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1.
Marcio Carvalho de Moretzsohn Mark S Hopkins Sharon E Mitchell Stephen Kresovich Jose Francisco Montenegro Valls Marcio Elias Ferreira 《BMC plant biology》2004,4(1):11
Background
The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors to allotetraploid A. hypogaea. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies. Microsatellite markers may also, to some extent, support phylogenetic inferences. Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives. 相似文献2.
Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species. 相似文献
3.
甘蔗属不同种及优良甘蔗栽培品种的SSR标记遗传多样性分析 总被引:2,自引:0,他引:2
应用21对SSR引物与毛细管电泳技术,分析了52个甘蔗属品种的遗传多样性。共检测出327个SSR标记,平均每对引物检测15.6个。选择141个共显性标记构建SSR标记指纹图谱数据库,利用DNAMAN软件与UPGMA统计方法分析参试材料遗传多样性。DNAMAN软件同源分析显示,新台糖16号与台优1号之间的同源性最高(87%),品种之间最小的同源性为55%;利用UPGMA统计方法可把参试材料分成4个遗传相似性较高的类群。结果表明,SSR标记与毛细管技术的结合,可构建甘蔗种质资源SSR标记指纹图谱、分析甘蔗种质资源遗传多样性。聚类分析显示参试甘蔗材料的遗传基础相近,为了提高甘蔗选育种效率,应拓宽甘蔗选育种亲本的遗传基础,提高杂交栽培品种的抗虫、抗病等特性。 相似文献
4.
Jifeng Tang Samantha J Baldwin Jeanne ME Jacobs C Gerard van der Linden Roeland E Voorrips Jack AM Leunissen Herman van Eck Ben Vosman 《BMC bioinformatics》2008,9(1):374
Background
Simple Sequence Repeat (SSR) or microsatellite markers are valuable for genetic research. Experimental methods to develop SSR markers are laborious, time consuming and expensive. In silico approaches have become a practicable and relatively inexpensive alternative during the last decade, although testing putative SSR markers still is time consuming and expensive. In many species only a relatively small percentage of SSR markers turn out to be polymorphic. This is particularly true for markers derived from expressed sequence tags (ESTs). In EST databases a large redundancy of sequences is present, which may contain information on length-polymorphisms in the SSR they contain, and whether they have been derived from heterozygotes or from different genotypes. Up to now, although a number of programs have been developed to identify SSRs in EST sequences, no software can detect putatively polymorphic SSRs. 相似文献5.
Variability of morphological characters and Inter Simple Sequence Repeat (ISSR) markers is studied in a mixed multispecies
sympatric growth of wild roses in Lugansk province of Ukraine. Several methods of data analysis are used, such as Principal
Coordinates Analysis, cluster analysis (UPGMA), and Bayesian analyses of population structure with the Structure 2.2 and NewHybrids
programs. The results indicate that there are four species growing at the site, viz. R. canina, R. villosa, R. dimorpha, and R. podolica, as well as various hybrids between them. The hybrid nature of the specimens is confirmed by molecular data, however they
are not intermediate between the parental species as to their morphology. The hybrids either coincide morphologically with
one of the parents, or demonstrate novel combinations of diagnostic characters. 相似文献
6.
Development and characterization of EST‐SSR markers for the genus Rhododendron section Brachycalyx (Ericaceae)
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Watanabe Yoichi Shota Sakaguchi Saneyoshi Ueno Nobuhiro Tomaru Koichi Uehara 《Plant Species Biology》2017,32(4):455-459
Simple sequence repeat (SSR) markers were developed from expressed sequence tags (ESTs) for Rhododendron section Brachycalyx in order to elucidate its evolutionary processes and reproductive ecology. Nineteen polymorphic EST‐SSR markers were developed from EST libraries of R. amagianum and R. hyugaense. Polymorphisms for these markers were assessed using four species of section Brachycalyx. The number of alleles ranged from 1 to 14, and the observed and expected heterozygosity ranged from 0.000 to 0.931 and 0.000 to 0.904, respectively. The EST‐SSR markers developed in this study will be useful for elucidating population genetic structure and breeding systems in section Brachycalyx. 相似文献
7.
? Premise of the study: A new set of pomegranate microsatellites was selected and characterized to assess the level of genetic diversity among cultivars and wild genotypes. ? Methods and Results: Nine Simple Sequence Repeat (SSR) markers were obtained using the Microsatellite-AFLP technique and were successfully amplified in 34 genotypes belonging to Italian, Spanish, and Turkish germplasm collections. The number of alleles per locus ranged from 1 to 5, and the total number of alleles was 22. ? Conclusions: Because only a few codominant markers are available for this species, the newly identified SSRs will facilitate genetic diversity studies, fingerprinting, and mapping. In addition, the 9 loci successfully amplified in P. granatum var. nana. No cross transferability was observed for Cuphea micropetala and Lagerstroemia indica (Lythraceae). 相似文献
8.
Samanthi K. Wasala B. M. Prasanna 《Journal of plant biochemistry and biotechnology.》2013,22(4):392-400
Maize (Zea mays L.) harbours significant genetic diversity not only in its centre of origin (Mexico) but also in several countries worldwide, including India, in the form of landraces. In this study, DNA fingerprinting of 48 landrace accessions from diverse regions of India was undertaken using 42 fluorescent dye-labeled Simple Sequence Repeat (SSR) markers, followed by allele resolution using DNA sequencer and analysis of molecular diversity within and among these landraces. The study revealed a large number of alleles (550), with high mean number of alleles per locus (13.1), and Polymorphism Information Content (PIC) of 0.60, reflecting the level of diversity in the landrace accessions. Besides identification of 174 unique alleles in 44 accessions, six highly frequent SSR alleles were detected at six loci (phi014, phi090, phi112, umc1367, phi062 and umc1266) with individual frequencies greater than 0.75, indicating that chromosomal regions harboring these SSR alleles are not selectively neutral. F statistics revealed very high genetic differentiation, population subdivision and varying levels of inbreeding in the landraces. Analysis of Molecular Variance showed that 63 % of the total variation in the accessions could be attributed to within-population diversity, and 37 % represented between population diversity. Cluster analysis of SSR data using Nei’s genetic distance and UPGMA revealed considerable genetic diversity in these populations, although no clear separation of accessions was observed based on their geographic origin. 相似文献
9.
Evaluation of allelic diversity at chloroplast microsatellite loci among common wheat and its ancestral species 总被引:14,自引:0,他引:14
T. Ishii N. Mori Y. Ogihara 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,103(6-7):896-904
Twenty four chloroplast microsatellite loci having more than ten mononucleotide repeats were identified from the entire chloroplast
DNA sequence of common wheat, Triticum aestivum cv Chinese Spring. For each microsatellite, a pair of primers were designed to produce specific PCR products in the range
of 100– 200 bp. The allelic diversity at the microsatellite loci was evaluated using 43 accessions from 11 Triticum and Aegilops species involved in wheat polyploid evolution. Polymorphic banding patterns were obtained at 21 out of 24 chloroplast microsatellite
loci. The three monomorphic microsatellites were found to be located in coding regions. For the polymorphic microsatellites,
the number of alleles per microsatellite ranged from 2 to 7 with an average of 4.33, and the diversity values (H) ranged from
0.05 to 0.72 with an average of 0.47. Significant correlations (P<0.01) were observed between the number of repeats and the number of alleles, and between the number of repeats and diversity
value, respectively. The genetic diversity explained by chloroplast microsatellites and nuclear RFLP markers were compared
using 22 tetraploid accessions. Although the number of alleles for nuclear RFLP markers was found to be higher than that for
chloroplast microsatellites, similar diversity values were observed for both types of markers. Among common wheat and its
ancestral species, the percentages of common chloroplast microsatellite alleles were calculated to examine their phylogenetic
relationships. As a result, Timopheevi wheat species were clearly distinguished from other species, and Emmer and common wheat
species were divided into two main groups, each consisting of a series of wild and cultivated species from tetraploid to hexaploid.
This indicates that the two types of chloroplast genomes of common wheat might have independently originated from the corresponding
types of wild and cultivated Emmer wheat species.
Received: 6 October 2000 / Accepted: 13 March 2001 相似文献
10.
Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.) 总被引:26,自引:0,他引:26
Microsatellite markers containing simple sequence repeats (SSR) are a valuable tool for genetic analysis. Our objective is to augment the existing RFLP map of rice with simple sequence length polymorphisms (SSLP). In this study, we describe 20 new microsatellite markers that have been assigned to positions along the rice chromosomes, characterized for their allelic diversity in cultivated and wild rice, and tested for amplification in distantly related species. Our results indicate that the genomic distribution of microsatellites in rice appears to be random, with no obvious bias for, or clustering in particular regions, that mapping results are identical in intersubspecific and interspecific populations, and that amplification in wild relatives ofOryza sativa is reliable in species most closely related to cultivated rice but becomes less successful as the genetic distance increases. Sequence analysis of SSLP alleles in three relatedindica varieties demonstrated the clustering of complex arrays of SSR motifs in a single 300-bp region with independent variation in each. Two microsatellite markers amplified multiple loci that were mapped onto independent rice chromosomes, suggesting the presence of duplicated regions within the rice genome. The availability of increasing numbers of mapped SSLP markers can be expected to increase the power and resolution of genome analysis in rice. 相似文献
11.
The present study was conducted to test the clonal homogeneity of six month old tissue culture raised plants of grapevine cv. Crimson Seedless using Inter Simple Sequence Repeat (ISSR) and Simple Sequence Repeat (SSR) markers. Visible assessment of these in vitro raised plants maintained in polyhouse did not show any morphological differences among themselves. However, to test the genetic homogeneity of these plants, we screened 50 ISSR primers out of which, 22 primers produced scorable and repeatable bands. These 22 primers were used further for assessing genetic homogeneity of in vitro raised plants of Crimson Seedless. These 22 ISSR primers generated 134 distinct band classes with a total of 3216 scorable bands. All the primers showed uniform banding pattern for all the in vitro raised plants and the mother plant. In case of 5 SSR primers (VS1, VVMD5, VVS2, VMCNG4c8 and VVMD31) used, a total of 288 scorable bands were obtained. The allele sizes ranged from 98 to 254 bp. Allelic composition of 23 in vitro raised plants and the mother plant at 5 SSR loci did not show any polymorphism. The results of the two marker systems in the present study revealed the genetic uniformity among the in vitro raised plants demonstrating the reliability of in vitro propagation system used for the cultivar. 相似文献
12.
Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa 总被引:11,自引:3,他引:8
N. Diwan J. H. Bouton G. Kochert P. B. Cregan 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):165-172
Cultivated alfalfa (Medicago sativa) is an autotetraploid. However, all three existing alfalfa genetic maps resulted from crosses of diploid alfalfa. The current
study was undertaken to evaluate the use of Simple Sequence Repeat (SSR) DNA markers for mapping in diploid and tetraploid
alfalfa. Ten SSR markers were incorporated into an existing F2 diploid alfalfa RFLP map and also mapped in an F2 tetraploid population. The tetraploid population had two to four alleles in each of the loci examined. The segregation of
these alleles in the tetraploid mapping population generally was clear and easy to interpret. Because of the complexity of
tetrasomic linkage analysis and a lack of computer software to accommodate it, linkage relationships at the tetraploid level
were determined using a single-dose allele (SDA) analysis, where the presence or absence of each allele was scored independently
of the other alleles at the same locus. The SDA diploid map was also constructed to compare mapping using SDA to the standard
co-dominant method. Linkage groups were generally conserved among the tetraploid and the two diploid linkage maps, except
for segments where severe segregation distortion was present. Segregation distortion, which was present in both tetraploid
and diploid populations, probably resulted from inbreeding depression. The ease of analysis together with the abundance of
SSR loci in the alfalfa genome indicated that SSR markers should be a useful tool for mapping tetraploid alfalfa.
Received: 10 September 1999 / Accepted: 11 November 1999 相似文献
13.
Saneyoshi Ueno Yuriko Taguchi Nobuhiro Tomaru Yoshihiko Tsumura 《Conservation Genetics》2009,10(5):1477-1485
Fagus crenata Blume is widely distributed throughout Japanese cool-temperate deciduous broad-leaved forests, but there are two divergent
groups of populations in areas with contrasting winter climates separated by Japan’s Central Mountain Range. To facilitate
investigations of adaptive genetic differentiation of the species using potentially functional genes, we have collected Expressed
Sequence Tags and developed Simple Sequence Repeat markers using a cDNA library constructed from cambium and surrounding tissues.
In total, 270 primer pairs were designed, and 87 of the corresponding loci showed polymorphism in 16 individuals, with 2–21
alleles per locus and expected heterozygosities ranging from 0.06 to 0.97. EST-SSR markers developed in the present study
will be useful for genomic analyses of F. crenata populations. 相似文献
14.
Umbreen Shahzad M. Awais Khan Muhammad Jaffar Jaskani Iqrar Ahmad Khan Schuyler S. Korban 《Conservation Genetics》2013,14(6):1161-1172
Moringa is a genus of the tropical flowering plant family Moringaceae containing 13 diverse species. Among the different species, only Moringa oleifera L. is cultivated. This species has great potential in serving as a high-value crop for food, medicinal products, as well as fodder for animals, particularly in developing tropical regions of the world. In this study, the genetic diversity and population structure of world-wide collections of M. oleifera were investigated using DNA markers. A total of 19 microsatellite or simple sequence repeat (SSR) markers along with a partial sequence of the chloroplast gene atpB were used to study genetic diversity within 161 accessions of M. oleifera collected from Asia, Africa, North and South America, and the Caribbean. On average, 8.3 alleles/per SSR were amplified in each accession. A total number of 158 alleles were detected in 131 accessions collected from the wild in Pakistan and from 30 accessions obtained from ECHO (Florida). Observed heterozygosity varied from 0.16 to 0.86, with an average of 0.58, while the average PIC value was 0.59. Partial sequencing of chloroplast genes of 43 of 161 plants generated mixed patterns. These findings have demonstrated that there is a large genetic diversity present in wild collections of M. oleifera collected in Pakistan; whereas low genetic diversity is detected in cultivated accessions obtained from ECHO. Taken together, these results agree with previous reports that M. oleifera is native to the Indo-Pakistan ecological region, and provides sufficient diversity for genetic exploration as well as for genetic improvement efforts. 相似文献
15.
Genetic variation assessment of acid lime accessions collected from south of Iran using SSR and ISSR molecular markers 总被引:1,自引:0,他引:1
Ata Allah Sharafi Asad Asadi Abkenar Ali Sharafi Mohammad Masaeli 《Physiology and Molecular Biology of Plants》2016,22(1):87-95
Iran has a long history of acid lime cultivation and propagation. In this study, genetic variation in 28 acid lime accessions from five regions of south of Iran, and their relatedness with other 19 citrus cultivars were analyzed using Simple Sequence Repeat (SSR) and Inter-Simple Sequence Repeat (ISSR) molecular markers. Nine primers for SSR and nine ISSR primers were used for allele scoring. In total, 49 SSR and 131 ISSR polymorphic alleles were detected. Cluster analysis of SSR and ISSR data showed that most of the acid lime accessions (19 genotypes) have hybrid origin and genetically distance with nucellar of Mexican lime (9 genotypes). As nucellar of Mexican lime are susceptible to phytoplasma, these acid lime genotypes can be used to evaluate their tolerance against biotic constricts like lime “witches’ broom disease”. 相似文献
16.
G. Werlemark M. Uggla H. Nybom 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(3-4):557-563
The dogroses, Rosa sect. Caninae, are polyploid and characterized by their unique meiosis with an unequal number of chromosomes in the male and female gametes.
The pollen cells have 7 chromosomes and the egg cells 21, 28 or 35 depending on the ploidy level of the species. The resulting
matroclinal inheritance was studied with both morphological and molecular markers in a pair of reciprocal crosses between
R. dumalis and R. rubiginosa (2n=35). A canonical discriminant analysis based on seven morphological characters showed only a minor overlapping between
the two progeny groups. In addition, the R. dumalis×R. rubiginosa offspring were more heterogeneous than the offspring from the reciprocal cross in each of the characters analysed. Eleven
RAPD markers specific for the R. dumalis parent and 10 RAPD markers specific for the R. rubiginosa parent were scored in the offspring. Each of the offspring exhibited either all, or all-but-one, of the seed parent markers.
The average number of pollen donor markers found in the offspring was 3.2 (R. dumalis×R. rubiginosa) and 2.7 (R. rubiginosa×R. dumalis). About half of the pollen donor markers were never transmitted to the progeny. This is, to our knowledge, the first time
the highly skewed chromosome distribution in Rosa sect. Caninae has been demonstrated with statistically evaluated morphological data and with molecular markers.
Received: 25 June 1998 / Accepted: 28 July 1998 相似文献
17.
R. K. Varshney M. Baum P. Guo S. Grando S. Ceccarelli A. Graner 《Molecular breeding : new strategies in plant improvement》2010,26(2):229-242
Detection and utilization of genetic variation available in the germplasm collection for crop improvement have been the prime
activities of breeders. Here a set of ICARDA barley germplasm collection comprising of 185 cultivated (Hordeum vulgare L.) and 38 wild (H. spontaneum L.) genotypes originated from 30 countries of four continents was genotyped with 68 single nucleotide polymorphism (SNP)
and 45 microsatellite or simple sequence repeat (SSR) markers derived from genes (expressed sequence tags, ESTs). As two SNP
markers provided 2 and 3 datapoints, a total of 71 SNPs were surveyed that yielded a total of 143 alleles. The number of SSR
alleles per locus ranged from 3 to 22 with an average of 7.9 per marker. Average PIC (polymorphism information content) value
for SSR and SNP markers were recorded as 0.63 and 0.38, respectively. Heterogeneity was recorded at both SNP and SSR loci
in an average of 5.72 and 12.42% accessions, respectively. Genetic similarity matrices for SSR and SNP allelic data were highly
correlated (r = 0.75, P < 0.005) and therefore allelic data for both markers were combined and analyzed for understanding the genetic relationships
among the germplasm surveyed. Majority of clusters/subclusters were found to contain genotypes from the same geographic origins.
While comparing the genetic diversity, the accessions coming from Middle East Asia and North East Asia showed more diversity
as compared to that of other geographic regions. Majority of countries representing Africa, Middle East Asia, North East Asia
and Arabian Peninsula included the genotypes that contained rare alleles. As expected, spontaneum accessions, as compared to vulgare accessions, showed a higher number of total alleles, higher number of alleles per locus, higher effective number of alleles
and higher allelic richness and a higher number of rare alleles were observed. In summary, the examined ICARDA germplasm set
showed ample natural genetic variation that can be harnessed for future breeding of barley as climate change and sustainability
have become important throughout all growing areas of the world, drought/heat tolerance being the most important ones. 相似文献
18.
Development of simple sequence repeat (SSR) markers for the assessment of gene flow between sea beet (Beta vulgaris ssp. maritima) populations 总被引:1,自引:0,他引:1
A. N. Cureton M. J. Burns B. V. Ford‐Lloyd H. J. Newbury 《Molecular ecology resources》2002,2(4):402-403
Molecular markers can be used to estimate gene flow indirectly by monitoring the relative frequency of alleles in adjacent populations. Sea beet (Beta vulgaris ssp. maritima) is a wild plant species found along the coastlines of many European countries and is closely related to cultivated beets. A set of six simple sequence repeat (SSR) markers that are polymorphic in UK populations have been developed for sea beet to assess the problems of indirect measurement of gene flow in these populations. 相似文献
19.
长期以来,螨类主要依靠其形态特征进行系统学研究。DNA标记是指能反映生物个体或物种间基因组中某种差异特征的DNA片段。近年来,DNA标记技术在螨类系统学研究中得到越来越广泛的应用。本文综述了随机扩增多态性RAPD、限制性内切酶片段长度多态性RFLP、微卫星SSR、核酸序列扩增、扩增片段长度多态性AFLP和直接扩增片段长度多态性DALP等6种DNA标记技术在螨类系统学研究中的应用现状及前景。 相似文献
20.
A. C. Chandra-Shekara B. M. Prasanna S. R. Bhat B. B. Singh 《Journal of plant biochemistry and biotechnology.》2007,16(1):23-28
Pearl millet [Pennisetum glaucum (L) R Br] is one of the widely grown cereal crops in the arid and semi-arid regions of Africa and India. We undertook a study to ascertain the genetic diversity in 21 elite inbreds (parental lines of 13 pearl millet hybrids in India) using 20 Random Amplified Polymorphic DNA (RAPD) and 21 Simple Sequence Repeat (SSR) markers. Based on Polymorphism Information Content (PIC) and unique banding profiles, 6 RAPD primers OPD12, OPA16, OPB6, OPA19, OPB5 and OPB1, and 3 SSR markers Xpsmp2208, Xpsmp2223 and Xpsmp2220, were found to be highly discriminative. The PIC values ranged from 0.28 to 0.48 for the RAPD and from 0.24 to 0.60 for the SSR markers. Cluster analysis and principal component analysis of the combined dataset of RAPD and SSR markers indicated moderate genetic divergence among the elite pearl millet germplasm, besides unraveling the genetic relationships among the male sterile lines and the restorers. 相似文献