Isolation of DNA for RAPD analysis from dry leaf material of some<Emphasis Type="Italic">Hesperis</Emphasis> L. specimens

An improved protocol for the isolation of DNA from dry material of someHesperis specimens is described. The isolated DNA is suitable for random amplification of polymorphic DNA (RAPD) analysis. Different DNA extraction protocols were examined to determine which might yield DNA from dry leaf tissue ofHesperis specimens. The methods examined include the protocols with hexadecyltrimethylammonium bromide (CTAB) described by Doyle and Doyle (1987); sodium dodecyl sulfate (SDS) by Dellaporta et al. (1983); and CTAB and SDS, the modified minipreparation, by Dellaporta et al (1983). None of these procedures yielded DNA of suitable purity for RAPD assay. We established an improved procedure involving CTAB and enzymatic digestion of proteins and RNA. The recovery of DNA with an average yield of 25 mg/g of leaf material was possible with this procedure. RAPD bands, which could be used to distinguish amongHesperis specimens, were generated.     

苹果乙烯不敏感基因EIN2片段的克隆及序列分析

分别以苹果果实总DNA和cDNA为模板,采用PCR、RT-PCR方法扩增、克隆乙烯不敏感基因(ethyleneinsensitive 2,EIN2),并利用生物信息学方法分析其核苷酸序列和蛋白质结构。结果表明:(1)以DNA和cDNA为模板的扩增结果完全相同,扩增的EIN2基因片段为4 378bp,尚未发现有内含子,开放阅读框全长3 282bp,编码1 093个氨基酸;苹果EIN2相对分子质量为118.9kD,等电点为5.52,其蛋白可能为脂溶性疏水蛋白。(2)所克隆苹果EIN2基因编码的氨基酸序列与拟南芥(AAD41077.1)、碧桃(ACY78397.1)和葡萄(CAN66374.1)EIN2基因编码的氨基酸序列一致性分别为52%、79%、62%。(3)构建的EIN2基因进化树显示,拟南芥、小盐芥、甜瓜、杨毛果EIN2基因亲缘关系较近,聚为一类;葡萄为一类;蒺藜苜蓿为一类;碧桃、矮牵牛、西红柿聚为一类;苹果单独为一类。而且苹果EIN2基因与碧桃等同源基因的亲缘关系相对较近,与拟南芥、小盐芥同源基因的亲缘关系相对较远。     

Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species

Genic microsatellites or simple sequence repeat markers derived from expressed sequence tags (ESTs), referred to as EST–SSRs, are inexpensive to develop, represent transcribed genes, and often have assigned putative function. The large apple (Malus × domestica) EST database (over 300,000 sequences) provides a valuable resource for developing well-characterized DNA molecular markers. In this study, we have investigated the level of transferability of 68 apple EST–SSRs in 50 individual members of the Rosaceae family, representing three genera and 14 species. These representatives included pear (Pyrus communis), apricot (Prunus armeniaca), European plum (P. domestica), Japanese plum (P. salicina), almond (P. dulcis), peach (P. persica), sour cherry (P. cerasus), sweet cherry (P. avium), strawberry (Fragaria vesca, F. moschata, F. virginiana, F. nipponica, and F. pentaphylla), and rose (Rosa hybrida). All 68 primer pairs gave an amplification product when tested on eight apple cultivars, and for most, the genomic DNA-derived amplification product matched the expected size based on EST (in silico) data. When tested across members of the Rosaceae, 75% of these primer pairs produced amplification products. Transferability of apple EST–SSRs across the Rosaceae ranged from 25% in apricot to 59% in the closely related pear. Besides pear, the highest transferability of these apple EST–SSRs, at the genus level, was observed for strawberry and peach/almond, 49 and 38%, respectively. Three markers amplified in at least one genotype within all tested species, while eight additional markers amplified in all species, except for cherry. These 11 markers are deemed good candidates for a widely transferable Rosaceae marker set provided their level of polymorphism is adequate. Overall, these findings suggest that transferability of apple EST–SSRs across Rosaceae is varied, yet valuable, thereby providing additional markers for comparative mapping and for carrying out evolutionary studies.     

A comparison of sap flux and water relations of leaves of various isolated trees with special reference to foundation movement in clay soil

Diurnal variation in sap flux (S) through stems of six trees, two each of Ulmus procera SALISB., Melaleuca styphelioides SM. and Prunus cerasifera EHRH. ‘Nigra’ (referred to hereafter by their generic names), were estimated from measurements of heat pulse velocities. Leaf water potential (ψ), stomatal conductance (g _s ) and transpiration from leaves (T) of all replicate trees were measured at 1300–1500h, once during the summer. On two separate occasions measurements were made of S, ψ, (g _s ) and T for one each of Ulmus and Melaleuca trees to study diurnal variations in these parameters. A 12×12 m² area around each tree was kept covered to simulate the condition of trees growing on pavements adjacent to residential properties. Sap flux for these tree species was in the order Melaleuca>Ulmus>Prunus. It is suggested that the smaller canopy and sapwood area in Prunus compared to the other two species is responsible for lower water potential and lower transpiration rate than the other species. Detailed analysis of the diurnal variation in sap flux and water relation of leaves of Melaleuca and Ulmus indicated sap flux of Melaleuca to be greater than that of Ulmus at the same transpiration rate per unit leaf area although the sapwood area of the two species was marginally different. This may have been due either to the difference in canopy conductance or in leaf area between the two species. With the assumption that sap flux closely resembles the rate of soil water extraction for both species, results indicate that Melaleuca is likely to extract soil water at a higher rate than Ulmus and hence is capable of causing greater shrinkage and soil movement than Ulmus.     

A rapid method for tissue collection and high-throughput isolation of genomic DNA from mature trees

Collection of tissue and subsequent isolation of genomic DNA from mature tree species often proves difficult. DNA extraction from needles, leaves, or buds is recommended in many protocols. Collecting these tissues from mature trees generally requires the use of firearms or climbing if sampling is to be nondestructive. As a result, sample collection is a major expense of many tree-based projects. Tree (and plant) tissues generally contain large amounts of polysaccharides and phenolic compounds that are difficult to separate from DNA. Many methods aim to overcom these problems, with most involving extraction in buffers containing the nonionic detergent cetyltrimethyl-ammonium bromide (CTAB), followed by numerous steps to clean contaminants from the DNA, using organic solvents and differential salt precipitation. These steps are time-consuming, such that isolation of DNA becomes the bottleneck in many molecular studies. This paper presents a new, efficient, cambium collection method for tree species and a DNA extraction protocol based on that of Doyle and Doyle (1987), with follow-up purification using the Wizard nuclei lysis and protein precipitation solutions (Promega). Results show a significant improvement in yield and DNA purity compared with other published methods, with consistently high yields of pure genomic DNA and high sample throughput. The relatively low cost per extraction, no requirement for use of liquid nitrogen, no requirement for freezer storage, and long-term sample stability after collection are important additional benefits.     

Detection of Prunus necrotic ring spot virus in plum,cherry and almond by serological and molecular techniques from India

Stone fruits are cultivated in the temperate and sub-temperate regions of India. During surveys in stone fruit growing areas, viral symptoms were observed in almond, cherry and plum. These samples were brought to the laboratory for further detection at serological and molecular levels to check the presence of virus. In the present study, incidence of PNRSV is reported on plum (Prunus domestica), almond (Prunus dulcis) and cherry (Prunus avium) using serological and molecular techniques. Coat protein gene of PNRSV was amplified from almond, cherry and plum. This is the first molecular evidence of PNRSV on these stone fruits reported from India.     

Influence of selected fruit tree pollen on life history of <Emphasis Type="Italic">Euseius stipulatus</Emphasis> (Acari: Phytoseiidae)

Euseius stipulatus (Athias-Henriot) is a predatory mite widespread in the Mediterranean region considered to be important for the biological control of spider mites in citrus orchards. Development, survival and reproduction of this phytoseiid mite feeding on seven commercially obtained pollen were studied under constant laboratory conditions (20 ± 1°C, RH 65 ± 5%, photoperiod 16L: 8D h). Mites were kept individually at rearing units with ample quantity of almond (Prunus amygdalus Batch), apple (Malus domestica Borkh), apricot (Prunus armeniaca L.), cherry (Prunus avium L.), pear (Pyrus communis L.), plum (Prunus domestica L.) and walnut (Juglans regia L.) pollen as food source. Developmental time from egg to adult varied between the several pollen tested from 8.38 ± 0.08 to 9.58 ± 0.11 days for females and from 8.23 ± 0.12 and 9.07 ± 0.12 days for males. Female longevity varied from 11.53 ± 1.22 to 51.38 ± 2.45 days, while fecundity ranged from 22.84 ± 2.30 to 43.61 ± 3.78 eggs/female. The predator was unable to reproduce when feeding on walnut pollen. Data were submitted to life table analysis and values of the intrinsic rate of increase were derived, ranging from 0.079 to 0.146 (day⁻¹). The cumulative Weibull function that was used to describe the age specific survival of females produced excellent fits to the survival data. Results show that almond, plum, cherry and apricot pollen possess higher nutritional value for E. stipulatus than pear and apple pollen and thus may contribute in sustaining and increasing the predator population in field conditions. Walnut pollen can be utilized by the predator only to survive during short periods of time when principal or alternative food sources are scarce.     

Host preference of the plum curculio

We assessed host preference of adult plum curculio, Conotrachelus nenuphar (Herbst) (Coleoptera: Curculionidae), based on the total number of mark‐released and wild adults recovered and the total distance moved by mark‐released adults in an orchard whose layout was designed to specifically allow foraging plum curculios to choose among host tree species. Host trees included apple, Malus domestica Borkh.; pear, Pyrus communis (L.); peach, Prunus persica (L.) Batsch; apricot, Prunus armeniaca L.; tart cherry, Prunus cerasus L.; sweet cherry, Prunus avium (L.); European plum, Prunus domestica L.; and Japanese plum, Prunus salicina Lindl. (all Rosaceae). We released 2900 marked adults and recovered 17.7%. We used screen traps to provide a measure of the number of adults that arrived at and climbed up particular host trees and found that significantly greater numbers of marked adults and the greatest number of wild adults were recovered from screen traps attached to Japanese plum. We sampled host tree canopies by tapping limbs to provide a measure of the number of adults within a tree canopy at a particular moment. Again, significantly greater numbers of marked and wild adults were recovered from plum species, with no difference between Japanese and European plum cultivars for marked individuals, but with significantly greater numbers of wild individuals recovered from Japanese plum. The preference index (PI) for Japanese plum based on total distances moved by all marked adults recovered on Japanese plum divided by the total distance moved by marked adults recovered on other host trees indicated that Japanese plum was the most highly preferred host, followed by European plum, peach, sweet cherry, tart cherry, apricot, apple, and pear, respectively.     

A rapid and efficient method for the extraction of total DNA from mature leaves of the data palm (Phoenix dactylifera L.)

A method is presented for the rapid isolation of high-molecular-weight DNA from mature leaves of date palm (Phoenix dactylifera L.), using a CTAB-based buffer. The method yields up to 800 μg of DNA from 1 g of leaf tissues. The procedure was also suitable for DNA extraction from callus or buds from tissue culture. The DNA obtained through this method was a good substrate for at least seventeen restriction endonucleases. This method was also used to extract DNA from mature leaves of coconut and may be applicable to other species of palms.     

Effect of host plants on developmental time and life table parameters of <Emphasis Type="Italic">Amphitetranychus viennensis</Emphasis> (Acari: Tetranychidae)

The effect of host plant species including black cherry (Prunus serotina cv. Irani), cherry (Prunus avium cv. siahe Mashhad) and apple (Malus domestica cv. shafi Abadi) was studied on biological parameters of Amphitetranychus viennensis (Zacher) in the laboratory at 25 ± 1°C, 70 ± 10% RH and 16L: 8D photoperiod. Duration of each life stage, longevity, reproduction rate, the intrinsic rate of natural increase (r _m ), net reproductive rate (R ₀ ), mean generation time (T), doubling time (DT), and finite rate of increase (λ) of the hawthorn spider mite on the three host plants were calculated. Differences in fertility life table parameters of the spider mite among host plants were analyzed using pseudo-values, which were produced by jackknife re-sampling. The results indicated that black cherry might be the most suitable plant for hawthorn spider mite due to the shorter developmental period (10.6 days), longer adult longevity (25.5 days), higher reproduction (65.6 eggs), and intrinsic rate of natural increase (0.194 females/female/day). Cherry was the least suitable host plant. To determine the effect of host shifts, the mite was transferred from black cherry onto cherry and apple. In the first generation after shifting to apple, the developmental period, reproduction and life table parameters were negatively influenced. However, population growth parameters in the first generation on cherry were actually better than after three generations on this new host. This underscores the relevance of the mites’ recent breeding history for life table studies.     

Genome size and ploidy level among wild and cultivated <Emphasis Type="Italic">Prunus</Emphasis> taxa in Slovakia

2C DNA content and ploidy level variation of Prunus spinosa and closely related taxa together with Prunus domestica L. and Prunus insititia L. was studied in Slovakia. The aim of the study was to define genome sizes and find differences between closely related taxa within Prunus spinosa sensu lato mentioned in previous works. According to our results, investigated taxa can be divided into three groups according to ploidy level: Prunus spinosa, Prunus dasyphylla, Prunus ×fruticans, Prunus ×dominii and Prunus ×schurii are tetraploids, Prunus ×fechtneri is pentaploid, and P. domestica and P. insititia are hexaploids. Genome size differences within tetraploid taxa were relatively small (Prunus spinosa: 1.40?±?0.02, P. ×domini: 1.44?±?0.01, P. ×fruticans: 1.48?±?0.02, P. ×schurii: 1.44?±?0.02), but statistically significant. Although further research is needed, it seems that the concept of several taxa as product of hybridization between P. spinosa and cultivated plum species has been supported by our study.     

Doubled haploid production in fruit crops

The interest of fruit breeders in haploids and doubled haploids (DH), lies in the possibility of shortening the time needed to produce homozygous lines compared to conventional breeding. Haplo-diploidization through gametic embryogenesis allows single-step development of complete homozygous lines from heterozygous parents. In a conventional breeding programme, a pure line is developed after several generations of selfing. With fruit crops, characterized by a long reproductive cycle, a high degree of heterozygosity, large size, and, sometimes, self-incompatibility, there is no way to obtain haploidization through conventional methods. This paper reviews the current status of research on doubled haploid production in the main fruit crops: Citrus, Malus domestica, Pyrus communis, Pyrus pyrifolia, Prunus persica, Prunus avium, Prunus domestica, Prunus armeniaca, Vitis vinifera, Actinidia deliciosa, Olea europaea, Morus alba, Actinidia deliziosa, [Musa balbisiana (BB)], Carica papaya, Annona squamosa, Feijoa sellowiana, Opuntia ficus-indica, Eriobotrya japonica.     

Molecular detection of <Emphasis Type="Italic">Entoloma</Emphasis> spp. associated with roots of rosaceous woody plants

Seventeen isolates of Entoloma clypeatum, a fungus associated with rosaceous woody plants and suspected to act as a root pathogen, were obtained from fruit-bodies collected at 7 localities in the Czech Republic. The fungus grew best on the medium supplied with cellobiose. The growth of E. clypeatum was inhibited by fungicide preparation Ridomil Gold MZ 68WP. A part of the LSU rRNA gene of 11 selected isolates was sequenced and two reverse primers recognizing the sequence motifs in the LSU rRNA gene of E. clypeatum and other related species associated with rosaceous woody plants were designed. One of these primers, NL4EC2, showed high specificity towards DNA of Entoloma spp. of interest and may be used for detection of these organisms in soil, in roots or in the substrate where the fruit trees are cultivated. The results of in vitro inoculation experiment suggest a resistance of roots of young Prunus domestica plants to colonization by Entoloma clypeatum, and the fungus could be detected only in the surrounding substrate. We were able to detect Entoloma spp. in soil and in roots of Prunus avium but only if the fructification of the fungus occurred at the locality. The method is robust towards the false positive detection caused by nonspecific amplification of DNA of other soil microorganisms.     

Characterization and genetic diversity of Pseudomonas syringae isolates from stone fruits in north‐western Iran

From 33 Iranian fluorescent Pseudomonas isolates originating from symptomatic tissues of peach (Prunus persica), plum (Prunus domestica), sweet (Prunus avium) and sour cherry (Prunus cerasus), 27 were identified as Pseudomonas syringae using LOPAT tests. Further characterization of those isolates by GATTa and L‐lactate utilization tests and the detection of syringomycin and coronatine and yersiniabactin coding genes showed that five of them belonged to race 1 and four to race 2 of P. syringae pv. morsprunorum (Psm) and eighteen other isolates were identified as P. syringae pv. syringae (Pss). Based on the analysis of the fingerprint patterns generated by REP, ERIC and BOX‐PCR, the strains were differentiated into three main groups at the 67% similarity level. Strains of the groups 1, 2 and 3 belong to Psm race 1, Psm race 2 and Pss, respectively. Rep‐PCR analysis showed high intra‐pathovar variation within the Pss isolates, which grouped into four distinct clusters. Using the REP primers, the percentage of polymorphic loci was 74.61%, whereas with BOX and ERIC primers, it was 60.5 and 55.21%, respectively. Finally, this study is the first report of the isolation of P. syringae pv. morsprunorum race 1 and 2 strains from stone fruit trees in Iran.     

A simple and efficient method for isolation of DNA in high mucilaginous plant tissues

A protocol is described for rapid DNA isolation from Malvaceae plant species and different tissues of Bixaceae that contain large amounts of polysaccharides, polyphenols, and pigments that interfere with DNA extractions. The method is a modification of Dellaporta et al. The current protocol is simple, and no phenolchloroform extraction, ethanol, or isopropranol precipitation is required. The method is based in the incubation of soluble DNA with silica, mix in batch during the extraction. The procedure can be completed in 2 h and many samples can be processed at the same time. DNA of excellent quality was recovered and used for polymerase chain reaction (PCR) amplification, restriction enzyme digestion, and Southern blot analysis. The method was used with healthy Bixa orellana and virus-infected Malvaceae plants.     

Large-scale,cost-effective screening of PCR products in marker-assisted selection applications

A simple, PCR-based method has been developed for the rapid genotyping of large numbers of samples. The method involves a alkaline extraction of DNA from plant tissue using a slight modification of the procedure of Wang et al. (Nucleic Acids Res 21:4153–4154, 1993). Template DNA is amplified using allelespecific associated primers (ASAPs) which, at stringent annealing temperatures, generate only a single DNA fragment and only in those individuals possessing the appropriate allele. This approach eliminates the need to separate amplified DNA fragments by electrophoresis. Instead, samples processing the appropriate allele are identified by direct staining of DNA with ethidium bromide. Total technician time required for extraction, amplification and detection of 96 samples is about 4 h, and this time requirement can be reduced by automation. Excluding labor, cost per sample is less than $0.40. The method is tested using the codominant isozyme marker, alcohol dehydrogenase (Adh-1) gene in pea (Pisum sativum), and applied to the screening of photoperiod genes in common bean (Phaseolus vulgaris L.).     

Isolation of genomic DNA from the earthworm speciesEisenia fetida

Our interest in detecting genotoxic exposure in earthworms led us to isolate high quality DNA from theEisenia fetida species. For that, we compared a modification of the conventional phenol-chloroform extraction procedure, usually refered to as the Maniatis procedure, to two commercially available kits reportedly eliminating multiple partitions in phenol and chloroform, namely the Qiagen and Nucleon protocols. From the 260 nm optical density values, the commercial kits extracts hinted toward higher DNA recovery with those procedures. However, the 260/280 nm ratios indicated that the quality of the DNA isolated with the modified Maniatis procedure was purer than that isolated with the commercial kits, the latter being most probably contaminated by proteins and/or RNA. The Maniatis procedure was slightly modified by the introduction of a potassium acetate step for protein precipitation and by shortening the proteinase K treatment from 12–18 h to only 2 h. The higher quality of the DNA isolated by phenol-chloroform extraction was confirmed by quantification with the fluorescent 3,5-diaminobenzoic acid assay. Preliminary results suggest that the modified Maniatis procedure herein described is not only applicable for DNA adducts studies using³²P-postlabelling techniques but is also suitable for DNA extraction from other earthworm species such asLumbricus terrestris.