scholarly journals Mapping expressed sequence tag sites on yeast artificial chromosome clones of Arabidopsis thaliana DNA.

1997 ◽  
Vol 7 (1) ◽  
pp. 1-9 ◽  
Author(s):  
F D Agyare ◽  
D A Lashkari ◽  
A Lagos ◽  
A F Namath ◽  
G Lagos ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Yeast Artificial Chromosome ◽  
Expressed Sequence Tag ◽  
Artificial Chromosome ◽  
Expressed Sequence

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

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1086-1092 ◽  
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.

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

1996 ◽  
Vol 23 (4) ◽  
pp. 453 ◽  
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.

Construction of an Overlapping YAC Library of the Arabidopsis thaliana Genome

1992 ◽  
Vol 19 (4) ◽  
pp. 341 ◽  
Author(s):  
R Schmidt ◽  
G Cnops ◽  
I Bancroft ◽  
C Dean
Keyword(s):  
Arabidopsis Thaliana ◽  
Yeast Artificial Chromosome ◽  
Artificial Chromosome ◽  
Rflp Markers ◽  
Collaborative Effort ◽  
Inverse Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Yac Library ◽  
Polymerase Chain ◽  
Arabidopsis Thaliana Genome

As part of an international effort to construct an overlapping yeast artificial chromosome (YAC) library of the Arabidopsis thaliana genome, we have been identifying and linking YAC clones that cover the top halves of chromosomes 4 and 5. All the available RFLP markers mapping to these regions were hybridised to filters carrying different YAC libraries. The YAC colonies were arrayed such that an entire library was contained on one small filter, greatly simplifying the screening procedure. The collaborative effort has currently resulted in 30% of the genome being represented in mapped YAC clones. Probes derived from the ends of the YAC inserts, using either inverse polymerase chain reaction (PCR) or left-end rescue, are now being used to walk out to link the YAC clones hybridising to adjacent RFLP markers.

scholarly journals Mapping quantitative trait loci and identification of genes that control fatness in poultry

2002 ◽  
Vol 61 (4) ◽  
pp. 441-446 ◽  
Author(s):  
David W. Burt ◽  
Paul M. Hocking
Keyword(s):  
Quantitative Trait Loci ◽  
Bacterial Artificial Chromosome ◽  
Quantitative Trait ◽  
Expressed Sequence Tag ◽  
Artificial Chromosome ◽  
Nouvelles Technologies ◽  
Trait Loci ◽  
Expressed Sequence

RésuméLa génomique de la volaille a bénéficié des avancements technologiques rapides acquis en génomique humaine et sur les organismes modèles. Certains outils et certains approches sont maintenant bien établis chez le poulet, y compris les cartes et marqueurs (génétiques comme physiques), mapping loci pour caractéres quantitatifs, mapping comparative, ressources expressed sequence tag et bacterial artificial chromosome, et mapping physique. De plus, la phase suivante de la découverte génétique, la génomique fonctionnelle, est en cours. Les progre`s dans le mapping de loci pour caracte`res quantitatifs de croissance et d'adiposité seront discutés pour illustrer ces nouvelles technologies et ces nouvelles approches dans l'étude de la génétique et de la physiologie avicole.

scholarly journals Potato Homologs of Arabidopsis thaliana Genes Functional in Defense Signaling—Identification, Genetic Mapping, and Molecular Cloning

2005 ◽  
Vol 18 (10) ◽  
pp. 1107-1119 ◽  
Author(s):  
Karolina M. Pajerowska ◽  
Jane E. Parker ◽  
Christiane Gebhardt
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Molecular Mechanisms ◽  
Expressed Sequence Tag ◽  
Quantitative Resistance ◽  
Erwinia Carotovora ◽  
Soft Rot ◽  
Signaling Cascades ◽  
Defense Signaling ◽  
Expressed Sequence

Defense against pests and pathogens is a fundamental process controlled by similar molecular mechanisms in all flowering plants. Using Arabidopsis thaliana as a model, steps of the signal transduction pathways that link pathogen recognition to defense activation have been identified and corresponding genes have been characterized. Defense signaling (DS) genes are functional candidates for controlling natural quantitative variation of resistance to plant pathogens. Nineteen Arabidopsis genes operating in defense signaling cascades were selected. Solanaceae EST (expressed sequence tag) databases were employed to identify the closest homologs of potato (Solanum tuberosum). Sixteen novel DS potato homologs were positioned on the molecular maps. Five DS homologs mapped close to known quantitative resistance loci (QRL) against the oomycete Phytophthora infestans causing late blight and the bacterium Erwinia carotovora subsp. atroseptica causing blackleg of stems and tuber soft rot. The five genes are positional candidates for QRL and are highly sequence related to Arabidopsis genes AtSGT1b, AtPAD4, and AtAOS. Full-length complementary DNA and genomic sequences were obtained for potato genes StSGT1, StPAD4, and StEDS1, the latter being a putative interactor of StPAD4. Our results form the basis for further studies on the contributions of these candidate genes to natural variation of potato disease resistance.

scholarly journals An Arabidopsis thaliana Gene on the Yeast Artificial Chromosome Can Be Transcribed in Tobacco Cells

CYTOLOGIA ◽  
2004 ◽  
Vol 69 (2) ◽  
pp. 235-240 ◽  
Author(s):  
Haibo Liu ◽  
Akira Kawabe ◽  
Sachihiro Matsunaga ◽  
Yeon Hee Kim ◽  
Tsunehito Higashi ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Yeast Artificial Chromosome ◽  
Artificial Chromosome ◽  
Tobacco Cells

Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 12-17 ◽  
Author(s):  
L D Chaves ◽  
J A Rowe ◽  
K M Reed
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Meleagris Gallopavo ◽  
Whole Genome Sequence ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Important Species ◽  
Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

Genome ◽  
2004 ◽  
Vol 47 (1) ◽  
pp. 141-155 ◽  
Author(s):  
H H Yan ◽  
J Mudge ◽  
D-J Kim ◽  
R C Shoemaker ◽  
D R Cook ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Glycine Max ◽  
Medicago Truncatula ◽  
Physical Mapping ◽  
Large Scale ◽  
Sequence Similarity ◽  
Artificial Chromosome ◽  
Bac Contig ◽  
Cross Hybridization ◽  
Bac Contigs

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1114-1121 ◽  
Author(s):  
Shu-Mei Jiang ◽  
Long Zhang ◽  
Jun Hu ◽  
Rui Shi ◽  
Guang-He Zhou ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Expressed Sequence Tag ◽  
Barley Yellow Dwarf Virus ◽  
Differentially Expressed ◽  
Addition Line ◽  
Alien Chromosome ◽  
Thinopyrum Intermedium ◽  
Barley Yellow Dwarf ◽  
Yellow Dwarf Virus ◽  
Expressed Sequence

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.

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