Antioxidant activity of minimally processed red chicory (Cichorium intybus L.) evaluated in xanthine oxidase-, myeloperoxidase-, and diaphorase-catalyzed reactions

Minimally processed red chicory products (Cichorium intybus L. var. silvestre) were studied for their polyphenol content and antioxidant activity evaluated by using the synthetic 2,2-diphenyl-1-(2,4,6-trinitrophenyl)hydrazyl radical and three model reactions catalyzed by relevant enzymatic sources of reactive oxygen species, namely, xanthine oxidase, myeloperoxidase, and diaphorase. Products were analyzed at the time of production and after storage at 4 degrees C within either a gas permeable film or a gas barrier film. The antioxidant activity and contents of hydroxycinnamic acids and flavonoids decreased by less than 20% during storage of the minimally processed red chicory products. Total phenolics were significantly correlated with the antioxidant activity evaluated with both the synthetic radical and the enzyme-catalyzed reactions. On a molar basis, red chicory phenolics were as efficient as the reference compound Trolox in scavenging the synthetic radical. However, red chicory phenolics had a much higher inhibitory activity than Trolox in the model enzymatic systems.     

Introgression between oilseed rape (Brassica napus L.) and its weedy relative B. rapa L. in a natural population

We investigated introgression in a mixed weedy population ofoilseed rape (Brassica napus) and itsrelative B. rapa usingspecies-specific AFLP-markers. The population wassituated in a field relayed from conventional to organic cultivation11 years ago. One-hundred-and-twoB. napus orB. rapa-like plantswere collected in a 3 m² plot. Of these, onewas a first generation hybrid (F₁) and nearlyhalf (44 plants) were introgressed, having bothB. napus andB. rapa specific markers.The remaining plants apparently corresponded to pure species, with 50having only B. rapa-and seven having only B.napus-specific markers. We compared thenumber of markers in the plants from the weedy population with thenumbers in controlled backcross generations (BC₁ andBC₂). The marker distribution in the weedy populationresembled the distribution in the second backcross generation mostclosely. Together with the cultivation history of the field, thissuggests that the introgression process in the weedy mixed populationhas been in progress for some time. This study is the first to showintrogression between B.napus and B.rapa under natural conditions.     

Survival,distribution, and gene transfer of bacteria in a compact soil microcosm system

Summary A microcosm has been designed for application in risk assessment. It was used to investigate the vertical distribution and survival of bacteria in a soil column. Plasmid transfer was studied in sterile and non-sterile soil, using the microcosm. The results show that bacteria can be isolated from deeper soil layers a few days after their introduction. Of the bacteria containing plasmid RP4, 14% lost their replicon within 13 days. A survival analysis of representative soil bacteria demonstrated a good survival of Bacillus subtilis and Pseudomonas fluorescens under the given conditions. The number of Escherichia coli decreased over 7 days. The conjugative plasmid RP4 was transferred between Gram-negative bacteria in sterile soil. Neither conjugation nor mobilization were observed in non-sterile soil.     

Ecogeographical distribution of wild, weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers’ knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.     

Could early gene flow have created similar allozyme-gene frequencies in cultivated and wild barley?

The possible role of early gene flow between wild and cultivated barley in their similar esterase gene frequencies was tested in a simulation study. The hypothetical population consisted of 99.9% wild forms possessing three alleles of an esterase gene and 0.01% domesticated forms possessing one of these esterase alleles. Various rates of inbreeding, selection coefficients against the wild form and shifting cultivation methods were tested for their effect on the establishment of the domesticated form and the esterase gene flow between the two barley types. Of these factors, inbreeding rates, in the range of 90–99%, had the smallest effect on the establishment of the domesticated form under primitive cultivation. Via gene flow, the esterase allelic frequency in the domesticated form could be similar to that of the wild form under 90% outcrossing in the domesticated form for 115–230 years, an unrealistic situation for barley which normally exhibits about 1% outcrossing. It seems, therefore, that the similar esterase allelic frequencies in wild and cultivated barley is only partly due to gene flow, and it is more plausibly accounted for by multiple domestications.     

Population structure,gene flow and genetic diversity analyses based on agro-morphological traits and microsatellite markers within cultivated and wild germplasms of okra [Abelmoschus esculentus (L.) Moench.]

Genetic Resources and Crop Evolution - Okra [Abelmoschus esculentus (L.) Monech.] is an annual herb of the family Malvaceae and has tremendous nutritional and industrial potential. However, the...     

Variation and population structure at microsatellite and isozyme loci in wild cabbage ( Brassica oleracea L.) in Dorset (UK)

We examined variation at four isozyme and seven microsatellite loci in natural populations of Brassica oleracea L. on the coast of Dorset. All loci were polymorphic, and the diversity index of isozyme loci was similar to that of the microsatellites. Both microsatellites and isozymes showed significant spatial differentiation of genetic variation, but the scale differed between the marker types. Significant non-random mating at isozyme loci was detected within small groups of about five plants, in which adjacent individuals were separated by less than 5 m. On the other hand, non-random mating at microsatellite loci was only detected within the Dorset region as a whole. F_ST was significant for all loci and there was evidence of isolation by distance at both microsatellite and isozyme loci. From these data we infer that there is low but significant amounts of gene flow among B. oleracea populations in Dorset. The differences in the genetic structure between the two types of marker may be due to higher mutation rates at the microsatellite loci; however, the data suggest that stepwise gain or loss of single repeat units is not the principal mechanism.     

Genetic Variation and Population Structure in a Eurasian Collection of <Emphasis Type="Italic">Isatis tinctoria</Emphasis> L.

Isatis tinctoria L. is a biennial species which was cultivated in Europe until the 18th century to produce indigo, a pigment used for dyestuffs. Today there is renewed interest in this ancient crop because of a market demand for natural dyes. Cultivation of the species appears to be particularly suitable for marginal areas. Information about the evolutionary and genetic patterns of I. tinctoria is needed if varieties or to be developed in future breeding programs. The aim of this study was to assess the genetic variation and similarity levels among and within natural populations of I. tinctoria from Europe and central Asia. Fifteen populations were used to carry out the genetic analyses with AFLP and SAMPL molecular markers. Data collected were analysed by the UPGMA method and were used to perform AMOVA. The results are consistent with the hypothesis that the crop originated in an eastern centre of origin and moved westward giving rise to a gene pool that is quite different from the original. The wide within-population variation revealed by this study suggests that effective breeding work to develop varieties suitable for marginal environments can be carried out easily.     

Development and characterization of microsatellite markers,genetic diversity and population structure analysis in Sapota (Manilkara zapota (L.) P. Royen)

Genetic Resources and Crop Evolution - Manilkara zapota (L.) P. Royen, a widely adapted and popular tree meant for its appetizing fruits in tropics with no genomic resources like microsatellite...     

Relationship of wild and cultivated forms of <Emphasis Type="Italic">Pisum</Emphasis> L. as inferred from an analysis of three markers,of the plastid,mitochondrial and nuclear genomes

Eighty-nine accessions of wild and cultivated peas (12 Pisum fulvum Sibth. et Smith., 7 P. abyssinicum A. Br., 31 wild and 42 cultivated forms of P. sativum L.) were analysed for presence of the variants of three functionally unrelated polymorphic markers referring to different cellular genomes. The plastid gene rbcL either contains or not the recognition site for restriction endonuclease AspLEI (rbcL+ vs. rbcL−); the mitochondrial gene cox1 either contains or not the recognition site for restriction endonuclease PsiI (cox1+ vs. cox1−); the nuclear encoded seed albumin SCA is represented by slow (SCA^S) or fast (SCA^F) variant. Most of the accessions possessed either of two marker combinations: 24 had SCA^F cox1+ rbcL+ (combination A) and 49 accessions had SCA^S cox1− rbcL− (combination B), 16 accessions represented 5 of the rest 6 possible combinations. All accessions of P. fulvum and P. abyssinicum had combination A, the overwhelming majority of cultivated forms of P. sativum had combination B while wild representatives of P. sativum had both combinations A and B, as well as rare combinations. This pattern indicates that combination A is the ancestral state in the genus Pisum L., inherited by P. fulvum and P. abyssinicum, while combination B seems to have arisen in some lineage of wild P. sativum which rapidly fixed mutational transitions of the three markers studied, most probably via a bottleneck effect during the Pleistocene. Then this ‘lineage B’ spread over Mediterranean and also gave rise to cultivated forms of P. sativum. Rare combinations may have resulted from occasional crosses between ‘lineage A’ and ‘lineage B’ in nature or during cultivation, or represent intermediate evolutionary lineages. The latter explanation seems relevant for an Egyptian cultivated form ‘Pisum jomardii Schrank’ (SCA^F cox1− rbcL−) which is here given a subspecies rank. Wild representatives of P. sativum could be subdivided in two subspecies corresponding to ‘lineage A’ and ‘lineage B’ but all available subspecies names seem to belong to lineage B only. Presently all wild forms would better be considered within a fuzzy paraphyletic subspecies P. sativum subsp. elatius (Bieb.) Schmalh. s. l.     

Genetic diversity and differentiation of <Emphasis Type="Italic">Camellia sinensis</Emphasis> L. (cultivated tea) and its wild relatives in Yunnan province of China,revealed by morphology,biochemistry and allozyme studies

We evaluated morphological, isozyme and biochemical diversity of a total of 87 accessions in the genus Camellia [Camellia sinensis var. sinensis (10), C. talinensis (7), C. sinensis var. dehungensis (3), C. crassicolumna (3) and C. sinensis var. assamica (64)]. Great variation of morphological characters was apparent within each taxa. Across the five taxa, all leaf and most flower quantitative characters showed significant differences while all fruit quantitative characters measured did not differ significantly, and, seven (i.e., life form, bud color, petal texture, pubescence on ovary, style number, stamen location and locule per fruit) of the 33 qualitative characters yield significant differences. As a whole, caffeine content had the highest variation with CV of 22.7%, water extract solid showed the least variation (13.4%) and content of polyphenols (20.0%) and free amino acids (18.8%) showed intermediate variations. Camellia taliensis and C. sinensis var. assamica had significantly higher content of polyphenols and water extract solid than in the other three taxa, while no significant differences were detected for the content of caffeine and free amino acids. For allozyme study, 14 loci presented good resolution, among which, nine loci (64%) were polymorphic in each taxon (AAT-3, FUM-1, 6PDG-1, G6PDH-1, G3PDH-1, ME-1, PGM-1, PGM-2 and SKD-1). The percentage of polymorphic loci (P) for each taxon was 21.4–50.0%. Mean heterozygosity per locus (H _e ) varied 0.114–0.218. F _ST value indicated that only 4.6% of the variations could be ascribable to genetic differences among taxa. Genetic relationships among the five taxa revealed by allozymes, were also exposed by the result of clustering of the morphological and biochemical characters.     

Assessment of genetic diversity in cultivars and wild accessions of Luohanguo (<Emphasis Type="Italic">Siraitia grosvenorii</Emphasis> [Swingle] A. M. Lu et Z. Y. Zhang), a species with edible and medicinal sweet fruits endemic to southern China,using RAPD and AFLP markers

Genetic variation of wild populations and cultivars of Luohanguo (Siraitia grosvenorii), a plant species endemic to southern China, was assessed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Based on the results for 130 individuals from seven populations, a high level of genetic diversity of Luohanguo was observed at the species level. The percentage of polymorphic loci (P) was 89.4%, Nei’s gene diversity (H _e) was 0.239, and Shannon’s information index (H _o) was 0.373 based on the combined AFLP and RAPD data. There was a high degree of genetic differentiation, with 45.1% of the genetic variation attributed to differences between the populations. The genetic diversity of the Luohanguo cultivars is much lower than that of wild populations (P = 41.8%, H _e = 0.141, H _o = 0.211), and a distinct genetic differentiation is observed between the cultivars and wild accessions. The pool of genetic variation in the wild populations provides an excellent gene resource for Luohanguo breeding.     

Nuclear DNA content estimations in wild olive ( Olea europaea L. ssp. europaea var. sylvestris Brot.) and Portuguese cultivars of O. europaea using flow cytometry

Olive tree (Olea europaea L.) is an economically important woody fruit crop widely distributed in the Mediterranean regions. In this work the genome size of six Portuguese cultivars of olive (O. europaea ssp. europaea var. europaea) and wild olive (O. europaea spp. europaea var. sylvestris) was estimated for the first time. The nuclear DNA content of O. europaea cultivars ranged between 2.90 ± 0.020 pg/2C and 3.07 ± 0.018 pg/2C and the genome size of wild olive was estimated as 3.19 ± 0.047 pg/2C DNA. These results suggest a low intraspecific variation at least among the studied cultivars and between them and wild olive. This is not in accordance with previous results in some Italian cultivars where high genome size heterogeneity was found. The methodology presented here seems appropriate for genome size estimations within this genus and opens good perspectives for a large screening of estimation of nuclear DNA content among O. europaea cultivars and Olea species that could clarify this issue.     

Microbial communities of Lumbricus terrestris L. middens: structure, activity, and changes through time in relation to earthworm presence

Background, aim, and scope  Earthworms make a major contribution to decomposition in ecosystems where they are present, mainly acting in the drilosphere, that is, galleries, burrows, casts, and middens. Earthworm middens are hot-spots of microbial activity and nutrient dynamics and represent a suitable model for studying earthworm-mediated influences on soil microbial communities by alteration of the patch structure of the microbial environment. We studied the structure and activity of the microbial communities in the soil system formed by middens of Lumbricus terrestris and the soil below and surrounding them and the role of earthworms in maintaining these structures through time. Material and methods  We set up an experiment in which middens were either left (control) or removed from their original place (translocated) and left in a nearby area free of earthworm activity for 2 months. After 1 and 2 months we sampled middens, soil below them, and surrounding soil. We analyzed the phospholipid fatty acid (PLFA) profiles and measured respiratory fluxes of CO₂ and CH₄. Results  Microbial communities of middens clearly differed from those of soil below and surrounding soil samples, showing higher bacterial and fungal PLFAs (p < 0.0001 and p < 0.01, respectively); furthermore, changes in microbial communities were stronger in control middens than in translocated middens. Moreover, gram positive and negative bacterial PLFAs were greater in translocated than control middens (p < 0.0001 and p < 0.001, respectively), as well as total organic carbon (p < 0.001). Microbial activity was higher in middens than in soil below and surrounding soil samples both for CO₂ (p < 0.0001) and CH₄ (p < 0.0001). Discussion  Soil bioturbation by the earthworm L. terrestris was strong in their middens, but there was not any effect on soil below and surrounding soil. Microbial communities of middens maintain their biomass and activity when earthworms were not present, whereas they decreased their biomass and increased their activity when earthworms were present. Conclusions  Earthworms strongly enhanced microbial activity measured as CO₂ production in middens, which indicates that there are hot spots for soil microbial dynamics and increasing habitat heterogeneity for soil microorganisms. Moreover, our data strongly support the fact that the impact of this earthworm species in this soil is restricted to their middens and increasing soil heterogeneity. Recommendations and perspectives  Our data indicate that it is not clear if earthworms enhance or depress microbial communities of middens since the microbial activity increased, but did not modify their biomass and this was not dependent on soil organic C content. These results indicate no competence for C pools between this anecic earthworm and microorganisms, which has been found for other earthworm species, mainly endogeics. Conversely, they suggest some type of facilitation due to the release of additional nutrient pools in middens when earthworms are present, through the digestion of middens' material or the addition of casts produced from other food sources.     

Comparison of the genetic structure of populations of wild emmer wheat, <Emphasis Type="Italic">Triticum turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides</Emphasis>, from Israel and Turkey revealed by AFLP analysis

The aim of the present study was to assess the genetic variation in several Israeli and Turkish populations of wild emmer wheat, Triticum turgidum ssp. dicoccoides, the progenitor of most domesticated wheat. Single spikes were collected in 2002 from 60 plants that grew in six different habitats in Ammiad, northeastern Israel (8–12 plants from each habitat), and in 1998 from 56 plants that grew in seven different habitats in Diyarbakir, southeastern Turkey (8 plants from each habitat). Seeds were planted in a nursery and DNA was extracted from every plant and analyzed by the fluorescent-based amplified fragment length polymorphism (AFLP) method. Seven primer combinations produced 788 discernible loci of which 48.6% were polymorphic in Israel and 40.5% in Turkey. The genetic diversity estimates P (frequency of polymorphic loci) and He (gene diversity) were higher in Ammiad than in Diyarbakir (means of P = 0.34 and He = 0.13 in Ammiad vs. P = 0.20 and He = 0.08 in Diyarbakir). Ammiad populations contained more unique alleles than Diyarbakir populations. The relative genetic diversity estimates (θ) values were 0.188 in Ammiad and 0.407 in Diyarbakir, suggesting better differentiation of the populations in Turkey. Genetic distance was larger between Israeli and Turkish populations than between populations of each country. The data indicate that the Israeli and Turkish populations are considerably diverged and that the Israeli populations are more polymorphic than the Turkish ones, having a larger within-populations genetic variation than among-populations one. The significance of the results in relation to the differentiation pattern of wild emmer in the Near East is discussed.     

Genetic diversity,population structure and linkage disequilibrium in Nordic spring barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L. subsp. <Emphasis Type="Italic">vulgare</Emphasis>)

Genetic diversity, population structure and genome-wide linkage disequilibrium (LD) was estimated in Nordic spring barley (Hordeum vulgare L. subsp. vulgare) by genotyping 180 breeding lines with 48 SSR markers and 7842 high-confidence SNPs using the Illumina Infinium 9K assay. In total 6208 SNPs were polymorphic and selected for further statistical analysis. A Mantel test revealed a strong positive correlation with a Pearson’s correlation coefficient (r) of 0.86, between the estimates of genetic distances based on SSR and SNP data. Population structure analysis identified two groups with a clear ancestry and one group with an admixed ancestry. The groups were primarily separated based on row-type and geographical origin. Average LD for the whole population decayed below a critical level of r² = 0.20 within a range of 0–4 cM. To avoid confounding effects of the strong population structure, LD decay for the different groups was analysed separately and ranged from 0 to 12 cM. A slower LD decay was found within the two-rowed lines compared to the six-rowed lines and the two-rowed lines originating from the northern part, which could be the result of strong selection for malting quality and yield in the southern part. No large difference in genetic diversity was observed between population sub-groups, but differences at certain chromosomal regions were evident.