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1.
Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the
use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting
cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic
diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers
could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging
from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer,
with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The
results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected
among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific
markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism
technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses
considerable potential for studying genetic diversity and relationships among peanut accessions. 相似文献
2.
Relationships among <Emphasis Type="Italic">Leymus</Emphasis> species assessed by RAPD markers 总被引:1,自引:0,他引:1
The DNA genetic diversity of 40 accessions of genus Leymus was analyzed by random amplified polymorphic DNA (RAPD) markers. A total of 352 products were amplified by 34 10-mer arbitrary
primers, among which 337 products (95.74 %) were found to be polymorphic. 5–14 polymorphic bands were amplified by each polymorphic
primer, with an average of 9.91 bands. The data of 352 RAPD bands were used to generate Jaccard’s similarity coefficients
and to construct a dendrogram by means of UPGMA. Great genetic diversity in genus Leymus was observed, the genetic diversity among the different species more abundant than that of the different accessions, and
the different accessions in a species or the species from the same areas were clustered together. 相似文献
3.
4.
K. -H. Ma K. -H. Kim A. Dixit I. -M. Chung J. -G. Gwag T. -S. Kim Y. -J. Park 《Biologia Plantarum》2010,54(2):272-278
The present study describes the assessment of genetic diversity and relationships among 79 Job’s tears (Coix lacrymajobi L.) accessions collected from China and Korea using 17 microsatellite markers. A total of 57 alleles were detected with an
average of 3.4 alleles per locus. A high frequency of rare alleles (36.3 %) was observed within the collection. Values for
observed (HO), expected heterozygosity (HE) and Shannon’s information index (I) within the analysis ranged from 0.00 (GBssrJT183) to 0.81 (GBssrJT130), from 0.01 (GBssrJT170)
to 0.65 (GBssrJT130) and from 0.034 (GBssrJt170) to 1.13 (GBssrJT130), respectively. The locus GBJT130 was the most informative
marker with the highest values for observed and effective alleles as well as for HO, HE and I. Based on the UPGMA algorithm, the majority of the Chinese accessions grouped in one cluster, whereas all the Korean
accessions grouped together in a separate cluster, indicating that Chinese accessions are genetically quite distinct from
Korean accessions. No relation between genetic relatedness among Job’s tears accessions and their place of collection was
observed. Chinese accessions exhibited greater within population polymorphism (P = 95 %, HE = 0.30, I = 0.52) than the accessions from Korea (P = 68 %, HE = 0.13, I =0.24), indicating their potentiality as a reservoir of novel alleles for crop improvement. However, in general
the low diversity within each population indicates a narrow genetic base within our collection. 相似文献
5.
A simple procedure was developed to convertLathyrus sativus defence-related expressed sequence tags (ESTs) into mappable genetic markers by using PCR. Twenty-nine STS primer pairs were
generated on the basis of sequence information from anL. sativus cDNA library. These primers were used to screen for polymorphisms between 2L. sativus accessions, ATC 80878 and ATC 80407, resistant and susceptible, respectively, toMycosphaerella pinodes infection. All 29 primer pairs amplified PCR products in both accessions, 11 of which amplified multiple RAPD-like products.
The remaining 18 primer pairs amplified single monomorphic products. Following cloning, sequencing, and database searches,
17 of 18 PCR products were confirmed to have amplified the targeted genome region. Ten of these 17 STS primer pairs revealed
polymorphisms between ATC 80878 and ATC 80407 when PCR products were digested with a range of restriction endonucleases. These
results suggest that the STS-based PCR analysis will be useful for generating informative molecular markers inL. sativus for future genome mapping experiments. 相似文献
6.
7.
Inter-simple sequence repeat (ISSR) amplification was used to analyze polymorphisms of micro-satellite sequences in the honeysuckle
genome and to evaluate genetic diversity among fourteen Polish and Russian blue honeysuckle accessions (Lonicera caerulea var. edulis, L. caerulea no. 7661, L. caerulea no. 7987, Jolanta, Atut, Wojtek, Czarna, Zielona, Dlinnoplodna, Czelabinka, Signoglazka, N1, N2 and A). The plant material
was selected from the Department of Pomology, the Dendrological Garden in Rogowo (Poland), and breeder collections. A total
of 40 primers, containing different simple sequence repeat motifs, were tested for amplification. Out of the 40 primers, only
11 gave interpretable banding patterns in all blue honeysuckle accessions. A total of 129 ISSR loci were amplified, of which
83 (64%) were polymorphic and 24 (19%) accession-specific. ISSR-PCR with genomic DNA from blue honeysuckle yielded DNA fragments
ranging from 260 to 3250 bp in size. UPGMA cluster analysis with bootstrapping (1000 replications) and used to construct a
dendrogram and to estimate the genetic distances between Lonicera accessions. The ISSR-based phylogeny was consistent with Lonicera caerulea origin based on morphological and phenological evidence. The phylogenetic relationships based on the accession studies and
the breeding usefulness are discussed. 相似文献
8.
Emmanuel Plas Otwe Daniel S. Agyirifo Isaac K. Galyuon John S Heslop-Harrison 《Tropical plant biology》2017,10(2-3):57-67
Cowpea [Vigna unguiculata L. (Walp)] is grown mainly for its protein-rich grains and is consumed in various forms in sub-Saharan Africa. Average grain yield in farmers’ fields is generally low due to a number of biotic and abiotic stresses. One hundred and six cowpea accessions from Ghana, which had previously been evaluated for seedling drought tolerance, were used for this study. This paper attempts to use three multi-locus PCR-based molecular markers; simple sequence repeats (SSR), inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphisms (REMAP), to analyse genetic diversity in the cowpea accessions. Analysis of the polymorphic bands data indicated that 101 alleles were amplified among 121 cowpea genotypes (83.4%) from 16 SSR primer pairs out of a total of 30 SSR primer pairs. Likewisely, a total of 66 (54.5%) polymorphic bands were obtained from IRAP and a total of 114 (94.2%) highly polymorphic bands obtained from REMAP analysis. The outcome indicated the highly polymorphic nature of the DNA markers, as small groups of these molecular markers were found to be able to identify each of the accessions used. Microsatellite markers (SSRs) and retrotransposon-based markers, like IRAP and REMAP, were found to be highly polymorphic and informative, suggesting that genomic fingerprinting has a major role in characterizing populations. 相似文献
9.
Yuvraj Yadav G. R. Lavanya Sushil Pandey Manjusha Verma Chet Ram Lalit Arya 《Acta Physiologiae Plantarum》2016,38(3):75
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. 相似文献
10.
Petr Smýkal Dana Šafářová Milan Navrátil Radmila Dostalová 《Molecular breeding : new strategies in plant improvement》2010,26(3):425-438
Traditional plant breeding relies upon crosses and subsequent selection of genotypes to meet desirable traits. The incorporation
of marker-assisted selection into breeding strategies would result in a reduction in the number of offspring to be propagated,
selected and tested. In the case of pea (Pisum sativum L.), the testing of resistance to viral pathogens such as pea seed-borne mosaic virus (PSbMV) is included in the breeding process. Resistance to the common strains of PSbMV is conferred by a single recessive
gene (eIF4E), localized on LG VI (sbm-1 locus). We have analyzed for variation in the eIF4E genomic sequences from 43 pea varieties and breeding lines, reported as donors of resistance. This enabled a comprehensive
investigation of the eIF4E gene structure and mutations responsible for PSbMV resistance were identified. Subsequently, PCR-based and gene-specific
single nucleotide polymorphism and co-dominant amplicon length polymorphism markers were developed. All together 60 accessions
were analyzed using sequence data and/or allele specific DNA markers. Developed allele specific markers were reproducibly
amplified across a broad spectra of pea varieties and breeding lines. These were found to be 100% accurate in detecting the
presence of the respective alleles when compared to symptomology and ELISA, testing (74% reliable). Hence, these molecular
markers will substantially speed-up PSbMV diagnosis and resistance breeding processes in pea. 相似文献
11.
Anthony F Combes C Astorga C Bertrand B Graziosi G Lashermes P 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(5):894-900
Molecular markers were used to assess polymorphism between and within the genetic bases of coffee (i.e. Typica and Bourbon) spread from Yemen since the early 18th century that have given rise to most arabica cultivars grown world-wide. Eleven Coffea arabica accessions derived from the disseminated bases were evaluated by amplified fragment length polymorphism (AFLP) using 37 primer combinations and simple-sequence repeats (SSRs) produced by six microsatellites. Four cultivars growing in Yemen and 11 subspontaneous accessions collected in the primary centre of diversity of the species were included in the study in order to define their relationship with the accessions derived from the genetic bases of cultivars. One hundred and seven AFLP markers were used to calculate genetic distances and construct a dendrogram. The accessions derived from the disseminated bases were grouped separately, according to their genetic origin, and were distinguished from the subspontaneous accessions. The Yemen cultivars were classified with the Typica-derived accessions. Except for one AFLP marker, all AFLP and SSR markers present in the cultivated accessions were also detected in the subspontaneous accessions. Polymorphism among the subspontaneous accessions was much higher than among the cultivated accessions. It was very low within the genetic bases, confirming the historical documentation on their dissemination. The results enabled a discussion of the genetic diversity reductions that successively occurred during the dissemination of C. arabica from its primary centre of diversity. 相似文献
12.
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
13.
Chandrawati Neha Singh Rajendra Kumar Sujit Kumar P. K. Singh V. K. Yadav S. A. Ranade Hemant Kumar Yadav 《Physiology and Molecular Biology of Plants》2017,23(1):207-219
The present investigation aimed to explore the level of genetic diversity, determine the population structure in a larger set of germplasm of linseed using microsatellite marker and identify linked markers through association mapping. A total of 168 accessions of linseed were evaluated for major agro-economic traits and SSRs markers deployed for diversity assessment. A total of 337 alleles were amplified by 50 SSRs ranging from 2 to 13 with an average of 6.74 ± 2.8 alleles per loci. The neighbor joining based clustering grouped all the accessions into three major clusters that were also confirmed by scatter plot of PCoA. While model based clustering determined four sub-populations (K = 4). Further, analysis of molecular variance analysis considering three population showed that maximum variation (79%) was within the population. We identified one putative SSR marker (Lu_3043) linked with days to 50% flowering through both GLM and MLM analysis of association mapping. The results of this preliminary study revealed genetic diversity, population structure in linseed and linked marker which could be utilized in future breeding program. 相似文献
14.
Moslem Papizadeh Mohammad Roayaei Ardakani Gholamhossein Ebrahimipour Hossein Motamedi 《World journal of microbiology & biotechnology》2010,26(7):1195-1200
Oil-polluted soils were sampled from National Iranian South Oil Company (NISOC) for isolation and screening of C–S and not
C–C targeted Dibenzothiophene (DBT) degrading microorganisms. Microbacterium sp. NISOC-06, a C–S targeted DBT degrading bacterium, was selected and its desulfurization ability was studied in aqueous phase and water-gasoline
biphasic systems. The 16srRNA gene was amplified using universal eubacteria-specific primers, PCR product was sequenced and
the sequence of nearly 1,500 bp 16srDNA was studied. Based on Gas Chromatography results Microbacterium sp. NISOC-06 utilized 94.8% of 1 mM DBT during the 2 weeks of incubation. UV Spectrophotometry and biomass production measurements showed
that the Microbacterium sp. NISOC-06 was not able to utilize DBT as a carbon source. There was no accumulation of phenolic compounds as Gibb’s assay showed. Biomass
production in a biphasic system for which DBT-enriched gasoline was used as the sulfur source indicated the capability of
Microbacterium sp. NISOC-06 to desulfurize gasoline. 相似文献
15.
Cláudia I Lima-Bittencourt Spartaco Astolfi-Filho Edmar Chartone-Souza Fabrício R Santos Andréa MA Nascimento 《BMC microbiology》2007,7(1):58
Background
Chromobacterium violaceum is a free-living bacterium able to survive under diverse environmental conditions. In this study we evaluate the genetic and physiological diversity of Chromobacterium sp. isolates from three Brazilian ecosystems: Brazilian Savannah (Cerrado), Atlantic Rain Forest and Amazon Rain Forest. We have analyzed the diversity with molecular approaches (16S rRNA gene sequences and amplified ribosomal DNA restriction analysis) and phenotypic surveys of antibiotic resistance and biochemistry profiles. 相似文献16.
Bettina Heider Meike S. Andersson Rainer Schultze-Kraft 《Biodiversity and Conservation》2007,16(6):1617-1631
Flemingia macrophylla (Willd.) Kuntze ex Merr., a multi-purpose legume with potential as dry-season forage crop, mainly occurs in subhumid to humid
environments of tropical and subtropical Asia. Despite increasing interest in conservation of germplasm suitable for low-input
production systems information on the genetic diversity of F. macrophylla is extremely scarce. The creation of baseline data is supposed to contribute to more efficient conservation management and
to identify collecting strategies of novel germplasm. Random amplified polymorphic (RAPD) markers were used to investigate
the genetic variation among 37 F. macrophylla accessions. Germplasm analysed in this study originated from Bac Kan province, Northeast Vietnam. Eight primers generated
a total of 47 amplified RAPD loci of which 38 were polymorphic. Jaccard’s similarity coefficients among accessions ranged
from 0.069 to 1 with a mean of 0.67. The UPGMA dendrogram revealed three clusters along with three outliers. No correspondence
between geographic and genetic distance was found (Mantel test: R = 0.21; P = 0.016). Analysis of molecular variance (AMOVA) revealed significant (P < 0.001) differentiation between accessions collected in lowland and upland regions. Results of UPGMA clustering were confirmed
by the pattern of principle coordinates analysis (PCO) plotting. Future collecting strategies should target populations at
large distances and along the altitudinal range. Ex situ conservation should encompass those accessions that showed genetic
divergence. In situ conservation may consist of establishing a system of interconnected population fragments to guarantee
continuing genetic exchange via corridors and of rehabilitating degraded habitats. 相似文献
17.
Background
Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. 相似文献18.
J. R. Demey Elizabeth Gamez Sandy Molina Diógenes Infante 《Plant Molecular Biology Reporter》2004,22(1):29-35
Two DNA-based marker systems, amplified fragment legnth polymorphism (AFLP) and inverse sequence-tagged repeat (ISTR), were
evaluated with respect to their discriminating capacity and efficiency in genetically analyzing henequen (Agave fourcroydes). Samples were taken from a mother plant, sucker-derived daughter plants, and bulbils. ISTR analysis produced more polymorphic
markers than AFLP and had a better capacity for quantifying genetic diversity through an average number of alleles per locus,
expected heterozygosis of polymorphic loci, expected heterozygosity, effective number of alleles per locus, and total number
of effective alleles. ISTR also showed superior discriminatory capacity. 相似文献
19.
Kyung-Ho Ma Nam-Soo Kim Gi-An Lee Sok-Young Lee Ju Kyong Lee Jung Yoon Yi Yong-Jin Park Tae-San Kim Jae-Gyun Gwag Soon-Jae Kwon 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(7):1247-1254
The numbers of SSR markers and their utilization have not been determined and investigated as extensively in Fagopyrum species as compared to other crop species. The current report presents 136 new SSR markers in Fagopyrum esculentum ssp. esculentum and their application to related species in the genus Fagopyrum. Of the 136 SSRs, 10 polymorphic SSR markers were utilized in a genetic diversity analysis of a common buckwheat population
consisting of 41 accessions of diverse origin. The study showed observed (H
O) and expected (H
E) heterozygosities ranging from 0.071 to 0.924 (mean = 0.53) and from 0.073 to 0.902 (mean = 0.412), respectively. Forty-one
of the 136 SSRs amplified sequences in other Fagopyrum species, including the cymosum and urophyllum groups. The phylogenetic relationships revealed using the SSRs was consistent
with results obtained using other marker systems, with one exception. The sequence and diversity information obtained using
these new SSRs and their cross-transferability to related Fagopyrum species will increase our understanding of genetic structures and species relationships within the Fagopyrum genus. 相似文献
20.
M. J. García-Moreno J. M. Fernández-Martínez L. Velasco B. Pérez-Vich 《Molecular breeding : new strategies in plant improvement》2011,28(3):367-379
Genetic control of the synthesis of high gamma-tocopherol (gamma-T) content in the seed oil of safflower (Carthamus tinctorius L.) and development of highly reliable molecular markers for this trait were determined through molecular tagging and candidate
gene approaches. An F2 population was developed by crossing the high gamma-T natural mutant IASC-1 with the CL-1 line (standard,
high alpha-T profile). This population segregated for the partially recessive gene Tph2. Bulked segregant analysis with random amplified polymorphic DNA (RAPD) and microsatellite (SSR) markers revealed linkage
of eight RAPD and one SSR marker loci to the Tph2 gene and allowed the construction of a Tph2 linkage map. RAPD fragments closest to the Tph2 gene were transformed into sequence-characterized amplified region markers. A gamma-T methyltransferase (gamma-TMT) locus
was found to co-segregate with Tph2. The locus/band was isolated, cloned and sequenced and it was confirmed as a gamma-TMT gene. A longer partial genomic DNA
sequence from this gene was obtained. IASC-1 and CL-1 sequence alignment showed one non-synonymous and two synonymous nucleotide
mutations. Intron fragment length polymorphism and insertion-deletion markers based on the gamma-TMT sequence diagnostic for
the Tph2 mutation were developed and tested across 22 safflower accessions, cultivars, and breeding lines. The results from this study
provide strong support for the role of the gamma-TMT gene in determining high gamma-T content in safflower and will assist
introgression of thp2 alleles into elite safflower lines to develop varieties with improved tocopherol composition for specific market niches. 相似文献