Conversion of chromosome-specific RAPDs into SCAR-based anchor markers for onion linkage maps and its application to genetic analyses in other Allium species

Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via cloning and sequencing of RAPD amplicons and designing of 24-mer oligonucleotide primers. Of the eight pairs of SCAR primers, seven resulted in the amplification of single bands of the original RAPDs, and the remaining primer set amplified an additional band. The results of Southern hybridization using RAPD amplicons from genomic DNA of Japanese bunching onion (Allium fistulosum L.)—shallot monosomic addition lines indicated that five SCAR markers were single shallot chromosome-specific markers and were not detected in genomic DNA of A. fistulosum. The eight SCAR primer pairs were applied to other Allium species and exhibited three types of amplification profiles, namely RAPD amplicons observed only in shallot, in shallot and Allium vavilovii, and in several Allium species. A mapping study using 65 F₂ plants generated by the selfing of one interspecific cross A. cepa × Allium roylei individual integrated the SCAR marker SAOE17₅₀₀ into chromosome 5 as expected. The results of the present study show that the eight SCAR primer sets specific to shallot can facilitate the mapping in A. cepa and can also serve as anchor points between maps of different Allium species.     

Characterization of a new fungal antagonist of Phytophthora capsici

The capacity of many microorganisms for antagonism towards pathogens is unknown and previously uncharacterized species may be potentially useful in this respect. This work presents the evaluation of the capacity of a previously uncharacterized Ascomycete, denominated here as UA to protect chili pepper (Capsicum annuum) against Phytophthora capsici, and other soil-borne plant pathogens and establishes the role of UA as a biocontrol agent. Inoculation of UA 2 days before the inoculation of P. capsici led to 77.8% survival of pepper plants. Simultaneous confrontation of both microorganisms in vitro led to 53.1% growth inhibition of P. capsici, while the inoculation of P. capsici 3 days after the inoculation with UA improved growth inhibition up to 73%. Simultaneous confrontation in vitro of UA with Fusarium oxysporum and Fusarium solani led to 41.2 and 50% growth inhibition, respectively, but had no effect on Rhizoctonia solani or a binucleate Rhizoctonia isolate. Moreover, formation of zoosporangia and the germination of zoospores were completely inhibited by exposure to undiluted filter sterilized filtrate. UA produces septate mycelia, but could not be classified in detail due to a lack of spores or reproductive structures. However, sequencing of Internal Transcribed Spacer 1, 2 and the 5.8S genes indicated that this fungus is a member of the Ascomycetes.     

Responses of eight chile peppers to saline water irrigation

Salt tolerance of five cultivars of Capsicum annuum L. Early Jalapeno, Golden Treasure, NuMex Sweet, NuMex Joe E. Parker, and Santa Fe Grande, two cultivars of C. chinense Jacq. Habanero and Pimienta De Chiera, and one accession of C. annuum, NMCA 10652, were evaluated in a field study. Seedlings were transplanted in late May to field raised beds containing loamy sand soils in a semi-arid environment. Plants were well irrigated throughout the experiment. Three saline solution treatments, prepared by adding NaCl, MgSO₄, and CaCl₂ to tap water at different amounts to create three salinity levels of 0.82 dS m⁻¹ (control, tap water), 2.5 dS m⁻¹, and 4.1 dS m⁻¹ electrical conductivity (EC), were initiated on 15th June and ended in late August. Among the eight varieties, NMCA 10652 had the highest survival percentage at 100% in the 4.1 dS m⁻¹ treatment, followed by ‘Early Jalapeno’, ‘NuMex Sweet’, ‘Pimienta De Chiera’, ‘Santa Fe Grande’, ‘Golden Treasure’, and ‘NuMex Joe E. Parker’. ‘Habanero’ had the lowest survival at 28%. Compared to control, final shoot dry weight of the plants irrigated with saline solution at 4.1 dS m⁻¹ was reduced by 92% in ‘Habanero’, followed by ‘Golden Treasure’ at 80%. For fruit fresh weight in 4.1 dS m⁻¹ vs. control, ‘Habanero’ had the highest reduction at 86%, followed by ‘Golden Treasure’ at 74%, while NMCA 10652 and ‘Santa Fe Grande’ had the least at 26% and 19%, respectively. NMCA 10652, the most tolerant to salinity, had the lowest leaf Na⁺ accumulation, while ‘Habanero’, the most sensitive to salinity, had the highest Na⁺ in the leaves. For leaf Cl⁻, ‘Early Jalapeno’ had the highest, while ‘Habanero’ had the lowest Cl⁻ accumulation in the leaves. Generally, sensitive varieties accumulated more Na⁺ and/or Cl⁻ in leaves, except for ‘Early Jalapeno’, which was relatively tolerant to salinity but had high Na⁺ and Cl⁻ accumulation in leaves.     

Towards crop improvement in bell pepper (Capsicum annuum L.): Transgenics (uid A::hpt II) by a tissue-culture-independent Agrobacterium-mediated in planta approach

Agrobacterium tumefaciens-mediated transformation has been one of the methods used to generate transgenic plants in bell pepper. An alternate transformation method that avoids/minimizes tissue culture would be beneficial for the improvement of bell pepper due to its recalcitrant nature. In this report, transgenic bell pepper plants have been developed by a tissue-culture-independent A. tumefaciens-mediated in planta transformation procedure. In the present study, two open pollinated varieties viz., Arka Gaurav and Arka Mohini were used for transformation. Agrobacterium strain EHA105 harboring the binary vector pCAMBIA1301 that carries the genes for β-glucuronidase (uid A) and hygromycin phosphotransferase II (hpt II) was used for transformation. GUS histochemical analysis of T₀ and T₁ plants at various stages of growth followed by molecular analysis using PCR, Southern analysis and RT-PCR allowed selection of transgenics. The method resulted in 17.8% and 11.4% of the T₀ plants in Arka Gaurav and Arka Mohini being selected as chimeric and 35.0% and 29.7%, respectively, were identified as stable transformants in the T₁ generation based on PCR analysis.     

黄瓜种质资源遗传亲缘关系的RAPD分析

利用ＲＡＰＤ技术对多个生态型的黄瓜材料的遗传亲缘关系进行了研究。从２００个１０碱基随机引物中筛选出２０个用于ＰＣＲ反应,３９．２％的扩增条带表现多态性;每个生态型品种都具有其特有的扩增（缺失）带以区别其他生态型品种;聚类分析将供试材料分为３大类群：华北类群、华南类群和欧洲温室类群。从分子水平验证了传统的黄瓜地域分类标准及黄瓜是遗传基础狭窄的蔬菜作物。对利用ＲＡＰＤ技术进行亲缘控制研究的可能性进行了探讨。     

灵芝菌株的DNA指纹分析

CTAB法提取灵芝菌丝体总DNA,再以核糖体DNA转录间隔区（ITSⅡ、IGR IPCR RFLP）结合随机引物扩增多态性（RAPD）标记分析30个灵芝菌株间的亲缘关系.结果表明,ITSⅡ、IGR I-PCR RFLP产生了47条带,其中42条显示出多态性,通过聚类分析将30个菌株分成七大类,包括紫芝、黑灵芝、树舌灵芝、薄树灵芝四大类,以及另外三个无法确定具体归属的类群,但没能将赤芝与松杉灵芝区分开.RAPD从247个随机引物中筛选出8个随机引物,共检测到69个多态性位点并全部显示出多态性,通过聚类分析将供试的30个灵芝菌株全部区分开.     

Genetic diversity in Tunisian olive accessions and their relatedness with other Mediterranean olive genotypes

Eighty-four olive accessions obtained from the National Conservatory of Boughrara-Sfax (Tunisia), previously evaluated for morphological traits, were analysed with 47 random amplified polymorphic DNA (RAPD) markers. They were compared with other olive genotypes originated from Eastern or Western Mediterranean. The highest and lowest similarities between genotypes, estimated by simple matching algorithm, were 0.98 and 0.40, respectively. A dendrogram based on Ward's method and a factorial correspondence analysis (FCA) showed that most of Tunisian accessions are closely related to olive genotypes originating from the Eastern Mediterranean and some are clustering with genotypes originated from the Western Mediterranean. These findings suggested multiple and complex origin of Tunisian olive. A comparative study between a previous morphological analysis and current RAPD assay was carried out and discussed.     

Induced synthesis of caffeoylserotonin in pepper fruits upon infection by the anthracnose fungus, Colletotrichum gloeosporioides

Caffeoylserotonin (CaS) is a serotonin derivative that belongs to the family of phenylpropanoid amides, but has not previously been identified in plants. In this study, pepper fruits challenged with the anthracnose fungus, Colletotrichum gloeosporioides, were found to synthesize CaS, which accumulated at concentrations of up to 2.3 μg/g fresh weight. The induction of CaS was accompanied by the upregulation of both 4-coumarate-CoA ligase (4CL) and serotonin N-hydroxycinnamoyl transferase (SHT) in unripe pepper fruits. However, no induction of SHT and 4CL was observed in ripe pepper fruits consistent with the lower level of CaS production.     

Confirmation of Clematis hybrids using molecular markers

The hybrid origin of progeny from crosses of Clematis tubulosa and Clematis brevicaudata was investigated using randomly amplified polymorphic DNA (RAPD) and single nucleotide polymorphisms (SNPs) from sequence analysis of chloroplast rbcL, accD genes, and the C. brevicaudatamatK gene. Plants collected from three and four populations of C. brevicaudata (C. brev) and C. tubulosa (C. tubu), respectively, from Mt. Songshan, Beijing, China were used as parents for hybridization. Morphological characters of pollen, seeds, and leaves were recorded in 2007. DNA from leaf samples of both parents and of C. brev × C. tubu and C. tubu × C. brev were extracted, and used for RAPD and SNPs from sequence data. A dendrogram was constructed by the branching neighbor-joining (IB-NJ) method. Proportionate population scores were generated by the admixture model using the STRUCTURE software. Based on morphological characters, C. brevicaudata was quite uniform. However, variations were detected in C. tubulosa. Hybrids of C. brev × C. tubu and C. tubu × C. brev showed intermediate morphological characters of the parents. Accessions of C. tubu × C. brev were clustered into 2 groups, with the majority of hybrids belonging to group IV b in the RAPD dendrogram, suggesting that this resulted from variations within C. tubulosa. In general, the hybrid origin of all progeny characterized by morphological characters was supported by the RAPD and SNPs data. These results indicate that RAPD results supported by SNPs data will be useful tool to verify hybrids.     

Agronomic characteristics and carotenoid content of five Bola-type paprika red pepper (Capsicum annuum L.) cultivars

The production of sweet paprika in Spain uses exclusively fruit of Bola-type Capsicum annuum L. This work describes the evaluation of the agronomic behaviour of five new cultivars of the Bola-type paprika red pepper, selected in the Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA), and grown in Extremadura for 3 years. The colour and the pigment content of the paprika elaborated following the traditional procedure of La Vera were also studied.     

RAPD analysis of genetic diversity among and within Portuguese landraces of common white bean (Phaseolus vulgaris L.)

Seventeen landraces of common beans (Phaseolus vulgaris L.) sampled in the North and Centre of Portugal were analyzed at population level for 689 RAPD loci amplified by using forty random primers. The two different parameters used to estimate the genetic variability in and between samples indicate that the inter-population component of the genetic variability is mainly responsible for the diversity found, since only about a 10% would be of an intra-population nature. In addition, the gametic disequilibrium was estimated and reached an average value of 40% for the different combinations of pairs in the 689 loci studied taking the 17 samples as a whole population. Self-pollination, genetic drift and adaptation would thus be favouring the formation of multilocus associations. In addition, the fingerprinting study suggests that each landrace produced unique amplification products allowing it to be distinguished from the other tested genotypes, but, nevertheless, the landraces show a considerable genetic similarity (56% and 70.5% using two different methods). The Neighbour-Joining dendrogram did not show any relation between the geographical distribution of landraces and genetic distance. The results suggest that these Portuguese landraces conserved an important genetic diversity that can be useful to widen the genetic base of currently cultivated beans.     

秀珍菇菌株遗传差异研究初报

分析了在不同国家和地区栽培的８个秀珍菇株的农艺性状,利用现代分子生物学技术扩增获得秀珍菇菌株ＲＡＰＤ的ＤＮＡ指纹图谱,并构建其树状遗传聚类图。结果表明,这些菌株存在较大的遗传差异。     

DNA content,morphometric and molecular marker analyses of Citrus limonimedica, C. limon and C. medica for the determination of their variability and genetic relationships within the genus Citrus

This work investigated the fingerprinting and phenotyping of Citrus germplasm; species selected were of historical importance belonging to Citrus limonimedica Lush. and its supposed ancestors, along with some other species of the Citrus genus. An integrated approach based on the exploitation of nuclear DNA content, morphological traits and molecular markers, such as RAPD fingerprints and ITS-based SNPs, was employed. We studied a core collection of 54 distinct accessions, including 43 genotypes of the Citrus species (18 species or supposed species) and 11 genotypes of the Poncirus genus, which was used as the reference outgroup. Morphological trait analysis and statistical analysis of DNA content and markers were useful for reconstructing a Citrus phylogeny. In particular, our experiments aimed at estimating the genetic variation within and the genetic relatedness among C limon (L.) Burm., C. limonimedica and C. medica L. to shed light on the hybrid origin hypothesis of C. limonimedica. The results of the multidisciplinary analyses allowed us to confirm a remarkable differentiation between Poncirus and Citrus genera and to highlight a close relationship among the three investigated Citrus species but a distinct difference between these three species and other species in the Citrus genus. RAPD fingerprints and ITS polymorphisms enabled us to point out a variation gradient between lemon and citron, with C. limonimedica as a possible intermediate species. Some accessions of C. medica and C. limonimedica that deviate from such a trend suggest recurrent introgression and/or hybridisation with other species of Citrus.     

Genetic variation and its relationship to root weight in the sweet potato as revealed by RAPD analysis

The aim of this work was to evaluate the genetic variations of the sweet potato by a random amplified polymorphic DNA (RAPD) assay with emphasis on correlations with morphological traits. Cuttings of superior and inferior lines derived from tissue culture-regenerated plants and asexually propagated plants of the Tainung 57 (TN57) and Tainung 66 (TN66) sweet potato were planted in the field. Three important agronomic traits, top weight, root weight, and root numbers, were measured 3 months after planting. The RAPD-PCR (polymerase chain reaction) technique was used for detecting genomic variations within and between varieties. Of the 160 primers tested in this study, 38 revealed clear and repeatable RAPD polymorphisms. Among the 38 primers, 8 showed consistent amplified band patterns among the plants with variations within and between varieties, while the others indicated polymorphisms within or between varieties. RAPD markers demonstrated a clear association with root weight. However, the presence and absence of these genetic markers did not correspond well with either the top weight or root number. Genetic instability revealed in the selection stress of superior and inferior plants was found to be independent of variety. In addition, both asexual propagated and tissue culture-induced somaclonal variations were observed in this study. Our results show that RAPD is a useful tool for detecting somaclonal variations from varietal and intra-varietal sweet potato for monitoring of DNA changes in somaclonal variants. The identification of regions which are associated with the character of root weight by RAPD markers enables us to use these markers as selection tools to improve root weight in sweet potato.     

Micropropagation of Capsicum frutescens L. using axillary shoot explants

A novel micropropagation protocol was established for Capsicum frutescens L. cv. ‘Uchithi’, a pungent chilli cultivar, through induction of axillary shoot proliferation of in vitro raised plantlets by decapitation and using the axillary shoots as explants for multiple shoot bud induction. About 2–6 axillary shoots were induced within 2 weeks when 4-week-old in vitro raised plantlets were decapitated. The axillary shoot-tip explants produced multiple shoot buds when cultured on Murashige and Skoog's (MS) medium containing 8.8–44.4 μM 6-benzylaminopurine (BAP) or 9.3–46.7 μM kinetin alone or 8.8–44.4 μM BAP with 4.6 μM kinetin or 5.7 and 28.5 μM indole-3-acetic acid (IAA). Maximum number of shoots (5.6) were induced on medium containing 22.2 μM BAP in combination with 4.65 μM kinetin. The separated shoots rooted and elongated on medium containing 2.8 μM IAA or 2.4–4.9 μM indole-3-butyric acid (IBA). Rooted plantlets were successfully established in the soil. Efficient mass multiplication of this important food crop was achieved.     

Interspecific variations in seed germination of Corylopsis

This study was initiated to investigate the differences in germination percentages and rates between Corylopsis coreana Uyeki and Corylopsis sinensis var. calvescens Rehder & E.H. Wilson following a warm stratification (WS) and cold stratification (CS), and to study the effect of different WS temperatures interacting with different durations of CS. Warm stratification at 10 °C, 15 °C, 20 °C, and 25 °C was given for 1 month (1 M 10 °C, 15 °C, 20 °C, and 25 °C WS) followed by 0 M, 1 M, 2 M, and 3 M of CS at 5 °C (0 M, 1 M, 2 M, 3 M CS) and seeds were germinated in an air conditioned greenhouse maintained at 18.5 °C/18 °C. On average, less than 1% of C. coreana seeds germinated when sown without any WS and CS or with 1 M 15 °C, 20 °C, and 25 °C WS without CS treatment. However, 26% C. coreana seeds germinated after 1 M 10 °C WS without any CS treatment. Germination was not affected by WS temperatures when followed by 2 M 5 °C CS. It is concluded that C. coreana exhibited low seed germination at 10 °C and that this temperature could be considered the upper limit of CS for C. coreana. Only 2 M CS was required for more than 90% seeds to germinate. However, C. sinensis var. calvescens required longer than 3 M CS for more than 29% seeds to germinate. This clearly shows that there is an interspecific variation in optimum dormancy-breaking requirements.     

利用RAPD技术评估金针菇种质资源

本文利用20个10核苷酸的随机引物对来源不同而具有代表性的16个金针菇菌株进行了RAPD分析研究。结果表明:所测试的20个随机引物中有6个引物的扩增产物DNA片断表现出明显的多态性,对所有供测试的金针菇菌株总共扩增出84条具重复性的DNA片断;同时也显示供试的16个金针菇菌株两两间的遗传相似性变化较大(相似系数从0.0592到0.8000)。另外,采用系统聚类法中的类平均法,对供试的16个菌株两两间的相似系数进行聚类,可将它们分为四大类,各大类的类间和类内菌株的遗传变异程度较大,其中以Ⅳ类内各菌株间的最高(平均相似系数为0.4353),Ⅰ类和Ⅱ类间各菌株间的最低(平均相似系数为0.6812)。但是,从整个被测试的16个金针菇菌株来看,它们之间的遗传变异并不丰富(总平均相似系数为0.5292)。同时,将RAPD技术应用于不同菌株间遗传差异的研究,具有反应迅速、不受外界环境条件影响、能从DNA分子水平上揭示菌株间的遗传差异等优点。因此,RAPD分析技术是一种快速准确评估食用菌种质资源的有效方法。     

Pollination with laser-irradiated pollens breaks cross-incompatibility between zicaitai (Brassica campestris var. purpurea) and ornamental kale (Brassica oleracea var. acephala) to produce hybrids with the aid of ovule culture

The objective of this study was to produce interspecific hybrids between an Ogura-cytoplasmic male sterile (CMS) line of zicaitai (Brassica campestris var. purupurea, 2n = 20) and cultivars of ornamental kale (Brassica oleracea var. acephala, 2n = 18) to develop a CMS system for hybrid seed production. Pollination with pollen grains of ornamental kales irradiated at a power output of 9.0 mW with a He–Ne laser for 3 min could overcome the cross-incompatibility between the species concerned. Intact hybrids could be efficiently produced from ovules cultured on Murashige and Skoog media supplemented by 0.2 mg l⁻¹ 6-benzyladenine. Chromosome number of hybrids was confirmed to be 2n = 19. Hybrids resembled ornamental kales in leaf morphology and in vernalization response. Pollens of hybrids had a sterile appearance. Moreover the hybridity of the putative hybrids was confirmed by RAPD data on a DNA fragment of 820 bp.     

Screening Capsicum species of different origins for high temperature tolerance by in vitro pollen germination and pollen tube length

Successful fruit set depends on several reproductive processes including pollen germination and tube growth processes. An experiment was conducted to determine the effects of temperature on pollen germination characteristics and to identify species/genotypic differences in Capsicum using the cumulative temperature response index (CTRI) concept. Pollen was collected from plants of seven genotypes from five Capsicum species, adapted to various parts of the world and grown outdoors in large pots. The pollen was subjected to in vitro temperatures ranging from 15 to 50 °C at 5 °C intervals. Pollen germination and tube lengths were recorded for all species after 24 h of incubation at the respective treatments. Species/genotypes differed significantly for in vitro pollen germination percentage and pollen tube length with mean values of 78% and 734 μm, respectively. The mean cardinal temperatures (T_min, T_opt, and T_max) averaged over genotypes, were 15.2, 30.7, and 41.8 °C for pollen germination and 12.2, 31.2, and 40.4 °C for pollen tube growth. The CTRI of each species/genotype calculated as the sum of eight relative individual stress response values, such as maximum pollen germination, maximum pollen tube length; T_min, T_opt, and T_max temperatures of pollen germination, and pollen tube lengths, identified species tolerance to high temperatures. Capsicum annum cv. Mex Serrano from Mexico was identified as tolerant, C. chacoense cv. 1312 and C. spp. cv. Cobanero from Argentina and Guatemala, respectively as intermediate and C. frutescens cv. Early Spring Giant from China, C. annum cv. Long Green from South Korea, C. spp. cv. NM89C130 and C. pubescens cv. 90002 from Guatemala as sensitive to high temperatures. The tolerant species/genotypes can be used in breeding programs to develop new genotypes that can withstand high temperature conditions both in the present climate and particularly in a future warmer climate.     

Genetic structure of Buxus sinica var. parvifolia, a rare and endangered plant

Buxus sinica var. parvifolia, a rare and endangered tree species in some semitropics alpine areas of China, plays an important role in the maintenance of the landscape and ecosystem. In this study, RAPD and ISSR markers were used to investigate the genetic diversity and structure of five natural populations and one tamed population of B. sinica var. parvifolia. 21 RAPD primers amplified 209 bands with 167 (79.90%) polymorphic and 21 ISSR primers amplified 518 bands with 467 (90.15%) polymorphic. The genetic diversity, estimated by Shannon’ index, was 0.4343 (by RAPDs) and 0.3661 (by ISSRs). Both RAPD and ISSR analyses revealed a high level of genetic diversity in natural populations of B. sinica var. parvifolia. Furthermore, analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations. The proportion of variation attributable to within-population differences was very high (69.2% by RAPDs; 84.51% by ISSRs). Moderate differentiation was detected among populations using RAPDs (30.80%), while only a small amount of variation (15.49%) was detected among populations using ISSRs. We suggest that the present genetic structure is due to high levels of environmental variability and gene flow, which still need further study to confirm. Conservation measures are suggested, including in situ and ex situ strategies, based on the observed population genetic information.