scholarly journals Detailed Comparative Mapping of Cereal Chromosome Regions Corresponding to the Ph1 Locus in Wheat

Genetics ◽  
1997 ◽  
Vol 147 (2) ◽  
pp. 801-807 ◽  
Author(s):  
Tracie Foote ◽  
Michael Roberts ◽  
Nori Kurata ◽  
Takuji Sasaki ◽  
Graham Moore
Keyword(s):  
Physical Mapping ◽  
Yeast Artificial Chromosome ◽  
Rice Genome ◽  
Rice Chromosome ◽  
Wheat Chromosome ◽  
Artificial Chromosome ◽  
Gene Isolation ◽  
Chromosome 9 ◽  
Ph1 Locus ◽  
Yac Contigs

Detailed physical mapping of markers from rice chromosome 9, and from syntenous (at the genetic level) regions of other cereal genomes, has resulted in rice yeast artificial chromosome (YAC) contigs spanning parts of rice 9. This physical mapping, together with comparative genetic mapping, has demonstrated that synteny has been largely maintained between the genomes of several cereals at the level of contiged YACs. Markers located in one region of rice chromosome 9 encompassed by the YAC contigs have exhibited restriction fragment length polymorphism (RFLP) using deletion lines for the Ph1 locus. This has allowed demarcation of the region of rice chromosome 9 syntenous with the ph1b and ph1c deletions in wheat chromosome 5B. A group of probes located in wheat homoeologous group 5 and barley chromosome 5H, however, have synteny with rice chromosomes other than 9. This suggests that the usefulness of comparative trait analysis and of the rice genome as a tool to facilitate gene isolation will differ from one region to the next, and implies that the rice genome is more ancestral in structure than those of the Triticeae.

A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽  
2001 ◽  
Vol 44 (1) ◽  
pp. 32-37 ◽  
Author(s):  
Shoko Saji ◽  
Yosuke Umehara ◽  
Baltazar A Antonio ◽  
Hiroko Yamane ◽  
Hiroshi Tanoue ◽  
...  
Keyword(s):  
Genetic Map ◽  
Dna Markers ◽  
Yeast Artificial Chromosome ◽  
Physical Map ◽  
Genome Structure ◽  
Rice Genome ◽  
Artificial Chromosome ◽  
Physical Length ◽  
Rice Chromosomes ◽  
Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4

Genetica ◽  
2010 ◽  
Vol 138 (11-12) ◽  
pp. 1277-1296 ◽  
Author(s):  
Tong Geon Lee ◽  
Yong Jin Lee ◽  
Dae Yeon Kim ◽  
Yong Weon Seo
Keyword(s):  
Physical Mapping ◽  
Rice Chromosome ◽  
Wheat Chromosome ◽  
Chromosome 4 ◽  
Chromosome Arm

A comprehensive large-insert yeast artificial chromosome library for physical mapping of the mouse genome

1996 ◽  
Vol 7 (10) ◽  
pp. 767-769 ◽  
Author(s):  
M. L. Haldi ◽  
C. Strickland ◽  
P. Lim ◽  
V. VanBerkel ◽  
X. -N. Chen ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Mouse Genome ◽  
Yeast Artificial Chromosome ◽  
Artificial Chromosome ◽  
Yeast Artificial Chromosome Library

Targeted molecular mapping of a major wheat QTL for Fusarium head blight resistance using wheat ESTs and synteny with rice

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 817-823 ◽  
Author(s):  
Sixin Liu ◽  
James A Anderson
Keyword(s):  
Fusarium Head Blight ◽  
Molecular Mapping ◽  
Fusarium Head Blight Resistance ◽  
Rice Chromosome ◽  
Wheat Chromosome ◽  
Artificial Chromosome ◽  
Sequence Information ◽  
Head Blight ◽  
Wheat Ests ◽  
Sts Markers

A major QTL for resistance to Fusarium head blight (FHB) in wheat, Qfhs.ndsu-3BS, has been identified and verified by several research groups. The objective of this study was to increase the marker density in this QTL region using STS (sequence-tagged site) markers developed from wheat expressed sequence tags (ESTs) near Qfhs.ndsu-3BS. Because wheat chromosome 3BS and rice chromosome 1S are syntenous, the sequences of P1-derived artificial chromosome (PAC) and (or) bacterial artificial chromosome (BAC) clones covering the sub-distal portion of rice chromosome 1S were used as queries for a BLASTn search to identify wheat ESTs most likely near Qfhs.ndsu-3BS. Sixty-eight out of 79 STS primer pairs designed from wheat ESTs amplified PCR products from the genomic DNA of Triticum aestivum 'Chinese Spring'. Twenty-eight STS markers were localized on chromosome 3BS by aneuploid analysis. Six out of the nine STS markers that could be mapped in the T. aestivum 'Sumai 3'/T. aestivum 'Stoa' population had higher R2 and LOD values for this QTL than the most significant marker reported previously. Therefore, leveraging genome sequence information available in rice for wheat genetics is an effective strategy to develop DNA markers for Qfhs.ndsu-3BS, and this strategy may have broad applications for targeted mapping of other traits in cereal crops.Key words: comparative mapping, genomics.

scholarly journals An ordered yeast artificial chromosome library covering over half of rice chromosome 6.

1996 ◽  
Vol 6 (10) ◽  
pp. 935-942 ◽  
Author(s):  
Y Umehara ◽  
H Tanoue ◽  
N Kurata ◽  
I Ashikawa ◽  
Y Minobe ◽  
...  
Keyword(s):  
Yeast Artificial Chromosome ◽  
Rice Chromosome ◽  
Artificial Chromosome ◽  
Chromosome 6 ◽  
Yeast Artificial Chromosome Library

Physical mapping of the 5S rDNA gene complex in rice (Oryza sativa)

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 658-661 ◽  
Author(s):  
Y. C. Song ◽  
J. P. Gustafson
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Rice Chromosome ◽  
5S Rdna ◽  
Rice Cultivar ◽  
Chromosome 9 ◽  
Gene Complex ◽  
Rdna Gene ◽  
Biotin Labelling

This study was designed to use biotin labelling in situ hybridization to physically map the 5S rDNA genes to a chromosome arm location in rice. Chromosome preparations were made using an improved protoplast technique, which resulted in more mitotic cells with less overlying cytoplasmic and cellular debris. Cells in which both chromatids were labelled were observed. The hybridization detection level for the 5S rDNA gene complex was 17.22%. The results established that the 5S rDNA gene complex of rice is located at the end of the short arm of chromosome 9 in rice cultivar IR36. The similarities and differences of the 5S rDNA gene complex location between rice and other cereals and advantages of in situ hybridization for physical mapping are discussed.Key words: biotin labelling, in situ hybridization.

Generation of a YAC contig encompassing the extra glume gene, eg, in rice

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1072-1077 ◽  
Author(s):  
Wim Van Houten ◽  
Nori Kurata ◽  
Yosuke Umehara ◽  
Takuji Sasaki ◽  
Yuzo Minobe
Keyword(s):  
Yeast Artificial Chromosome ◽  
Single Gene ◽  
Rice Variety ◽  
Rice Chromosome ◽  
Artificial Chromosome ◽  
Chromosome 1 ◽  
Flower Morphogenesis ◽  
Molecular Map ◽  
Yac Contig ◽  
Extra Glume

We have used DNA markers from a high density molecular map of rice (Oryza sativa) to tag a single gene expressed as a flower morphogenesis mutation, extra glume (eg). Using an F2 population segregating for eg, obtained from a cross between IR24 and F136 (eg/eg), we constructed a partial molecular map and located eg relative to restriction fragment length polymorphism markers. The region between two markers appears to span the eg locus on rice chromosome 1 and extends to a genetic length of 3.8 cM. The yeast artificial chromosome (YAC) library obtained from rice variety 'Nipponbare', which carries the wild-type allele of eg, was screened to completely cover the locus by overlapping YAC clones. The eg allele should be contained in two overlapping YACs. YAC size determination by pulsed-field gel electrophoresis indicated that this region has a physical length of approximately 400 kb. We anticipate that the tagging of eg in a relatively short stretch of DNA will allow a molecular characterization of this gene through map-based cloning. Key words : rice, gene tagging, YAC contig, flower morphogenesis, extra glume.

Physical characterization of the homoeologous Group 5 chromosomes of wheat in terms of rice linkage blocks, and physical mapping of some important genes

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 191-198 ◽  
Author(s):  
R N Sarma ◽  
L Fish ◽  
B S Gill ◽  
J W Snape
Keyword(s):  
Physical Mapping ◽  
Comparative Mapping ◽  
Rice Chromosome ◽  
Chromosome 9 ◽  
Deletion Mapping ◽  
Homoeologous Group ◽  
Conserved Synteny ◽  
Deletion Lines ◽  
Mapping Approach ◽  
Group 5

The wheat homoeologous Group 5 chromosomes were characterized physically in terms of rice linkage blocks using a deletion mapping approach. All three chromosomes, 5A, 5B, and 5D, were shown to have a similar structure, apart from the 4A-5A translocation on the distal end of chromosome arm 5AL. The physical mapping of rice markers on the deletion lines revealed that the whole of rice chromosome 9 is syntenous to a large block, proximal to the centromere, on the long arm. Likewise, a small segment of the distal end of the long arm showed conserved synteny with the distal one-third end of the long arm of rice chromosome 3. In between those conserved regions, there is a region on the long arm of the Group 5 chromosomes which shows broken synteny. The proximal part of the short arms of the Group 5 chromosomes showed conserved synteny with a segment of the short arm of rice chromosome 11 and the distal ends showed conserved synteny with a segment of rice chromosome 12. The physical locations of flowering time genes (Vrn and earliness per se) and the gene for grain hardness (Ha) on the Group 5 chromosomes were determined. These results indicate that comparative mapping using the deletion mapping approach is useful in the study of genome relationships, the physical location of genes, and can determine the appropriate gene cloning strategy. Key words: wheat, rice, comparative mapping, deletion lines.

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