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1.
Molecular mapping of rice chromosomes 总被引:108,自引:0,他引:108
S. R. McCouch G. Kochert Z. H. Yu Z. Y. Wang G. S. Khush W. R. Coffman S. D. Tanksley 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1988,76(6):815-829
Summary We report the construction of an RFLP genetic map of rice (Oryza sativa) chromosomes. The map is comprised of 135 loci corresponding to clones selected from a PstI genomic library. This molecular map covers 1,389 cM of the rice genome and exceeds the current classical maps by more than 20%. The map was generated from F2 segregation data (50 individuals) from a cross between an indica and javanica rice cultivar. Primary trisomics were used to assign linkage groups to each of the 12 rice chromosomes. Seventy-eight percent of the clones assayed revealed RFLPs between the two parental cultivars, indicating that rice contains a significant amount of RFLP variation. Strong correlations between size of hybridizing restriction fragments and level of polymorphism indicate that a significant proportion of the RFLPs in rice are generated by insertions/delections. This conclusion is supported by the occurrence of null alleles for some clones (presumably created by insertion or deletion events). One clone, RG229, hybridized to sequences in both the indica and javanica genomes, which have apparently transposed since the divergence of the two cultivars from their last common ancestor, providing evidence for sequence movement in rice. As a by product of this mapping project, we have discovered that rice DNA is less C-methylated than tomato or maize DNA. Our results also suggest the notion that a large fraction of the rice genome (approximately 50%) is single copy. 相似文献
2.
The purpose of this study was to construct a comparative RFLP map of an allotetraploid wild rice species, Oryza latifolia, and to study the relationship between the CCDD genome of O. latifolia and the AA genome of O. sativa. A set of RFLP markers, which had been previously mapped to the AA genome of cultivated rice, were used to construct the comparative map. Fifty-eight F2 progeny, which were derived from a single F1 plant, were used for segregation analysis. The comparative RFLP map contains 149 DNA markers, including 145 genomic DNA markers from cultivated rice, 3 cDNA markers from oat, and one known gene (waxy, from maize). Segregation patterns reflected the allotetraploid ancestry of O. latifolia, and the CC and DD genomes were readily distinguished by most probes tested. There is a high degree of conservation between the CCDD genome of O. latifolia and the AA genome of O. sativa based on our data, but some inversions and translocations were noted. 相似文献
3.
Chloroplast DNA insertions into the nuclear genome of rice: the genes,sites and ages of insertion involved 总被引:1,自引:0,他引:1
Rice (Oryza sativa) is one of three predominant grain crops, and its nuclear and organelle genomes have been sequenced. Following genome analysis
revealed many exchanges of DNA sequences between the nuclear and organelle genomes. In this study, a total of 45 chloroplast
DNA insertions more than 2 kb in length were detected in rice nuclear genome. A homologous recombination mechanism is expected
for those chloroplast insertions with high similarity between their flanking sequences. Only five chloroplast insertions with
high sequence similarity between two flanking sequences from an insertion were found in the 45 insertions, suggesting that
rice might follow the non-homologous end-joining (NHEJ) repair of double-stranded breaks mechanism, which is suggested to
be common to all eukaryotes. Our studies indicate that the most chloroplast insertions occurred at a nuclear region characterized
by a sharp change of repetitive sequence density. One potential explanation is that regions such as this might be susceptible
target sites or “hotspots” of DNA damage. Our results also suggest that the insertion of retrotransposon elements or non-chloroplast
DNA into chloroplast DNA insertions may contribute significantly to their fragmentation process. Moreover, based on chloroplast
insertions in nuclear genomes of two subspecies (indica and japonica) of cultivated rice, our results strongly suggest that they diverged during 0.06–0.22 million years ago.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
Chen M Presting G Barbazuk WB Goicoechea JL Blackmon B Fang G Kim H Frisch D Yu Y Sun S Higingbottom S Phimphilai J Phimphilai D Thurmond S Gaudette B Li P Liu J Hatfield J Main D Farrar K Henderson C Barnett L Costa R Williams B Walser S Atkins M Hall C Budiman MA Tomkins JP Luo M Bancroft I Salse J Regad F Mohapatra T Singh NK Tyagi AK Soderlund C Dean RA Wing RA 《The Plant cell》2002,14(3):537-545
Rice was chosen as a model organism for genome sequencing because of its economic importance, small genome size, and syntenic relationship with other cereal species. We have constructed a bacterial artificial chromosome fingerprint–based physical map of the rice genome to facilitate the whole-genome sequencing of rice. Most of the rice genome (~90.6%) was anchored genetically by overgo hybridization, DNA gel blot hybridization, and in silico anchoring. Genome sequencing data also were integrated into the rice physical map. Comparison of the genetic and physical maps reveals that recombination is suppressed severely in centromeric regions as well as on the short arms of chromosomes 4 and 10. This integrated high-resolution physical map of the rice genome will greatly facilitate whole-genome sequencing by helping to identify a minimum tiling path of clones to sequence. Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes. 相似文献
5.
Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population 总被引:13,自引:0,他引:13
Hong-Bin Zhang Sangdun Choi Sung-Sick Woo Zhikang Li Rod A. Wing 《Molecular breeding : new strategies in plant improvement》1996,2(1):11-24
Rice is a leading grain crop and the staple food for over half of the world population. Rice is also an ideal species for genetic and biological studies of cereal crops and other monocotyledonous plants because of its small genome and well developed genetic system. To facilitate rice genome analysis leading to physical mapping, the identification of molecular markers closely linked to economic traits, and map-based cloning, we have constructed two rice bacterial artificial chromosome (BAC) libraries from the parents of a permanent mapping population (Lemont and Teqing) consisting of 400 F9 recombinant inbred lines (RILs). Lemont (japonica) and Teqing (indica) represent the two major genomes of cultivated rice, both are leading commercial varieties and widely used germplasm in rice breeding programs. The Lemont library contains 7296 clones with an average insert size of 150 kb, which represents 2.6 rice haploid genome equivalents. The Teqing library contains 14208 clones with an average insert size of 130 kb, which represents 4.4. rice haploid genome equivalents. Three single-copy DNA probes were used to screen the libraries and at least two overlapping BAC clones were isolated with each probe from each library, ranging from 45 to 260 kb in insert size. Hybridization of BAC clones with chloroplast DNA probes and fluorescent in situ hybridization using BAC DNA as probes demonstrated that both libraries contain very few clones of chloroplast DNA origin and are likely free of chimeric clones. These data indicate that both BAC libraries should be suitable for map-based cloning of rice genes and physical mapping of the rice genome. 相似文献
6.
Characterization and genetic mapping of a short, highly repeated, interspersed DNA sequence from rice (Oryza sativa L.). 总被引:8,自引:0,他引:8
Summary A short, highly repeated, interspersed DNA sequence from rice was characterized using a combination of techniques and genetically mapped to rice chromosomes by restriction fragment length polymorphism (RFLP) analysis. A consensus sequence (GGC)n, where n varies from 13–16, for the repeated sequence family was deduced from sequence analysis. Southern blot analysis, restriction mapping of repeat element-containing genomic clones, and DNA sequence analysis indicated that the repeated sequence is interspersed in the rice genome, and is heterogeneous and divergent. About 200000 copies are present in the rice genome. Single copy sequences flanking the repeat element were used as RFLP markers to map individual repeat elements. Eleven such repeat elements were mapped to seven different chromosomes. The strategy for characterization of highly dispersed repeated DNA and its uses in genetic mapping, DNA fingerprinting, and evolutionary studies are discussed. 相似文献
7.
Alm V Fang C Busso CS Devos KM Vollan K Grieg Z Rognli OA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,108(1):25-40
A genetic linkage map has been constructed for meadow fescue (Festuca pratensis Huds.) (2n=2x=14) using a full-sib family of a cross between a genotype from a Norwegian population (HF2) and a genotype from a Yugoslavian cultivar (B14). The two-way pseudo-testcross procedure has been used to develop separate maps for each parent, as well as a combined map. A total number of 550 loci have been mapped using homologous and heterologous RFLPs, AFLPs, isozymes and SSRs. The combined map consists of 466 markers, has a total length of 658.8 cM with an average marker density of 1.4 cM/marker. A high degree of orthology and colinearity was observed between meadow fescue and the Triticeae genome(s) for all linkage groups, and the individual linkage groups were designated 1F–7F in accordance with the orthologous Triticeae chromosomes. As expected, the meadow fescue linkage groups were highly orthologous and co-linear with Lolium, and with oat, maize and sorghum, generally in the same manner as the Triticeae chromosomes. It was shown that the evolutionary 4AL/5AL translocation, which characterises some of the Triticeae species, is not present in the meadow fescue genome. A putative insertion of a segment orthologous to Triticeae 2 at the top of 6F, similar to the rearrangement found in the wheat B and the rye R genome, was also observed. In addition, chromosome 4F is completely orthologous to rice chromosome 3 in contrast to the Triticeae where this rice chromosome is distributed over homoeologous group 4 and 5 chromosomes. The meadow fescue genome thus has a more ancestral configuration than any of the Triticeae genomes. The extended meadow fescue map reported here provides the opportunity for beneficial cross-species transfer of genetic knowledge, particularly from the complete genome sequence of rice.Communicated by P. Langridge 相似文献
8.
Rhonda J. Honeycutt Bruno W.S. Sobral Michael McClelland Alan G. Atherly 《The Plant journal : for cell and molecular biology》1992,2(1):133-135
The technique of pulsed-field gel electrophoresis (PFE) has been used to study chromosomal regions and entire genomes of several organisms. Techniques are presented for the isolation of high molecular weight DNA from embedded soybean protoplasts and the conditions for separating large DNA fragments using PFE. Digestion was detected by Southern hybridization using single copy nodulin clones. These data are being used to generate a physical map of the nodulin region(s) of the soybean genome. 相似文献
9.
Characterization of rice transformed via an Agrobacterium-mediated inflorescence approach 总被引:4,自引:0,他引:4
Dong Jinjiang Kharb Pushpa Teng Weimin Hall Timothy C. 《Molecular breeding : new strategies in plant improvement》2001,7(3):187-194
Rice inflorescences were inoculated with Agrobacterium tumefaciens strain LBA4404 carrying plasmid pJD4 with application of vacuum infiltration. After co-cultivation, callus was initiated and subjected to hygromycin selection, and plants were regenerated from resistant callus lines. Based on the total number of co-cultivated inflorescences bearing flowers 1 to 3 mm in length, the average frequency for recovering independent transgenic rice plants was at least 30%. Seeds from selfed R0 plants were harvested within 6 months after initiation of the experiments. Genomic DNA blot analysis showed that genes in the T-DNA of the binary plasmid were stably integrated into the rice genome, typically at low copy number. In most, but not all, cases the transgene was transmitted to R1 progeny at a frequency characteristic for Mendelian inheritance of a single dominant trait. For selfed progeny of one two-locus insertion line, reactivation of GUS expression was observed for a single copy locus that segregated from a silenced multicopy locus. For this line and some additional plants, fluorescence in situ hybridization was used to visualize the chromosomal location of the transgene insert. 相似文献
10.
Robert Fjellstrom Anna M. McClung A. Robert Shank 《Molecular breeding : new strategies in plant improvement》2006,17(2):149-157
Pi-z is a disease resistance gene that has been effectively used to combat a broad-spectrum of races of the rice blast fungus
Magnaporthe grisea. Although DNA markers have been reported for selection of the Pi2(t) and Pi-z resistance genes at the Pi-z locus, markers that are more tightly linked to the Pi-z locus would benefit rapid and effective cultivar development. Analysis of the publicly available genome sequence of Nipponbare
near the Pi-z locus revealed numerous SSRs that could be converted into markers. Three SSRs on rice PAC AP005659 were found to be very
tightly linked to the Pi-z locus, with one marker, AP5659-3, co-segregating with the Pi-z resistance reaction. The Pi-z factor conferring resistance to two races of blast was mapped to a 57 kb region on the physical map of Nipponbare in a location
where the Pi2(t) gene was physically mapped. Two SSR marker haplotypes were unique for cultivars carrying the Pi-z gene, which indicates these markers are useful for selection of resistance genes at the Pi-z locus in rice germplasm. 相似文献
11.
Arabitol dehydrogenase as a selectable marker for rice 总被引:3,自引:0,他引:3
Arabitol dehydrogenase has been adapted for use as a plant selectable marker. Arabitol is a five-carbon sugar alcohol that
can be used by E. coli strain C, but not by the laboratory K12 strains. The enzyme converts the non-plant-metabolizable sugar arabitol into xylulose,
which is metabolized by plant cells. Rice was transformed with a plant-expression-optimized synthetic gene using Biolistic-mediated
transformation. Selection on 2.75% arabitol and 0.25% sucrose yielded a transformation efficiency (9.3%) equal to that obtained
with hygromycin (9.2%). Molecular analyses showed that the atlD gene was integrated into the rice genome of selected plants and was inherited in a Mendelian manner. This study indicates
that arabitol could serve as an effective means of plant selection. 相似文献
12.
13.
W. Kennard R. Phillips R. Porter A. Grombacher R. L. Phillips 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(5):793-799
We present the first genetic map of wild rice (Zizania palustris L., 2n=2x=30), a native aquatic grain of northern North America. This map is composed principally of previously mapped RFLP (restriction
fragment length polymorphism) genetic markers from rice (Oryza sativa 2n=2x=24). The map is important as a foundation for genetic and crop improvement studies as well as a reference for genome organization
comparisons among species of Gramineae. A comparative mapping approach with rice is especially useful because wild rice is
grouped in the same subfamily, Oryzoideae, and no other mapping comparison has yet been made within the subfamily. As rice
is the reference point for mapping and gene cloning in cereals, establishing a consensus map within the subfamily identifies
conserved and unique regions. The genomes of wild rice and rice differ in total DNA content (wild rice has twice that of rice)
and the number of chromosome pairs (wild rice=15 versus rice=12). The wild rice linkage map reported herein consists of 121
RFLP markers on 16 linkage groups spanning 1805 cM. Two linkage groups consist of only two markers. Colinear markers were
found representing all rice linkage groups except #12. The majority of rice loci mapped to colinearly arranged arrays in wild
rice (92 of 118). Features of the map include duplication of portions of three rice linkage groups and three possible translocations.
The map gives basic information on the composition of the wild rice genome and provides tools to assist in the domestication
of this important food source.
Received: 25 August 1998 / Accepted: 20 February 1999 相似文献
14.
Berruyer R Adreit H Milazzo J Gaillard S Berger A Dioh W Lebrun MH Tharreau D 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,107(6):1139-1147
Rice blast disease is a major constraint for rice breeding. Nevertheless, the genetic basis of resistance remains poorly understood for most rice varieties, and new resistance genes remain to be identified. We identified the resistance gene corresponding to the cloned avirulence gene ACE1 using pairs of isogenic strains of Magnaporthe grisea differing only by their ACE1 allele. This resistance gene was mapped on the short arm of rice chromosome 8 using progenies from the crosses IR64 (resistant) × Azucena (susceptible) and Azucena × Bala (resistant). The isogenic strains also permitted the detection of this resistance gene in several rice varieties, including the differential isogenic line C101LAC. Allelism tests permitted us to distinguish this gene from two other resistance genes [Pi11 and Pi-29(t)] that are present on the short arm of chromosome 8. Segregation analysis in F2 populations was in agreement with the existence of a single dominant gene, designated as Pi33. Finally, Pi33 was finely mapped between two molecular markers of the rice genetic map that are separated by a distance of 1.6 cM. Detection of Pi33 in different semi-dwarf indica varieties indicated that this gene could originate from either one or a few varieties.Communicated by D.J. Mackill 相似文献
15.
Ammiraju JS Yu Y Luo M Kudrna D Kim H Goicoechea JL Katayose Y Matsumoto T Wu J Sasaki T Wing RA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(8):1596-1607
The International Rice Genome Sequencing Project has recently announced the high-quality finished sequence that covers nearly
95% of the japonica rice genome representing 370 Mbp. Nevertheless, the current physical map of japonica rice contains 62 physical gaps corresponding to approximately 5% of the genome, that have not been identified/represented
in the comprehensive array of publicly available BAC, PAC and other genomic library resources. Without finishing these gaps,
it is impossible to identify the complete complement of genes encoded by rice genome and will also leave us ignorant of some
5% of the genome and its unknown functions. In this article, we report the construction and characterization of a tenfold
redundant, 40 kbp insert fosmid library generated by random mechanical shearing. We demonstrated its utility in refining the
physical map of rice by identifying and in silico mapping 22 gap-specific fosmid clones with particular emphasis on chromosomes
1, 2, 6, 7, 8, 9 and 10. Further sequencing of 12 of the gap-specific fosmid clones uncovered unique rice genome sequence
that was not previously reported in the finished IRGSP sequence and emphasizes the need to complete finishing of the rice
genome.
Fosmid library reported here is publicly available from our web site 相似文献
16.
Dan E. Wells Laura Gutierrez Zhenkang Xu Vladimir Krylov Jaroslav Macha Kerstin P. Blankenburg Matthew Hitchens Larry J. Bellot Mary Spivey Derek L. Stemple Andria Kowis Yuan Ye Shiran Pasternak Jenetta Owen Thu Tran Renata Slavikova Lucie Tumova Tereza Tlapakova Eva Seifertova Steven E. Scherer Amy K. Sater 《Developmental biology》2011,(1):507
We present a genetic map for Xenopus tropicalis, consisting of 2886 Simple Sequence Length Polymorphism (SSLP) markers. Using a bioinformatics-based strategy, we identified unique SSLPs within the X. tropicalis genome. Scaffolds from X. tropicalis genome assembly 2.0 (JGI) were scanned for Simple Sequence Repeats (SSRs); unique SSRs were then tested for amplification and polymorphisms using DNA from inbred Nigerian and Ivory Coast individuals. Thus identified, the SSLPs were genotyped against a mapping cross panel of DNA samples from 190 F2 individuals. Nearly 4000 SSLPs were genotyped, yielding a 2886-marker genetic map consisting of 10 major linkage groups between 73 and 132 cM in length, and 4 smaller linkage groups between 7 and 40 cM. The total effective size of the map is 1658 cM, and the average intermarker distance for each linkage group ranged from 0.27 to 0.75 cM. Fluorescence In Situ Hybridization (FISH) was carried out using probes for genes located on mapped scaffolds to assign linkage groups to chromosomes. Comparisons of this map with the X. tropicalis genome Assembly 4.1 (JGI) indicate that the map provides representation of a minimum of 66% of the X. tropicalis genome, incorporating 758 of the approximately 1300 scaffolds over 100,000 bp. The genetic map and SSLP marker database constitute an essential resource for genetic and genomic analyses in X. tropicalis. 相似文献
17.
O. V. Galaev G. Yu. Shevchuk V. V. Dudchenko Yu. M. Sivolap 《Cytology and Genetics》2011,45(4):208-213
A molecular genetic analysis of soriz genotypes (Sorghum oryzoidum), its parental form Sorghum bicolor (L.) Moench (grain sorghum), possible parents (Sorghum sudanense (Piper.) Stapf. (Sudan grass) and Oryza sativa L. (Rice planting), as well as its closest relatives, has been carried out with the use of microsatellite loci of sorghum
and rice. Based on the obtained data, the genetic distances were calculated and the examined species were clustered. It was
shown that soriz did not carry rice DNA fragments, but its genome contained DNA fragments, which belonged to Sudan grass.
This confirms that the origin of soriz is associated with representatives of Sorghum sudanense. 相似文献
18.
Naoki Kishimoto Majid R. Foolad Etsuo Shimosaka Seiji Matsuura Akira Saito 《Plant cell reports》1993,12(7-8):457-461
Application of genetic linkage maps in plant genetics and breeding can be greatly facilitated by integrating the available classical and molecular genetic linkage maps. In rice, Oryza sativa L., the classical linkage map includes about 300 genes which correspond to various important morphological, physiological, biochemical and agronomic characteristics. The molecular maps consist of more than 500 DNA markers which cover most of the genome within relatively short intervals. Little effort has been made to integrate these two genetic maps. In this paper we report preliminary results of an ongoing research project aimed at the complete integration and alignment of the two linkage maps of rice. Six different F2 populations segregating for various phenotypic and RFLP markers were used and a total of 12 morphological and physiological markers (Table 1) were mapped onto our recently constructed molecular map. Six linkage groups (i.e., chr. 1, 3, 7, 9, 11 and 12) on our RFLP map were aligned with the corresponding linkage groups on the classical map, and the previous alignment for chromosome 6 was further confirmed by RFLP mapping of an additional physiological marker on this chromosome. Results from this study, combined with our previous results, indicate that, for most chromosomes in rice, the RFLP map encompasses the classical map. The usefulness of an integrated genetic linkage map for rice genetics and breeding is discussed.Abbreviations RFLP
restriction fragment length polymorphism
- chr
chromosome
- cM
centiMorgan 相似文献
19.
Flow cytometric analysis of nuclear genome of the Ethiopian cereal tef [Eragrostis tef (Zucc.) Trotter] 总被引:1,自引:0,他引:1
Flow cytometric analysis of nuclear DNA content was performed by using nuclei isolated from young leaf tissue of tef (Eragrostis tef). The method was very useful for rapid screening of ploidy levels in cultivars and lines of tef representing the phenotypic variability of this species in Ethiopia. The results of the analysis showed that all cultivars were tetraploid. Flow cytometry was also used to determine nuclear DNA content in absolute units (genome size) in four tef cultivars. Nuclei isolated from tomato (Lycopersicon esculentum, 2C=1.96 pg) were used as an internal reference standard. The 2C DNA content of individual tef cultivars ranged from 1.48 to 1.52 pg (1C genome size: 714 Mbp-733 Mbp), the differences among them being statistically nonsignificant. The fact that the nuclear genome of tef is only about 50% larger than that of rice should make it amenable for analysis and mapping at the molecular level. 相似文献
20.
Evelyn Tait Moyra C. Simon Susan King Alistair J. Brown Neil A.R. Gow Duncan J. Shaw 《Fungal genetics and biology : FG & B》1997,21(3):308-314
A new project to map the genome of the pathogenic fungus,Candida albicans,has been started. The entire genome was cloned as 5088 cosmids, stored in individual microtiter plate wells. DNA was prepared and fingerprinted using restriction digestion, fluorescent labeling, and analysis on an ABI sequencer. These data are being used to construct contigs of the genome. Simultaneously, a DNA pooling system has been set up, suitable for PCR-based isolation of cosmids containing any known gene. Ultimately, these approaches will lead to the creation of a physically based map of theC. albicansgenome, providing the means to localize precisely all the genes, act as a substrate for genome sequencing projects, and provide probes for future studies of genome rearrangement and comparative genomics. 相似文献