suggest S. sitiens and S. lycopersicoides attract different pollinators than S. chilense and S. peruvianum. The four Solanum spp. native or endemic to Chile provide a variety of novel traits which, through hybridization and introgression with cultivated tomato, could facilitate development of improved varieties, as well as research on a variety of basic topics, including plant-pollinator interactions, abiotic stress responses, and evolution of reproductive barriers.     

Agro-morphological characterisation of common vetch and its close relatives

The Vicia sativa aggregate, which includes the common vetch, is a complex of six closely related tax a which combines cultivated, weedy and wild forms. In this study 454 accessions with an emphasis on Mediterranean and Central Asian accessions have been compared for 22 key agro-morphological and phonological characters. The agronomic potential of the different members of the aggregate is assessed and useful variation existing in the collection is determined. Geographic patterns of the agronomic variation are studied to determine sources of useful variation. In both sub sp. cordata and sub sp. sativa accessions were found which had higher yields than the checks, consisting of three promising accessions. Sub sp. macrocarpa needs a longer growing season than the other tax a to reach its full potential. The other three tax a in the aggregate all had quite low yields. Important variation in shattering of pod sand in tolerance to moderate frost and resistance to the Sitona weevil was found in most subspecies of the aggregate. Variation in phenological characters appeared to be related to the latitude from which the accession was collected. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity of Brassica napus L. Germplasm from China and Europe assessed by some agronomically important characters

Summary The genetic diversity and relationships among 63 rapeseed accessions, including 34 Chinese, 22 Czech, 2 Swedish, 2 German, one French and 2 Canadian accessions, were evaluated by nine agronomically important characters in the field at Yangling, Shaanxi, China. Significant differences between Chinese and European group in plant height, setting position of the first primary branch, number of siliques of the terminal raceme, thousand seed weight and seed yield per plant were detected. There were significant variations in nine agronomic characters among the tested rapeseed accessions. Ward’s minimum variance cluster analysis based on Mahalanobis distances on the raw data of nine agronomic characters clearly separated the European accessions from the Chinese ones. However, the Chinese accessions with erucic acid free and/or low glucosinolates could not be separated from those Chinese accessions with both high erucic acid and glucosinolates. In general, cluster analysis of the 63 accessions based on the selected agronomic characters was consistent with known pedigree information and geographic origin, as well as the previous RAPD results of these accessions. The European rapeseed could be important germplasm resources for enriching the genetic background of Chinese rapeseed, and vice versa.