Genetic diversity of Pistachio (Pistacia vera, Anacardiaceae) Germplasm based on Randomly Amplified Polymorphic DNA (RAPD) markers

We used Randomly Amplified Polymorphic DNA (RAPD) markers to examine patterns of relatedness among 29 pistachio (Pistacia vera L.) cultivars and accessions. These included 13 cultivars that we had previously described, and an additional 16 items from the USDA National Clonal Germplasm Repository/Davis comprising cultivars and land races originating further east of the cultivars described previously, and material from wild P. vera stands in or near the putative center of origin for pistachio in South Central Asia. The results show high levels of polymorphism in the species emphasizing the importance of preservation of the remaining wild stands of P. vera. Analyses support the concept that cultivars in use west of the Zagros-Caucasus ranges likely originate from a limited germplasm base. The newly examined cultivated material shows greater genetic diversity, consistent with the hypothesis that pistachio cultivation originated in or near South Central Asia. Results also indicate that for at least two cases, material identified differently in two collections are the same clones, thus illustrating the value of molecular marker techniques in describing and maintaining germplasm collections for clonally propagated species.

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Résumé  En este trabajo se ha empleado la técnica del ADN polimórfico amplificado al azar (RAPD) para examinar la similitud genética entre 29 cultivares y accesiones de pistachero (Pistacia vera L). Este material incluye 13 cultivares considerados en un trabajo anterior y 16 nuevas accesiones del Banco Nacional de Germoplasma Clonal del USDA en Davis que incluyen cultivares y razas locales de regiones más orientales que las consideradas anteriormente así como material procedente de basques naturales de P. vera situados en las proximidades del presunto centro de origen del pistachero. Los resultados obtenidos muestran un alto grado de polimorfismo, lo que indica la necesidad de conservar el germoplasma de P. vera todavía existente en estado natural. Además se confirma la hipótesis de que los cultivares procedentes del oeste de la zona Caucásica y del Zagros se originaron a partir de una base genética limitada. El nuevo material estudiado muestra una mayor diversidad genética lo que corrobora la idea de que el cultivo del pistachero se inició en Asia Central. Al menos en dos de los casos estudiados, el material identificado en dos colecciones diferentes como distintos genotipos, en realidad se trata del mismo clon, lo que demuestra la utilidad de los marcadores moleculares en la descripción y mantenimiento de colecciones de germoplasma en especies de reproducción vegetativa.

     

Pistillate and staminate flower development in dioecious Pistacia vera (Anacardiaceae)

The development of staminate and pistillate flowers in the dioecious tree species Pistacia vera L. (Anacardiaceae) was studied by scanning electron microscopy with the objective of determining organogenetic patterns and phenology of floral differentiation. Flower primordia are initiated similarly in trees of both sexes. Stamen and carpel primordia are initiated in both male and female flowers, and the phenology of organ initiation is essentially identical for flowers of both sexes. Vestigial stamen primordia arise at the flanks of pistillate flower apices at the same time functional stamens are initiated in the staminate flowers. Similarly, a vestigial carpel is initiated in staminate flowers at the same time the primary, functional carpel is initiated in pistillate flower primordia. Differences between the two sexes become apparent early in development as, in both cases, development of organs of the opposite sex becomes arrested at the primordial stage. Male flowers produce between four and six mature functional stamens and female flowers produce a gynoecium with one functional and two sterile carpels.     

In vitro Micrografting of Mature Pistachio (Pistacia vera var. Siirt)

The success of various in vitro micrografting methods of shoot tips of pistachio (Pistacia vera L. var. Siirt) have been examined. Excised zygotic embryos that germinated in vitro were used as rootstocks. Current year shoot tips from mature trees of pistachio micrografted onto in vitro juvenile rootstocks, resulted in the restoration of shoot-bud proliferation. Variables tested include a size of microscion, grafting method, effects of culture medium and effects of time of the year at which shoot tips were used. The results indicate that the easiest and most successful method for grafting was slit micrografting. High levels of micrograft take were achieved with 2–4 mm (56.75%) and 4–6 mm (79.25%) long scions obtained from the regenerated shoot tips. The survival rate of the shoot tips was directly related to time of the year. The best growth of microscion was obtained with the in vitro forced shoot tips rather than with shoot tips excised from tree. Slow growth and lack of axillary shoot development on the micrografts was noticeable when the micrografts were cultured on hormone-free and germination medium. In vitro micrografted plantlets were successfully weaned and no problems were encountered with the establishment of micrografted plants in vivo.     

RAPD analysis of the genetic diversity of mango (Mangifera indica) germplasm in Brazil

We evaluated genetic variability of mango (Mangifera indica) accessions maintained in the Active Germplasm Bank of Embrapa Meio-Norte in Teresina, Piauí, Brazil, using RAPDs. Among these accessions, 35 originated from plantings in Brazil, six from the USA and one from India. Genomic DNA, extracted from leaf material using a commercial purification kit, was subjected to PCR with the primers A01, A09, G03, G10, N05, and M16. Fifty-five polymorphic loci were identified, with mean of 9.16 ± 3.31 bands per primer and 100% polymorphism. Application of unweighted pair group method using arithmetic average cluster analysis demonstrated five genotypic groups among the accessions examined. The genotypes Rosa 41, Rosa 48 and Rosa 49 were highly similar (94% similarity), whereas genotypes Sensation and Rosa 18 were the most divergent (only 7% similarity). The mango accessions were found to have considerable genetic variability, demonstrating the importance of analyzing each genotype in a collection in order to efficiently maintain the germplasm collection.     

The comparison of RFLP,RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis

The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.Abbreviations RFLP restriction fragment length plymorphism - RAPD random-amplified polymorphic DNA - AFLP amplified fragment length polymorphism - SSR simple sequence repeat - PCR polymerase chain reaction - TBE Tris-borate-EDTA buffer - MI marker index - SENA sum of effective numbers of alleles     

The genetic analysis and germplasm identification of the gametophytes of Undaria pinnatifida (Phaeophyceae) with RAPD method

Eleven pairs of Undaria pinnatifida (Harv.) Suringar gametophytes were identified with random amplified polymorphic DNA (RAPD) technique. After screening 100 primers, 20 ten-base primers were determined for the RAPD analysis. A total of 312 polymorphic loci were obtained, of which 97.7% were polymorphic. The primer S198 was found to distinguish all the selected Undaria pinnatifida gametophytes. The genetic distances between each two of the twenty-two U. pinnatifida gametophytes ranged from 0.080 to 0.428, while the distances to the Laminaria was 0.497 on average. After reexamination, two sequences characterized amplification region (SCAR) markers were successfully converted, which could be applied to U. pinnatifida germplasm identification. All these results demonstrated the feasibility of applying RAPD markers to germplasm characterization and identification of U. pinnatifida gametophytes, and to provide a molecular basis for Undaria breeding.     

Determination of genetic diversity among Saccharina germplasm using ISSR and RAPD markers

Various species of genus Saccharina are economically important brown macroalgae cultivated in China. The genetic background of the conserved Saccharina germplasm was not clear. In this report, DNA-based molecular markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) were used to assess the genetic diversity and phylogenetic relationships among 48 Saccharina germplasms. A total of 50 ISSR and 50 RAPD primers were tested, of which only 33 polymorphic primers (17 ISSR and 16 RAPD) had an amplified clear and reproducible profile, and could be used. Seventeen ISSR primers yielded a total of 262 bands, of which 256 were polymorphic, and 15.06 polymorphic bands per primer were amplified from 48 kelp gametophytes. Sixteen RAPD primers produced 355 bands, of which 352 were polymorphic, and 22 polymorphic bands per primer were observed across 48 individuals. The simple matching coefficient of ISSR, RAPD and pooled ISSR and RAPD dendrograms ranged from 0.568 to 0.885, 0.670 to 0.873, and 0.667 to 0.862, revealing high genetic diversity. Based on the unweighted pair group method with the arithmetic averaging algorithm (UPGMA) cluster analysis and the principal components analysis (PCA) of ISSR data, the 48 gametophytes were divided into three main groups. The Mantel test revealed a similar polymorphism distribution pattern between ISSR and RAPD markers, the correlation coefficient r was 0.62, and the results indicated that both ISSR and RAPD markers were effective to assess the selected gametophytes, while matrix correlation of the ISSR marker system (r = 0.78) was better than that of the RAPD marker system (r = 0.64). Genetic analysis data from this study were helpful in understanding the genetic relationships among the selected 17 kelp varieties (or lines) and provided guidance for molecular-assisted selection for parental gametophytes of hybrid kelp breeding.     

Genetic relatedness of Brazilian Colletotrichum truncatum isolates assessed by vegetative compatibility groups and RAPD analysis

The genetic variation among nine soybean-originating isolates of Colletotrichum truncatum from different Brazilian states was studied. Nitrate non-utilizing (nit) mutants were obtained with potassium chlorate and used to characterize vegetative compatibility reactions, heterokaryosis and RAPD profile. Based on pairings of nit mutants from the different isolates, five vegetative complementation groups (VCG) were identified, and barriers to the formation of heterokaryons were observed among isolates derived from the same geographic area. No complementation was observed among any of the nit mutants recovered from the isolate A, which was designed heterokaryon-self-incompatible. Based on RAPD analysis, a polymorphism was detected among the wild isolate C and their nit1 and NitM mutants. RAPD amplification, with five different primers, also showed polymorphic profiles among Brazilian C. truncatum isolates. Dendrogram analysis resulted in a similarity degree ranging between 0.331 and 0.882 among isolates and identified three RAPD groups. Despite the lack of a correlation between the RAPD analysis and the vegetative compatibility grouping, results demonstrated the potential of VCG analysis to differentiate C. truncatum isolates genotypically similar when compared by RAPD.     

小麦耐盐种质遗传多样性的RAPD分析

选用２２个引物对２４份小麦耐盐种质进行ＲＡＰＤ分析,共产生２００条扩增片段,多态性片段数为１７２条,扩增片段的多态性百分率为８６％,利用ＮＹＳＴＳ软件根据Ｊａｃｃａｒｄ系统分析ＲＡＰＤ结果,并按ＵＰＧＭＡ类平均法进行聚类。２４份材料相似系数在０．２１￣０．９７之间,其中含有多枝赖草、黑麦和偃麦草等外源染色体的多１７４、ＷＲ８３０和南前１２７被分别在３个独立的组,多１７４和南前１２７的亲关系最远,相     

三个地理群体赤眼鳟遗传多样性的RAPD分析

利用RAPD技术对宿鸭湖、青龙湖和丹江口水库3个野生赤眼鳟群体的遗传多样性进行分析.9个RAPD引物共获得93个扩增位点,其中多态位点56个,多态位点比例为60.22%.3个群体的多态位点比例分别为53.01%、54.12%和57.95%,遗传距离分别为0.1548、0.1613和0.1764,Shannon信息指数分别为0.2249、0.2318和0.2437.群体间遗传距离以宿鸭湖和青龙湖群体最近(0.1257),青龙湖与丹江口水库群体最远(0.1416).结果表明3个赤眼鳟群体的遗传多样性均较丰富,但群体间地理遗传分化差异并不明显.     

Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers

Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.     

Genetic relatedness of Portuguese almond cultivars assessed by RAPD and ISSR markers

Randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to analyse the genetic diversity of Portuguese Prunus dulcis cultivars and their relationship to important foreign cultivars. Of the primers tested, 6 (out of 60) RAPD and 5 (out of 18) ISSR primers were selected for their reproducibility and high polymorphism. Out of 124 polymerase chain reaction fragments that were scored, 120 (96.8%) were polymorphic. All the plants could be discriminated and constitute a very heterogeneous group. Five unidentified almond plants found in the region of Foz Côa (north Portugal) and wild almond (P. webbii) from Italy and Spain were also included. Four main groups of plants could be distinguished: P. dulcis cultivars; one Foz Côa plant; P. webbii; and P. persica (outgroup). The segregating Foz Côa plant may represent a feral individual or a hybrid between P. dulcis and P. webbii.Abbreviations dNTP Deoxynucleotide triphosphate - CTAB Cetyltrimethylammonium bromide - ISSR Inter-simple sequence repeats - PCR Polymerase chain reaction - RAPD Randomly amplified polymorphic DNA - RASTM Regional Agricultural Services of Trás-os-Montes - TE Tris-EDTA buffer - UPGMA Unweighted pair group method with arithmetical averagesCommunicated by P. Puigdoménech     

Genetic diversity inChaenomeles (Rosaceae) revealed by RAPD analysis

Genetic relatedness inChaenomeles was studied by RAPD analysis in 42 plants representing accessions of three wild species and one hybrid taxon. Amplification with 17 primers yielded a total of 156 polymorphic RAPD bands. Estimates of genetic relatedness suggest thatC. cathayensis andC. japonica are the most distantly related species, and that the former is comparatively homogeneous.Chaenomeles speciosa, which may have arisen through hybridization betweenC. cathayensis andC. japonica, takes an intermediate position between these two species. Analysis of diagnostic bands demonstrate that neitherC. speciosa norC. ×superba has any bands that do not occur in at least one ofC. cathayensis orC. japonica. Moreover,C. speciosa and the partly overlapping taxonC. ×superba are comparatively heterogeneous, which is also in accordance with a hybrid origin. Intraspecific variation was studied mainly inC. japonica; plants obtained from different sources of material formed well separated groups in the cluster analysis.     

Vegetative anatomy of Pachycortnus (Anacardiaceae)

Pachycormus discolor , an arborescent desert perennial endemic to Baja California, has small, pinnately compound, hypostomatic, bifacial leaves produced on short shoots and photosynthetic stem phelloderm covered by exfoliating translucent phellem. Tightly packed laminal palisade cells are filled with tannins and lack chloroplasts. Spongy mesophyll is the major photosynthetic tissue. Leaves possess unicellular trichomes with secondary walls and uniseriate trichomes with glandular heads. Schizogenous resin ducts occur in primary phloem of stems, leaves and roots as well as all living tissues of the bark. Developmental studies reveal that initiation and differentiation of foliar primordia resembles that of other dicotyledons except that tannin cells and secretory ducts arise precociously. Primary vasculature is an open sympodial system with three principal traces diverging toward each foliar primordium. The wood is highly specialized and comprises mostly unlignified cells packed with starch grains. Thick bark is mainly produced as annual layers of secondary phloem marked by a ring of secretory ducts each surrounded by tannin cells. The possible adaptive significance of these unusual anatomical features is discussed.     

Identification of hazelnut (Corylus avellana) cultivars by RAPD analysis

The random amplified polymorphic DNA (RAPD) technique offers a useful tool to detect DNA polymorphisms. It can also be used to distinguish different clones and cultivars. We have developed a comprehensive RAPD-based procedure for the routine molecular typing of various plants. Here we report the application of this technique for the correct identification of six hazelnut cultivars (Corylus avellana) widespread in the Campania region (south Italy). The analysed hazelnut cultivars were successfully distinguished by their RAPD fingerprints using the DNA primers U2, U3, U4, U11 and U14. However, in each cultivar we observed very low genetic heterogeneity among the clonal variants. Since this technique is among the simplest and easiest methods used to fingerprint DNA, it could be easily transferred to less sophisticated laboratory infrastructures (e.g. outstations of crop regulatory agencies). Received: 20 December 1997 / Revision received: 6 August 1998 / Accepted: 13 November 1998     

In vitro conservation and cryopreservation of mature pistachio (Pistacia vera L.) germplasm

As genetic erosion of pistachio (Pistacia vera L.) has been occurring in the Mediterranean, Central and West Asia and North Africa, experiments were conducted to conserve two cultivars (‘Atl?’ and ‘Siirt’) of mature pistachio germplasm by assessing both medium- and long-term conservation techniques. In medium-term conservation, our results showed that it was feasible to conserve both cultivars in the form of either microshoots or encapsulated shoot apices up to 12 months at 4°C in the dark. As regards long-term conservation, encapsulation-dehydration and droplet-vitrification techniques were assessed for cryopreservation of cold-hardened and osmoprotected shoot apices of mature ‘Atl?’ cultivar. Among the methods tested, 13.6% of regrowth was achieved with incubation of explants in the droplets of vitrification solution for 150 min at 0°C followed by direct immersion in liquid nitrogen (LN), rapidly thawed and then cultured on Murashige and Skoog’s (MS) medium containing 1 mg L^?1 BA and 0.5 mg L^?1 GA_3. The developed droplet-vitrification technique appeared as a promising procedure for long-term preservation of shoot apices of mature pistachio germplasm. Moreover, assesment of genetic fidelity by Random Amplified Polymorphic DNA analysis (RAPD) revealed out high levels of genetic stability between donor plant and cryopreserved plants (similarity indexes between 0.959 and 0.973) after they were subcultured for at least 3 months. The detected low level of genetic instability could be due to the toxic effect of PVS2 and regeneration phase. The optimized conservation techniques, especially slow growth storage, could be applied to preserve other Pistacia species.     

Inflorescence structure and affinities of Laurophyllus (Anacardiaceae)

WANNAN, B. S. & QUINN, C. J., 1992. Inflorescence structure and affinities of Laurophyllus (Anacardiaceae). The inflorescence structure, pollen and floral anatomy are investigated in Laurophyllus . The inflorescence is a panicle sensu Briggs & Johnson, but with marked differences between the male and female. Sistergroup comparison with the Burseraceae indicates that the plesiomorphic inflorescence in the Anacardiaceae is a thyrsoid, the apomorph being the panicle. Laurophyllus has Rhus -type pollen and therefore has no close affinity with Dobinea or Campylopeialum . Floral anatomy reveals that Laurophyllus is unicarpellary with a dorsally attached style and an apically attached ovule. These characters suggest that rather than being related to Anacardium or Mangifera , it has some affinity with Blepharocarya or perhaps with one of the poorly known African or Madagascan genera.     

Karyotype differentiation among Spondias species and the putative hybrid Umbu-cajá (Anacardiaceae)

Spondias L. comprises at least nine Neotropical species, including the widely cultivated S. monbim and S. tuberosa. Umbu‐cajá, a putative hybrid between these two species, is also grown. In this paper, the karyotypes of five Spondias species and Umbu‐cajá were analysed for evidence of this hybridization. Chromosome banding with chromomycin A₃ and the distribution of 5S and 45S rDNA sites were used to characterize the plants, also genomic in situ hybridization using nuclear DNA from both putative parents and the hybrid as probes. All material presented the same chromosome number (2n = 32) and morphology, but differed in the number and distribution of bands. Spondias monbim and S. tuberosa, the supposed relatives of Umbu‐cajá, displayed similar banding patterns, with five to six chromosome pairs having terminal bands, whereas Umbu‐cajá exhibited bands on both members of nine chromosome pairs. The three other species, S. venulosa, S. cytherea and S. purpurea, showed less closely related karyotypes, with bands in 12–18 chromosome pairs. In situ hybridization with 5S and 45S rDNA probes revealed one site of each probe per haploid chromosome complement in all material. However, in S. tuberosa, the location of 5S rDNA was different from the other species and found no counterpart in Umbu‐cajá. Several tests with total DNA from S. mombin and S. tuberosa against metaphase chromosomes of Umbu‐cajá failed to differentiate the individual genomes in the hybrid. From the chromosome banding and the distribution of rDNA sites, as well as from the genomic in situ hybridization, it seems clear that Umbu‐cajá is related closely to S. monbim and S. tuberosa, but it is karyotypically homozygous and distinct from theses other species. Karyotypically, the three other investigated species were related less closely to Umbu‐cajá. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155 , 541–547.     

Determination of variability in monosporidial lines of Tilletia indica by RAPD analysis

Genetic variability in 23 monosporidial lines developed from five isolates of Tilletia indica causing Karnal bunt of wheat isolated from four wheat growing states of India was determined by using 19 rapid amplified polymorphic DNA (RAPD) markers. Amplification profile generated with all the 19 primers produced 3–16 numbers of bands of 1.5–5 kb size. High level of polymorphism (95.2%) suggested wide range of variability. Maximum Jaccard's similarity coefficient (80%) was observed between KB2MsB and KB2MsC followed by KB5MsC and KB5MsE with 75% similarity, whereas it was minimum between KB3MsA and Kb4MsB (47%). The dendrogram derived from the fingerprint analysis with 19 RAPD primers by using UPGMA showed different levels of genetic similarity among monosporidial lines. At 35% genetic similarity, the monosporidial lines were grouped in two clusters. Some primers, viz., OPN-1, OPN-6, OPN-9, OPN-12, OPN-13, OPN-18, OPM-2, OPM-8, OPM-10, OPB-8, OPB-17 and OPB-20 showed 100% polymorphism. The RAPD fingerprint generated by OPN-1 and OPM-3 were analysed and showed high range of variation in genetic make-up of monosporidial lines.     

Strains differentiation of Microsporum canis by RAPD analysis using (GACA)4 and (ACA)5 primers

Molecular analysis of dermatophytes (based on PCR fingerprinting) revealed high clonal differentiation between the genus and species. Microsporum canis (zoophilic dermatophyte, belonging to genus Microsporum), responsible for most cases of tinea capitis in children, tinea corporis in adults and dermatophytoses in cats, is very unique in comparison with other dermatophytes. Results of most molecular studies show that there is no clonal differentiation within M. canis as distinct from other species. The aim of this study was application of (GACA)4 repetitive primer and (ACA)5 primer for typing of M. canis strains isolated from human and animals in Central Poland. Fungal strains: 32 clinical isolates of M. canis, originated from patients from Central Poland; 11 strains isolated from infected cats (6) and dogs (7), reference strains of M. canis (CBS 113480), T rubrum (CBS 120358), T mentagrophytes (CBS 120357) and E. floccosum (CBS 970.95). The genomic DNAs of the strains were used as a template in RAPD reaction. No differentiation was observed for the analyzed M. canis strains using (GACA)4 and (ACA)5 typing.