Diversity and relationships among Turkish okra germplasm by SRAP and phenotypic marker polymorphism

Germplasm characterization is essential and molecular markers provide valuable information for breeding programs. Sequence-related amplified polymorphism (SRAP) and phenotypic markers were studied to determine diversity and relationships among 23 okra (Abelmoschus esculentus (L) Moench) genotypes. The 39 combinations of forward and reverse SRAP primers were used to evaluate the 21 Turkish and two randomly selected USA genotypes as outgroups, and produced 97 scorable markers, of which 50% was polymorphic for all 23 genotypes. Seventeen out of the 23 genotypes (74%) were distinguished from each other with mean similarity of 0.93. As to phenotypic markers, 33 heritable traits were evaluated in field with ten replications, 28 of them (85%) were found to be polymorphic. The UPGMA (unweighted-pair group method arithmetic average) dendrogram based on the 33 phenotypic markers distinguished all genotypes, but failed to detect any geographic association of okra genotypes, being consistent with previous study. It can be concluded that SRAP markers are useful for studying diversity and relationships among okra germplasm, and have potential in marker-aided selection, linkage mapping, and evolutionary studies.     

大豆种质资源SRAP分子标记中的引物筛选

以113个大豆栽培品种和20个野生品种为材料,从288对引物组合中筛选出12对多态性丰富、条带清晰、可重复性好的SRAP引物组合。用筛选出的12对引物组合对大豆品种进行PCR扩增,获得了带型丰富和清晰可辨的DNA的PAGE指纹图谱;共扩增出251条谱带,其中多态性条带220条,多态性谱带比率为87.6%,平均每个引物扩增出18.3条谱带。结果显示,所筛选出的12对引物组合可以有效的应用于大豆种质资源的SRAP分析。     

The emergence of okra enation leaf curl virus—an important begomovirus,infecting okra in several states across India

Okra enation leaf curl virus (OELCuV), a begomovirus, is an emerging serious constraint for okra production in India. OELCuV was earlier reported in Haryana, Gujarat and Karnataka. In the current study, a survey was conducted on okra crop in the other predominant okra growing regions of India and identified for the first time, a widespread symptomology of OELCuV. The disease incidence was recorded between 5 and 74% in all the surveyed regions. The diseased samples collected from all the locations were amplified with coat protein specific new primer in PCR. The amplicons were sequenced and deposited to NCBI Gene Bank. The finding could be highly useful in okra breeding programs against OELCuV.     

Evaluation of Genetic Diversity in Lemons and Some of Their Relatives Based on SRAP and SSR Markers

Genetic diversity was evaluated by sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers among 45 lemons (Citrus limon (L.) Burm. f.), five citrons (Citrus medica L.), four rough lemons (Citrus jambhiri Lush), and two Citrus volkameriana accessions. Twenty-one SRAP primer combinations produced a total of 141 (77%) polymorphic fragments with an average of 6.7 fragments per primer combinations whereas 13 SSR primers produced a total of 26 (76%) polymorphic fragments with an average of 2.0 per primer. The unweighted pair-group method arithmetic average analysis as assessed with combined SRAP and SSR data demonstrated that the accessions had a similarity range from 0.65 to 1.00. Rough lemons and C. volkameriana accessions were relatively closely related. In lemon group, accessions from hybrid origin were distant from the others. We also applied principal components analysis (PCA) for a better presentation of relation among the accessions studies. Using PCA, 88.7% of the total variation in the original dimensions could be represented by just the two dimensions defined by the first two PCs. Although nearly all accessions could be distinguished, there was a low level of genetic diversity detected among lemon cultivars.     

Genetic diversity assessment of a germplasm collection of Salvia miltiorrhiza Bunge. based on morphology,ISSR and SRAP markers

Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants for its therapeutic effects. In the present study, morphological traits, ISSR (inter-simple sequence related) and SRAP (sequence-related amplified polymorphism) markers were used to analyze the genetic diversity of 59 S. miltiorrhiza phenotypes. Out of the 100 ISSR primers and 100 SRAP primer combinations screened, 13 ISSRs and 7 SRAPs were exploited to evaluate the level of polymorphism and discriminating capacity. The results showed that the 13 ISSRs generated 190 repeatable amplified bands, of which 177 (93.2%) were polymorphic, with an average of 13.6 polymorphic fragments per primer. The 7 SRAPs produced 286 repeatable amplified bands, of which 266 (93.4%) were polymorphic, with an average of 38.1 polymorphic fragments per primer. Cluster analysis readily separated different morphological accessions, wild and cultivated controls based on morphological traits, ISSR and SRAP markers. The study indicated that morphological traits, ISSR and SRAP markers were reliable and effective for assessing the genetic diversity of phenotypic S. miltiorrhiza accessions. The overall results suggested that the introduction of genetic variation from morphology-based germplasms enlarged the genetic base for the collection, conservation and further breeding program of S. miltiorrhiza germplasm.     

Occurrence of whitefly-transmitted geminiviruses in crops in Burkina Faso, and their serological detection and differentiation

Whitefly-transmitted geminiviruses were found to be associated with four diseases of crop plants in Burkina Faso: cassava mosaic, okra leaf curl, tobacco leaf curl and tomato yellow leaf curl. Tomato yellow leaf curl is an economically serious disease, reaching a high incidence in March, following a peak population of the vector whitefly, Bemisia tabaci, in December. Okra leaf curl is also a problem in the small area of okra grown in the dry season but is not important in the main period of okra production in the rainy season. The geminiviruses causing these four diseases, African cassava mosaic (ACMV), okra leaf curl (OLCV), tobacco leaf curl (TobLCV) and tomato yellow leaf curl (TYLCV) viruses, were each detected in field-collected samples by triple antibody sand-wich-ELISA with cross-reacting monoclonal antibodies (MAbs) to ACMV. Epitope profiles obtained by testing each virus isolate with panels of MAbs to ACMV, OLCV and Indian cassava mosaic virus enabled four viruses to be distinguished. ACMV and OLCV had similar but distinguishable profiles. The epitope profile of TobLCV was the same as that of one form of TYLCV (which may be the same virus) and was close to the profile of TYLCV from Sardinia. The other form of TYLCV reacted with several additional MAbs and had an epitope profile close to that of TYLCV from Senegal. Only minor variations within each of these four types of epitope profile were found among geminivirus isolates from Burkina Faso. Sida acuta is a wild host of OLCV.     

Evaluation of bamboo genetic diversity using morphological and SRAP analyses

Bamboo is an important member of the giant grass subfamily Bambusoideae of Poaceae. In this study, 13 bamboo accessions belonging to 5 different genera were subjected to morphological evaluation and sequence-related amplified polymorphism (SRAP) analysis. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis was used to construct a dendrogram and to estimate the genetic distances among accessions. On the basis of morphological characteristics, the 13 accessions were distinctly classified into 2 major clusters; 3 varieties, PPYX, PGNK, and PLYY were grouped as cluster A, and 10 accessions were categorized under cluster B. Similarity coefficients ranging from 0.23 to 0.96 indicated abundant genetic variation among bamboo varieties. Approximately 38 SRAP primer combinations generated 186 bands, with 150 bands (80.65%) showing polymorphisms among the 13 accessions. Based on SRAP analysis, 13 bamboo accessions were grouped into 3 major clusters. Five species comprised Cluster I (PASL, PLYY, PTSC, SCNK, and BMAK), which belongs to genus Phyllostachys. Cluster II consisted of 5 varieties, PASL, PLYY, PTSC, SCNK, and BMAK; Cluster III included 3 varieties, PGNK, PLSY, and BMRS. Comparison of the results generated by morphological and SRAP analyses showed that the classification based on SRAP markers was more concordant to the taxonomic results of Gamble than that performed using morphological characters, thus suggesting that SRAP analysis is more efficient in evaluating genetic diversity in bamboos compared to morphological analysis. The SRAP technique serves as an alternative method in assessing genetic diversity within bamboo collections.     

油莎豆SRAP指纹图谱构建及遗传多样性分析

利用SRAP分子标记构建了14份不同地理来源、表型具有差异的油莎豆品系的分子指纹图谱并进行遗传多样性分析。结果表明100对引物中共有多态性引物42对,扩增出多态性带328条,平均每对引物7.8条。28对引物在12个品系上具有特征谱带,除品系4和14外,均可用1对引物进行鉴定;采用引物组合法仅用Me2/Em6和Me8/Em11这2对引物就可将14份材料区分开,并利用这2对引物构建了上述品系的数字指纹图谱。UPGMA聚类分析表明,所有参试材料间的遗传距离在0.12～0.75之间,平均为0.42,表明我国不同地理来源的油莎豆品系遗传差异较大,具有较为丰富的遗传多样性。     

Genetic diversity of Dioscorea dumetorum (Kunth) Pax using Amplified Fragment Length Polymorphisms (AFLP) and cpDNA

We have utilized Amplified Fragment Length Polymorphisms (AFLP) in conjunction with chloroplast DNA (cpDNA) sequence data to study the genetic diversity in 53 accessions of Dioscorea dumetorum from six countries in West and Central Africa. Our results provide a comparison of the two marker systems with regards to their applicability to differentiate intraspecific genotypes and the grouping of the accessions based on localities of collection. A total of 1052 AFLP fragments (of which 94.1% were polymorphic) produced from twelve primer combinations indicate a relatively high level of polymorphism among the accessions. Three major genetic groups that do not strictly follow a geographic distribution pattern were identified using Neighbour-joining and the principal coordinate (PCo) analyses. Accessions from Togo showed higher numbers of private fragments and the highest percentage polymorphism (59.4%). The detection of highest genetic diversity in accessions from Nigeria and Togo and their relationship to other accessions suggest that these countries are the centre of origin and diversity of D. dumetorum. The moderately high genetic diversity (average of 61%) is suggesting great influence on the D. dumetorum germplasms through exchange and transfer of cultivars among local farmers in the sub-region. In contrast, DNA sequence data from the psbA-trnH and the rpoB-trnC chloroplast regions revealed no variation among accessions from the different localities and clearly differentiated by AFLP patterns. The results demonstrate the usefulness of the AFLP marker in generating high polymorphism in the D. dumetorum accessions from West and Central Africa and hence may be used for agronomic purposes.     

Vegetative Compatibility and Virulence Diversity of <i>Verticillium dahliae</i> from Okra (<i>Abelmoschus esculentus</i>) Plantations in Turkey and Evaluation of Okra Landraces for Resistance to <i>V. dahliae</i>

Forty-four V. dahliae isolates were collected from symptomatic vascular tissues of okra plants each from a different field in eight provinces located in the eastern Mediterranean and western Anatolia regions of Turkey during 2006- 2009. Nitrate-nonutilizing (nit) mutants of V. dahliae from okra were used to determine heterokaryosis and genetic relatedness among isolates. All isolates from okra plants were grouped into two vegetative compatibility groups (VCGs) (1 and 2) and three subgroups as 1A (13.6%, 6/44), 2A (20.5%, 9/44) and 2B (65.9%, 29/44) according to international criteria. Pathogenicity tests were performed on a susceptible local okra (A. esculentus) landrace in greenhouse conditions. All isolates from VCG1A and VCG2B induced defoliation (D) and partial defoliation (PD) symptoms, respectively. Other isolates from VCG2A gave rise to typical leaf chlorosis symptoms without defoliation. The obtained data showed that the virulence level of V. dahliae isolates from okra was related to their VCG belongings. Eighteen okra landraces from diverse geographical origins were screened for resistance to VCG2B and VCG1A of V. dahliae. The results indicated that all landraces were more susceptible to highly virulent VCG1A-D pathotype displaying D or PD symptoms depending on their susceptibility levels with a mean disease severity index of 3.52 than to less virulent VCG2B-PD pathotype of V. dahliae displaying PD and ND symptoms with a mean disease severity index of 2.52. Significant differences were observed among the landraces; however, none of them exhibited a level of resistance. Okra landraces; Çorum, Hatay Has and Şanlıurfa displayed the lowest level of susceptibility or little tolerance to both D and PD pathotypes. VCG2B of PD was prevailing in the surveyed areas and VCG1A of D was the most virulent of the VCGs identified. Introduction of resistant genotypes to Turkish okra germplasm from different sources and breeding new resistant okra cultivars are critical for the sustainability of okra production.     

鸭茅种质资源遗传多样性的SRAP研究

利用SRAP(Sequence-related amplified polymorphism)标记对来自国内外的45份鸭茅（Dactylis glomerata L.）种质资源进行遗传多样性研究。21对引物扩增出438个条带,多态性条带为363条,多态性条带比率为82.08%,每对引物组合的多态性带数平均为17.29条。GS值范围在0.6248-0.9686间,平均GS值为0.7958,显示来源广泛的鸭茅种质资源间存在着丰富的遗传变异。聚类分析及主成分分析能将所有材料聚为4类,能较准确的反映材料的来源分布情况及供试材料的染色体倍性差异,表明鸭茅的遗传多样性与染色体倍性及地理分布密切相关。同时清楚的揭示出国产鸭茅品种遗传基础较为狭窄。本研究为育种和探讨鸭茅种质资源遗传变异奠定了较好的理论基础。     

Genetic diversity and relationships within sweet kernel apricot and related Armeniaca species based on sequence-related amplified polymorphism markers

Sequence-related amplified polymorphism (SRAP) markers were employed to detect the genetic variation among 28 sweet kernel apricot and related Armeniaca accessions from China. Fifteen SRAP primer combinations were used and 252 polymorphic bands out of 286 with an average of 16.8 per primer combination were observed. The unweighted pair-group method (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.55 to 0.91 with a mean of 0.7, and there were three clusters with two groups of sweet kernel apricots distinctly separated from the related Armeniaca vulgaris and Armeniaca sibirica at the similarity level of 0.58, indicating more extensive genetic variation among sweet kernel apricot. The origin of sweet kernel apricot has also been discussed. This suggested there are abundant germplasm resources of sweet kernel apricot from China for further breeding and biodiversity conservation.     

Genetic relationships among a collection of Musa germplasm by fluorescent-labeled SRAP

Edible banana and plantains of the Musa genus are important staple food crops cultivated in humid tropical and subtropical climatic zones. These crops are important for subsistence farming in rural communities and also to generate significant employment and income. In an effort to increase the genetic variability of available cultivars, indexed accessions have been introduced into a regional collection in southeastern Mexico, through the Banana Bioversity International Program. The aim of this study was to use the fluorescently labeled sequence-related amplified polymorphism (SRAP) molecular marker system to characterize the genetic variability within 71 accessions of the existing collection and resolved uncertainties for the better management of the collection, as a preliminary step to establishing a breeding program. These accessions, which included wild species and cultivars of different subgroups, were consistently identified and separated by SRAP markers. A total of 330 polymorphic bands were detected using 12 primer combinations. The average number of polymorphic bands per primer pair was 27.5. The genetic similarity between accessions ranged between 0.44 and 0.97, as estimated using Jaccard's coefficient. Moreover, SRAP marker system probed to be useful to identify closely related accessions in the genus Musa and facilitated the recognition of duplicates to be eliminated and clarified uncertainties or mislabeled banana accessions introduced to the collection.     

Assessment of genetic diversity of coffee leaf rust pathogen Hemileia vastatrix using SRAP markers

Coffee leaf rust caused by the fungus Hemileia vastatrix (Berk and Br.) is a major disease occurring in coffee plantations. Although the rust fungus exists in different physiological races, the genetic difference between them is meagrely understood. In this study, genetic diversity of 14 identified and two unidentified leaf rust races was determined by sequence‐related amplified polymorphism (SRAP) markers. Of 48 SRAP primer pairs tested, 35 primers are polymorphic and generated 347 distinct scorable fragments. The number of fragments ranged from 4 to 18 with a mean of 9.97 fragments per primer combination. Of the total 347 amplified fragments, 185 fragments (53.31%) are polymorphic with an average of 5.41 fragments per primer combination. The average resolving power (Rp) and the average polymorphism information content (PIC) of the 35 SRAP primer combinations were 13.60 and 0.356, respectively. Of 35 SRAP primer pairs, 15 primer pairs were more informative and generated 25 unique fragments, which are useful for race discrimination. The study demonstrated the existence of genetic variability among various leaf rust races and this information will be helpful in coffee breeding programmes.     

Identification of Genetic Diversity Among Cultivars of <Emphasis Type="Italic">Phyllostachys violascens</Emphasis> Using ISSR,SRAP and AFLP Markers

Bamboo is one of the most important forest resources with a strong carbon fixation capability. To utilize genetic resource of Phyllostachys violascens, ISSR (inter-simple sequence repeat), SRAP (sequence-related amplified polymorphism), and AFLP (amplified fragment length polymorphism) techniques were used for the first time for the assessment of genetic diversity within its different cultivars. A total of 209 (136 polymorphic), 222 (152 polymorphic), and 434 (253 polymorphic) bands were detected using 15 ISSR primers, 15 primer combinations of SRAP, and 15 primer combinations of AFLP, respectively. The mean genetic similarity of Ph. violascens was 0.872, 0.867 or 0.871 for the ISSR, SRAP and AFLP analyses, respectively. Based on genetic diversity, all the cultivars of Ph. violascens could be divided into four groups, which are reflected by their morphologies. Our data demonstrated that all three methods are useful in the identification of genetic diversity in Ph.violascens, but AFLP is the most efficient.     

Musa Genetic Diversity Revealed by SRAP and AFLP

The sequence-related amplified polymorphism (SRAP) technique, aimed for the amplification of open reading frames (ORFs), vis-â-vis that of the amplified fragment length polymorphisms (AFLP) were used to analyze the genetic variation and relationships among forty Musa accessions; which include commercial cultivars and wild species of interest for the genetic enhancement of Musa. A total of 403 SRAP and 837 AFLP amplicons were generated by 10 SRAP and 15 AFLP primer combinations, of which 353 and 787 bands were polymorphic, respectively. Both cluster analysis of unweighted pair-grouping method with arithmetic averages (UPGMA) and principal coordinate (PCO) analysis separated the forty accessions into their recognized sections (Eumusa, Australimusa, Callimusa and Rhodochlamys) and species. The percentage of polymorphism amongst sections and species and the relationships within Eumusa species and subspecies varied between the two marker systems. In addition to its practical simplicity, SRAP exhibited approximately threefold more specific and unique bands than AFLP, 37 and 13%, respectively. SRAP markers are demonstrated here to be proficient tools for discriminating amongst M. acuminata, M. balbisiana and M. schizocarpa in the Eumusa section, as well as between plantains and cooking bananas within triploid cultivars.     

亚洲棉种内群体异常偏分离的分子标记检测

利用3个形态标记、20个SSR和11个SRAP多态性标记,研究它们在“如东鸡脚桠果”与“美国中棉971”杂交的F2群体中的分离情况。结果表明,77.42%的分子标记表现为偏分离,所有的偏分离标记都偏向母本“如东鸡角桠果”;如此高的偏分离比例以及偏分离标记都偏向一个亲本,这种现象在棉花中是比较罕见的。3种类型的SSR标记和非物种特异性的SRAP标记都表现偏分离,而形态标记则表现为正常分离,这表明该异常偏分离现象是由材料本身的遗传特性所决定的。通过分析偏分离的共显性标记的等位基因频率(p=q)以及各种基因型频率(p2:2pq:q2)的F2分布,发现大多数标记的等位基因频率差异显著而F2基因型频率分布正常,表明这些标记产生偏分离可能是配子体选择的结果。     

甜瓜种质资源遗传多样性的SRAP分析

为研究甜瓜材料之间的亲缘关系及其分类, 更有效地利用种质资源, 为培育新品种提供依据, 文章采用 SRAP (Sequence-related amplified polymorphism)技术对61份甜瓜种质资源的遗传多样性进行研究。结果表明: 从42对引物组合中筛选出16对扩增条带清晰、多态性高的引物组合分析供试材料, 共检测出452个位点, 其中265个为多态性位点, 多态性比率达58.63％, 平均每对引物组合产生28.56个位点和16.56个多态性位点。61份材料间的相似系数为0.48～0.93, 平均为0.73。这些结果说明, 供试甜瓜材料具有较为丰富的遗传多样性。聚类分析结果表明, 61个甜瓜品种中首先可分为薄皮甜瓜与厚皮甜瓜两大类, 彼此亲缘关系最远。以遗传相似系数0.74为截值, 可把供试材料分为5个类群。在生态区域中, 新疆厚皮甜瓜的Nei’s基因多样性指数(0.2231)和Shannon’s信息指数(0.3422)最高。     

Neutral and functional marker based genetic diversity in kodo millet (<Emphasis Type="Italic">Paspalum scrobiculatum</Emphasis> L.)

Kodo millet (Paspalum scrobiculatum L.) is known for its high nutritive value, dietary fiber, antioxidant activity, as well as for drought tolerance. It is primarily grown as a grain in India and in Africa it is either cultivated or harvested in wild. Neutral—ISSR (inter simple sequence repeat) as well as functional—SCoT (start codon targeted) and SRAP (sequence-related amplified polymorphism) markers were employed for genetic diversity studies in 96 accessions of kodo millet collected from diverse regions of India. The genetic diversity parameters like average bands per primer, Polymorphic information content, Nei’s gene diversity and Shannon’s information index of 11.22, 9.69; 0.12, 0.11; 0.15 ± 0.14, 0.13 ± 0.13 and 0.26 ± 0.21, 0.22 ± 0.19 was observed with neutral and functional markers respectively. Neutral markers were showing higher values as compared to functional markers for the genetic diversity parameters as discussed. Structure based analysis placed all the accessions into four sub-groups not strictly according to their geographical locations. The accessions from Bihar followed by Karnataka were showing high diversity based on both the marker systems useful for designing exploration, conservation and germplasm enrichment strategies. Further, the set of diverse accessions selected based on these markers would serve as potential sources of unique alleles and may be exploited in future for enhancement and utilization of kodo millet germplasm. Usage of African gene pool and wild species for broadening the genetic base of Indian kodo millet was also suggested based on the present studies.     

Yellow Vein Mosaic Disease in Okra (<i>Abelmoschus esculentus</i> L.): An Overview on Causal Agent,Vector and Management

Okra (Abelmoschus esculentus L.) belongs to the Malvaceae family and is one of the most essential and popular vegetables globally. It is rich in proteins, carbohydrates, and vitamins. Abiotic and biotic factors threaten okra productivity. Okra yellow vein mosaic disease (OYVMD) is the most destructive disease of okra. The causal agent, [(i.e., Okra yellow vein mosaic virus (OYVMV)] of this disease belongs to the family Geminiviridae and genus Begomovirus. OYVMV is a monopartite with additional ssDNA molecule. This virus has two components DNA-A for protein coding and DNA-B for symptoms induction. Whitefly transmits OYVMV in persistent manner. Characteristic symptoms of OYVMV infected okra plants are chlorosis, dwarfing, and yellowing of veins and fruits. High temperatures with moderate rainfall enhance the development of OYVMV disease and the whitefly population. However, high humidity with low temperature and rainfall has no significant role in developing the OYVMD and whitefly population. Moreover, the virus also affects the secondary metabolites in the infected okra plants. The virus can be managed through various strategies including the application of plant defense activators, the development of resistant varieties and by controlling its vector via pesticides and plant extracts. Various plant defense activators such as monopotassium phosphate (KH₂PO), salicylic acid, benzoic acid, and citric acid enhance resistance in okra against OYMVD. In addition, the resistance to OYMVD can also be achieved by successfully incorporating high yielding but resistant cultivars of acceptable quality. In this review, we have discussed history, economic impact, symptomology, disease development under a natural environment, genetics and management of OYVMV.