An assessment of genetic variability and relationships within Asian pears based on AFLP (amplified fragment length polymorphism) markers

A total of 100 Pyrus L. accessions native mainly to East Asia were subjected to amplified fragment length polymorphism (AFLP) analysis to evaluate genetic variability and relationships among the accessions. Six AFLP primer combinations produced a total of 459 fragments, of which 410 were polymorphic with a polymorphism percentage of 89%. The Dice's similarity coefficient among pear accessions ranged from 0.671 (P. betulaefolia Bge and P. elaeagrifolia Pall.) to 0.947 (‘Umajirou’ and ‘Immuraaki’). Occidental pears generally had low similarities to Asian pears. The dendrogram generated from all the accessions by unweighted pair-group method of arithmetic analysis (UPGMA) cluster analysis clearly distinguished Occidental pears from accessions of East Asia. P. ussuriensis Maxim., P. betulaefolia and P. communis L. clustered separately into independent groups in accordance with their morphological classification. Japanese pear cultivars formed two groups with some Chinese white pears and Chinese sand pears. Chinese white pears and Chinese sand pears independently formed their own groups and also mingled into mixed groups in the dendrogram. Therefore, Chinese white pears were treated as a cultivated group or an ecotype of P. pyrifolia: P. pyrifolia White Pear Group. The information obtained from this study will be of great help for understanding the origin and evolution of Asian pear cultivars.     

Genetic analysis of Tunisian fig (Ficus carica L.) cultivars using amplified fragment length polymorphism (AFLP) markers

Genetic diversity of forty fig cultivars collected from five regions in Tunisia was investigated using amplified fragment length polymorphism (AFLP). A total of 342 reproducible bands amplified with six AFLP primer combinations were obtained. The high percentage of polymorphic bands (%PB) of 97.5 and the resolving power (Rp) collective rate value of 143 were scored. In addition, the polymorphism information content (PIC) values varied from 0.61 to 0.87 with an average of 0.77. Although cluster (UPGMA) and principal components analyses indicate that the cultivars’ clustering made independently both from the geographical origin, horticultural classifications and/or from the sex of trees. In addition, the observed variation suggests considerable differentiation among fig cultivars. The present data supports the common origin of the fig cultivars. Analysis of molecular variance (AMOVA) revealed that average Φ_ST value overall loci was 0.026, and the overall distribution pattern of molecular variation indicated that about 97.43% of the total variance was accounted by the within-region variance component. The remaining 2.5% (P < 0.001) of the variation was founded among cultivars of the prospected regions. Our results proved that AFLP markers are useful for germplasm discrimination as well as for investigation of fig patterns variation. The information may be useful to define conservation management program.     

Assessment of genetic diversity in common bean (Phaseolus vulgaris L.) germplasm using amplified fragment length polymorphism (AFLP)

AFLP technique was applied to assess genetic diversity among 44 common bean accessions that included 6 exotic accessions, 15 Indian land races and 23 released varieties. Eight AFLP primer pairs were used that produced 820 products of which 698 were polymorphic (85.12%). Wide variations were observed among all the accessions for the number of amplification products, percent polymorphism and average polymorphism information content (PIC). The Jaccard's similarity indices (J) based on the AFLP profiles were subjected to UPGMA cluster analysis. The dendrogram generated revealed seven major groups. Seventeen out of 23 released varieties were restricted to clusters VI and VII. The value of r = 0.934 in Mantel's test for cophenetic corrlelation applied to the cluster analysis indicated the high fitness of the accessions to a group. The germplasm used in the present study had narrow genetic base, although moderate to high genetic diversity was observed. The details of diversity analysis and the potential use of Indian common bean accessions in common bean breeding programme are provided in the present study.     

Amplified fragment length polymorphism (AFLP) markers for fingerprinting of Argyranthemum frutescens cultivars

Argyranthemum frutescens is a commercially important ornamental species with extensive breeding programmes in several countries. Since it is vegetatively propagated there is a great need for tools for identification of cultivars. Vegetatively propagated species require clean-up from diseases, often performed through meristem-tip cultures. Forty-three cultivars of A. frutescens propagated by meristem-tip culture and traditional cuttings were analyzed for genetic relatedness and possible somaclonal variation using AFLP. Five primer combinations resulted in a relatively high degree of polymorphism. Ten molecular markers generated by one primer combination could distinguish between all 43 cultivars. Differences in fingerprints between meristem-tip culture and cuttings from the same cultivars were found, but the proportion of fragments being specific for either tissue culture or cuttings was relatively low. Some cultivars that did not display somaclonal variation as judged by the AFLP-fingerprints may still be genetically unstable since some morphological variation was observed in the true to type test.     

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。     

Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs)

Sequence related amplified polymorphism (SRAP) markers were used to detect molecular marker polmorphisms among 86 citrus and their relatives in Aurantioidea. Twenty-one SRAP primer combinations produced a total of 376 polymorphic fragments with an average of 17.9 per primer combination and an average polymorphism information content (PIC) of 0.86. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.28 to 1.00 with a mean of 0.64. The subtribe Clauseninae (tribe Clauseneae) separated from the subtribes of the tribe Citreae. The subtribe Balsamocitrinae (tribe Citreae) was the most distant from the others. In the Citrinae, ‘primitive citrus fruit trees’ and ‘near citrus fruit trees’ groups did not clearly separate from each other but all genera in these groups were distinct. On the other hand, subgenus Papeda and subgenus Citrus were not separated clearly in the dendrogram. C. maxima, C. medica and C. reticulata separated into three distinct clusters in agreement with three ‘true basic species’ thesis. Similarity-based analyses supported the theory of few ancestral species in Aurantioidea.     

扁桃种质资源的AFLP分析

利用AFLP分子标记技术对国内外49份扁桃材料的亲缘关系进行了鉴定,使用3对选择性引物组合,每对引物扩增出136条带,并对其进行聚类分析。结果表明,不同种以及不同品种间的遗传距离不同。在相似系数小于0.68时,大多数栽培品种聚为一类,并可将野生扁桃组、苦巴旦组、榆叶梅,以及桃、中国樱桃、欧洲甜樱桃分开。栽培品种中,同一种源区的大多数栽培品种能聚类在一起。我国的扁桃资源与国外的扁桃资源遗传差异较大。     

荔枝品种亲缘关系的AFLP分析

 应用AFLP技术，对39个荔枝品种进行了遗传多样性分析及分类研究。筛选出适于荔枝AFLP分析的最佳引物组合3对，分别为EcoRI AAC+MseI CTG，EcoPd AGC+MseI CAT，EcoRI ACC+Msel CAT。在分子水平上，荔枝品种的遗传多样性并非形态学性状所体现的那样丰富。AFLP分析将39个荔枝品种分成了6组，与传统的以果皮龟裂片隆起类型为分类标准的分类没有一致性。初步建立起荔枝主要栽培品种的分子标记标准图谱。应用AFLP技术对来自两个不同地方的两个荔枝品种(桂味、妃子笑)进行了鉴别。     

Genetic diversity and population genetic structure of pomegranate (Punica granatum L.) in Iran using AFLP markers

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits. It is native to Iran and spread from Iran to other areas. In this study amplified fragment length polymorphism (AFLP) was used to detect intra- and inter-population genetic diversity of pomegranate. A group of 67 accessions belonged to 4 populations from Iran was studied using eight primer combinations. A total of 221 scorable bands were amplified, of which, 118 (54.13%) were polymorphic. Resolving power (Rp) ranged from 5.70 to 9.21, and the average of polymorphism information content (PIC) per primer pair was 0.40. According to Nei's gene diversity and allelic statistics, Isfahan population had a highest genetic diversity (H = 0.3646, I = 0.5327, N_e = 1.6467). Coefficient of gene differentiation between populations (GST) was 0.124, indicated that mainly proportion of genetic variation (87.6%), was within populations and the remaining (12.4%) of the variation was among populations that, also supported by analysis of molecular variance (AMOVA). The gene flow (Nm) varied from 0.969 to 10.404 between pair-wise populations and was 3.504 among all of the populations. The Jaccard similarity coefficient between individuals ranged from 0.26 to 0.88. The UPGMA dendrogram clustered all 67 accessions into 6 groups. In some cases accessions from same region were grouped together but in most cases, there was gene exchange. To study the genetic relationships among populations, a principal coordinate analysis (PCoA) based on Nei's genetic distances was performed. Results of this study showed that AFLP marker can be a useful tool for investigating the genetic diversity of pomegranate genotypes.     

草莓品种亲缘关系的AFLP分子标记分析

 利用AFLP技术对我国国家草莓资源圃内保存的107个草莓品种进行了DNA多态性分析。从64对“2 + 2”引物中筛选出10对引物应用于扩增基因组DNA, 共获得清晰可辨的581条带, 其中412条为多态性带。UPGMA方法聚类分析结果显示, AFLP分子鉴定结果与其系谱关系非常一致, 表明AFLP指纹图谱分析能很好地鉴别草莓品种之间的遗传关系。     

Characterization of Tunisian pomegranate (Punica granatum L.) cultivars using amplified fragment length polymorphism analysis

The amplified fragment length polymorphism (AFLP) analysis of DNA was used to characterize 34 pomegranate cultivars. By using a combination of six primers, a total of 327 markers were scored with a mean of 57.5. The high percentage of polymorphic bands (ppb) of 94.7 and the resolving power (R_p) collective rate value of 129.14 were scored. Data proved that the tested primers were informative to discriminate among cultivars and to survey the genetic diversity in this fruit crop. It has been assumed that the local pomegranate germplasm is characterized by a typically continuous genetic diversity. The derived dendrogram proved that cultivars are clustered independently from their geographical origin and their denomination. In addition, AFLP permitted the generation of a nearly unlimited number of molecular markers that are reliable in differentiating the cultivars and/or the polyclonal varieties.     

Genetic relationships among nine cultivated taxa of Calliandra Benth. (Leguminosae: Mimosoideae) using random amplified polymorphic DNA (RAPD) markers

Random amplified polymorphic DNA (RAPD) marker was used to assess genetic diversity and inter-specific relationships among nine taxa of Calliandra (Leguminosae: Mimosoideae) grown in Indian gardens. DNA from leaf sample was isolated and RAPD analysis was performed using 22 primers. The genetic similarities were analyzed from the dendrogram constructed by the RAPD data using a similarity index which supported the segregation of the nine taxa of the genus into two groups; the sect. Androcallis with seven taxa, viz. C. haematocephala, C. haematocephala var. alba, C. surinamensis, C. tweedii, C. tergemina var. emarginata and C. selloi and sect. Calliandra having two species namely, C. inermis and C. calothyrsus. The intra-generic classification and phylogeny inferred from molecular markers supported the traditional classification of the genus based on morphological characters at the level of sections and series except in case of C. selloi (C. brevipes) which did not show much genetic similarity with C. tweedii and C. surinamensis; all the three species being members of the sect. Androcallis series Androcallis.     

Genetic relationships among loquat cultivars and some wild species of the genus Eriobotrya based on the internal transcribed spacer (ITS) sequences

The phylogenetic relationships among seven wild species and 25 loquat cultivars of genus Eriobotrya were studied by comparing sequences of the internal transcribed spacer (ITS) region. The length of ITS1 region of Eriobotrya was 223 bp and the lengths of ITS2 were ranged from 201 bp to 203 bp. The G + C contents varied from 64.1% to 65.5% in ITS1 and from 68.5% to 72.1% in ITS2. The aligned sequences were analyzed by neighbor-joining (NJ) and maximum parsimony (MP) methods. The ITS1 spacer region comprised 223 characters, of which 44 were variable sites and 34 were parsimony informative sites. The NJ tree had very similar topology to the MP tree. E. malipoensis and E. seguinii had only one different character in ITS2 region and both of them could be the most primitive species of Eriobotrya genus. ITS2 evolved much faster and had more parsimony informative sites than ITS1. ITS2 presented much more precise information about the phylogenetic relationships. Based on ITS2 regions, the evolution order of the studied taxa in this paper could be concluded, which was E. bengalensis f. angustifolia, E. prinoides var. dadunensis, E. prinoides (E. bengalensis), E. dayaoshanensis and E. japonica Lindl.     

Genetic structure of phenotypic variants and somaclones of the genus Cereus (Cactaceae) as revealed by AFLP markers

The amplified fragment length polymorphism (AFLP) technique was used to investigate the genetic relationship among somaclonal variants and cultivated varieties of Cereus at the molecular level. Samples of tortuosus and monstruosus varieties, as well as cacti with typical erect shoots, monstruosus somaclones, and somaclones with erect shoots were analyzed using six AFLP primer pairs. The highest value for genetic diversity was detected among the monstruosus somaclones. High identity values were detected among erect, monstruosus, and tortuosus varieties as well as among erect and monstruosus somaclones. The AFLP markers revealed divergences in the in vitro cultures and in the natural environment (in vivo), and also illustrated the potential of the monstruosus and tortuosus varieties as well as the Cereus somaclones for generating new varieties of ornamental value.     

Genetic diversity and phylogenic relationships in date-palms (Phoenix dactylifera L.) as assessed by random amplified microsatellite polymorphism markers (RAMPOs)

Random amplified microsatellite polymorphisms (RAMPOs) were used to assess genetic diversity among 30 date-palm cultivars and 10 male trees. Using 18 primers combinations, 197 bands were scored and 186 were polymorphic suggesting the high level of polymorphism among studied cultivars. Moreover, taking into account the high percentage of polymorphic bands (ppb), the resolving power (R_p) together with the polymorphism information content (PIC) scored values, all the tested primer sets contribute strongly in the discrimination of date-palm genotypes. In addition, the topology of the derived UPGMA dendrogram exhibited cultivars’ clustering made independently both from the geographical origin and/or from the sex of trees. The present data support the Mesopotamian origin of the date-palm domestication. Thus we assume that the used method is efficient to assess genetic diversity within date-palm cultivars. Data are discussed in relation with the opportunity of the RAMPO method to provide additional molecular markers suitable in the improvement of the date-palms germplasm characterisation.     

Analysis of genetic variation in eggplant and related Solanum species using sequence-related amplified polymorphism markers

Collection and characterization of all sorts of germplasm resources are required for the development of new cultivars. Molecular characterization is more reliable than morphological characterization. Here, we employed sequence-related amplified polymorphism (SRAP) markers to evaluate genetic variation in a diverse collection of 56 Solanum accessions. Fifty-five SRAP primer combinations were used and a total of 635 polymorphic bands were observed. Cluster analysis by the unweighted pair-group method with arithmetic averages based on similarity matrices indicated that there were three clusters: (i) S. melongena; (ii) S. aethiopicum; (iii) S. surattense. The coefficients of genetic similarity among all the accessions ranged from 0.04 to 0.96 with an average of 0.73, and averaged 0.78 among S. melongena accessions originated from China, indicating extensive genetic variation. These results demonstrated that SRAP can be efficiently used to estimate genetic diversity and analyze phylogenetic relationship.     

Assessing Rosa persica genetic diversity using amplified fragment length polymorphisms analysis

The genetic diversity among 128 Iranian Rosa persica (R. persica) accessions in the different populations was analyzed. Amplified fragment length polymorphisms (AFLP) technique was used to produce 171 polymorphic fragments. The number of polymorphic loci ranged from 101 to 147 and the polymorphism information content (PIC) varied from 0.289 to 0.073, with an average of 0.16. This shows extreme variability and genetic diversity among the studied R. persica populations. An indirect estimate of the number of migrants per generation (Nm = 0.376) indicated that gene flow was relatively low among populations of the species. Cluster analysis using the UPGMA method grouped all accessions into six clusters. The results did not show relative agreement with the genotypes’ region of origin. Based on an analysis of molecular variance, 48% of the genetic variation of R. persica was within population and 52% was among populations. The present analysis revealed that Iranian R. persica genotypes are highly variable and genetically distinct from their origins. The apparent unique nature of the R. persica genotypes revealed by our results supports the case for the implementation of more intense characterization and conservation strategies, and provides useful information to address breeding programmes and germplasm resource management in Rosa spp.     

Genetic diversity in Apium graveolens and related species revealed by SRAP and SSR markers

Genetic diversity is essential to crop improvement. However, lack of molecular markers prevents the understanding of genetic diversity in celery and related species. In this study, SRAP and SSR markers was firstly used to evaluate genetic variation in 68 accessions of Apium graveolens and related species. A total of 888 bands were generated by 40 primer combinations of SRAP and 32 bands were produced by eight SSR markers. Of the 920 bands, 95.1% were polymorphic between A. graveolens and related species, and 49.2% were polymorphic within A. graveolens. Cluster and structure analysis could distinguish local celery, celery, and related species. These results suggested that both SRAP and SSR technologies can be efficiently used to characterize genetic variation and analyze genetic relationship in celery and related species.     

A preliminary genetic linkage map of chrysanthemum (Chrysanthemum morifolium) cultivars using RAPD,ISSR and AFLP markers

A genetic linkage map of chrysanthemum (Chrysanthemum morifolium) was constructed by genotyping 142 F₁ progeny of the bi-parental cross ‘Yuhualuoying’ × ‘Aoyunhanxiao’ with a combination of RAPD, ISSR and AFLP markers in a double pseudo-testcross mapping strategy. A total of 567 polymorphic markers, including 153 RAPDs, 61 ISSRs and 353 AFLPs, were used in linkage mapping. 336 of 567 (60%) markers were grouped on the two parental maps, leaving 231 (40%) markers unlinked. In the ‘Yuhualuoying’ linkage map, 210 markers including 116 testcross and 94 intercross markers were placed in 12 major and 32 minor (8 triplets and 24 doublets) linkage groups, covering 1034 cM with an average map distance of 6.2 cM between adjacent markers. In ‘Aoyunhanxiao’ linkage map, 190 markers consisting of 113 testcross and 77 intercross markers were resolved into 9 major and 24 minor linkage groups, with genome coverage of 1095 cM and a mean inter-marker separation of 6.9 cM between adjacent markers. Six pairs of homologous linkage groups were established on the basis of 64 intercross markers shared by the two parental maps. The maps lay a foundation for further quantitative traits loci (QTL) mapping and marker-assisted breeding of chrysanthemum.     

Molecular diversity of Chinese Cucurbita moschata germplasm collections detected by AFLP markers

Cucurbita moschata is an important vegetable crop. Although a total of 1032 landraces of C. moschata are maintained in China, little is known about their genetic diversity. Molecular characterization is needed to facilitate the use of this C. moschata germplasm collection in breeding. Seventy-four Chinese accessions and 15 accessions from other countries were selected for evaluation based upon variation in fruit traits and geographical origin of molecular diversity with AFLP analysis. Nine pairs of EcoRI/MseI primers produced 500 fragments, of which 75.57% were polymorphic, indicating a high degree of diversity. The accessions from China were classified into two clusters, which were clearly differentiated from the accessions originating from Mexico, Guatemala, Honduras, and Ecuador. Chinese group genetically more closely related to other Asian countries group (India and Japan). In general, the accessions from the Americas had a greater number of unique loci than those from China. The differences are probably due to a limited number of introductions and genetic drift. The Americas are the center of origin of C. moschata and therefore more diverse. With AFLP analysis, the accessions did not clearly group according to fruit shape; however, sub-clusters exist in acorn- and dumbbell-shaped accessions. The assessment of genetic distance, along with some unique traits among the different genotypes, could be useful in further genetic studies and the selection of the most adequate accessions for use in breeding programs.