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1.
Genetic and physical mapping of new EST-derived SSRs on the A and B genome chromosomes of wheat 总被引:2,自引:0,他引:2
A. Gadaleta A. Giancaspro S. L. Giove S. Zacheo G. Mangini R. Simeone A. Signorile A. Blanco 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(5):1015-1025
The availability of genetic maps and phenotypic data of segregating populations allows to localize and map agronomically important
genes, and to identify closely associated molecular markers to be used in marker-assisted selection and positional cloning.
The objective of the present work was to develop a durum wheat intervarietal genetic and physical map based on genomic microsatellite
or genomic simple sequence repeats (gSSR) markers and expressed sequence tag (EST)-derived microsatellite (EST-SSR) markers.
A set of 122 new EST-SSR loci amplified by 100 primer pairs was genetically mapped on the wheat A and B genome chromosomes.
The whole map also comprises 149 gSSR markers amplified by 120 primer pairs used as anchor chromosome loci, two morphological
markers (Black colour, Bla1, and spike glaucousness, Ws) and two seed storage protein loci (Gli-A2 and Gli-B2). The majority of SSR markers tested (182) was chromosome-specific. Out of 275 loci 241 loci assembled in 25 linkage groups
assigned to the chromosomes of the A and B genome and 34 remained unlinked. A higher percentage of markers (54.4%), localized
on the B genome chromosomes, in comparison to 45.6% distributed on the A genome. The whole map covered 1,605 cM. The B genome
accounted for 852.2 cM of genetic distance; the A genome basic map spanned 753.1 cM with a minimum length of 46.6 cM for chromosome
5A and a maximum of 156.2 cM for chromosome 3A and an average value of 114.5 cM. The primer sets that amplified two or more
loci mapped to homoeologous as well as to non-homoeologous sites. Out of 241 genetically mapped loci 213 (88.4%) were physically
mapped by using the nulli-tetrasomic, ditelosomic and a stock of 58 deletion lines dividing the A and B genome chromosomes
in 94 bins. No discrepancies concerning marker order were observed but the cytogenetic maps revealed in some cases small genetic
distance covered large physical regions. Putative function for mapped SSRs were assigned by searching against GenBank nonredundant
database using TBLASTX algorithms. 相似文献
2.
Anja Weise Peter Harbarth Uwe Claussen Thomas Liehr 《The journal of histochemistry and cytochemistry》2003,51(4):549-551
Fluorescence in situ hybridization (FISH) on human chromosomes in meta- and interphase is a well-established technique in clinical and tumor cytogenetics and for studies of evolution and interphase architecture. Many different protocols for labeling the DNA probes used for FISH have been published. Here we describe for the first time the successful use of Photoprobe biotin-labeled DNA probes in FISH experiments. Yeast artificial chromosome (YAC) and whole chromosome painting (wcp) probes were tested. 相似文献
3.
4.
In an effort to provide useful information about parasites important in tropical diseases, the WHO has initiated genome mapping projects for a number of parasites. One goal of this effort is to establish physical maps of the genomes of the targeted parasites. Multicellular parasites (helminths) contain various numbers of chromosomes, some large, that condense during the cell cycle. Here Hirohisa Hirai and Phil LoVerde present details of fluorescence in situ hybridization as a means to localize genes and DNA fragments to schistosome chromosomes. Although the techniques presented are for schistosome chromosomes, they are applicable to any system where the chromosomes condense at metaphase. 相似文献
5.
Human genomic mapping has been greatly advanced by the independent development of three new methods: large DNA fragment cloning in yeast artificial chromosomes, amplification from complex DNAs of human specific segments by Alu-PCR, and high-resolution localization of complex DNA probes by fluorescent in situ hybridization. We describe here the combination of these three analytical tools for efficient and accurate localization of randomly screened or especially selected human YAC recombinants to chromosome 11. We map a YAC clone encompassing the pepsinogen A (PGA) locus to 11q13.1-11q13.3. 相似文献
6.
Rütten KB Pietsch C Olek K Neusser M Beukeboom LW Gadau J 《Cytogenetic and genome research》2004,105(1):126-133
Nasonia vitripennis is a small parasitic hymenopteran with a 50-year history of genetic work including linkage mapping with mutant and molecular markers. For the first time we are now able to anchor linkage groups to specific chromosomes. Two linkage maps based on a hybrid cross (N. vitripennis x N. longicornis) were constructed using STS, RAPD and microsatellite markers, where 17 of the linked STS markers were developed from single microdissected banded chromosomes. Based on these microdissections we anchored all linkage groups to the five chromosomes of N. vitripennis. We also verified the chromosomal specificity of the microdissection through in situ hybridization and linkage analyses. This information and technique will allow us in the future to locate genes or QTL detected in different mapping populations efficiently and fast on homologous chromosomes or even chromosomal regions. To test this approach we asked whether QTL responsible for the wing size in two different hybrid crosses (N. vitripennis x N. longicornis and N. vitripennis x N.giraulti) map to the same location. One QTL with a major effect was found to map to the centromere region of chromosome 3 in both crosses. This could indicate that indeed the same gene/s is involved in the reduction of wing in N. vitripennis and N. longicornis. 相似文献
7.
Silahtaroglu A Pfundheller H Koshkin A Tommerup N Kauppinen S 《Cytogenetic and genome research》2004,107(1-2):32-37
Fluorescence in situ hybridization (FISH) is a highly useful technique with a wide range of applications including the delineation of complex karyotypes, prenatal diagnosis of aneuploidies, screening for diagnostic or prognostic markers in cancer cells, gene mapping and gene expression studies. However, it is still a fairly time-consuming method with limitations in both sensitivity and resolution. Locked Nucleic Acids (LNAs) constitute a novel class of RNA analogs that have an exceptionally high affinity towards complementary DNA and RNA. Substitution of DNA oligonucleotide probes with LNA has shown to significantly increase their thermal duplex stability as well as to improve the discrimination between perfectly matched and mismatched target nucleic acids. To exploit the improved hybridization properties of LNA oligonucleotides in FISH, we have designed several LNA substituted oligonucleotide probes specific to different human-specific repetitive elements, such as the classical satellite-2, telomere and alpha-satellite repeats. In the present study we show that LNA modified oligonucleotides are excellent probes in FISH, combining high binding affinity with short hybridization time. 相似文献
8.
Phylogenetic diversity and relationship among Gossypium germplasm using SSRs markers 总被引:1,自引:0,他引:1
Gossypium species represent a vast resource of genetic multiplicity for the improvement of cultivated cotton. To determine genetic
diversity and relationships within a diverse collection of Gossypium, we employed 120 SSR primers on 20 diploid species representing seven basic genome groups of the genus Gossypium, five AD allotetraploid cotton accessions while T. populnea served as an outgroup species. Out of 120 SSR primers, 49 pairs are polymorphic, which produced a total of 99 distinct alleles
with an average of 2.0 alleles per primer pair. A total of 1139 major SSR bands were observed. Genetic similarities among
all the diploid species ranged from 0.582 (between G. herbaceum and G. trilobum) up to 0.969 (between G. arboreum and G. herbaceum). Phylogenetic trees based on genetic similarities were consistent with known taxonomic relationships. The results also indicated
that G. raimondii is the closest living relative of the ancestral D-genome donor of tetraploid species and the A-genome donor is much similar
to the present-day G. herbaceum and G. arboreum. Ancient tetraploid cotton species were formed by hybridizing and chromosome doubling between them, then different tetraploid
cotton species appeared by further geographical and genetic isolation and separating differentiation. The results showed that
SSRs could be an ideal means for the identification of the genetic diversity and relationship of cotton resources at the genomic
level. 相似文献
9.
Ken Sahara Atsuo Yoshido Fukashi Shibata Noriko Fujikawa-Kojima Takuya Okabe Makiko Tanaka-Okuyama Yuji Yasukochi 《Insect biochemistry and molecular biology》2013,43(8):644-653
Since the Bombyx mori genome sequence was published, conserved synteny between B. mori and some other lepidopteran species has been revealed by either FISH (fluorescence in situ hybridization) with BAC (bacterial artificial chromosome) probes or linkage analysis. However, no species belonging to the Noctuidae, the largest lepidopteran family which includes serious polyphagous pests, has been analyzed so far with respect to genome-wide conserved synteny and gene order. For that purpose, we selected the noctuid species Helicoverpa armigera and Mamestra brassicae, both with n = 31 chromosomes. Gene-defined fosmid clones from M. brassicae and BAC clones from a closely related species of H. armigera, Heliothis virescens, were used for a FISH analysis on pachytene chromosomes. We recognized all H. armigera chromosomes from specific cross-hybridization signals of 146 BAC probes. With 100 fosmid clones we identified and characterized all 31 bivalents of M. brassicae. Synteny and gene order were well conserved between the two noctuid species. The comparison with the model species B. mori (n = 28) showed the same phenomenon for 25 of the 28 chromosomes. Three chromosomes (#11, #23 and #24) had two counterparts each in H. armigera and M. brassicae. Since n = 31 is the modal chromosome number in Lepidoptera, the noctuid chromosomes probably represent an ancestral genome organization of Lepidoptera. This is the first identification of a full karyotype in Lepidoptera by means of BAC cross-hybridization between species. The technique shows the potential to expand the range of analyzed species efficiently. 相似文献
10.
D. E. Delaney S. Nasuda T. R. Endo B. S. Gill S. H. Hulbert 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(4):568-573
We have constructed cytologically based physical maps (CBPMs), depicting the chromosomal distribution of RFLP markers, of the group-2 chromosomes of common wheat (Triticum aestivum L. em Thell). Twenty-one homozygous deletion lines for 2A, 2B, and 2D were used to allocate RFLP loci to 19 deletion-interval regions. A consensus CBPM was colinearily aligned with a consensus genetic map of group-2 chromosomes. The comparison revealed greater frequency of recombination in the distal regions. Several molecularly tagged chromosome regions were identified which may be within the resolving power of pulsed-field gel electrophoresis. The CBPMs show that the available probes completely mark the group-2 chromosomes, and landmark loci for sub-arm regions were identified for targeted-mapping. 相似文献
11.
D. E. Delaney S. Nasuda T. R. Endo B. S. Gill S. H. Hulbert 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1995,91(5):780-782
Cytologically based physical maps for the group 3 chromosomes of wheat were constructed by mapping 25 Triticum aestivum deletion lines with 29 T. tauschii and T. aestivum RFLP probes. The deletion lines divide chromosomes 3A, 3B, and 3D into 31 discrete intervals, of which 18 were tagged by marker loci. The comparison of the consensus physical map with a consensus RFLP linkage map of the group 3 chromosomes of wheat revealed a fairly even distribution of marker loci on the long arm, and higher recombination in the distal region. 相似文献
12.
Microsatellite, or simple sequence repeat (SSR), loci can be identified by mining expressed sequence tag (EST) databases, and where these are available, marker development time and expense can be decreased considerably over conventional strategies of probing the entire genome. However, it is unclear whether they provide information on population structure similar to that generated by anonymous genomic SSRs. We performed comparative population genetic analyses between EST-derived SSRs (EST-SSRs) and anonymous SSRs developed from genomic DNA for the same set of populations of the insect Diabrotica virgifera, a beetle in the family Chrysomelidae. Compared with noncoding, nontranscribed regions, EST-SSRs were generally less polymorphic but had reduced occurrence of null alleles and greater cross-species amplification. Neutrality tests suggested the loci were not under positive selection. Across all populations and all loci, the genomic and EST-SSRs performed similarly in estimating genetic diversity, F(IS), F(ST), population assignment and exclusion tests, and detection of distinct populations. These findings, therefore, indicate that the EST-SSRs examined can be used with confidence in future genetic studies of Diabrotica populations and suggest that EST libraries can be added as a valuable source of markers for population genetics studies in insects and other animals. 相似文献
13.
Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers 总被引:1,自引:0,他引:1
Goro Ishikawa Toshiki Nakamura Taizo Ashida Mika Saito Shuhei Nasuda Takashi R. Endo Jianzhong Wu Takashi Matsumoto 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(3):499-514
PCR-based Landmark Unique Gene (PLUG) markers are EST-PCR markers developed based on the orthologous gene conservation between
rice and wheat, and on the intron polymorphisms among the three orthologous genes derived from the A, B and D genomes of wheat.
We designed a total of 960 primer sets from wheat ESTs that showed high similarity with 951 single-copy rice genes. When genomic
DNA of Chinese Spring wheat was used as a template, 872 primer sets amplified one to five distinct products. Out of these
872 PLUG markers, 531 were assigned to one or more chromosomes by nullisomic-tetrasomic analysis. For each wheat chromosome,
the number of loci detected ranged from 32 for chromosome 6A to 73 for chromosome 7D, with an average of 48 loci per chromosome.
Several novel synteny perturbations were identified using deletion bin-mapping of markers. Furthermore, we demonstrated that
PLUG markers can be used as probes to simultaneously identify BAC clones that contain homoeologous regions from all three
genomes.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
14.
Ignacio Tagarro Antonia M. Fernández-Peralta Juan J. González-Aguilera 《Human genetics》1994,93(4):383-388
Classical satellites I, II and III are composed of a mixture of repeated sequences. However, each of them contains a simple family of repeated sequences as a major component. Satellites 2 and 3 are simple families of repeated sequences that form the bulk of human classical satellites II and III, respectively, and are composed of closely related sequences based on tandem repeats of the pentamer ATTCC. For this reason, extensive cross-hybridizations are probably responsible for the similar in situ hybridization patterns obtained for satellites II and III. We have used a fluorescent in situ hybridization method with highly specific oligonucleotides for satellites 2 and 3, respectively, as probes. Our results show that satellite 2 is mainly located on chromosomes 1, 2, 10 and 16, whereas the major domain of satellite 3 is on chromosome 9. Furthermore, minor sites of satellites 2 and 3 are shown. Two-colour in situ hybridizations have enabled us to define the spatial relationships existing between the major domains of both satellites and centromeric alpha satellite sequences. These experiments indicate that the heterochromatin regions of chromosomes 1, 9 and 16 have different molecular organizations. 相似文献
15.
Chromosomal detection of simple sequence repeats (SSRs) using nondenaturing FISH (ND-FISH) 总被引:1,自引:0,他引:1
Simple Sequence Repeats (SSRs) are known to be scattered and present in high number in eukaryotic genomes. We demonstrate
that dye-labeled oligodeoxyribonucleotides with repeated mono-, di-, tri, or tetranucleotide motifs (15-20 nucleotides in
length) have an unexpected ability to recognize SSR target sequences in non-denatured chromosomes. The results show that all
these probes are able to invade chromosomes, independent of the size of the repeat motif, their nucleotide sequence, or their
ability to form alternative B-DNA structures such as triplex DNA. This novel and remarkable property of binding SSR oligonucleotides
to duplex DNA targets permitted the development of a non-denaturing fluorescence in situ hybridization method that quickly
and efficiently detects SSR-enriched chromosome regions in mitotic, meiotic, and polytene chromosome spreads of different
model organisms. These results have implications for genome analysis and for investigating the roles of SSRs in chromosome
structure and function. 相似文献
16.
Human metaphase chromosomes were digested with StuI and subsequently hybridized in situ using chromosome 9 alphoid DNA and classical satellite III DNA as probes. The data obtained suggest that it is not possible to establish a general rule regarding the cytological effects induced by restriction enzymes in particular chromosome regions and that a number of factors, such as DNA sequences, DNA-protein interaction and enzyme structure, play a role in determining such effects. 相似文献
17.
The vast majority of probes used in fluorescence in situ hybridization (FISH) contain repetitive DNA. This DNA is usually
competed out of a hybridization reaction by the addition of an unlabeled blocking agent, Cot-1 DNA. We have successfully removed
repetitive DNA from two complex FISH probe sets: a degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) single
human chromosome library and genomic DNA. The procedure involved hybridizing in solution a DOP-PCR-amplifiable probe set with
a 50-fold excess of biotin-labeled Cot-1 DNA, and capturing the Cot-1 DNA-containing hybrids using streptavidin magnetic particles,
followed by purification and reamplification of the unbound fraction. Probes were checked for depletion of repeats by hybridization
to chromosomes without Cot-1 DNA. Results showed hybridization patterns comparable to those achieved with untreated probes
hybridized with Cot-1 DNA.
Received: 21 January 1997 / Accepted: 2 April 1997 相似文献
18.
19.
Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes 总被引:8,自引:0,他引:8
The short arm of Triticeae homeologous group 1 chromosomes is known to contain many agronomically important genes. The objectives of this study were to physically localize gene-containing regions of the group 1 short arm, enrich these regions with markers, and study the distribution of genes and recombination. We focused on the major gene-rich region ("1S0.8 region") and identified 75 useful genes along with 93 RFLP markers by comparing 35 different maps of Poaceae species. The RFLP markers were tested by gel blot DNA analysis of wheat group 1 nullisomic-tetrasomic lines, ditelosomic lines, and four single-break deletion lines for chromosome arm 1BS. Seventy-three of the 93 markers mapped to group 1 and detected 91 loci on chromosome 1B. Fifty-one of these markers mapped to two major gene-rich regions physically encompassing 14% of the short arm. Forty-one marker loci mapped to the 1S0.8 region and 10 to 1S0.5 region. Two cDNA markers mapped in the centromeric region and the remaining 24 loci were on the long arm. About 82% of short arm recombination was observed in the 1S0.8 region and 17% in the 1S0.5 region. Less than 1% recombination was observed for the remaining 85% of the physical arm length. 相似文献
20.
Intergenomic translocations between wheat, Hordeum chilense and Hordeum vulgare have been obtained in tritordeum background. Advanced lines from the crosses between three disomic chromosome addition lines for chromosome 2Hv, 3Hv, and 4Hv of barley (Hordeum vulgare) in Triticum aestivum cv. Chinese Spring (CS) and hexaploid tritordeum (2n = 6x = 42, AABBHchHch) were analyzed. Multicolor FISH using both genomic DNA from H. chilense and H. vulgare were used to establish the presence and numbers of H. vulgare introgressions into tritordeum. Interspecific H. vulgare/H. chilense and intergeneric wheat/H. vulgare and wheat/H. chilense translocations were identified. Frequencies of plants containing different kinds of intergenomic translocations between chromosome arms are presented. These lines can be useful for introgressing into tritordeum characters of interest from H. vulgare. 相似文献