Relationships Among some Pears Genotypes (Pyrus Communis L.) Based on ISSR and RAPD Analysis

Thirty one pears genotypes from east blacksea region were evaluated for genetic relationships by using Randomly Amplified Polymorphic DNA (RAPD) and ISSR (Inter-Simple Sequence Repeats) markers from total 70 RAPD and ISSR primer investigated, 22 could amplify clearly and consistently. Cluster analysis of the pears genotypes was performed based on data from polymorphic bands RAPD and ISSR by using Jaccard’s similarity coefficient and the Unweighted pair-group method with arithmetic average (UPGMA) clustering method. The 31 pear genotypes were classified into two major groups. Cluster A was divided into 2 subclusters: Gumushane pears and Trabzon pears. Cluster B consisted of Artvin pears. The similarity matrix values ranged between 0.105 and 0.968.     

RAPD markers reveal polymorphism among some Iranian pomegranate (Punica granatum L.) genotypes

In this study RAPD markers were used to determine the diversity level among 24 Iranian pomegranate genotypes. One hundred decamer random primers were used for PCR reactions, among which 16 showed reliable polymorphic patterns. These primers produced 178 bands, of which 102 were polymorphic. Cluster analysis of the genotypes was performed based on data from polymorphic RAPD bands, using Jaccard's similarity coefficient and UPGMA clustering method. The highest and lowest similarities detected between genotypes were 0.89 and 0.29, respectively. At a similarity of 60%, the genotypes were divided into four sub-clusters. Cophenetic correlation coefficient between similarity matrix and cophenetic matrix of dendrogram was relatively high (r = 0.9) showing the goodness of fit of the dendrogram. RAPD markers showed to be a useful tool for studying the genetic diversity of pomegranate.     

Study of Genetic Diversity of Pear Genotypes and Cultivars (<Emphasis Type="Italic">Pyrus communis</Emphasis> L.) Using Inter<Emphasis Type="Italic">-</Emphasis>Simple Sequence Repeat Markers (ISSR)

ISSR molecular marker was used to investigate genetic diversity of ‘Dare Gazi’ genotypes of Mashhad Esteghlal orchard and its relationship with other commercial and native cultivars of pear. Among ‘Dare Gazi’ genotypes of Mashhad Esteghlal orchard 23 genotypes were selected base on difference in tree vigor, leaf color, shape and color of fruit and also 33 other commercial and native pear cultivars from Esteghlal orchard and other Mashhad commercial orchards were studied. A total number of 230 DNA fragments were obtained using 11 primers of which 225 were polymorphic. On average, each primer produced 20.9 bands. Dice similarity coefficient ranged from 0.27 (between ‘Dom Kaj’ and Asian pear) to 1 (between ‘Dare Gazi’ 1 and 2 genotypes). Sample cluster dendrogram indicated that 56 genotypes were divided into 12 distinct clusters. The dendogram generated on the principle of Unweight Pair Wise Method using Arithmetic Average (UPGMA) was constructed by Dice coefficient and the genotypes were grouped into 12 clusters. ‘Dare Gazi’ genotypes did not show 100% similarity due to seed propagation or mutation, as ‘Dare Gazi’ 3 and 18 genotypes had the lowest similarity coefficient (0.64). Asian pears were placed in a separate group from European pears. And ‘Dare Gazi’ genotypes from different orchards were grouped separately, but all of them are called as ‘Dare Gazi’ pear for convenience. ISSR molecular marker can well identify the genetic variability among genotypes and cultivars and found suitable for grouping them.     

Identification of RAPD marker linked to fruit skin color in Japanese pear (Pyrus pyrifolia Nakai)

In Japanese pear, fruit skin color is a very important trait for growers because the russet skin protects the fruit against external stress caused by disease, insects, bad weather, and shipping. This report describes the development of a randomly amplified polymorphic DNA (RAPD) marker linked to major genes controlling the fruit skin color in Japanese pear. Two F₁ progenies from the cross of ‘Kousui’ × ‘Kinchaku’ and ‘Niitaka’ × ‘Chikusui’ segregated by fruit skin color were used for bulked segregant analysis. Four kinds of bulked DNA were constructed and used for the polymerase chain reaction in RAPD analysis. After 200 random primers were screened against four bulks, a band named OPH-19₄₂₅ was selected in cooperation with green bulks. The recombination rate between OPH-19₄₂₅ and the green skin phenotype was 7.3%. The RAPD marker (OPH-19₄₂₅) could select green fruit with probability as high as approximately 92%. The marker was apparently useful for the selection of green-skinned individuals in a breeding program. This is the first report on developing a DNA marker closely linked to the fruit phenotype in Japanese pear.     

部分中国砂梨和日本梨的RAPD分析

 采用RAPD分子标记技术, 对来自福建和浙江的6份中国砂梨和36份日本梨的亲缘关系进行了分析。27个引物产生了可记录的多态性条带261条。聚类分析将这些梨品种和类型分为4个中国砂梨群和5个日本梨群。其中4个日本梨群中都包含有日本高知县的品种或类型。尽管由于取样的偏差, 中国砂梨和日本梨在聚类分析中没有混合聚为大群, 但中国砂梨品种与部分日本梨, 特别是来自高知县的日本梨的相似系数高于与中国梨之间的相似系数。     

Molecular assessment of polymorphism among local Jordanian genotypes of the common fig (Ficus carica L.)

This research was conducted to assess polymorphism among local genotypes of common fig available in Jordan (one of countries of origin). Leaf samples were collected in spring for DNA isolation from 20 different local genotypes (5 cultivars and 15 landraces). Two more wild types and one foreign cultivar were included. The genotypes were assessed using the randomly amplified polymorphic DNA (RAPD) technique. Six of the 19 screened primers showed reproducible polymeric profiles. Out of 62 amplified bands, 48 were polymorphic (77%). They generated 1104 data entries (591 for present and 513 for absent bands). After determining Jaccard similarity index, some genotypes showed high genetic similarity (90% between F20 and F22), while other were less similar (3–18% between F11 and all other genotypes). Moreover, the primers were evaluated for their discriminating power, where primer RAPD06 showed the weakest power (0.431), while highest values of 0.989 and 0.996 were achieved for primers RAPD02 and RAPD13, respectively.     

应用RAPD分析新疆主要梨品种的遗传关系

利用RAPD分析了新疆18个梨品种间的亲缘关系。从160个随机十聚体引物中筛选出12条RAPD引物。18份材料共扩增133条带,平均每条引物扩增约11条带,其中14条带为所有材料的共有带,有119个多态性位点,占总带数的89.47%,Nei相似系数为0.5～0.923。用PHYLIP构建MP树,认为(1)对选用的形态学经典分类已较明确的新疆梨、白梨、砂梨、西洋梨、秋子梨,RAPD分析数据完全与其相符;(2)几个芽变品种间高度相似;(3)杂种新梨1号与砀山梨、杂种新梨6号与香梨、杂种早酥梨与苹果梨分别并类;(4)苹果梨独立于供试的5个种之外;(5)库尔勒香梨归属于新疆梨。     

Inter- and intra-specific genetic diversity among cyclamen accessions investigated by RAPD markers

Random amplified polymorphic DNA (RAPD) analysis was used to characterize genetic diversity of 26 Cyclamen persicum and Cyclamen com accessions. Eighty-four arbitrary primers tested, among which nine primers showed reliable polymorphic banding patterns and yielded 104 polymorphic markers. Jaccard's similarity coefficient among accessions ranged from 0.99 to 0.08. At a similarity of 68%, accessions were divided into three clusters. The cophenetic correlation coefficient between the similarity matrix and the dendrogram was relatively high (r = 0.9) showing the goodness of fit of the dendrogram. The RAPD analysis offered a rapid and reliable tool for the estimation of inter- and intra-specific variability in cyclamens. The wide genetic variation observed for cyclamens within Iran guarantees a promising future of breeding.     

Genetic diversity analysis in date palm (Phoenix dactylifera L.): a comparative assessment using ISSR and RAPD marker assays

SUMMARY

A comparative study was conducted to evaluate genetic diversity in 45 genotypes of date palm (Phoenix dactylifera L.), including both male and female plants, employing RAPD and ISSR marker systems. The data were analysed to calculate the total number of bands, the number of polymorphic bands, the percentage polymorphism, the average number of bands per primer, the effective multiplex ratio (EMR), the polymorphic information content (PIC), the marker index (MI), and genetic similarity coefficients. The 37 RAPD and 53 ISSR primers used generated 363 and 608 scorable amplified products, respectively, of which 95.0% and 90.9% were polymorphic. The ISSR markers produced more information than the RAPD markers due to their higher EMR and MI values. Jaccard similarity values among male plants, female plants, and between all male and all female plants varied between 0.72 – 0.80. The results indicate the effectiveness of these two marker systems for demonstrating genetic relationships among date palm genotypes.     

甘肃中部梨种质资源的AFLP分析

采用AFLP分子标记技术对甘肃中部梨种质资源的遗传多样性进行分析。结果表明,6对AFLP引物在40份甘肃梨种质中共扩增出472条带,其中多态性带为404条,多态率高达86%,显示了甘肃中部梨资源丰富的遗传多样性。任何一对引物可以鉴别所有40份资源,显示了很高的鉴别能力。采用UPGMA聚类分析法构建的系统树在相似系数为0.72时将40份种质分为7个组:西洋梨、新疆梨、白梨(砂梨)、木梨、褐梨组和2个秋子梨组。所有白梨品种与唯一的砂梨品种黄花梨聚为一个大组。形态学上归属不明的品种分别聚类到西洋梨、白梨、木梨和秋子梨组中。研究表明基于AFLP标记的梨资源分类体系可以反映甘肃地方梨品种和类型间的遗传多样性和亲缘关系。     

梨品种资源遗传差异的RAPD分析

明确种质间的遗传差异,对杂交育种中亲本的选择和搭配具有重要意义。利用随机扩增多态性DNA(RAPD)技术,从40个随机引物中筛选出了33个多态性好的引物,在21个品种间进行了分析,最终得到339个清晰稳定的扩增位点,其中多态性位点为292个,占86.1%。利用UPGMA(非加权配对算术平均)法进行了品种间相似系数的计算以及聚类分析,揭示了这些品种间遗传上的差异程度。     

Genetic relationships of pear cultivars in Xinjiang,China, as measured by RAPD markers

Summary

Thirteen native pear species have been identified in China, of which P. armeniacaefolia Yu and P. sinkiangensis Yu are specific to Xinjiang. P. armeniacaefolia grows wild and a few cultivars have been assigned to this species. Cultivars of P. sinkiangensis have been suspected to be of hybrid origin involving P. communis L. and P. bretschneideri Rehd. In this study, traditional pear cultivars in Xinjiang were evaluated using RAPD markers and compared with representatives of Occidental pear species, cultivars of P. communis and East Asian pear accessions. The combination of 72 pear accessions and 20 selected primers produced 231 scorable polymorphic RAPD bands, of which some were specific to certain species. Five main groups of pear accessions could be distinguished from UPGMA analysis: 1) P. xerophila Yu, its relatives and one cultivar of P. ussuriensis Max., 2) cultivars of P. sinkiangensis, 3) cultivars of P. pyrifolia Nakai and P. bretschneideri, 4) wild Occidental species, cultivars of P. communis and P. armeniacaefolia, and 5) hybrids between P. communis and Chinese or Japanese pear cultivars. The result of PCA generally agrees with that based on UPGMA. Based on RAPD data, some cultivars traditionally classified as P. bretschneideri should be assigned to P. sinkiangensis. Some heirloom cultivars assigned to P. communis were found to be of hybrid origin involving the Chinese white pear (P. bretschneideri) or sand pear (P. pyrifolia). Our results confirmed that P. sinkiangensis is of hybrid origin and at least P. communis, P. armeniacaefolia and Chinese white pears or sand pears have been involved. A further study is needed to understand how pear species and cultivars in Xinjiang are related to those originated from countries in Central Asia.     

Development of SCAR markers to differentiate between mume (Prunus mume Sieb. et Zucc.) and apricot (P. armeniaca L.)

Summary

Mume (Prunus mume Sieb. et Zucc.) and apricot (P. armeniaca L.) are similar in fruit and tree morphology, and exhibit high cross- and graft-compatibility with each other. It is therefore difficult to differentiate mume and apricot cultivars on the basis of morphological and phenotypical characteristics. Molecular markers were developed to differentiate nine mume from ten apricot cultivars. Four dominant, random amplified polymorphic DNA (RAPD) markers that can discriminate between mume and apricot cultivars (designated OPA15₆₂₈, OPO10₅₅₀, OPO20₂₅₉, and OPU03₄₁₅) were identified from 21 decamer primers. Two RAPD markers (OPO10₅₅₀ and OPU03₄₁₅) were developed into dominant sequence-characterised amplified region (SCAR) markers (SCO10 and SCU03). These SCAR markers could differentiate between all mume and apricot cultivars.     

Clone identification and genetic relationship among vine cacti from the genera Hylocereus and Selenicereus based on RAPD analysis

Clones of Hylocereus and of Selenicereus species were distinguished from each other by the banding pattern generated by one to nine 10-mer oligonucleotide primers in the random amplified polymorphic DNA (RAPD) reaction. RAPD analysis was also applied to estimate the genetic relationship among five Hylocereus and nine Selenicereus species. A dendrogram was constructed based on a data matrix of 173 polymorphic bands originated by nine primers. Two groups were identified, one consisting of Hylocereus species and the other consisting of Selenicereus species. These results are consistent with the accepted taxonomic classification of the genera studied. The principal coordinate analysis (PCO), i.e. the plot drawn on the basis of the RAPD data, clearly distinguished between three groups, namely, Hylocereus species, S. megalanthus and the rest of the Selenicereus species studied. PCO thus strongly support the notion that the tetraploid S. megalanthus is an exception among the Selenicereus group. The RAPD results support our hypothesis regarding the allopolyploid (rather than autopolyploid) origin of this species.     

DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD,ISSR and SRAP markers

Three molecular marker systems, RAPD (random amplified polymorphic DNA), ISSR (inter-simple sequence repeat) and SRAP (sequence-related amplified polymorphism), were employed for identification and genetic diversity analysis of 35 elite late-bolting radish cultivars. Detected by 35 RAPD primers, 22 ISSR primers and 17 SRAP primer combinations, the proportions of polymorphic bands were 85.44%, 85.2% and 85.41%, respectively, and the mean genetic similarity coefficients between pairs of genotypes were 0.781, 0.787 and 0.764, respectively. Each of the three molecular marker systems can identify all the cultivars. Five sets of three-RAPD primers, 3 sets of three-ISSR primers and 16 sets of three-SRAP primer combinations were able to distinguish all the cultivars. A linear relationship was observed between Resolving power (Rp) of a primer and its ability to distinguish genotypes. The 35 cultivars were clustered into three major groups based on the RAPD, ISSR and marker combination data with UPGMA, which are in high accordance with their own origins and main characteristics. The results demonstrated that these three marker systems could be useful for identification and genetic diversity analysis of radish cultivars.     

Cultivar identification and genetic diversity analysis of broccoli and its related species with RAPD and ISSR markers

A total of 18 genotypes of broccoli were subjected to random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) marker analysis. Seventy-four RAPD and eight ISSR primers generated 344 and 67 polymorphic bands, respectively. All broccoli genotypes could be distinguished with two-primer combinations, indicating that RAPD and ISSR markers can be used to efficiently identify broccoli cultivars. These 18 broccoli genotypes could be separated into two major sub-groups. The first major sub-group (A) included 13 genotypes and the second major sub-group (B) was comprised of five genotypes belonging to early-maturating cultivars. Genetic diversity analysis was performed on the 18 broccoli genotypes, one radish genotype, and six related Brassica accessions. All accessions could be clustered into two groups (radish and Brassica) based on the unweighted pair group of arithmetic average (UPGMA) cluster analysis. The UPGMA analysis indicated that broccoli is most closely related to cauliflower, than to cabbage and Chinese cabbage.     

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.     

Analysis of genetic diversity among Indian short-day onion (Allium cepa L.) cultivars using RAPD markers.

Summary

Randomly amplified polymorphic DNA (RAPD) markers were used to estimate genetic diversity among 24 cultivars of short-day onions. Total genomic DNA was extracted and subjected to RAPD analysis using 90 arbitrary 10-mer primers. Of these, 15 primers were selected which yielded 137 bands, 91.24% of which were polymorphic. None of the primers produced a unique banding pattern for each cultivar. RAPD data were used to calculate a Squared-Euclidian Distance matrix which revealed a minimum genetic distance between cultivars ‘AFLR-722’ and ‘PBR-140’, and a maximum genetic distance between cultivars ‘PBR-139’ and ‘A.Kalyan’, and ‘MS-48’ and ‘A.Kalyan’. Based on the distance matrix, cluster analysis was done using a minimum variance algorithm.The dendrogram thus generated, based on Ward’s method, grouped the 24 onion cultivars into two major clusters. The first cluster consisted of cultivars from the northern region, and the second of cultivars from the southern region of India. The present study shows that there is high diversity among the onion cultivars selected and indicates the potential of RAPD markers for identification and maintenance of onion germplasm for crop improvement purposes.     

番茄种质资源遗传多样性的RAPD分析

利用RAPD分子标记技术,对63份番茄种质资源进行了遗传多样性研究。结果表明:从180个RAPD引物当中,筛选出22条稳定性好、多态性强的RAPD引物,共扩增出多态性带207条,多态性条带比率为86.96%,63份番茄栽培品种或品系间的相似系数介于0.28～0.99之间,说明RAPD能很好的对番茄野生种、近缘野生种和栽培种进行多态性分析。采用UPGMA进行聚类分析,得到与生物学分类地位基本一致的结果。     

梨果实酸/低酸性状的SSR分析

以八月红(Pyrus communis L.‘Bayuehong')×砀山酥梨(P.× bretshneider‘Dangshansuli')F1代杂交分离群体(共118株)为试材,测定了成熟果实的酸含量,从表型上分析了梨果实含酸量的遗传规律.利用225对源自梨和苹果基因组的SSR引物,结合分离群体分离分析法(Bulk...