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

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.

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Genetic and contig map of a 2200-kb region encompassing 5.5 cM on chromosome 1 of Arabidopsis thaliana

Genome ◽

10.1139/g96-136 ◽

1996 ◽

Vol 39 (6) ◽

pp. 1086-1092 ◽

Cited By ~ 5

Author(s):

Christian S. Hardtke ◽

Thomas Berleth

Keyword(s):

Arabidopsis Thaliana ◽

Positional Cloning ◽

Yeast Artificial Chromosome ◽

Physical Map ◽

Primary Root ◽

Artificial Chromosome ◽

Chromosome 1 ◽

Rflp Markers ◽

Caps Markers ◽

Yac Contig

In the course of the isolation of the MONOPTEROS (MP) gene, required for primary root formation in Arabidopsis thaliana, a yeast artificial chromosome (YAC) contig encompassing approximately 2200 kilobases corresponding to 5.5 cM on the top arm of chromosome 1 was established. Forty-six YAC clones were characterized and 12 new restriction fragment length polymorphism (RFLP) markers are presented. Three new codominant amplified polymorphic sequence (CAPS) markers were generated that enabled high resolution genetic mapping and correlation of physical and genetic distances along the contig. The map contributes to the completion of a physical map of the Arabidopsis genome and should facilitate positional cloning of other genes in the region as well as studies on genome organization. We also present another set of 11 physically linked probes, as well as mapping data for additional RFLP markers within a broader interval of 10.4 cM. Key words : Arabidopsis, CAPS markers, MONOPTEROS gene, physical map, RFLP markers, YAC contig.

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

Genome ◽

10.1139/g00-076 ◽

2001 ◽

Vol 44 (1) ◽

pp. 32-37 ◽

Cited By ~ 11

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.

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A 2.8 megabase YAC contig spanning D8S339, which is tightly linked to the Werner syndrome locus

Genome ◽

10.1139/g97-010 ◽

1997 ◽

Vol 40 (1) ◽

pp. 77-83

Author(s):

R. Bruskiewich ◽

M. Schertzer ◽

S. Wood

Keyword(s):

Human Chromosome ◽

Genetic Marker ◽

Yeast Artificial Chromosome ◽

Werner Syndrome ◽

Physical Map ◽

Artificial Chromosome ◽

Sequence Tagged Sites ◽

Yeast Artificial Chromosome Contig ◽

Yac Contig ◽

Chromosome 8P

A number of gene loci, including the locus for Werner syndrome (WRN), map to proximal human chromosome 8p near the genetic marker D8S339. In this report, we present a long range physical map of an approximately 2.8 megabase yeast artificial chromosome contig centred on D8S339. In this map, we localize the WRN-linked polymorphic sequence-tagged sites (STS) D8S339 and D8S1055, as well as a novel polymorphic STS, D8S2297. We also refine the positions of three known gene loci, GTF2E2, GSR, and PPP2CB, relative to the location of WRN within the map.Key words: WRN, GTF2E2, GSR, PPP2CB, physical map, human chromosome 8p.

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Dosage and Imprinting Effects in Abnormalities of Human Chromosome 15

Acta geneticae medicae et gemellologiae twin research ◽

10.1017/s0001566000001136 ◽

1996 ◽

Vol 45 (1-2) ◽

pp. 83-83 ◽

Cited By ~ 1

Author(s):

D.H. Ledbetter ◽

S.L. Christian ◽

T. Kubota ◽

A. Mutirangura ◽

J.S. Sutcliffe ◽

...

Keyword(s):

Yeast Artificial Chromosome ◽

Cpg Island ◽

Uniparental Disomy ◽

Artificial Chromosome ◽

Chromosome 15 ◽

Diagnostic Strategy ◽

Str Analysis ◽

Paternal Grandmother ◽

Cosmid Contigs ◽

Yac Contig

Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are distinct mental retardation disorders caused by paternal deficiency (PWS) or maternal deficiency (AS) of gene(s) in 15qll.2-ql3. We have constructed a 3.5 Mb yeast artificial chromosome (YAC) contig of the PWS/AS region and cosmid contigs of selected YACs at D15S13, SNRPN, S10, and S113. Cosmid clones have been used for fluorescence in situ hybridization (FISH) detection of deletions in PWS and AS patients. In addition, a total of 28 short tandem repeat polymorphisms (STRs) have been mapped to specific YACs in the contig, providing a highly informative set of markers for detection of deletion or uniparental disomy (UPD) in PWS and AS patients. Use of the 3 most informative markers in this region (S542, S128, and ASSCA-1) plus 3 markers distal on 15q (S123, S125, and S131) provide an efficient diagnostic strategy for UPD15.A combination of FISH and STR analysis has identified small deletions in one sporadic and one familial case of PWS (family O). Both deletions involve all or part of the SNRPN gene but do not extend telomeric to PAR-5 or PAR-1, two novel transcripts expressed exclusively from the paternal chromosome. However, expression of SNRPN, PAR-5, and PAR-1 is lost in both cases, implying the presence of an imprinting control region near SNRPN. The smallest deletion in family O is estimated at approximately 30-40 kb in size and involves a newly identified CpG island at the 5′ end of SNRPN which is methylated on the maternal chromosome. This small deletion in two PWS affected siblings was present in the father and the paternal grandmother, both of whom were phenotypically normal.

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Construction of a YAC Contig of 2 Megabases Around the MS1 Gene in Arabidopsis thaliana

Functional Plant Biology ◽

10.1071/pp9960453 ◽

1996 ◽

Vol 23 (4) ◽

pp. 453 ◽

Cited By ~ 3

Author(s):

RM Chapple ◽

AM Chaudhury ◽

KC Blomer ◽

LB Farrell ◽

ES Dennis

Keyword(s):

Arabidopsis Thaliana ◽

Yeast Artificial Chromosome ◽

Artificial Chromosome ◽

Rflp Markers ◽

Chromosome Walking ◽

Chromosome 5 ◽

Plant Populations ◽

Recombinant Plant ◽

Yac Contig ◽

The Relationship

The ms1 mutation of Arabidopsis thaliana causes male sterility by preventing the development of normal microspores in the developing anther. The gene is located on a region of chromosome 5 containing the RFLP markers g4111, g4560 and g21503. Using yeast artificial chromosome (YAC) libraries, we have constructed a contig of 38 YACs spanning approximately 2.1 megabases (approximately 2% of the genome) around MS1 and redefined the order of these RFLP markers. Chimeric YACs and repetitive DNA caused problems in chromosome 'walking'. A method for cloning YAC right ends by plasmid rescue was applied to arabidopsis. One YAC end contained a portion of the A. thaliana sucrose synthase gene ASUSI, hence locating this gene on chromosome 5 near MS1. Using recombinant plant populations containing ms1 and flanking markers, MS1 was localised to a 200 kb region within the YAC contig. In this contig the relationship between physical and genetic distance varied from less than 100 kb to 720 kb per centimorgan.

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