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1.
Conservation of microsatellite loci within the genus Vitis 总被引:7,自引:0,他引:7
G. Di Gaspero E. Peterlunger R. Testolin K. J. Edwards G. Cipriani 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):301-308
Eleven microsatellites isolated from grapevine (Vitis vinifera) were used to study the degree of conservation of these sequences across different Vitis species. Nine microsatellites were newly isolated, the remaining two (VVS2 and VVS5) came from the literature. A preliminary
assay on the conservation of priming sites was carried out on 14 non-V. vinifera species, including relevant taxa for breeding. Parthenocissus quinquefolia was added as representative of a related genus. Cross-species amplification was obtained in 94% of the 176 genotype×locus
tested combinations. Three microsatellite loci were then cloned and sequenced in ten species. The microsatellite repeat was
found present in all cases. The repeat region was often longer in V. vinifera than in the other species. Furthermore the non-source species showed interruptions in the repeat. In spite of these constraints,
which could reduce the polymorphism of microsatellites in non-source species, the results demonstrate the possibility of extending
the use of microsatellite markers to wild germplasm and inter-specific hybrids. Point mutations have been found in microsatellite
flanking regions and these variations have been used to investigate the genetic relationship among taxa. The Neighbor-joining
tree that was obtained on the basis of ten nucleotide variations, showed that there is not a clear cut difference between
American, Asian and European species and that the actual taxonomy which reflects the geographical distribution of species
must most likely be revised. Moreover, in general, nucleotide variations which occur in microsatellite flanking regions provide
new molecular tools for investigating the evolution of species.
Received: 24 October 1999 / Accepted: 11 November 1999 相似文献
2.
Characterization and analysis of microsatellite loci in Elymus caninus (Triticeae: Poaceae) 总被引:4,自引:0,他引:4
G.-L. Sun B. Salomon R. V. Bothmer 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,96(5):676-682
Microsatellites are highly variable DNA sequences that can be used as markers for the genetic analysis of plants. The potential
of microsatellite markers for use in a genetic diversity study in Elymus species was evaluated. Genomic libraries of Elymus caninus were constructed. The libraries were screened with two dinucleotide, (GA)n and (GT)n, and two trinucleotide repeats, (TCT)n
and (CAC)n. A total of 19 positive clones were found for the two dinucleotide repeats; no positive clone was found for the
trinucleotide repeats. Positive clones were sequenced to confirm the presence of microsatellites and to generate polymerase
chain reaction (PCR) primers based on the sequences flanking the microsatellite. All sequenced (GA)n clones have repeats of
n>10; over half of the (GT)n microsatellites have n<10 repeats. Primer pairs were designed and evaluated for 8 selected microsatellites. PCR products were amplified from 15
Elymus caninus accessions. The number of alleles found for the eight loci varied from 1 for ECGA89 and ECGT35 to 13 for ECGA22, as determined by non-denaturing polyacrylamide electrophoresis. Six microsatellite loci were found to be polymorphic in
E. caninus. The eight primer pairs were tested on three other species; seven were successful in amplifying DNA from Elymus alaskanus and E. mutabilis, and four amplified DNA from E. caucasicus. Based on these results, microsatellites appear to be useful markers in detecting variation in E. caninus.
Received: 8 September 1997/Accepted: 6 October 1997 相似文献
3.
Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium 总被引:3,自引:0,他引:3
P. A. Butcher S. Decroocq Y. Gray G. F. Moran 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(8):1282-1290
Microsatellite markers were developed in Acacia mangium Willd. to provide highly variable co-dominant markers for linkage mapping and studies of the breeding system. After an enrichment
procedure 40% of colonies contained microsatellites in contrast with less than 1% from a non-enriched library. The majority
of microsatellite sequences were AC repeats. Co-dominant segregation of alleles in two full-sib crosses of A. mangium was demonstrated at 33 microsatellite loci. The markers were highly variable relative to restriction fragment lengths polymorphisms
(RFLPs). In the two pedigrees 53% of microsatellite loci were fully informative compared with 15% of RFLPs. Based on alleles
detected among four parental genotypes, the microsatellites consisting of dinucleotide repeats were more polymorphic than
those with tri- and tetra-nucleotide repeats. The microsatellite markers were not as transferable across species in the genus
Acacia as RFLPs. Two thirds of the primers developed in A. mangium (subgenus Phyllodineae, section Juliflorae) amplified DNA from other species within the same section but failed to amplify
in species from the subgenus Acacia. The availability of multiallelic, PCR-based, co-dominant microsatellite loci makes possible
efficient studies of gene flow and breeding systems in A. mangium, a species with low allozyme variation.
Received: 30 December 1999 / Accepted: 10 May 2000 相似文献
4.
Merdinoglu Didier Butterlin Giséle Bevilacqua Lucie Chiquet Vincent Adam-Blondon Anne-Françoise Decroocq Stéphane 《Molecular breeding : new strategies in plant improvement》2005,15(4):349-366
Despite their numerous advantages, the use of microsatellites as genetic markers could be limited because of the low number of loci that can be simultaneously analysed per experiment. To increase the information per simple sequence repeat (SSR) assay in the grapevine, we developed a large set of new markers suitable for multiplexing and multi-loading. We produced microsatellite motif-enriched genomic libraries containing preferentially large size inserts which allowed us to design primers generating a wide range of allele sizes in a very standard and unique PCR condition. Three hundred and fifty clones were sequenced and 190 of them (54%) contained microsatellite motifs with suitable flanking regions for primer design. We developed 169 new SSR markers giving suitable signal with fluorescent-based DNA detection. The total number of alleles detected varied from 1 to 8 per locus with an average of 3.5 and the mean expected heterozygosity was 0.544 (range: 0 0.86). Sixty-eight loci (40%) were perfect types, 73 (43%) were imperfect and 28 (17%) were compound or imperfect-compound. The number of alleles generated by perfect and imperfect type loci was positively correlated to the length of the microsatellite motif. Forty-six multiplex sets based on 125 selected loci were developed. Considering their allele size range, up to four PCR multiplex were pooled together for multi-loading. The 169 SSR loci developed in this study represent a new and informative set of markers easy to combine for multiplexing and multi-loading according to the needs of any user and suitable for large scale genetic analyses in grapevine. 相似文献
5.
Molecular characterization and genetic mapping of random amplified microsatellite polymorphism in barley 总被引:10,自引:0,他引:10
J. A. Dávila Y. Loarce E. Ferrer 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(2):265-273
This study has analyzed the molecular basis and genetic behaviour of the polymorphism generated by the amplification of barley
genomic DNA with primers complementary to microsatellites. Primers anchored at the 5′ end, used alone or in combination with
arbitrary sequence primers, generated random amplified microsatellite polymorphisms (RAMPs). Unanchored primers were also
used as single primers in a microsatellite primed-PCR (MP-PCR). Twenty six randomly selected RAMP DNA fragments which showed
polymorphism between the cultivars Steptoe and Morex were cloned and sequenced. All sequences showed the expected repeated
motif at the end of the insert, with the number of repeats ranging from five to ten. Genomic sequences containing low numbers
of microsatellite motifs were preferentially amplified; therefore, only a fraction of the polymorphism could be attributed
to variation in the number of microsatellite motifs at the priming site. Some sequences contained either cryptic simple sequences
or members of families of repeated DNA. Polymorphism at the internal cryptic simple sequences was detected by RAMP bands inherited
as co-dominant markers. Four MP-PCR bands were cloned and sequenced. A number of repeats identical to the primer itself were
found at each end of the insert. Two allelic bands were polymorphic for an internal microsatellite. The potential use of cloned
bands as fingerprinting tools was investigated by employing them as hybridization probes in Southern blots containing digested
barley DNA from a sample of cultivars. RAMP probes produced complex hybridization band patterns. MP-PCR probes produced either
a highly variable single locus or low-copy number loci. Segregations for 31 RAMPs and three MP-PCR bands were studied in a
population of 70 doubled-haploids from the Steptoe/Morex cross. One third of all markers were co-dominantly inherited. Markers
were positioned on an RFLP map and found to be distributed in all barley chromosomes. The new markers enlarged the overall
length of the map to 1408 cM.
Received: 6 May 1998 / Accepted: 20 July 1998 相似文献
6.
K. M. Sefc M. S. Lopes F. Lefort R. Botta K. A. Roubelakis-Angelakis J. Ibáñez I. Pejić H. W. Wagner J. Glössl H. Steinkellner 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(3-4):498-505
Nine microsatellite markers (VVMD5, VVMD7, VVS2, ssrVrZAG21, ssrVrZAG47, ssrVrZAG62, ssrVrZAG64, ssrVrZAG79 and ssrVrZAG83)
were chosen for the analysis of marker information content, the genetic structure of grapevine cultivar gene pools, and differentiation
among grapevines sampled from seven European vine-growing regions (Greece, Croatia, North Italy, Austria and Germany, France,
Spain and Portugal). The markers were found to be highly informative in all cultivar groups and therefore constitute a useful
set for the genetic characterization of European grapevines. Similar and high levels of genetic variability were detected
in all investigated grapevine gene pools. Genetic differentiation among cultivars from different regions was significant,
even in the case of adjacent groups such as the Spanish and Portuguese cultivars. No genetic differentiation could be detected
between vines with blue and white grapes, indicating that they have undergone the processes of cultivar development jointly.
The observed genetic differentiation among vine-growing regions suggested that cultivars could possibly be assigned to their
regions of origin according to their genotypes. This might allow one to determine the geographical origin of cultivars with
an unknown background. The assignment procedure proved to work for cultivars from the higher differentiated regions, as for
example from Austria and Portugal.
Received: 10 April 1999 / Accepted: 25 May 1999 相似文献
7.
The use of microsatellites for germplasm management in a Portuguese grapevine collection 总被引:2,自引:0,他引:2
M. S. Lopes K. M. Sefc E. Eiras Dias H. Steinkellner M. Laimer Câmara Machado A. Câmara Machado 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(3-4):733-739
To initiate the characterization of the Portuguese grapevine genepool, we have genotyped 49 Portuguese grapevine cultivars at 11 microsatellite loci. The markers proved to be informative in the Portuguese cultivars, with expected heterozygosity ranging from 0.67 to 0.84. At most loci, an excess of heterozygous individuals was observed, while the deficiency of heterozygotes at 1 locus (VVMD6) indicated the presence of null alleles. On the basis of the microsatellite allele data several previously assumed synonyms were verified: (1) ’Fernão Pires’=’Maria Gomes’, (2) ’Moscatel de Setúbal’=’Muscat of Alexandria’, (3) ’Boal Cachudo’=’Boal da Madeira’=’Malvasia Fina’, (4) ’Síria’=’Crato Branco’= ’Roupeiro’ and (5) ’Periquita’=’Castelão Francês’=’João de Santarém’=’Trincadeira’. Although the three varieties ’Verdelho da Madeira’, ’Verdelho dos Açores’, and ’Verdelho roxo’ are regarded by the Lista Nacional de Sinónimos as distinct cultivars, they displayed identical SSR profiles at 17 loci and appear to represent types of 1 single cultivar. The genetic profiles of all 49 cultivars were searched for possible parent-offspring groups. The data obtained revealed the descendence of ’Boal Ratinho’ from ’Malvasia Fina’ and ’Síria’. 相似文献
8.
B. Sosinski M. Gannavarapu L. D. Hager L. E. Beck G.J. King C. D. Ryder S. Rajapakse W. V. Baird R. E. Ballard A. G. Abbott 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(3):421-428
Microsatellites have emerged as an important system of molecular markers. We evaluated the potential of microsatellites for
use in genetic studies of peach [Prunus persica (L.) Batsch]. Microsatellite loci in peach were identified by screening a pUC8 genomic library, a λZAPII leaf cDNA library,
as well as through database searches. Primer sequences for the microsatellite loci were tested from the related Rosaceae species
apple (Malus×domestica) and sour cherry (Prunus cerasus L.). The genomic library was screened for CT, CA and AGG repeats, while the cDNA library was screened for (CT)n- and (CA)n-containing clones. Estimates of microsatellite frequencies were determined from the genomic library screening, and indicate
that CT repeats occur every 100 kb, CA repeats every 420 kb, and AGG repeats every 700 kb in the peach genome. Microsatellite-
containing clones were sequenced, and specific PCR primers were designed to amplify the microsatellite- containing regions
from genomic DNA. The level of microsatellite polymorphism was evaluated among 28 scion peach cultivars which displayed one
to four alleles per primer pair. Five microsatellites were found to segregate in intraspecific peach-mapping crosses. In addition,
these microsatellite markers were tested for their utility in cross-species amplification for use in comparative mapping both
within the Rosaceae, and with the un- related species Arabidopsis thaliana L.
Received: 18 June 1999 / Accepted: 6 December 1999 相似文献
9.
J. P. Varghese B. Rudolph M. I. Uzunova W. Ecke 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):115-119
Microsatellite markers have assumed great significance in biological research. The isolation and characterisation of microsatellites
involves DNA library construction and screening, DNA sequencing, primer design and PCR optimisation. When a microsatellite
is situated close to the beginning or end of a cloned fragment, specific primers cannot be designed for one of the flanking
sequences, thus hindering the utilisation of such microsatellites as markers. The present approach was to use one 5′-anchored
primer complementary to the microsatellite sequence in combination with one specific Cy5- labelled primer with a view to retrieving
useful microsatellites, which would otherwise be lost. Six pairs of a 5′ anchored primer and a specific primer were used across
a set of 31 Brassica napus winter cultivars and one accession each of five additional Brassica species. Using laser fluorometry a single labelled product was observed after amplification with each of four primer pairs,
and one primer pair gave two labelled products. Three products corresponded in size with the products expected if 5′ anchoring
was effective, indicating the amplification of locus-specific full-length products including all of the microsatellite repeats.
All six primer pairs showed polymorphisms across the Brassica species examined, but only one primer pair showed polymorphisms within B. napus, making it useful for genetic analysis in rapeseed cultivars. The other primer pairs could be useful in studying gene introgression
into B. napus or for investigating interspecific crosses involving different Brassica species.
Received: 5 August 1999 / Accepted: 1 November 1999 相似文献
10.
The contribution of short repeats of low sequence complexity to large conifer genomes 总被引:6,自引:0,他引:6
A. Schmidt R. L. Doudrick J. S. Heslop-Harrison T. Schmidt 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(1-2):7-14
The abundance and genomic organization of six simple sequence repeats, consisting of di-, tri-, and tetranucleotide sequence
motifs, and a minisatellite repeat have been analyzed in different gymnosperms by Southern hybridization. Within the gymnosperm
genomes investigated, the abundance and genomic organization of micro- and minisatellite repeats largely follows taxonomic
groupings. We found that only particular simple sequence repeat motifs are amplified in gymnosperm genomes, while others such
as (CAC)5 and (GACA)4 are present in only low copy numbers. The variation in abundance of simple sequence motifs reflects a similar situation to
that found in angiosperms. Species of the two- and three-needle pine section Pinus are relatively conserved and can be distinguished from Pinus strobus which belongs to the five-needle pine section Strobus. The hybridization pattern of Picea species, bald cypress and gingko were different from the patterns detected in the Pinus species. Furthermore, sequences with homology to the plant telomeric repeat (TTTAGGG)n have been analyzed in the same set of gymnosperms. Telomere-like repeats are highly amplified within two- and three- needle
pine genomes, such as slash pine (Pinus elliottii Engelm. var. elliottii), compared to P. strobus,
Picea species, bald cypress and gingko. P. elliottii var. elliottii was used as a representative species to investigate the chromosomal organization of telomere-like sequences by fluorescence
in situ hybridization (FISH). The telomere-like sequences are not restricted to the ends of chromosomes; they form large intercalary
and pericentric blocks showing that they are a repeated component of the slash pine genome.Conifers have genomes larger than
20000 Mbp, and our results clearly demonstrate that repeats of low sequence complexity, such to (CA)8, (GA)8, (GGAT)4 and (GATA)4, and minisatellite- and telomere-like sequences represent a large fraction of the repetitive DNA of these species. The striking
differences in abundance and genome organization of the various repeat motifs suggest that these repetitive sequences evolved
differently in the gymnosperm genomes investigated.
Received: 1 October 1999 / Accepted: 3 November 1999 相似文献
11.
Development and characterization of microsatellite markers in Cucumis 总被引:21,自引:0,他引:21
Y. Danin-Poleg N. Reis G. Tzuri N. Katzir 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(1):61-72
This study provides a set of useful SSR markers and describes their development, characterization and application for diversity
studies.Sixty one Cucumis SSR markers were developed, most of them (46) from melon (Cucumis melo L.) genomic libraries. Forty of the markers (30 melon and 10 cucumber SSRs) were evaluated for length polymorphism in a sample
of 13 melon genotypes and 11 cucumber (Cucumis sativus L.) genotypes. PCR-amplification revealed up to six size alleles among the melon genotypes and up to five alleles among the
cucumber genotypes, with mean gene-diversity values of 0.52 and 0.28 for melon and cucumber, respectively. These differences
are in accordance with the known narrower genetic background of the cucumber. SSR data were applied to phylogenetic analysis
among the melon and cucumber genotypes. A clear distinction between the ’exotic’ groups and the sweet cultivated groups was
demonstrated in melon. In cucumber, separation between the two sub-species, C.sativus var. sativus and C.sativus var. hardwickii,was obtained. Conservation of SSR loci between melon and cucumber was proven by sequence comparisons.
Received: 17 April 2000 / Accepted: 16 May 2000 相似文献
12.
P. B. Cregan J. Mudge E. W. Fickus D. Danesh R. Denny N. D. Young 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(5):811-818
The soybean cyst nematode (SCN) (Heterodera glycines Inchinoe) is the most economically significant soybean pest. The principal strategy to reduce or eliminate damage from this
pest is the use of resistant cultivars. Identifying resistant segregants in a breeding program is a difficult and expensive
process which is complicated by the oligogenic nature of the resistance and genetic variability in the pathogen. Fortunately,
resistance at one SCN-resistance locus, rhg1, is generally accepted as a necessity for the development of resistant genotypes using any source of resistance and when challenged
by any SCN race. Thus, the development of SCN resistant cultivars would be expedited if an effective and rapid system were
available to identify breeding lines carrying a resistance allele at the rhg1 locus. In this study we report two simple sequence repeat (SSR) or microsatellite loci that cosegregate and map 0.4 cM from
rhg1. Allelic variation at the first of these loci, BARC-Satt309, distinguished most, if not all, SCN-susceptible genotypes from
those carrying resistance at rhg1 derived from the important SCN-resistance sources ’Peking’, PI 437654, and PI 90763. BARC-Satt309 was also effective in distinguishing
SCN resistance sources PI 88788 and PI 209332 from many, but not all, susceptible genotypes. BARC-Satt309 cannot be used in
marker-assisted selection in populations developed from typical southern US cultivars crossed with the important resistance
sources PI 88788 or PI 209332 because these genotypes all carry the identical allele at the BARC-Satt309 locus. A second SSR
locus, BARC-Sat_168, was developed from a bacterial artificial chromosome (BAC) clone that was identified using the primers
to BARC-Satt309. BARC-Sat_168 distinguished PI 88788 and PI 209332 from southern US cultivars such as ’Lee’, ’Bragg’ and ’Essex’.
Both BARC-Satt309 and BARC-Sat_168 were used to assay lines from SCN-susceptible×SCN-resistant crosses and proved to be highly
effective in identifying lines carrying rhg1 resistance from those carrying the allele for SCN susceptibility at the rhg1 locus.
Received: 5 November 1998 / Accepted: 3 February 1999 相似文献
13.
Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris spp.) 总被引:1,自引:0,他引:1
S. J. Rae C. Aldam I. Dominguez M. Hoebrechts S. R. Barnes K. J. Edwards 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(8):1240-1248
A set of informative simple sequence repeat markers has been identified for use in the marker-assisted breeding of Beta vulgaris. Highly enriched small insert genomic libraries were constructed, consisting of 1536 clones (with inserts of between 250–900
bp). Screening the clones with CA, CT, CAA, CATA and GATA nucleotide-repeat probes revealed positive hybridisation to over
50% of the clones. Of these 340 were sequenced. Primer pairs were designed for sequences flanking the repeats and, of these,
57 pairs revealed length polymorphism with 12 Beta accessions. Heterozygosity levels of the SSR loci ranged from 0.069 to 0.809. Heterozygosity levels were found to be similar
to those detected employing RFLP probes with the same accessions. Phenetic analysis using the markers, indicated relationships
in accordance with known pedigrees. Twenty three of the SSR markers were polymorphic in one or both of two F2 mapping populations, and were placed relative to a framework of RFLP probes. The markers are distributed over all nine linkage
groups of sugar beet.
Received: 14 July 1999 / Accepted: 27 October 1999 相似文献
14.
M. Rossetto A. McLauchlan F. C. L. Harriss R. J. Henry P. R. Baverstock L. S. Lee T. L. Maguire K. J. Edwards 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(6-7):1091-1098
The sequencing of 831 clones from an enriched microsatellite library of Melaleuca alternifolia (Myrtaceae) yielded 715 inserts containing repeat motifs. The majority of these (98%) were dinucleotide repeats or trinucleotide
repeats averaging 22 and 8 repeat motifs respectively. The AG/GA motif was the most common, accounting for 43% of all microsatellites.
From a total of 139 primer pairs designed, 102 produced markers within the expected size range. The majority of these (93)
were polymorphic. Primer pairs were tested on five selected M. alternifolia genotypes. Loci based on dinucleotide repeats detected on average a greater number of alleles (4.2) than those based on trinucleotide
repeats (2.9). The loci described will provide a large pool of polymorphisms useful for population studies, genetic mapping,
and possibly application in other Myrtaceae.
Received: 28 July 1998 / Accepted: 8 October 1998 相似文献
15.
An integrated genetic linkage map of avocado 总被引:5,自引:0,他引:5
D. Sharon P. B. Cregan S. Mhameed M. Kusharska J. Hillel E. Lahav U. Lavi 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(5-6):911-921
An avocado genomic library was screened with various microsatellite repeats. (A/T)n and (TC/AG)n sequences were found to be the most frequent repeats. One hundred and seventy-two positive clones were sequenced successfully
of which 113 were found to contain simple sequence repeats (SSR). Polymerase chain reaction primers were designed to the regions
flanking the SSR in 62 clones. A GenBank search of avocado DNA sequences revealed 1 sequence containing a (CT)10 repeat. A total of 92 avocado-specific SSR markers were screened for polymorphism using 50 offspring of a cross between the
avocado cultivars ‘Pinkerton’ and ‘Ettinger’. Both are standard avocado cultivars which are normally outcrossed and highly
heterozygous. Fifty polymorphic SSR loci, 17 random amplified polymorphic DNA (RAPD) and 23 minisatellite DNA Fingerprint
(DFP) bands were used to construct the avocado genetic map. The resulting data were analyzed with various mapping programs
in order to assess which program best accommodated data from progeny of heterozygous parents. The analyses resulted in 12
linkage groups with 34 markers (25 SSRs, 3 RAPDs and 6 DFP bands) covering 352.6 cM. This initial map can serve as a basis
for developing a detailed genomic map and for detection of linkage between markers and quantitative trait loci.
Received: 2 April 1996 / Accepted: 28 February 1997 相似文献
16.
Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes 总被引:11,自引:0,他引:11
P. B. Cregan J. Mudge E. W. Fickus L. F. Marek D. Danesh R. Denny R. C. Shoemaker B. F. Matthews T. Jarvik N. D. Young 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(6-7):919-928
Simple sequence repeats (SSRs) are versatile DNA markers that are readily assayed and highly informative. Unfortunately,
non-targeted approaches to SSR development often leave large genomic regions without SSR markers. In some cases these same
genomic regions are already populated by other types of DNA markers, especially restriction fragment length polymorphisms
(RFLPs), random amplified polymorphic DNAs (RAPDs), and amplified fragment length polymorphisms (AFLPs). To identify SSR markers
in such regions, bacterial artificial chromosome (BAC) clones can be used as intermediaries. First, one or more BAC clones
in a region of interest are identified through the use of an existing DNA marker. BAC clones uncovered in this initial step
are then used to create a small insert DNA library that can be screened for the presence of SSR-containing clones. Because
BAC inserts are often 100-kb pairs or more in size, most contain one or more SSRs. This strategy was applied to two regions
of the soybean genome near genes that condition resistance to the soybean cyst nematode on molecular linkage groups G and
A2. This targeted approach to identifying new DNA markers can readily be extended to other types of DNA markers, including
single nucleotide polymorphisms.
Received: 13 August 1998 / Accepted: 13 October 1998 相似文献
17.
Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) 总被引:49,自引:0,他引:49
X. Chen S. Temnykh Y. Xu Y. G. Cho S. R. McCouch 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(4):553-567
Ninety-four newly developed microsatellite markers were integrated into existing RFLP framework maps of four rice populations,
including two doubled haploid, a recombinant inbred, and an interspecific backcross population. These simple sequence repeats
(SSR) were predominantly poly(GA) motifs, targetted because of their abundance in rice. They were isolated from a previously
described sheared library and a newly constructed enzyme-digested library. Differences in the average length of poly(GA) tracts
were observed for clones isolated from the two libraries. The length of GA motifs averaged 21 repeat units for clones isolated
from the Tsp-509-digested library, while motifs averaged 17 units for clones from the sheared library. There was no evidence of clustering
of microsatellite markers near centromeres or telomeres. Mapping of the 94 newly developed markers as well as of 27 previously
reported microsatellites provided genome-wide coverage of the 12 chromosomes, with an average distance of 1 SSLP (simple sequence
repeat polymorphism) per 16–20 cM.
Received: 13 February 1997/Accepted: 28 February 1997 相似文献
18.
G. Cipriani G. Lot W.-G. Huang M. T. Marrazzo E. Peterlunger R. Testolin 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(1-2):65-72
We report the sequences of 17 primer pairs of microsatellite loci, which we have cloned and sequenced from two genomic libraries
of peach [Prunus persica (L) Batsch] ‘Redhaven’, enriched for AC/GT and AG/CT repeats respectively. For ten of these microsatellite loci we were able
to demonstrate Mendelian inheritance in a segregating back-cross population; the remainder did not segregate. The polymorphism
of the microsatellites was evaluated in a panel of ten peach genotypes, including true-to-type peaches, nectarines and one
canning-peach. Fifteen microsatellites (88%) were polymorphic showing 2–4 alleles each. The mean heterozygosity, averaged
over all loci, was 0.32 and significantly higher than that reported in the literature for isozymes and molecular markers,
such as RFLPs and RAPDs. We have also assayed the cross-species transportability and found that ten microsatellite (59%) gave
apparently correct amplification in all Prunus species surveyed, namely P. domestica (European plum), P. salicina (Japanese plum), P. armeniaca (apricot), P. dulcis (almond), P. persica var. vulgaris (peach), P. persica var. laevis (nectarine), P. avium (sweet cherry) and P. cerasus (sour cherry), with three of them also being amplified in Malus (apple). The remaining microsatellites gave less-extensive amplification. Because of their appreciable polymorphism and wide
cross-species transportability, most of these new markers can be integrated into the linkage maps which are currently being
constructed in peach, as well as in other stone fruit crops, such as almond, apricot, cherry and plum.
Received: 3 September 1998 / Accepted: 28 November 1998 相似文献
19.
Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci 总被引:20,自引:3,他引:20
H. Akagi Y. Yokozeki A. Inagaki T. Fujimura 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(1):61-67
Microsatellites consisting of AT repeats are highly polymorphic in rice genomes and can be used to distinguish between even
closely related japonica cultivars in Japan. Polymorphisms of 20 microsatellite loci were determined using 59 japonica cultivars,
including both domestic and modern Japanese cultivars. Although the polymorphisms of these 20 microsatellite loci indicated
that the Japanese cultivars were genetically quite similar, microsatellites consisting of AT repeats showed high gene diversity
even among such closely related cultivars. Combinations of these hypervariable microsatellites can be employed to classify
individual cultivars, since the microsatellites were stable within each cultivar. An identification system based on these
highly polymorphic microsatellites could be used to maintain the purity of rice seeds by eliminating contamination. A parentage
diagnosis using 17 polymorphic microsatellite loci clearly demonstrated that plants which carried desired chromosome regions
had been selected in breeding programs. Thus, these hypervariable microsatellites consisting of AT repeats should promote
the selection of plants which carry desired chromosomes from genetically similar parents. Backcrossing could also help to
eliminate unnecessary chromosome regions with microsatellite polymorphisms at an early stage in breeding programs.
Received: 8 July 1996 / Accepted: 12 July 1996 相似文献
20.
G. J. Bryan A. J. Collins P. Stephenson A. Orry J. B. Smith M. D. Gale 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,94(5):557-563
The development of large panels of simple-to-analyse genetic markers for tagging agronomically important genes and diversity
studies in hexaploid bread wheat is an important goal in applied cereal genetic research. We have isolated and sequenced over
200 clones containing microsatellites from the wheat genome and have tested 153 primer pairs for genetic polymorphism using
a panel of ten wheat varieties, including the parents of our main mapping cross. A subset comprising 49 primer pairs detects
76 loci, of which 74 can be unequivocably allocated to one of the wheat chromosomes. A relatively low frequency of the loci
detected are from the D genome, and these loci show less polymorphism than those from the A and B genomes. Generally, the
microsatellites show high levels of genetic polymorphism and an average of 3.5 alleles per locus with an average polymorphism
information content (PIC), value of 0.51. The observed levels of polymorphism are positively correlated with the length of
the microsatellite repeats. A high proportion, approximately two-thirds, of primer pairs designed to detect simple sequence
repeat (SSR) variation in wheat do not generate the expected amplification products and, more significantly, often generate
unresolvable PCR products. In general, our results agree closely with those obtained from other recent studies using microsatellites
in plants.
Received: 19 March 1996 / Accepted: 28 June 1996 相似文献