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1.
Amplified fragment length polymorphism fingerprinting of 16 banana cultivars (Musa cvs.) 总被引:4,自引:0,他引:4
Banana is one of the most important subtropical crops. The genetic system, however, is relatively unknown and is complicated by specific interhybridization, heterozygosity, and polyploidy, which are common in most clones. These factors make identification of closely related banana cultivars difficult, particularly when sterile. Amplified fragment length polymorphism (AFLP) analysis using eight primer combinations was carried out on 16 banana cultivars. Results showed that AFLP could be used to distinguish the different cultivars by their unique banding patterns. Unique AFLP molecular markers were detected for 12 banana cultivars, which can be used to develop specific probes for identification purposes. The cluster analysis also revealed the need for a link between genotype studies using molecular techniques and the current system of classification of Musa cultivars based purely on morphological traits. 相似文献
2.
Chun Jiang Zhou Hong Zhu Song Jin Hua Li Jian Wei Sun Min De Jin Qi Wen Zhang Bin Wang 《Plant Molecular Biology Reporter》2005,23(1):39-51
The genusPopulus L. (Salicaceae) can be divided into 5 sections with distribution throughout the world. Accurate identification ofPopulus clones and species is essential for effective selection, breeding, and management of genetic resources. In this study, amplified
fragment length polymorphism (AFLP) analysis, which was reported as a reliable technique with high efficiency in detecting
polymorphism, was used to conduct analyses of genetic diversity and variety identification of 44 species, clones, and cultivars
ofPopulus that represent a wide range of breeding and commercially available germplasms. Cluster analysis of the 44 samples was carried
out, and a dendrogram of genetic relatedness was developed on the basis of the AFLP data. DNA fingerprints of the 44 samples
were developed from 12 selected bands amplified with 2 primer combinations (M-CAG/E-TA and M-CAG/E-TC). Each sample has its
unique fingerprint pattern and can be distinguished from the others. Furthermore, 1 specific AFLP band of the cultivarPopulus canadensis cl. Guariento coming from fragments amplified by primer combination M-CTC/E-AG was successfully converted into a sequence-characterized
amplified region (SCAR) marker. The results indicate that AFLP analysis should be considered as the preferred technique for
the study of polymorphism inPopulus. This research is the first report concerning the use of AFLP analysis in genetic diversity and germplasm identification
among all sections ofPopulus. 相似文献
3.
Mukesh K. Dubey Ajit K. Shasany Omp. Dhawan Ashutosh K. Shukla Suman P. S. Khanuja 《Journal of genetics》2010,89(1):9-19
Downy mildew (DM) caused by Peronospora arborescens, is a serious disease in opium poppy (Papaver somniferum), which has a world-wide spread. The establishment of DM-resistant cultivars appears to be a sustainable way to control the
disease. In this paper, we present the results of a study aimed at the identification of amplified fragment length polymorphism
(AFLP) markers for DM-resistance in opium poppy. Three opium poppy genotypes (inbred over about 10 years): Pps-1 (DM-resistant),
Jawahar-16 (DM-susceptible) and H-9 (DM-susceptible) were crossed in a diallel manner and the F1 progeny along with the parents
were subjected to AFLP analysis of chloroplast (cp) and nuclear DNA with seven and nine EcoRI / MseI primer combinations, respectively. cpDNA AFLP analysis identified 24 Pps-1 (DM-resistant)-specific unique fragments that
were found to be maternally inherited in both the crosses, Pps-1 × Jawahar-16 and Pps-1 × H-9. In the case of nuclear DNA
AFLP analysis, it was found that 17 fragments inherited from Pps-1 were common to the reciprocal crosses of both (i) Pps-1
and Jawahar-16 as well as (ii) Pps-1 and H-9. This is the first molecular investigation on the identification of polymorphism
between DM-resistant and DM-susceptible opium poppy genotypes and development of DM-resistant opium poppy genotype-specific
AFLP markers. These AFLP markers could be used in future genetic studies for analysis of linkage to the downy mildew resistance
trait. 相似文献
4.
The results of AFLP study of 14 Capsicum annuum cultivars are presented. In spite of the known low genomic variation of large-fruited sweet pepper, AFLP analysis proved to be suitable for detecting polymorphism and genotyping pepper cultivars. Nine primer pairs were selected to allow identification of the cultivars under study. Among-cultivar polymorphism detectable with these primers was estimated at 16.5%. A characteristic AFLP pattern was obtained for each cultivar. Several cultivar-specific fragments were revealed for seven cultivars. On the basis of the AFLP data, genetic distances between cultivars were determined and a tree was constructed by means of hierarchic cluster analysis (UPGMA) with the Jacquard coefficient. It was assumed that this information is useful in breeding programs involving the cultivars examined. 相似文献
5.
AFLP and RAPDmarkers were employed in sixteen diploid cotton (Gossypium sp) cultivars for genetic diversity estimation and cultivar identification. Polymorphism information content (PIC) and percent polymorphism were found to be more for AFLP markers as compared to RAPD markers. Average Jaccard’s genetic similarity index was found to be almost similar using either AFLP or RAPD markers. All the cultivars could be distinguished from one another using AFLP markers and also by the combined RAPD profiles. Cultivar identification indicators like resolving power, marker index and probability of chance identity of two cultivars suggested the usefulness of AFLP markers over the RAPD markers. AFLP and RAPD analyses revealed limited genetic diversity in the studied cultivars. Cluster analysis of both RAPD and AFLP data produced two clusters, one containing cultivars of G. herbaceum and another containing cultivars of G. arboreum species. Highly positive correlation between cophenetic matrices using RAPD and AFLP markers was observed. AFLP markers were found to be more efficient for genetic diversity estimation, polymorphism detection and cultivar identification. 相似文献
6.
Identification of molecular markers in soybean comparing RFLP,RAPD and AFLP DNA mapping techniques 总被引:16,自引:0,他引:16
Jhy-Jhu Lin Jonathan Kuo Jin Ma James A. Saunders Hunter S. Beard Margaret H. MacDonald William Kenworthy George N. Ude Benjamin F. Matthews 《Plant Molecular Biology Reporter》1996,14(2):156-169
Three different DNA mapping techniques—RFLP, RAPD and AFLP—were used on identical soybean germplasm to compare their ability
to identify markers in the development of a genetic linkage map. Polymorphisms present in fourteen different soybean cultivars
were demonstrated using all three techniques. AFLP, a novel PCR-based technique, was able to identify multiple polymorphic
bands in a denaturing gel using 60 of 64 primer pairs tested. AFLP relies on primers designed in part on sequences for endonuclease
restriction sites and on three selective nucleotides. The 60 diagnostic primer pairs tested for AFLP analysis each distinguished
on average six polymorphic bands. Using specific primers designed for soybean fromEco RI andMse I restriction site sequences and three selective nucleotides, as many as 12 polymorphic bands per primer could be obtained
with AFLP techniques. Only 35% of the RAPD reactions identified a polymorphic band using the same soybean cultivars, and in
those positive reactions, typically only one or two polymorphic bands per gel were found. Identification of polymorphic bands
using RFLP techniques was the most cumbersome, because Southern blotting and probe hybridization were required. Over 50% of
the soybean RFLP probes examined failed to distinguish even a single polymorphic band, and the RFLP probes that did distinguish
polymorphic bands seldom identified more than one polymorphic band. We conclude that, among the three techniques tested, AFLP
is the most useful. 相似文献
7.
Ghada Baraket Khaled Chatti Olfa Saddoud Ahmed Ben Abdelkarim Messaoud Mars Mokhtar Trifi Amel Salhi Hannachi 《Plant Molecular Biology Reporter》2011,29(1):171-184
This study characterises the genetic variability of fig, Ficus carica L., using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. It compares the efficiency
and utility of the two techniques in detecting variation and establishing genetic relationships among Tunisian fig cultivars.
Our results show that using both marker systems, the Tunisian fig germ plasm is characterised by having a large genetic diversity
at the deoxyribonucleic acid level, as most of AFLP bands were detected and all SSR markers were polymorphic. In fact, 351
(342 polymorphic) and 57 (57 polymorphic) bands were detected using AFLP and SSR primers, respectively. SSR markers were the
most polymorphic with an average polymorphic information content value of 0.94, while AFLP markers showed the highest effective
multiplex ratio (56.9) and marker index (45.2). The effective marker index was recorded highest (4.19) for AFLP markers and
lowest (0.70) for the SSR ones. Our results demonstrate that (1) independent as well as combined analyses of cluster analyses
of SSR and AFLP fragments showed that cultivars are clustered independently from their geographical origin, horticultural
classifications and tree sex; (2) the analysis of molecular variance allowed the partitioning of genetic variation within
and among fig groups and showed greater variation within groups and (3) AFLP and SSR markers datasets showed positive correlation.
This study suggests the SSR and AFLP markers are suitable for diversity analysis and cultivars fingerprinting. An understanding
of the genetic diversity and population structure of F. carica in Tunisia can also provide insight into the conservation and management of this species. 相似文献
8.
Selective isolation, molecular identification and AFLP were used to investigate the distribution of the various species of
endophytic and epiphytic Trichoderma associated with banana roots and to compare and contrast their genetic structure. Three specific groups of Trichoderma were observed in the roots of banana. Group one, which made up the largest population, comprised T. asperellum, T. virens, and Hypocrea lixii, which were isolated from both inside and on the surface of the banana roots, while group two, made up of T. atroviride and T. koningiopsis, existed on the surface only. Group three, comprising only T. brevicompactum was isolated from the inside of the roots. The AFLP analysis revealed Nei’s diversity indices of 0.15 and 0.26 for epiphytic
T. asperellum and T. virens, respectively. The index values of 0.11 and 0.11 were obtained for endophytic T. asperellum and T. virens, respectively. The genetic diversity within endophytic T. asperellum and T. virens was lower than that within the epiphytes. This suggests that endophytic Trichoderma has a higher genetic conservation and is compatible with the relatively stable microenvironments inside roots. 相似文献
9.
10.
Khanna Harjeet Becker Doug Kleidon Jennifer Dale James 《Molecular breeding : new strategies in plant improvement》2004,14(3):239-252
Centrifugation-assisted Agrobacterium-mediated transformation (CAAT) protocol, developed using banana cultivars from two economically important genomic groups (AAA and AAB) of cultivated Musa, is described. This protocol resulted in 25-65 plants/50mg of settled cell volume of embryogenic suspension cells, depending upon the Agrobacterium strain used, and gave rise to hundreds of morphologically normal, transgenic plants in two banana cultivars from the two genomic groups. Development of a highly efficient Agrobacterium-mediated transformation protocol for a recalcitrant species like banana, especially the Cavendish group (AAA) cultivars, required the identification and optimisation of the factors affecting T-DNA delivery and subsequent plant regeneration. We used male-flower-derived embryogenic cell suspensions of two banana cultivars (Cavendish and Lady Finger) and Agrobacterium strains AGL1 and LBA4404, harbouring binary vectors carrying hpt (hygromycin phosphotransferase) and gusA (-glucuronidase) or nptII (neomycin phosphotransferase) and a modified gfp (green fluorescent protein) gene in the T-DNA, to investigate and optimise T-DNA delivery and tissue culture variables. Factors evaluated included pre-induction of Agrobacterium, conditions and media used for inoculation and co-cultivation, and the presence of acetosyringone and Pluronic F68 in the co-cultivation media. One factor that led to a significant enhancement in transformation frequency was the introduction of a centrifugation step during co-cultivation. Post co-cultivation liquid-media wash and recovery step helped avoid Agrobacterium overgrowth on filters supporting suspension culture cells. Marker-gene expression and molecular analysis demonstrated that transgenes integrated stably into the banana genome. T-DNA:banana DNA boundary sequences were amplified and sequenced in order to study the integration profile. 相似文献
11.
12.
Single nucleotide polymorphism (SNP) is the most abundant form of genetic variation among individuals within a species. SNPs
can be used as markers for gene discovery and for assessment of diversity. We established a practical strategy for identification
of SNPs in fruiting mei (Prunus mume Sieb. et Zucc.) from amplified fragment length polymorphism (AFLP) fragments. The main modification of this procedure was
optimization of the reamplification of bands excised from an AFLP gel by using a single enzyme (EcoRI) in digestion reaction to generate large AFLP fragments and to lower the number of bands on gels, using lower-concentration
polyacrylamide gels (4%) and loading each sample into 4 continuous lanes, using a newly modified protocol for purification
of AFLP bands from the gel, and using additional cycles for reamplification of AFLP bands. In this study, 15 groups of bands
with identical migration distances from 10 fruiting mei cultivars were selected for purification. Eighty-one of the 150 chosen
bands were successfully reamplified, and 67 of these reamplified polymerase chain reaction products yielded reliable sequences
belonging to 13 groups. The alignment of 13 group sequences yielded 95 SNPs, for a total of 5252 bp. Among these SNPs, 73
were heterozygous in the loci of some individual cultivars. The SNP distribution was 58% transition, 40% transversion, and
2% indels. There was also 1 dinucleotide polymorphism and 1 tetranucleotide deletion. 相似文献
13.
Establishment of AFLP technique and assessment of primer combinations for mei flower 总被引:2,自引:0,他引:2
Chaodong Yang Junwei Zhang Qiang Xu Caifeng Xiong Manzhu Bao 《Plant Molecular Biology Reporter》2005,23(1):79-80
Mei flower is one of the most famous ornamental flowers in eastern Asia for its blossoming in early spring. Amplified fragment
length polymorphism (AFLP) is one of the most frequently used techniques for analysis of genetic variation and is used herein
for the first time inPrunus mume. This research provides a detailed and modified AFLP protocol for Mei genomic DNA digested withEcoRI/PstI restriction endonuclease combinations. The 10 best primer pairs of high polymorphism were screened from 256 primer combinations
that could reliably and repetitively distinguish 14 Mei samples and would be suitable for genetic analysis of more cultivars.
Ten primer pairs produced up to a total of 524 AFLP bands and up to 233 polymorphic bands. The ratio of polymorphic bands
scoped from 35.71% to 59.67%, and the average ratio was 44.46% in the 10 primers. AFLP is an effective, inexpensive, and timesaving
technique for the genetic differentiation of the Mei cultivars, as evidenced in this study. 相似文献
14.
Susan Groenewald Noëlani Van Den Berg Walter F.O. Marasas Altus Viljoen 《Mycological Research》2006,110(3):297-305
Fusarium oxysporum f. sp. cubense (Foc) is responsible for fusarium wilt of bananas. The pathogen consists of several variants that are divided into three races and 21 vegetative compatibility groups (VCGs). Several DNA-based techniques have previously been used to analyse the worldwide population of Foc, sometimes yielding results that were not always consistent. In this study, the high-resolution genotyping method of AFLP is introduced as a potentially effective molecular tool to investigate diversity in Foc at a genome-wide level. The population selected for this study included Foc isolates representing different VCGs and races, isolates of F. oxysporum f. sp. dianthi, a putatively non-pathogenic biological control strain F. oxysporum (Fo47), and F. circinatum. High-throughput AFLP analysis was attained using five different infrared dye-labelled primer combinations using a two-dye model 4200s LI-COR automated DNA analyser. An average of approx. 100 polymorphic loci were scored for each primer pair using the SAGAMX automated AFLP analysis software. Data generated from five primer pair combinations were combined and subjected to distance analysis, which included the use of neighbour-joining and a bootstrap of 1000 replicates. A tree inferred from AFLP distance analysis revealed the polyphyletic nature of the Foc isolates, and seven genotypic groups could be identified. The results indicate that AFLP is a powerful tool to perform detailed analysis of genetic diversity in the banana pathogen Foc. 相似文献
15.
Genetic diversity among 26 Russian and European cultivars of the common hop (Humulus lupulusL.) was studied using the ISSR–PCR technique. Twenty-one primers used provided amplification of 183 DNA fragments, 106 of which (57.9%) were found to be polymorphic. The ISSR markers, specific for some cultivars were revealed. Based on the genetic distances, cluster analysis was performed and a dendrogram was constructed, on which most of the hop cultivars formed two clusters according to their origin. Advantages of the ISSR–PCR analysis in breeding studies for classification and identification of common hop cultivars are discussed. 相似文献
16.
M. Kavino N. Kumar T. Damodaran S. Harish D. Saravanakumar 《Archives Of Phytopathology And Plant Protection》2013,46(11):1069-1078
Abstract Panama disease of banana (Musa spp) caused by the fungus Fusarium oxysporum f. sp. Cubense (FOC), is a serious constraint both to the commercial production of banana and cultivation for subsistence agriculture. Chemical control is not economically effective and is also hazardous to the environment and human health. Breeding for disease resistance is an alternative strategy, which leads to the development of resistance clones. Field evaluation is the most reliable method of screening for disease resistance, but it is demanding in terms of cost, manpower and space requirements. Another approach of screening hybrids at the sucker's stage (planting material) through biochemical markers has been found to be effective in early identification of resistant hybrids. The resistance mechanisms involving the role of phenol, PAL, oxidative enzymes like peroxidase (PO), polyphenol oxidase (PPO), superoxide dismutase (SOD), catalase and PR-proteins like chitinase, β-1-3 glucanase were studied and they showed relatively higher activity in resistant hybrids than susceptible hybrids. Isozyme analysis of peroxidase (PO) and polyphenol oxidase (PPO) was also carried out in cultivars and hybrids, which revealed the induction of specific isoforms in the resistant hybrids upon challenge inoculation. This could be a useful tool for early identification of F. oxysporum f. sp. cubense resistance banana clones. 相似文献
17.
Genetic similarity among cultivars of Phyllostachys pubescens 总被引:1,自引:0,他引:1
Xin Chun Lin Xiao Sai Ruan Yong Feng Lou Xiao Qin Guo Wei Fang 《Plant Systematics and Evolution》2009,277(1-2):67-73
Phyllostachys pubescens is the most important economic bamboo species in China, which grows widely in the South of China. There are more than ten cultivars in this species but their genetic relationship still remains unknown. We used both amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) techniques to determine genetic similarity among ten cultivars of P. pubescens and two related species. Eight hundred and twenty seven bands, in which 495 are polymorphic, were detected using 15 pairs of AFLP primers whereas total 231 bands, in which 154 bands are polymorphic, were scored using 16 ISSR primers. Statistic analysis showed that the genetic similarity matrices obtained from these two sets of molecular markers had a significant correlation (R = 0.959, P = 0.013). The dendrogram generated with AFLP and ISSR markers could clearly genetically identify ten cultivars of P. pubescens that had high similarity with genetic distances ranging from 0.023 to 0.108, and could be divided into three groups based on their genetic variation and similarity. Our results suggest that these molecular markers are useful to genetically classify cultivars or varieties of a species, particularly a bamboo species. 相似文献
18.
An assessment of the genetic diversity within Ganoderma strains with AFLP and ITS PCR-RFLP 总被引:1,自引:0,他引:1
Ganoderma lucidum is one of the most important medicinal materials and plant pathogens. Because of its specific interhybridization, the genetic background, however, is relatively unclear. It made identification of Ganoderma strains, especially closely related strains difficulty. Amplified fragment length polymorphism (AFLP) using 14 primer combinations and internal transcribed spacer (ITS) PCR-RFLP were used in a comparative study which was designed to investigate the closely related Ganoderma strains genetic relations at molecular level. The analysis of 37 Ganoderma strains showed there were 177 polymorphic AFLP markers and 12 ITS PCR-RFLP markers, and all accessions could be uniquely identified. Among the Ganoderma accessions, similarity coefficients ranged from 0.07692 to 0.99194 in AFLP. The Ganoderma strains formed a tight cluster in nine groups in AFLP whereas seven groups in ITS PCR-RFLP. The cluster analysis revealed that the taxonomical system of subgenus Ganoderma is composed of Sect. Ganoderma and Sect. Phaeonema, and the strain 22 should be a variant form of strain 21. All methods delineated the Ganoderma strains from the different regions seeming to show a greater level of genetic diversity. It indicated that the genotype study at molecular level is a useful complement method to the current classification system of Ganoderma strains based on morphological traits. The congruency of the experiments was analyzed using the biostatistical software DPS V3.01. 相似文献
19.
Castro I D'Onofrio C Martín JP Ortiz JM De Lorenzis G Ferreira V Pinto-Carnide O 《Molecular biotechnology》2012,52(1):26-39
Grapevine germplasm, including 38 of the main Portuguese cultivars and three foreign cultivars, Pinot Noir, Pinot Blanc and Chasselas, used as a reference, and 37 true-to-type clones from the Alvarinho, Arinto, Loureiro, Moscatel Galego Branco, Trajadura and Vinh?o cultivars were studied using AFLP and three retrotransposon-based molecular techniques, IRAP, REMAP and SSAP. To study the retrotransposon-based polymorphisms, 18 primers based on the LTR sequences of Tvv1, Gret1 and Vine-1 were used. In the analysis of 41 cultivars, 517 IRAP, REMAP, AFLP and SSAP fragments were obtained, 83% of which were polymorphic. For IRAP, only the Tvv1Fa primer amplified DNA fragments. In the REMAP analysis, the Tvv1Fa-Ms14 primer combination only produced polymorphic bands, and the Vine-1 primers produced mainly ISSR fragments. The highest number of polymorphic fragments was found for AFLP. Both AFLP and SSAP showed a greater capacity for identifying clones, resulting in 15 and 9 clones identified, respectively. Together, all of the techniques allowed for the identification of 54% of the studied clones, which is an important step in solving one of the challenges that viticulture currently faces. 相似文献
20.
Sirapope Wongniam Jamorn Somana Sasivimon Swangpol Tosak Seelanan Piyarat Chareonsap Supachitra Chadchawan Thaya Jenjittikul 《Biochemical Systematics and Ecology》2010
A large amount of banana genetic resource has been found in Thailand which is believed to be one of the centers of its origins. To assess genetic diversity and determine genetic relationships of edible bananas in Thailand, 110 accessions of banana species and cultivars collected from villages and natural locations were investigated. UPGMA clustering of numerical data from Amplified Fragment Length Polymorphism (AFLP) patterns showed two large groups which corresponded to genome designations of Musa acuminata (AA) and Musa balbisiana (BB), the known ancestors of most edible cultivars. The AFLP data suggested that among Thai bananas, AA and AAA cultivars were closely related to M. acuminata subsp. malaccensis, while some of ‘B’ genome contained ones closely related to wild M. balbisiana in Thailand and some may have been imported. Eight species-specific PCR-based primer pairs, generated from the AFLP results clearly identify ‘A’ and ‘B’ genomes within cultivars and hybrids. The analyses were useful to readily and easily infer progenitors of these cultivars and pronounce wide genetic diversity of the bananas in Thailand. 相似文献