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Male sterility is widely utilized for hybrid seed production. In this study, two new found male sterile mutants SauS4 and SauS5 were obtained from space flighted seeds of maize inbred line RP125. Then, genetic analysis, molecular markers identification, and cytological observation were conducted to confirm their male sterile types. For genetic analysis, the above two male sterile mutants were continuously backcrossed with two maize inbred line 18Hong and RP125, and four stable male sterile lines SauS4(18Hong), SauS5(18Hong), SauS4(RP125), SauS5(RP125) were generated by six-generation backcross. Restoring and maintaining relationship analysis showed that both Hui313 and Zifeng1 didn't rescue the male sterility SauS4(18Hong) and SauS5(18Hong). Using CMS mitochondria-specific primers for PCR detection suggested that only a 440 bp band unique to CMS-T type was amplified in SauS4(18Hong), SauS5(18Hong), SauS4(RP125), and SauS5(RP125). Sequencing results showed that these bands sequences were identical in DNA level which compared with T-urf13. Cytological observations showed that the main abortion stages of SauS4 and SauS5 were at the middle stage of uninucleate microspores under the two nuclear backgrounds of 18Hong and RP125, exhibiting the characteristics of sporophyte sterility. All the above results pointed out the two male sterile mutants SauS4 and SauS5 belonged to the CMS-T type. Interestingly, some mitochondrial genome difference between SauS4(RP125) and SauS5(RP125) were revealed by AFLP analysis. [ABSTRACT FROM AUTHOR]

A molecular marker approach was used to analyse the genetic diversity of endemic Triticum aethiopicum wheat accessions that were collected from the same sites in Ethiopia by N.I. Vavilov in 1927 and by the Joint Ethiopian-Russian Biological Expedition in 2012, which allowed the assessment of changes in the gene pool structure of this species over 85 years. The level of genetic diversity in the accessions from Vavilov's collection was higher than that of the accessions collected in 2012. Analysis of molecular variance indicated that differentiation between the two groups of accessions was 17% (PhiPT = 0.169; p < 0.010). A Bayesian clustering approach and principal coordinates analysis showed that these two groups of accessions were notably different in their genetics. In this regard, this article discusses the problem of in situ and ex situ conservation of wheat landraces: their evolution, stability and genetic drift. [ABSTRACT FROM AUTHOR]

Common DNA-based species determination methods fail to distinguish some blow flies in the forensically and medically important genus Lucilia Robineau-Desvoidy. This is a practical problem, and it has also been interpreted as casting doubt on the validity of some morphologically defined species. An example is Lucilia illustris and L. caesar, which co-occur in Europe whilst only L. illustris has been collected in North America. Reports that these species shared both mitochondrial and nuclear gene sequences, along with claims that diagnostic morphological characters are difficult to interpret, were used to question their separate species status. We report here that amplified fragment length polymorphism profiles strongly support the validity of both species based on both assignment and phylogenetic analysis, and that traditional identification criteria based on male and female genital morphology are more reliable than has been claimed.

The genetic diversity of 123 apple accessions from the collection of the research and production base Pushkin and Pavlovsk Laboratories of VIR, including landraces, Soviet cultivars, and commercial Russian and foreign cultivars, was for the first time estimated using the AFLP technique. A total of 355 fragments were obtained, 319 of which were polymorphic (89.86%), and each of the accessions had a unique set of AFLP fragments. The level of diversity of modern commercial cultivars was lower (74.11%, Не = 0.202, I = 0.302) as compared with landraces (89.20%, Не = 0.238, I = 0.366). A wide range of genetic differences between the studied accessions (0.99–0.63) was demonstrated. The statistical analysis of the data obtained made it possible to divide the studied samples into two groups. The first group included most of the analyzed landraces; with no clear differentiation of these landraces by origin. The second group included modern commercial Russian and foreign apple cultivars, Soviet cultivars, and some landraces. [ABSTRACT FROM AUTHOR]

Italy represents a territory rich in common bean landraces, most of which have not yet been characterized. Therefore, the proximal composition and metabolic profiles (fatty acid composition, total and free amino acids) as well as total polyphenols and antioxidant capacities of both 'Cerato' and 'Curniciello' dry beans, cultivated in Caserta's rural areas (Southern Italy) were evaluated, in comparison with other local known dry beans. 'Cerato' dry beans have a lower content of crude proteins (21.18 vs 23.41 g/100 g), lipids (1.27 vs 2.08 g/100 g) and total amino acids (16.01 vs. 17.89 g/100 g) with respect to 'Curniciello' dry beans, considering the average values of two different harvest years (2020–2021), although slight statistical differences were found when the two harvest years were analysed separately. Two essential fatty acids (n-6 linoleic and n-3 alpha-linolenic) and oleic acid were the most abundant fatty acids in both dry beans, (∼90% of the total). Subsequently, the trypsin and chymotrypsin inhibitory activities in raw and boiled (2 h) dry beans, as well as the α-amylase and α-glucosidase inhibitory activities were investigated, considering their capability to reduce crude protein and carbohydrates intake and assimilation. In addition, AFLP analysis of two landraces shows different polymorphic patterns useful for their authentication and traceability. Overall, our data provide a starting point for promoting the cultivation and consumption of 'Cerato' and 'Curniciello' dry beans, thus contributing to the preservation of local culinary traditions and Italian biodiversity. • Southern Italy is the place of origin of several bean landraces. • 'Cerato' and 'Curniciello' are bean landraces from Campania region, Italy. • Both landraces show different chemometric traits. • AFLP profiles are important for authentication/traceability of these beans. [ABSTRACT FROM AUTHOR]

Biodiversity of Rottboellia cochinchinensis from different areas were studied by morphological traits and amplified fragment length polymorphism (AFLP) analysis for classify of an allelopathic ability. The correlation of the similarity/distance between AFLP markers (Jaccard coefficient) and morphological traits (Euclidean distance) was significant with r = − 0.84**. Itchgrass could be divided into two groups from both UPGMA and STRUCTURE analyses: the group A consisted of itchgrass from Chaehom-Lampang, Si Thep-Phetchabun, Phrom Phiram-Phitsanulok, Amphur Muang-Nakhon Sawan, Kamalasai-Kalasin, Amphur Muang-Chachoengsao and Bang Yai-Nonthaburi, whereas itchgrass from Amphur Muang-Chiang Mai, Pak Chong-Nakhon Ratchasima and Kamphaeng Saen-Nakhon Pathom constituted the group B. Allelopathic properties of itchgrass as representative from different group were determined in bioassay test, the result showed that the aqueous extract of itchgrass from Chaehom-Lampang area has a strong allelopathic ability on growth of Echinochloa crus-galli L., Bidens pilosa L. and Lactuca sativa L. than the other group. The molecular analysis was strongly supported in morphological analysis clustering with bioassay test for allelopathic ability, specific morphological traits were soft trichomes, and the dark purple stems and roots which can be used for the preliminary classification of allelopathic ability. Our findings suggest that classification of itchgrass by morphological traits is related to the analysis of the genetic relationship of itchgrass with AFLP analysis, that allowing the assessment of the bio-diversity of itchgrass and their allelopathic potentials.

Common DNA-based species determination methods fail to distinguish some blow flies in the forensically and medically important genus Lucilia Robineau-Desvoidy. This is a practical problem, and it has also been interpreted as casting doubt on the validity of some morphologically defined species. An example is Lucilia illustris and L. caesar, which co-occur in Europe whilst only L. illustris has been collected in North America. Reports that these species shared both mitochondrial and nuclear gene sequences, along with claims that diagnostic morphological characters are difficult to interpret, were used to question their separate species status. We report here that amplified fragment length polymorphism profiles strongly support the validity of both species based on both assignment and phylogenetic analysis, and that traditional identification criteria based on male and female genital morphology are more reliable than has been claimed. [ABSTRACT FROM AUTHOR]

AFLP analysis of 144 samples of tetraploid wheat species, including cultivars and landraces of Triticum durum from Azerbaijan, was conducted. We obtained 249 fragments, 189 (76%) of which were polymorphic. The Dice genetic similarity index ranged from 0.67 to 0.99. Principal coordinate analysis revealed clear differences between the group of wheat with AABB genome and the group of wheat with AAGG genome. Within the group of wheat with AABB genome, differentiation was less pronounced, and this group was not divided into separate subclusters. It was shown that the Azerbaijani varieties of durum wheat were fairly similar to each other and with other species of Triticum durum. [ABSTRACT FROM AUTHOR]

AFLP analyses were used to assess the genetic similarity among selected accessions at the South China Tobacco Breeding Research Centre (Yunnan province, Southwest China). 154 AFLP polymorphic fragments out of 561 fragments were used to assess the genetic diversity among 28 tobacco accessions. The average number of polymorphic bands per AFLP primer pair was 15.4. AFLPs seemed to be an effective classification tools for germplasm conservation and breeding. Limited genetic variation was detected within this group of accessions. The relationship of cultivars was estimated by cluster analysis based on AFLP data.

Coffee leaf rust is the most limiting disease for coffee cultivation in Brazil. Despite its importance, relatively little is known about the genetic diversity of Hemileia vastatrix, the rust causal agent. In this work, the DNA from 112 monopustule isolates from different geographic locations and coffee genotypes were analysed by amplified fragment length polymorphisms ( AFLP). The objectives were to assess the influence of the host and geographic origin on the diversity and population differentiation in H. vastatrix. The fungal population showed a low level of genotypic diversity. Gene diversity ( h) was 0·027 and the hypothesis of random mating in the total population was rejected, but evidence for recombination was found for two subpopulations (São Paulo and Paraná). The analysis of molecular variance revealed that 90% of the genetic distribution of the pathogen occurs among isolates within the subpopulation (states or host of origin). There was no correlation between geographic and genetic distance ( r = −0·024, P = 0·74), which together with the high number of migrants and the low degree of differentiation in populations of H. vastatrix, is consistent with the fact that the inoculum is probably easily dispersed by wind over long distances, allowing dispersal of the pathogen among coffee growing areas in Brazil. Therefore, it is difficult to predict the durability of resistant sources to coffee rust. The recommendation for the breeding programmes is thus to incorporate multigenic resistance as a control strategy. [ABSTRACT FROM AUTHOR]

The first molecular genetic analysis of the apple species and varieties from Russian collections with the AFLP marker system was performed in order to study the genetic diversity of the genus Malus, as well as to clarify the phylogeny and solve some systematic issues of the genus. Nienty-one apple accessions, including species from five sections of the genus Malus and hybrid species, were examined. The level of polymorphism constituted 90.2%. It was demonstrated that the classical taxonomy of the genus Malus, which identifies five sections based on differences in their morphological characters, is valid and may be used to classify apple species. The species assignment of the Antonovka landraces was established. All of them belonged to the species M. domestica. It was demonstrated that the Yakutskaya apple variety is a domesticated species of the section Gymnomeles, presumably, M. baccata. AFLP analysis confirmed the hybrid nature of many species. The relationships between apple varieties of the Golden group with American wild species were demonstrated. The data suggest that the species M. sieversii was the ancestor of not only the domesticated apple but also of other species of the Section Malus. [ABSTRACT FROM AUTHOR]

Phytophthora austrocedrae is a recently discovered pathogen that causes severe mortality of Austrocedrus chilensis in Patagonia. The high level of susceptibility of the host tree, together with the distribution pattern of the pathogen, have led to the hypothesis that P. austrocedrae was introduced into Argentina. The aim of this study was to assess the population structure of P. austrocedrae isolates from Argentina in order to gain an understanding of the origin and spread of the pathogen. Genetic diversity was determined based on amplified fragment length polymorphisms ( AFLPs). In total, 48 isolates of P. austrocedrae were obtained from infected A. chilensis trees, representing the geographical range of the host. Four primer combinations were used for the AFLP analysis. Of the 332 scored bands, 12% were polymorphic. Gene diversity ( h) ranged from 0·01 to 0·03; the Shannon index ( I) ranged from 0·01 to 0·04. A high degree of genetic similarity was observed among the isolates (pairwise S values = 0·958-1; 0·993 ± 0·009, mean ± SD). A frequency histogram showed that most of the isolate pairs were identical. Principal coordinate analysis using three-dimensional plots did not group any of the isolates based on their geographical origin. The low genetic diversity (within and between sites) and absence of population structure linked to geographic origin, together with the aggressiveness of the pathogen and the disease progression pattern, suggest that P. austrocedrae might have been introduced into Argentina. [ABSTRACT FROM AUTHOR]

A simple, efficient protocol for direct in vitro shoot organogenesis and regeneration was established for three species of Miscanthus including two clones of Miscanthus x giganteus, one clone of M. sinensis and one clone of M. sacchariflorus. Shoots were induced from the axillary nodes of both M. x giganteus and M. sacchariflorus and from apical meristems of both M. sinensis and M. sacchariflorus. A tillering method was used to accelerate shoot proliferation. Shoots were rooted in a wet perlite substrate in pots in the greenhouse. Subsequently, rooted plants were transferred to the field. The genetic uniformity of regenerated plants was evaluated using amplified fragment length polymorphism analysis and compared to that of rhizome-propagated plants. A total of 33,443 fragments were generated, representing 869 markers. There were 21 fragments (0.06 % of the fragments) or 19 markers (2.19 % of the markers) that were polymorphic, and almost all of these were singletons. The three species showed similar polymorphisms. Genetic variability was also found in the rhizome-propagated plants, sometimes at a higher rate than in the in vitro culture, indicating that the genetic uniformity was not altered by the protocol. This protocol may help breeders produce new clones of Miscanthus in the future. [ABSTRACT FROM AUTHOR]

Alternaria blight on araliaceous plants is a common disease caused by Alternaria panax Whetzel and occurs worldwide. Genetic diversity among 58 isolates of A. panax from different araliaceous hosts in Korea was determined by amplified fragment length polymorphism (AFLP) analysis. Selected isolates from genetic groups (determined by AFLP analysis) were examined based on the results of phylogenetic analyses of eight genes (Alt a1, BT1, BT2, EF-1α, gpd, H3, ITS, and RPB2), morphological characteristics, and pathogenicity tests. Isolates were divided into two distinct genetic groups (A and B) by AFLP analysis and based on the results of sequence analyses of the BT1, BT2, gpd, and RPB2 genes. Isolates from ginseng plants ( Panax ginseng and P. quinquefolius) fell into group B, whereas isolates from the other araliaceous plants clustered in group A. Morphologically, although some overlap was observed among isolates in the two groups, isolates in group B had longer and narrower conidia, distinct sporulation patterns at 15 °C, and did not secrete pigment into PDA media. Pathogenicity tests revealed that isolates in groups A and B only induced severe disease symptoms on leaves of their hosts, such as isolates in group A on Aralia elata, Aralia continentalis, and in group B on Panax ginseng. The results indicate that the two genetic groups of Alternaria from araliaceous plants should be considered as two different species, and we propose that group A is a candidate of new Alternaria species distinguished from A. panax. [ABSTRACT FROM AUTHOR]

Genetic changes were investigated in two sets of independently synthesized Brasscia napus allopolyploids by the AFLP approach in the present study. We found that 1.17 % of the loci showed genetic changes following both hybridization and genome doubling in the synthesized B. napus F04J2 relative to its diploid progenitors, B. rapa (AA genome) and B. oleracea (CC genome). No significant difference between the proportion of A-genome-specific genetic changes and that of C-genome-specific genetic changes was detected in B. napus F04J2. Approximately 0.6 % of the loci displayed genetic changes following somatic genome doubling in the amphidiploid B. napus DCE11 relative to the amphihaploid in the dimorphic plants. This study showed that rapid genetic changes occurred after hybridization and/or genome doubling in synthesized B. napus allopolyploids and indicated that both hybridization and genome doubling could affect the genomic architecture in newly formed allopolyploids. [ABSTRACT FROM AUTHOR]

Abstract: Flowering cherry trees (Prunus subgenus Cerasus) are characterized by beautiful flowers along with the existence of hundreds of flower ornamental cultivars. The long history of cultivation of flowering cherries, however, has caused significant confusion over names and origins. We conducted experimental crosses and AFLP analysis to reveal the origins or parentages of early-flowering cherry cultivars, Prunus × kanzakura cv. Atami-zakura and Prunus × kanzakura cv. Kawazu-zakura. Multivariate analysis based on pairwise genetic similarity (principal coordinate analysis; PCoA), and Bayesian statistical methods to find genetic group (STRUCTURE analysis) and to classify samples into different hybrid classes (NewHybrids) clearly demonstrated that (1) Prunus × kanzakura cv. Atami-zakura is the F1 hybrid between P. jamasakura and P. campanulata, and (2) Prunus × kanzakura cv. Kawazu-zakura is the F1 hybrid between P. lannesiana var. speciosa and P. campanulata. The experimental crosses revealed the significant difficulty of generating these hybrids. In addition, 18 of 20 and six of six samples of Prunus × kanzakura cv. Atami-zakura and Prunus × kanzakura cv. Kawazu-zakura, respectively, are classified into a single AFLP genotype. It is apparent that the original trees or genets of these taxa have long been propagated by grafting over several tens to one hundred years. [Copyright &y& Elsevier]

Brachypodium, a monocot grass with wide distribution in temperate areas, has been considered a new model plant for many grass species, such as turfgrass or miscanthus, due to its small genome size, self-pollination, rapid life cycle, higher seed yield, and small stature. The objectives of this study were to compare the genetic diversity of natural and artificial populations, and to determine the effects of γ-radiation on genetic variability when evaluated by amplified fragment length polymorphism (AFLP) markers. Two populations used in this study include 66 plant introductions (PI) from the U.S. Department of Agriculture (USDA; POP1), and 43 mutants derived from one of the plant introductions, Bd43 (PI 227011; POP2) treated with a γ-irradiation ranging from 100 to 600 Gy. The highest performance of the phenotypic traits was observed at 200 Gy for germination rate, 100 Gy for height, and 600 Gy for tiller number, implying that the LD50 for determining of optimum dosage depends on the physiological parameters measured. Based on AFLP analysis, POP2 showed higher polymorphism (79.4%), PIC (polymorphism information content; 0.162), and genetic diversity (0.195) than POP1 (59.4%, 0.113, and 0.130, respectively). Those three genetic parameters were evaluated for the mutants derived at various γ-radiation dosages and were found to be the highest when irradiated at 300 Gy. Artificial mutagenesis using γ-radiation improved genetic diversity compared to that of the natural population, and 300 Gy was a useful dosage to enlarge genetic variability in Brachypodium. Results suggest that a dosage maximizing the genetic diversity when evaluated with AFLP markers is an alternative index to LD50 for determining the optimum level for mutation induction. [ABSTRACT FROM AUTHOR]

Species of the genus Myceliophthora and its teleomorph Corynascus have attracted increasing interest due to their potential to produce thermostable enzymes. This study re-assessed the phylogenetic relationship of 49 isolates of nine species belonging to Myceliophthora and Corynascus. One species, M. vellerea, was shown not to belong to the genus Myceliophthora and should be placed in the genus Ctenomyces. The other species belonged to two phylogenetic clusters: mesophilic fungi with the type species M. lutea and C. sepedonium, and thermophilic fungi with M. thermophila, M. hinnulea and C. thermophilus. The phylogenetic data provides no clear separation of the two genera Corynascus and Myceliophthora. To avoid confusion in future taxonomic studies, it is proposed that all existing Corynascus species be renamed to Myceliophthora, which is the old name and the one more frequently used. Furthermore, this study identified two groups within the isolates listed as M. thermophila and assigned one group (five isolates) to M. heterothallica based on AFLP analysis and mating behavior. This study provides new insights into the genetic differences within the genus Myceliophthora and will therefore be essential for the interpretation of future genomic and physiological studies of these species. [ABSTRACT FROM AUTHOR]

Phylogenetic analysis of LSU/ITS sequence data revealed two distinct lineages among 44 morphologically similar fruiting bodies of natural black morels {Morchella elata group) sampled at three non-burn locations in the St Joe and Kanisku National Forests in northern Idaho. Most of the sampled isolates (n = 34) represented a dominant LSU/ITS haplotype present at all three sites and identical to the Mel-12 phylogenetic lineage (GU551425) identified in a previous study. Variation at 1-3 nucleotide sites was detected among a small number of isolates (n = 6) within this well supported clade (94%). Four isolates sampled from a single location were in a well supported clade (97%) distinct from the dominant haplotypes and may represent a previously unsampled, cryptic phylogenetic species. Species-specific SNP and SCAR markers were developed for Mel-12 lineage isolates by cloning and sequencing AFLP amplicons, and segregation of AFLP markers were studied from single ascospore isolates from individual fruiting bodies. Based on the segregation of AFLP markers within single fruiting bodies, split decomposition analyses of two SCAR markers, and population genetic analyses of SNP, SCAR, and AFLP markers, it appears that members of the Morchella sp. Mel-12 phylogenetic lineage are heterothallic and outcross in nature similar to yellow morels. This is the first set of locus-specific molecular markers that has been developed for any Morchella species, to our knowledge. These markers will prove to be valuable tools to study mating system, gene flow and genetic structure of black morels at various spatial scales with field-collected fruiting bodies and eliminate the need to culture samples in vitro. [ABSTRACT FROM AUTHOR]

Abstract: Population diversity, susceptibility to antibiotics including carbapenems of 277 Acinetobacter baumannii strains collected in 17 Italian hospitals over a 6-months’ period was assessed. Semi-automated rep-PCR was used for screening strains for genotypic relatedness. AFLP analysis and MLST were used as definitive methods for strain, species and/or clone identification. Among the 277 strains, 49 rep-PCR types were distinguished with four types (1–4) predominant, indicating both intra- and interhospital spread. AFLP analysis allowed to distinguish 51 types and largely confirmed rep-typing results. Isolates with predominant rep-types 1 and 2 (in 3 and 9 hospitals) were allocated to EU clones I and II, respectively. Rep-type 3 (8 hospitals) belonged to a new clone (“Italian clone”). Rep-type 4 was found in 2 neighbouring hospitals. Two isolates from 2 locations belonged to EU clone III. Twenty-five isolates were identified by AFLP-analysis to A. pittii, emphasizing misidentification by phenotypic methods. MLST confirmed clone identification by AFLP; demonstrating also that the “Italian clone” was ST78, recently detected in different Mediterranean countries. Multidrug resistance, defined as resistance to 9 out of the 11 drugs tested, was common in 10 out of 17 hospitals. The high prevalence of carbapenem resistance was associated with OXA-58 found in 9 out of the 10 hospitals. A high percentage of noted very major errors in susceptibility testing, especially for amikacin and meropenem, was probably due to heteroresistant strains. The occurrence of carbapenem and multidrug resistance in A. baumannii was mainly confined to a limited number of clonal lineages of A. baumannii. [Copyright &y& Elsevier]

While there is evidence that the genetic structure of invasive populations may be distinct from native populations, it has proved difficult to establish the causes of any variation owing in part to the range of evolutionary processes involved. In order to assess differences in the genetic structure of invasive populations of Gunnera tinctoria, five native populations were compared to 23 geographically widely dispersed invasive populations using amplified fragment length polymorphic markers (AFLPs). In total, 221 individuals were sampled at three spatial scales: inter-regional, within-region, and at a high-resolution local scale. It was observed that there were high levels of genetic variation between most populations, that invasive populations were generally distinct from both native populations and from each other and that genetic variation away from founding populations can occur relatively quickly and within a small geographic area. Changes in the pattern of genetic variation observed in invasive populations strongly indicated that founder effects and genetic drift played a significant role in shaping their genetic structure. It was further concluded that gene flow had a homogenizing effect on the structure of invasive populations occurring in close proximity, increasing their allele content and potentially contributing to their successful establishment. [ABSTRACT FROM AUTHOR]

Codiaeum variegatum (L.) Blume, commonly known as crotons, are among the most popular ornamental foliage plants cultivated for either landscaping or interior-scaping. Currently, more than 300 cultivars are available; each has a distinct phenotype, particularly in leaf morphology. Thus far, there is no information regarding their genetic relationships. In this study, genetic relatedness of 44 cultivars of C. variegatum was investigated using amplified fragment length polymorphism (AFLP) markers. Fourteen primer combinations generated a total of 549 AFLP fragments, which were used to estimate genetic distances and construct dendrograms based on the neighbor-joining method. The 44 cultivars were divided into seven clusters, which concurred with the known history of croton geographical isolation, adaptation, introduction, and breeding activities but differed from the classification made by the Croton Society. based on leaf morphology. The established genetic relationships could be important for future germplasm identification and conservation and new cultivar development. Additionally, genetic distance among the 44 cultivars was 0.322 or less, indicating that they have a narrow genetic base. The narrow genetic base may indicate that the cultivars were derived from a common progenitor. On the other hand, 81% of the 549 fragments were polymorphic and the average polymorphic information content was 0.22, which suggests that the cultivars are genetically highly polymorphic. The high polymorphisms may be attributed to significant gene loss or gain facilitated by mutation and/or chromosome variation, thus contributing to a wide range of leaf morphological differences among cultivars. [ABSTRACT FROM AUTHOR]

Abstract: Arcobacter cryaerophilus is a heterogeneous species in which two distinct subgroups have been reported. In the present study, the taxonomic status of these subgroups was reassessed using amplified fragment length polymorphism and heat shock protein 60 gene sequence analysis. The results demonstrated that A. cryaerophilus has a complex taxonomic structure, which consists of multiple cores of strains that share intermediate levels of DNA–DNA hybridisation and exhibit low levels of DNA–DNA hybridisation towards other Arcobacter species. One of these cores consisted of the majority of strains and included most subgroup 2 strains from previous studies. A. cryaerophilus subgroup 1 strains represented three distinct cores, among which the type strain occupied a distinct position. These results therefore also demonstrate that the current subgroup nomenclature in A. cryaerophilus should be abandoned, and that the type strain is genetically aberrant and poorly represents strains belonging to this species. [Copyright &y& Elsevier]

Abstract: Recent investigations clearly indicate that the probiotic bacterium Lactobacillus paracasei IMPC2.1 can be incorporated into vegetables to obtain innovative probiotic foods whose marketing has been authorized by the Italian Ministry of Health. In this study, strain IMPC2.1 was characterized at a molecular level in order to define its taxonomic position and to develop a PCR test for strain-specific identification. Molecular methods, such as 16S rRNA gene sequencing and multiplex PCR, have provided evidence that strain IMPC2.1 indeed belongs to the L. paracasei species. In addition, a cluster analysis of fluorescent amplified fragment length polymorphism (f-AFLP) data strongly indicated that strain IMPC2.1 and nine other L. paracasei strains (including strain ATCC 334) belong to the same species and are definitely differentiated from the type strain L. casei ATCC 393. The f-AFLP technique was also used to identify a strain-specific DNA fragment of L. paracasei IMPC2.1 — encoding an amino acid sequence similar to a glycosyltransferase of probiotic strain L actobacillus rhamnosus HN001 — which enabled us to develop a rapid PCR test for strain-specific identification. The strain-specificity of the PCR test was assessed by comparison with a total of 73 bacterial strains mainly isolated from vegetable products that did not produce any amplified fragment. These strains belonged to the L. paracasei species, to 6 additional species of Lactobacillus and to Weissella cibaria, W. confusa, Lactococcus lactis, Leuconostoc mesenteroides and Pediococcus pentosaceus. A method similar to the one used in this study can be adopted to develop easy, rapid detection techniques for monitoring other bacteria in complex microbiota. [Copyright &y& Elsevier]

Brachypodium distachyon (brachypodium) is a small grass with the biological and genomic attributes necessary to serve as a model system for all grasses including small grains and grasses being developed as energy crops (e.g., switchgrass and Miscanthus). To add natural variation to the toolkit available to plant biologists using brachypodium as a model system, it is imperative to establish extensive, well-characterized germplasm collections. The objectives of this study were to collect brachypodium accessions from throughout Turkey and then characterize the molecular (nuclear and organelle genome), morphological, and cytological variation within the collection. We collected 164 lines from 45 diverse geographic regions of Turkey and created 146 inbred lines. The majority of this material (116 of 146 inbred lines) was diploid. The similarity matrix for the diploid lines based on AFLP analysis indicated extensive diversity, with genetic distances ranging from 0.05 to 0.78. Organelle genome diversity, on the other hand, was low both among and within the lines used in this study. The geographic distribution of genotypes was not significantly correlated with either nuclear or organelle genome variation for the genotypes studied. Phenotypic characterization of the lines showed extensive variation in flowering time (7-22 weeks), seed production (4-193 seeds/plant), and biomass (15-77 g). Chromosome morphology of the collected brachypodium accessions varied from submetacentric to metacentric, except for chromosome 5, which was acrocentric. The diverse brachypodium lines developed in this study will allow experimental approaches dependent upon natural variation to be applied to this new model grass. These results will also help efforts to have a better understanding of complex large genomes (i.e., wheat, barley, and switchgrass). [ABSTRACT FROM AUTHOR]

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1. Plant defence theory predicts trade-offs among defence traits as a result of resource limitation or pleiotropic effects. Although theoretically widely accepted, empirical demonstrations of such trade-offs are surprisingly scarce and mechanistic explanations are usually lacking. 2. We quantified cyanogenesis (the release of hydrogen cyanide (HCN)) as a direct defence and the emission of volatile organic compounds (VOCs) as an indirect defence against herbivores. To elucidate whether the trade-offs occur at the genetic or phenotypic level we investigated cultivated and wild-type accessions of lima bean (Fabaceae: Phaseolus lunatus L.) and compared different leaf developmental stages. Genetic relationships among the accessions were studied using amplified fragment length polymorphism (AFLP) analysis. 3. Cyanogenesis and the release of VOCs differed significantly among the accessions and were negatively correlated: high cyanogenic accessions released low amounts of VOCs and vice versa. The same remained true for the ontogenetic stages, since primary leaves of all accessions hardly ever produced HCN at all, yet regularly showed high release rates of VOCs. 4. Low and high cyanogenic accessions of lima bean formed distinct clades in an AFLP-based dendrogram, while wild-types and cultivars did not separate. The first pattern indicates that the underlying defensive syndromes are genetically conserved, while the latter is likely to be caused by a multiple origin of cultivated lima beans or an extensive gene flow among cultivated and wild plants. 5. Synthesis. Trade-offs between cynogenesis and VOC release were obvious both between accessions and at the ontogenetic level, and thus cannot be explained by pleiotropy. We contend that allocation restrictions and/or adaptations to different enemy pressures are most likely to explain why lima bean can invest into cyanogenesis or VOCs, but not both. [ABSTRACT FROM AUTHOR]

Abstract: Approximately 50 single-basidiospore isolates (SBIs) obtained from each of 16 field isolates of Thanatephorus cucumeris AG-1 IC were examined for heterokaryon formation. All SBIs obtained from each field isolate were divided into two mating groups (SBIs-M1 and SBIs-M2), and tufts of mycelia were formed in the contact zone between colonies of paired SBIs-M1 and -M2 based on 0.5 % charcoal agar medium. Tufts were produced from all possible pairing between SBIs from non-parental field isolates. Hyphal anastomosis reactions indicated no cell death and random cell death at the contact cell, and was not related to tuft formation. AFLP phenotypes of SBIs from each field isolate were not identical to each other and were different from their parental field isolate. AFLP phenotypes of the tuft isolates formed from SBIs-M1 and SBIs-M2 from each field isolate were heterokaryotic. Moreover, several SBIs also formed tufts with their parental and non-parental field isolates. AFLP phenotypes of these tuft isolates suggested that they were all heterokaryotic. Results of these experiments suggest that T. cucumeris AG-1 IC is heterothallic and bipolar, and that genetic exchange can occur between homokaryotic and heterokaryotic isolates (Buller phenomenon). [Copyright &y& Elsevier]

The aims of this study were to determine whether a multidrug-resistant Acinetobacter baumannii clone, known to be endemic in three tertiary-care Portuguese hospitals, had disseminated throughout Portugal, and whether this clone was related to one of the European clones I–III described previously. The isolates were first screened by pulsed-field gel electrophoresis and/or M13 random amplified polymorphic DNA fingerprint analysis. Ten representative isolates were compared by amplified fragment length polymorphism (AFLP) analysis, and were also compared with isolates contained in the AFLP library of the Leiden University Medical Centre. All of the Portuguese isolates clustered in European clone II (clone delineation level >80%). Following AFLP analysis, seven isolates clustered at >96%, indicating a striking degree of genetic relatedness and suggesting recent spread of a (sub)clone. Three isolates were slightly more separated from this main group, but all isolates clustered at 87.4%. Thus, the Portuguese multidrug-resistant isolates formed a sub-cluster of European clone II, suggesting that they belong to a recent lineage within clone II. [ABSTRACT FROM AUTHOR]

Here we use amplified fragment length polymorphism (AFLP) to assess genetic differentiation of Helicoverpa armigera and H. assulta. The results indicated that both species-specific fingerprints and cluster analysis showed the ability of AFLP technique to discriminate the two sibling species; among a total 1963 AFLP markers amplified from nine primer combinations: 777 (39.6%) were H. armigera-specific, 602 (30.7%) were H. assulta-specific, and 584 (29.7%) were common bands. The mean number of H. armigera-specific bands was significantly more than that of H. assulta-specific bands for nine primer combinations ( P < 0.05); the intraspecific distance of H. armigera and H. assulta was 0.123 0 and 0.110 7 respectively, and the interspecific distance was 0.178 3. In addition, the percentage of polymorphic loci and estimated average heterozygosity were used to estimate genetic diversity of the two species. This study therefore demonstrates that AFLP analysis is a sensitive and reliable technique to study genetic differentiation and genetic relationships between species and provides sufficient molecular markers for future linkage map construction, location and eventual cloning of genes involved in traits differentiation. [ABSTRACT FROM AUTHOR]

Unweighted pair-group (UPGMA) cluster, neighbor-joining (NJ), and parsimony analyses using amplified fragment length polymorphism (AFLP) data revealed the presence of three taxa within Carex digitalis Willd. (var. digitalis, var. floridana, var. macropoda). Even when taxa occur syntopically, genetic distinctiveness is maintained (Hertford Co., North Carolina populations of var. macropoda and var. floridana). Clades or clusters corresponding with vars. digitalis and floridana were well supported in all analyses. However, the var. macropoda clade was poorly supported on most trees. Despite our inability to fully resolve taxon relationships, AFLP data substantiate ongoing morphological and phytogeographic studies that show the presence of additional species diversity within sect. Careyanae and the eastern North American Carex flora. [ABSTRACT FROM AUTHOR]

Paspalum notatum Flügge is a warm-season forage grass with sexual diploid and apomictic tetraploid races. Genetic improvement was achieved in out-breeding diploids. The acquisition of artificial sexual tetraploids has raised the possibility of performing crosses and plant improvement at the tetraploid level. The objective of our study was to obtain a genetic and cytoembryological characterization of a germplasm collection of P. notatum, including 31 accessions from seven countries of America and 11 experimentally obtained genotypes. Morphology of mature gametophytes was observed to assess the mode of reproduction of the accessions. A total of 1342 AFLP fragments were generated across the 42 genotypes and from two reference taxa: P. urvillei and P. procurrens. AFLP data were converted into a binary matrix and similarity relationships were established. The genetic distance among all the accessions showed a maximum value of 0.36. In addition, eleven AFLP fragments were observed exclusively in apomictic plants, which could be linked to genomic regions implicated in the control of apospory. [ABSTRACT FROM AUTHOR]

Objective . To assess the relationship between the presence of mixed infection of Helicobacter pylori and both antimicrobial susceptibility and virulence markers. Material and methods . Thirty-six patients with H. pylori infection were included in the study. Three colonies were selected from each positive biopsy sample collected from each host for a total of 108 H. pylori strains. The genetic variability was evaluated through the amplified fragment length polymorphism (AFLP) analysis; the antibiotic susceptibility to amoxicillin, clarithromycin, moxifloxacin, rifabutin and tinidazole was determined using the minimum inhibitory concentrations (MICs) with the agar dilution method. Moreover, the vac A, cag A, ice A and bab A2 statuse were detected by polymerase chain reaction (PCR). Results . There was a strong connection between mixed H. pylori infection and antimicrobial resistance. In particular, H. pylori strains with genetic variability, in the same host, expressed more resistance to clarithromycin, moxifloxacin and tinidazole than that expressed in strains with a unique genetic host pattern. Vac A s1m1/s1m2 genotypes were found in 70% of strains isolated in mixed infection, whereas the same allelic combinations were found in 42% of strains, isolated in single infection. The cag A + status prevailed both in patients with mixed (97%) and in those with single infection (85%) without significant differences. The ice A1 status was more commonly found in patients with mixed infection, whereas the bab A2 status was significantly prevalent in single H. pylori infection. Conclusions . Mixed H. pylori infection harbouring in one patient is significantly related to strains that are more resistant to antibiotics and with a more virulent genotype ( vac A s1m1/s1m2, cag A, ice A1) than strains responsible for single infection. [ABSTRACT FROM AUTHOR]

Crown rust ( Puccinia coronata) resistance (CRres), which had been introgressed from meadow fescue ( Festuca pratensis) into the Italian ryegrass ( Lolium multiflorum) background, was genetically mapped with amplified fragment length polymorphism (AFLP) and sequence tagged site (STS) markers to a terminal segment of chromosome 5. Comparative mapping had previously shown that this region of the Lolium/ Festuca genome has a degree of conserved genetic synteny with chromosomes 11 and 12 of rice. Sequences from rice chromosome 12 were used as templates for identifying further STS markers that cosegregated with CRres. The relative genomic positions of molecular markers associated with CRres in L. multiflorum, L. perenne, F. pratensis and oats is discussed, along with their relationships to physical positions on rice chromosomes C11 and C12. [ABSTRACT FROM AUTHOR]

Abstract: The genetic diversity of 79 Nomuraea rileyi isolates from various lepidopteran hosts in Asia, North America, and South America was evaluated using amplified fragment length polymorphism (AFLP) analysis. Cluster analysis separated the N. rileyi isolates into two major groups and seven subgroups. The resulting dendrogram generally classified the N. rileyi isolates based on insect host and geographical region. The haplotypic diversity index of N. rileyi subpopulations from each location and host origin was ranging from 0.8788 to 1.000. However, analysis of molecular variance (AMOVA) demonstrated no significant differences (p =0.3421) among N. rileyi isolates from different continents. Whereas the genetic variation among the N. rileyi populations from the different host insects within each continent was significantly different (p <0.0001). [Copyright &y& Elsevier]

Abstract: Bacterial canker of citrus is a serious disease of citrus worldwide. Five forms of the disease have been described, cankers “A”, “B”, “C”, “D”, and “E”. Although considerable genetic diversity has been described among the causal agents of the five forms of citrus canker and supports multiple taxons, the causal agents currently are classified as pathovars citri (“A”), aurantifolii (“B/C/D”) and citrumelo (“E”) of a single species, Xanthomonas campestris pv. citri (or X. axonopodis pv. citri). To determine the taxonomic relatedness among strains of X. campestris pv. citri, we conducted DNA–DNA relatedness assays, sequenced the 16S-23S intergenic spacer (ITS) regions, and performed amplified fragment length polymorphism (AFLP) analysis, using 44 strains representative of the five recognized forms of citrus canker. Under stringent DNA reassociation conditions (T m−15°C), three distinct genotypes of citrus pathogens were revealed: taxon I included all “A” strains; taxon II contained all “B”, “C”, and “D” strains; and taxon III contained all “E” strains. The three citrus taxa showed less than 50% (mean) DNA–DNA relatedness to each other and less than 30% (mean) to X. campestris pv. campestris and X. axonopodis pv. axonopodis. Taxa I and II strains share over 70% DNA relatedness to X. campestris pv. malvacearum and X. campestris pv. phaseoli var. fuscans, respectively (at T m−15°C). Taxon III strains share 70% relatedness to X. campestris pv. alfalfae. Previous and present phenotypic data support these DNA reassociation data. Taxon II strains grow more slowly on agar media than taxa I and III strains. Taxa I and III strains utilize maltose, and liquefy gelatin whereas taxon II strains do not. Taxon I strains hydrolyze pectate (pH 7.0) whereas Taxon II strains do not. Taxon III strains utilize raffinose whereas Taxon I strains do not. Each taxon can be differentiated by serology and pathogenicity. We propose taxa I, II, and III citrus strains be named, respectively, Xanthomonas smithii subsp. citri (ex Hasse, 1915) sp. nov. nom. rev. comb. nov., Xanthomonas fuscans subsp. aurantifolii (ex Gabriel et al., 1989) sp. nov. nom. rev. comb. nov., and Xanthomonas alfalfae subsp. citrumelo (ex Riker and Jones) Gabriel et al., 1989 nov. rev. comb. nov. Furthermore, based on the analysis of 40 strains of 19 other xanthomonads, we propose to reclassify X. campestris pv. malvacearum (ex Smith, 1901) Dye 1978 as X. smithii subsp. smithii sp. nov. comb. nov. nom. nov.; X. campestris pv. alfalfae (ex Riker and Jones) Dye 1978 as X. alfalfae subsp. alfalfae (ex Riker et al., 1935) sp. nov. nov. rev.; and “var. fuscans” (ex Burkholder 1930) of X. campestris pv. phaseoli (ex Smith, 1897) as X. fuscans subsp. fuscans sp. nov. [Copyright &y& Elsevier]

The article presents a pathogenic and genetic analysis of Macrophomina phaseolina (Tassi) Goid on different hosts. Pathogenicity and AFLP (amplified fragment length polymorphisms) were used to analyze the diversity patterns of the fungus Macrophomina phaseolina isolates coming from Mexico and other countries. Species of Zea mays, Phaseolus vulgaris, Glycine max, Arachis hypogea, Sesamum indicum, and Cicer arietinum were investigated. Results show that sesame and soybean were mostly affected by M. phaseolina and maize the lowest. The AFLP reveals a great genetic diversity in M. phaseolina.

Summary: Forty three rhizobial strains isolated from root nodules of Genista tinctoria growing in England, Ukraine, and Poland were compared with 21 representatives of the recognized rhizobial species and two unclassified Bradyrhizobium sp. (Lupinus) strains by performing a numerical analysis of 102 phenotypic features and with the reference bradyrhizobia by simplified AFLP analysis with one restriction enzyme PstI and one selective primer PstI-A. All Genista tinctoria microsymbionts were slow-growing bradyrhizobia with generation time of 10–14 h, acid tolerant, salt sensitive, and antibiotic resistant. Cluster analysis based on the phenotypic properties of all bacteria included, grouped dyer''s broom rhizobia together with Bradyrhizobium strains, and classified them into three major phena according to their geographic origin. Genista tinctoria nodule isolates were separated into three clusters with the strain composition as in a phenogrouping by AFLP patterns. The presented results, suggest the relationship of G. tincoria microsymbionts to Bradyrhizobium species and show the usefulness of AFLP analysis for differentiation and classification of the studied rhizobia. [Copyright &y& Elsevier]

To assess diversification of indica rice, fingerprinting of 42 Indian rice varieties (Oryza sativa L) and one accession of O. brachyantha Chev. et Roehr. was taken up using amplified fragment length polymorphism (AFLP). Six primer combinations of PstI and MseI were used for this purpose. On denaturing polyacrylamide sequencing gel, on average 41 scorable AFLP bands were obtained of which 81% were polymorphic. Each variety revealed a distinct fingerprint. Data were scored on the basis of presence and absence of bands and cluster analysis was performed using Dice similarity coefficients. The resultant dendrogram showed four major clusters and traits. Some varieties especially landraces revealed more polymorphism and unique loci. Such study will be a valuable tool for proper choice of parents in mapping populations or breeding programs to produce heterotic several inexplicable minor clusters. Some varieties were grouped according to parentages of the cross while some were grouped according to physiological combinations apart from providing a characteristic fingerprint. [ABSTRACT FROM AUTHOR]