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1.
The comparison of RFLP,RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis 总被引:71,自引:0,他引:71
Wayne Powell Michele Morgante Chaz Andre Michael Hanafey Julie Vogel Scott Tingey Antoni Rafalski 《Molecular breeding : new strategies in plant improvement》1996,2(3):225-238
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 相似文献
2.
西瓜(Citrullus lanatus (Thunb.) Mansf.)种质资源的鉴定与评价是对其有效利用的基础.以往的研究表明, 西瓜是一种遗传资源特别狭窄的作物,在用同工酶、RAPD及SSR技术对西瓜种质资源进行鉴定时,发现很难将品种完全区分开来.本研究利用高效可靠的AFLP技术,对30个西瓜核心种质材料进行了遗传分析,最终建立了这30个材料的DNA指纹图谱.在该图谱中,每个材料均有其独特的"指纹",材料之间可以相互区分开来.为了进一步利用AFLP分子标记,将重要抗病种质材料"PI296341"的AFLP特异带转化成了生产上可以直接利用的SCAR标记. 相似文献
3.
综述了限制性长度多态性(RFLP)、随机扩增多态性DNA(RAPD)、扩增片段长度多态性(AFLP)、简单重复序列(SSR)等不同类型分子标记在草莓指纹图谱构建、品种鉴别、遗传多样性、进化、遗传作图以及相关性状的标记等方面的应用,分析了草莓分子标记研究中的关键问题,提出了今后研究方向。 相似文献
4.
Morand-Prieur ME Vedel F Raquin C Brachet S Sihachakr D Frascaria-Lacoste N 《Molecular ecology》2002,11(3):613-617
Restriction fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and simple sequence repeat (SSR or microsatellites) analyses were performed to detect chloroplast DNA polymorphisms between two ash species, Fraxinus excelsior and F. angustifolia. Only one SSR locus was found to be polymorphic, confirming the very close relatedness of these species. Inheritance of this marker was studied in hybrids obtained from controlled crosses between the two tree species. Results indicated, for the first time in Oleaceae, that chloroplasts are maternally inherited. This chloroplast SSR marker is now used concomitantly with nuclear markers to analyse ash populations in sympatric areas. 相似文献
5.
Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR 总被引:10,自引:0,他引:10
Tam SM Mhiri C Vogelaar A Kerkveld M Pearce SR Grandbastien MA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,110(5):819-831
The retrotransposon-based sequence-specific amplification polymorphism (SSAP) marker system was used to assess the genetic diversities of collections of tomato and pepper industrial lines. The utility of SSAP markers was compared to that of amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. On the basis of our results, SSAP is most informative of the three systems for studying genetic diversity in tomato and pepper, with a significant correlation of genetic relationships between different SSAP datasets and between SSAP, AFLP and SSR markers. SSAP showed about four- to ninefold more diversity than AFLP and had the highest number of polymorphic bands per assay ratio and the highest marker index. For tomato, SSAP is more suitable for inferring overall genetic variation and relationships, while SSR has the ability to detect specific genetic relationships. All three marker results for pepper showed general agreement with pepper types. Additionally, retrotransposon sequences isolated from one species can be used in related Solanaceae genera. These results suggest that different marker systems are suited for studying genetic diversity in different contexts depending on the group studied, where discordance between different marker systems can be very informative for understanding genetic relationships within the study group. 相似文献
6.
Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena
in plants. Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation
to phenotypes provide us with requisite landmarks for elucidation of genetic variation. Genetic or DNA based marker techniques
such as RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA), SSR (simple sequence repeats)
and AFLP (amplified fragment length polymorphism) are routinely being used in ecological, evolutionary, taxonomical, phylogenic
and genetic studies of plant sciences. These techniques are well established and their advantages as well as limitations have
been realized. In recent years, a new class of advanced techniques has emerged, primarily derived from combination of earlier
basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques. The newer
methods also incorporate modifications in the methodology of basic techniques to increase the sensitivity and resolution to
detect genetic discontinuity and distinctiveness. The advanced marker techniques also utilize newer class of DNA elements
such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through
increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns
of gene expression and uncover the genetic basis of biological responses. The review details account of techniques used in
identification of markers and their applicability in plant sciences. 相似文献
7.
8.
Zhou C Chen C Cao P Wu S Sun J Jin D Wang B 《Molecular genetics and genomics : MGG》2007,278(6):723-728
Southern corn rust (SCR) is a fungal disease caused by Puccinia polysora Underw, which can infect maize and may result in substantial yield losses in maize production. The maize inbred line Qi319
carries the SCR resistance gene RppQ. In order to identify molecular markers linked to the RppQ gene, several techniques were utilized including random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and
amplified fragment length polymorphism (AFLP). In addition, sequence characterized amplified region (SCAR) techniques combined
with bulked segregant analysis (BSA) were used. Seven RAPD markers, eight SSR markers, and sixty-three AFLP primer combinations
amplified polymorphisms between two parents and two bulk populations. A large F2 population was used for genetic analysis and for fine mapping of the RppQ gene region. One AFLP polymorphic band, M-CAA/E-AGC324, was converted to a SCAR marker, MA7, which was mapped to a position 0.46 cM from RppQ. Finally, the RppQ gene was mapped between the SCAR marker MA7 and the AFLP marker M-CCG/E-AGA157 with distances of 0.46 and 1.71 cM, respectively. 相似文献
9.
Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato 总被引:10,自引:0,他引:10
Milbourne Dan Meyer Rhonda Bradshaw John E. Baird Eileen Bonar Nicky Provan Jim Powell Wayne Waugh Robbie 《Molecular breeding : new strategies in plant improvement》1997,3(2):127-136
The application of AFLPs, RAPDs and SSRs to examine genetic relationships in the primary northwestern European cultivated potato gene pool was investigated. Sixteen potato cultivars were genotyped using five AFLP primer combinations, 14 RAPD primers, and 17 database-derived SSR primer pairs. All three approaches successfully discriminated between the 16 cultivars using a minimum of one assay. Similarity matrices produced for each marker type on the basis of Nei and Li coefficients showed low correlations when compared with different statistical tests. Dendrograms were produced from these data for each marker system. The usefulness of each system was examined in terms of number of loci revealed (effective multiplex ratio, or EMR) and the amount of polymorphism detected (diversity index, or DI). AFLPs had the highest EMR, and SSRs the highest DI. A single parameter, marker index (MI), which is the product of DI and EMR, was used to evaluate the overall utility of each marker system. The use of these PCR-based marker systems in potato improvement and statutory applications is discussed.Abbreviations: PCR, polymerase chain reaction; AFLP, amplified fragment length polymorphism; RAPD, randomly amplified polymorphic DNA; DNA, deoxyribonucleic acid; EMR, effective multiplex ratio; DI, diversity index; MI, marker index; RFLP, restriction fragment length polymorphism. 相似文献
10.
本文介绍了目前在蕈菌研究中的酯酶同工酶标记,RAPD标记,RFLP标记,AFLP标记,简单重复序列标记和电泳核型等分子标记和生化标记在蕈菌遗传育种、菌株鉴定、遗传多样性研究、亲缘关系和基因定位等方面的研究、应用现状,包括原理、应用领域及最新研究进展。 相似文献
11.
Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population 总被引:26,自引:8,他引:18
J. M. Costa A. Corey P. M. Hayes C. Jobet A. Kleinhofs A. Kopisch-Obusch S. F. Kramer D. Kudrna M. Li O. Riera-Lizarazu K. Sato P. Szucs T. Toojinda M.I. Vales R. I. Wolfe 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(2-3):415-424
A phenotypically polymorphic barley (Hordeum vulgare L.) mapping population was developed using morphological marker stocks as parents. Ninety-four doubled-haploid lines were
derived for genetic mapping from an F1 using the Hordeum bulbosum system. A linkage map was constructed using 12 morphological markers, 87 restriction fragment length polymorphism (RFLP),
five random amplified polymorphic DNA (RAPD), one sequence-tagged site (STS), one intron fragment length polymorphism (IFLP),
33 simple sequence repeat (SSR), and 586 amplified fragment length polymorphism (AFLP) markers. The genetic map spanned 1,387
cM with an average density of one marker every 1.9 cM. AFLP markers tended to cluster on centromeric regions and were more
abundant on chromosome 1 (7H). RAPD markers showed a high level of segregation distortion, 54% compared with the 26% observed
for AFLP markers, 27% for SSR markers, and 18% for RFLP markers. Three major regions of segregation distortion, based on RFLP
and morphological markers, were located on chromosomes 2 (2H), 3 (3H), and 7 (5H). Segregation distortion may indicate that
preferential gametic selection occurred during the development of the doubled-haploid lines. This may be due to the extreme
phenotypes determined by alleles at morphological trait loci of the dominant and recessive parental stocks. Several molecular
markers were found to be closely linked to morphological loci. The linkage map reported herein will be useful in integrating
data on quantitative traits with morphological variants and should aid in map-based cloning of genes controlling morphological
traits.
Received: 23 August 2000 / Accepted: 15 December 2000 相似文献
12.
Santiago García-Martínez Lorella Andreani Marta Garcia-Gusano Filippo Geuna Juan J Ruiz 《Génome》2006,49(6):648-656
Cultivated tomato (Solanum lycopersicum L.) germplasm shows limited genetic variation. Many DNA marker systems have been used for genetic diversity studies in wild and cultivated tomatoes, but their usefulness for characterizing phenotypic differences among very closely related cultivars remains uncertain. We have used 19 selected simple sequence repeat (SSR) markers and 7 amplified fragment length polymorphism (AFLP) primer combinations to characterize 48 cultivars of tomato, mainly traditional cultivars from the south-east of Spain. The main types were Solanum lycopersicum L. 'Muchamiel', 'De la pera', and 'Moruno'. The robustness of the dendrograms and the discrimination power reached with each marker type were similar. Unique fingerprinting even of the most closely related tomato cultivars could be obtained using a combination of some SSR and AFLP markers. A better grouping of the 'Muchamiel' cultivars was observed with SSR markers, whereas the grouping of cultivars of 'De la pera' type was best achieved with AFLPs. However, both types of markers adequately grouped cultivars of the main types, confirming the utility of SSR and AFLP markers for the identification of traditional cultivars of tomato. 相似文献
13.
Comparison of Linkage Disequilibrium in Elite European Maize Inbred Lines using AFLP and SSR Markers 总被引:4,自引:0,他引:4
Benjamin Stich Hans P. Maurer Albrecht E. Melchinger Matthias Frisch Martin Heckenberger Jeroen Rouppe van der Voort Johan Peleman Anker P. Sørensen Jochen C. Reif 《Molecular breeding : new strategies in plant improvement》2006,17(3):217-226
Application of association mapping to plant breeding populations has the potential to revolutionize plant genetics. The main
objectives of this study were to (i) investigate the extent and genomic distribution of linkage disequilibrium (LD) between
pairs of amplified fragment length polymorphism (AFLP) markers, (ii) compare these results with those obtained with simple
sequence repeat (SSR) markers, and (iii) compare the usefulness of AFLP and SSR markers for genomewide association mapping
in plant breeding populations. We examined LD in a cross-section of 72 European elite inbred lines genotyped with 452 AFLP
and 93 SSR markers. LD was significant (p < 0.05) for about 15% of the AFLP marker pairs and for about 49% of the SSR marker pairs in each of the two germplasm groups,
flint and dent. In both germplasm groups the ratio of linked to unlinked loci pairs in LD was higher for AFLPs than for SSRs.
The observation of LD due to linkage for both marker types suggested that genome-wide association mapping should be possible
using either AFLPs or SSRs. The results of our study indicated that SSRs should be favored over AFLPs but the opposite applies
to populations with a long history of recombination. 相似文献
14.
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
15.
遗传多样性是生物学研究中的一个重要领域,研究鸡的遗传多样性,不仅能加强生物多样性的保护。同时对起源进化、分类鉴定及遗传育种等都有重要的意义。本文对目前DNA水平鸡的遗传多样性的研究方法和研究进展进行了详细的阐述。重点介绍了DNA分子标记的特征;概括了在鸡遗传多样性分子标记的方法,包括微卫星分子标记(SSR)、扩增片段长度多态性(AFLP)、随机扩增多态性标记(RAPD)、限制性片段长度多态性标记(RFLP)和单核苷酸多态性标记(SNP)。本文综述了最近有关鸡DNA水平的遗传多样性的研究方法在系统学、遗传结构、生物地理等研究中的应用情况;提出在研究鸡遗传多样性时,可根据研究的目的,选择合适的方法。 相似文献
16.
DNA fingerprinting techniques for microorganisms 总被引:13,自引:0,他引:13
Mario Vaneechoutte 《Molecular biotechnology》1996,6(2):115-142
A whole array of DNA-fingerprinting techniques, which provide indirect access to DNA sequence polymorphism in order to assess
species or clonal identity of bacterial organisms or in order to study bacterial genome composition, have been described during
past decades. Nomenclature has been sometimes erroneous and/or confusing, also because of hybrid techniques that combine different
approaches. It can be shown that most techniques study the sequence polymorphism of only the chromosome, or only the plasmid(s)
or only a gene or gene fragment and that the sequence polymorphism is revealed by AFLP (amplified fragment length polymorphism)
or by RFLP (restriction fragment length polymorphism) or by special electrophoresis techniques. Starting from these considerations,
some taxonomy of techniques, which enables more appropriate nomenclature, can be developed. 相似文献
17.
Mastan SG Sudheer PD Rahman H Ghosh A Rathore MS Ravi Prakash Ch Chikara J 《Molecular biology reports》2012,39(4):4383-4390
Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits.
Very few attempts were made to understand the extent of genetic diversity of J. curcas germplasm. In the present study, efforts were made to analyze the genetic diversity among the elite germplasms of J. curcas, selected on the basis of their performance in field using random amplified polymorphic DNA (RAPD), amplified fragment length
polymorphism (AFLP) and simple sequence repeats (SSR). The plants were selected on the basis of height, canopy circumference,
number of seeds per fruit, weight of 100 seeds, seed yield in grams per plant and oil content. Out of 250 RAPD (with 26 primers),
822 AFLP (with 17 primers) and 19 SSR band classes, 141, 346 and 7 were found to be polymorphic, respectively. The percentage
polymorphism among the selected germplasms using RAPD, AFLP and SSR was found to be 56.43, 57.9, and 36.84, respectively.
The Jaccard’s similarity coefficient was found 0.91, 0.90 and 0.91 through RAPD, AFLP and SSR marker systems, respectively.
Principle component analysis (PCA) and dendrogarm analysis of genetic relationship among the germplasm using RAPD, AFLP and
SSR data showed a good correlation for individual markers. The germplasm JCC-11, 12, 13, 14 and 15 whose yield found to be
high were clustered together in dendrogram and PCA analysis though JCC11 is geographically distinct from others. In overall
analysis JCC6 (in RAPD), JCC8 (in AFLP) and JCC 6 and JCC10 (in SSR) were found genetically diverse. Characterization of geographically
distinct and genetically diverse germplasms with varied yield characters is an important step in marker assisted selection
(MAS) and it can be useful for breeding programs and QTL mapping. 相似文献
18.
Dunna Vijay Malvika Dadlani Polumetla Ananda Kumar Siva Kumar Panguluri 《Plant Molecular Biology Reporter》2009,27(3):282-291
Storage of seeds for extended periods causes a number of degradative changes related to the aging process such as decreased
seedling vigor and reduced germination. In this study, molecular markers were used to study the aging process in seeds of
two different plants species. Seeds of three differentially aged seed groups, including control (un-aged), naturally aged,
and accelerated aging, from soybean (Glycine max) and safflower (Carthamus tinctorius) were evaluated for genetic variability using random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism
(AFLP), and simple sequence repeat (SSR) markers. For both plant species, naturally aged and accelerated aged groups clustered
together with RAPD markers, whereas control and naturally aged seeds showed similarity in both AFLP and SSR profiles. Based
on these findings, it can be concluded that observed changes in DNA profiles of seeds from different aged groups did not contribute
to accumulation of genetic variations of the same magnitude. Therefore, seed of similar viability must be selected for molecular
marker analysis for plant variety protection, among other comparative studies. 相似文献
19.
The yellow mustard plant in Northern Shaanxi is a precious germplasm, and the yellow seed trait is controlled by a single recessive gene. In this report, amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) techniques were used to identify markers linked to the brown seed locus in an F(2) population consisting of 1258 plants. After screening 256 AFLP primer combinations and 456 pairs of SSR primers, we found 14 AFLP and 2 SSR markers that were closely linked to the brown seed locus. Among these markers, the SSR marker CB1022 showed codominant inheritance. By integrating markers previously found to be linked to the brown seed locus into the genetic map of the F(2) population, 23 markers were linked to the brown seed locus. The two closest markers, EA02MC08 and P03MC08, were located on either side of the brown seed locus at a distance of 0.3 and 0.5 cM, respectively. To use the markers for the breeding of yellow-seeded mustard plants, two AFLP markers (EA06MC11 and EA08MC13) were converted into sequence-characterized amplified region (SCAR) markers, SC1 and SC2, with the latter as the codominant marker. The two SSR markers were subsequently mapped to the A9/N9 linkage group of Brassica napus L. by comparing common SSR markers with the published genetic map of B. napus. A BLAST analysis indicated that the sequences of seven markers showed good colinearity with those of Arabidopsis chromosome 3 and that the homolog of the brown seed locus might exist between At3g14120 and At3g29615 on this same chromosome. To develop closer markers, we could make use of the sequence information of this region to design primers for future studies. Regardless, the close markers obtained in the present study will lay a solid foundation for cloning the yellow seed gene using a map-based cloning strategy. 相似文献
20.
Thomas C. de Bang Adebola A. Raji Ivan L. Ingelbrecht 《Plant Molecular Biology Reporter》2011,29(3):655-662
Current methods for molecular fingerprinting of cassava (Manihot esculenta Crantz) have limited throughput or are costly, thus preventing the characterization of large germplasm collections such as
those held by the International Agricultural Research Centers or National Research Institutions, which comprise hundreds to
thousands of accessions. Here, we report the development of a fluorescence-based multiplex simple sequence repeat (SSR) marker
kit that enables accurate and cost-effective cassava fingerprinting. The kit comprises 16 SSR markers assembled into five
multiplex panels and was tested on 21 cassava cultivars alongside one accession of Manihot epruinosa, a wild relative. A total of 68 alleles were detected with, on average, 4.25 alleles per locus and a polymorphism information
content of 0.53. The marker kit reported here is comparable to previously published amplified fragment length polymorphism
and SSR marker systems in terms of discriminating power and informativeness while offering significant advantages in speed
and cost of marker analysis. Previous molecular genetic diversity studies have suggested that cassava germplasm collections
contain duplicate entries based on the occurrence of identical genetic profiles. Using the newly developed microsatellite
kit, three out of six putative duplicate accessions could be readily differentiated, showing that these are distinct genotypes.
The relevance of these findings with respect to the characterization and management of large cassava germplasm collections
is discussed. 相似文献