scholarly journals Molecular characterization of the duplicated meristem identity genes HvAP1a and HvAP1b in barley

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 905-912 ◽  
Author(s):  
Liuling Yan ◽  
Jarislav von Zitzewitz ◽  
Jeffrey S Skinner ◽  
Patrick M Hayes ◽  
Jorge Dubcovsky
Keyword(s):  
Structural Changes ◽  
Growth Habit ◽  
Physical Map ◽  
Single Copy ◽  
Bacterial Artificial Chromosomes ◽  
Vernalization Gene ◽  
Artificial Chromosomes ◽  
Physical Maps ◽  
Meristem Identity

The vernalization gene VRN-1 has been identified as a MADS-box transcription factor orthologous to the meristem identity gene APETALA1 (AP1). A single copy of this gene was found in diploid wheat, but 2 copies were reported in barley. In this study, we present a detailed characterization of these 2 copies to understand their respective roles in the vernalization response. We identified 2 groups of barley bacterial artificial chromosomes (BACs), each containing 1 AP1 copy designated hereafter as HvAP1a and HvAP1b. A physical map of the VRN-H1 region showed that the HvAP1a BACs were part of the VRN-H1 region but that the HvAP1b BACs were not. Numerous structural changes were observed between the barley and wheat VRN-1 physical maps. In a population segregating for VRN-H1, the HvAP1a gene cosegregated with growth habit, suggesting that HvAP1a is the barley vernalization gene VRN-H1. The other copy, HvAP1b, was mapped on the centromeric region of chromosome 1H, the chromosome where vernalization gene VRN-H3 was previously mapped. We developed a mapping population segregating for VRN-H3 and showed that 2 molecular makers flanking HvAP1b locus were not linked to growth habit. The HvAP1b copy has a complete deletion of the first 2 exons, suggesting that it is a truncated pseudogene and not a candidate for VRN-H3. In summary, this study contributed a detailed physical map of the barley VRN-H1 region, showed several structural differences with the orthologous wheat region, and clarified the identity of the barley VRN-H1 gene.Key words: barley, vernalization, Vrn-1, physical map.

Karyotype stability in the genus Phaseolus evidenced by the comparative mapping of the wild species Phaseolus microcarpus

Genome ◽  
2013 ◽  
Vol 56 (6) ◽  
pp. 335-343 ◽  
Author(s):  
Artur Fonsêca ◽  
Andrea Pedrosa-Harand
Keyword(s):  
Common Bean ◽  
Wild Species ◽  
5S Rdna ◽  
Single Copy ◽  
Rdna Site ◽  
Phylogenetic Distance ◽  
Bacterial Artificial Chromosomes ◽  
Telomeric Dna ◽  
Artificial Chromosomes ◽  
Rdna Sites

The genus Phaseolus L. (Fabaceae) is monophyletic and comprises approximately 75 species distributed into two principal clades. The five cultivated species, including the common bean (Phaseolus vulgaris), were placed in clade B. Clade A comprises only wild species, with more limited distribution. In the present work, bacterial artificial chromosomes (BACs) previously mapped in common bean (2n = 22) were used as probes in fluorescent in situ hybridization (FISH) in this comparative study of Phaseolus microcarpus (2n = 22), a species from clade A. We also analyzed the chromomycin A3 (CMA)/4′,6-diamidino-2-phenylindole (DAPI) banding pattern and the localization of rDNA and telomeric DNA sites. The single 45S rDNA site from P. microcarpus was mapped to chromosome 6, showing conservation to the P. vulgaris homeolog. Of the two 5S rDNA sites identified in both species, only the site on chromosome 10 appeared conserved. In spite of the phylogenetic distance between the two species, all of the single-copy BACs demonstrated conservation of synteny. However, four collinearity breaks were observed, probably caused by para- and pericentric inversions. Some variation in the repetitive fraction of the genome was also observed. Thus, a broader analysis of the genus confirms that few, rare inversions seem to represent the main karyotype changes during the evolution of this genus.

Soybean genomic survey: BAC-end sequences near RFLP and SSR markers

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 572-581 ◽  
Author(s):  
Laura Fredrick Marek ◽  
Joann Mudge ◽  
Laura Darnielle ◽  
David Grant ◽  
Nadja Hanson ◽  
...  
Keyword(s):  
Physical Map ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Soybean Genome ◽  
Bacterial Artificial Chromosomes ◽  
University Of Minnesota ◽  
Artificial Chromosomes ◽  
Metabolic Functions ◽  
Wide Range ◽  
End Sequences

We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC-end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.Key words: Glycine max, sequencing, physical map, contig.

scholarly journals Construction and characterization of bacterial artificial chromosomes harboring the full-length genome of a highly attenuated vaccinia virus LC16m8

PLoS ONE ◽  
2018 ◽  
Vol 13 (2) ◽  
pp. e0192725 ◽  
Author(s):  
Tomoki Yoshikawa ◽  
Hikaru Fujii ◽  
Akiko Okutani ◽  
Miho Shibamura ◽  
Natsumi Omura ◽  
...  
Keyword(s):  
Vaccinia Virus ◽  
Full Length ◽  
Bacterial Artificial Chromosomes ◽  
Artificial Chromosomes ◽  
Full Length Genome

Correlating the Genetic and Physical Map of Barley Chromosome 3H Revealed Limitations of the FISH-Based Mapping of Nearby Single-Copy Probes Caused by the Dynamic Structure of Metaphase Chromosomes

2017 ◽  
Vol 152 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Fernanda O. Bustamante ◽  
Lala Aliyeva-Schnorr ◽  
Jörg Fuchs ◽  
Sebastian Beier ◽  
Andreas Houben
Keyword(s):  
Dna Sequences ◽  
Physical Map ◽  
Dynamic Structure ◽  
Single Copy ◽  
Physical Distance ◽  
Genetic Distances ◽  
Genetic Maps ◽  
Metaphase Chromosomes ◽  
Physical Maps

Genetic maps are based on the recombination frequency of molecular markers which often show different positions in comparison to the corresponding physical maps. To decipher the position and order of DNA sequences genetically mapped to terminal and interstitial regions of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization (FISH) on mitotic metaphase chromosomes was performed with 16 genomic single-copy probes derived from fingerprinted BAC contigs. Long genetic distances at subterminal regions translated into short physical distances, confirming that recombination events occur more often at distal regions of chromosome 3H. Nonoverlapping FISH signals were frequently obtained for probes with a physical distance of at least 30-60 kb. Only 8% of the analyzed chromosomes showed a symmetric order of FISH signals on both sister chromatids. Due to the dynamic packing of metaphase chromatin, the order of 2 adjacent single-copy signals along the chromosome arms outside the (peri)centromeric region can only reliably be determined if the cytological distance is approximately 3%, corresponding to 21.6 Mb.

FISH of a maize sh2-selected sorghum BAC to chromosomes of Sorghum bicolor

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 475-478 ◽  
Author(s):  
Martha I. Gómez ◽  
M. Nurul Islam-Faridi ◽  
Sung-Sick Woo ◽  
Don Czeschin Jr. ◽  
Michael S. Zwick ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Sorghum Bicolor ◽  
Fluorescence In Situ Hybridization ◽  
Artificial Chromosome ◽  
Single Copy ◽  
Bacterial Artificial Chromosomes ◽  
Extra Copy ◽  
Artificial Chromosomes ◽  
Sorghum Plant

Fluorescence in situ hybridization (FISH) of a 205 kb Sorghum bicolor bacterial artificial chromosome (BAC) containing a sequence complementary to maize sh2 cDNA produced a large pair of FISH signals at one end of a midsize metacentric chromosome of S. bicolor. Three pairs of signals were observed in metaphase spreads of chromosomes of a sorghum plant containing an extra copy of one arm of the sorghum chromosome arbitrarily designated with the letter D. Therefore, the sequence cloned in this BAC must reside in the arm of chromosome D represented by this monotelosome. This demonstrates a novel procedure for physically mapping cloned genes or other single-copy sequences by FISH, sh2 in this case, by using BACs containing their complementary sequences. The results reported herein suggest homology, at least in part, between one arm of chromosome D in sorghum and the long arm of chromosome 3 in maize.Key words: sorghum, maize, shrunken locus, physical mapping, fluorescence in situ hybridization, bacterial artificial chromosomes.

Framework for a Physical Map of the Human 22q13 Region Using Bacterial Artificial Chromosomes (BACs)

Genomics ◽  
1996 ◽  
Vol 33 (1) ◽  
pp. 9-20 ◽  
Author(s):  
Holger Schmitt ◽  
Ung-Jin Kim ◽  
Tatiana Slepak ◽  
Nikolaus Blin ◽  
Melvin I. Simon ◽  
...  
Keyword(s):  
Physical Map ◽  
Bacterial Artificial Chromosomes ◽  
Artificial Chromosomes

scholarly journals Molecular and cytogenetical characterization of the 10A1-2 band and adjoining region in the Drosophila melanogaster polytene X chromosome.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 1063-1073 ◽  
Author(s):  
T u Kozlova ◽  
V F Semeshin ◽  
I V Tretyakova ◽  
E B Kokoza ◽  
V Pirrotta ◽  
...  
Keyword(s):  
X Chromosome ◽  
Physical Map ◽  
Chromosome Region ◽  
Chromosome Rearrangements ◽  
P Element ◽  
Induced Mutations ◽  
Physical Maps ◽  
Break Points ◽  
Chromosome Bands

Abstract Some 300 kb of DNA from the 9F12-10A7 X chromosome region (seven bands) uncovered by Df(1)vL3 were cloned and 31 break points of chromosome rearrangements within the region were mapped. Positions of 12 genes found earlier in genetic saturation experiments, transcripts and P element-induced mutations were located on the physical map using either chromosome rearrangements or Southern blot hybridizations. Data on the position of the break points, genes and polytene chromosome bands allow the following conclusions to be made. (1) The size of the bands in the region varies between 4 kb (10A6 and 7) and 183-195 kb (10A1-2). The compaction ratio of DNA in bands varies from 8-36 (10A6 + 7) to 151-161 (10A1-2). Therefore, fine and thick bands appear to have different kinds of DNP packaging. (2) The bands differ in genetic content. Fine bands contain from one to three genes. In contrast, the 10A1-2 band contains three genes and at least six transcribed DNA fragments. (3) Comparison of genetic and physical maps shows that in this region 0.01 centiMorgan corresponds to 3.3 kb of DNA.

scholarly journals The Selection and Use of Sorghum (Sorghum propinquum) Bacterial Artificial Chromosomes as Cytogenetic FISH Probes for Maize (Zea maysL.)

2011 ◽  
Vol 2011 ◽  
pp. 1-16 ◽  
Author(s):  
Debbie M. Figueroa ◽  
James D. Davis ◽  
Cornelia Strobel ◽  
Maria S. Conejo ◽  
Katherine D. Beckham ◽  
...  
Keyword(s):  
Bac Library ◽  
Chromosome 9 ◽  
Bacterial Artificial Chromosomes ◽  
Fish Mapping ◽  
Artificial Chromosomes ◽  
Physical Maps ◽  
Sorghum Propinquum ◽  
Marker Loci ◽  
Single Clone

The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescencein situhybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and comparedin silicoBAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented along with an example of transgenomic BAC FISH mapping. This strategy has been used to facilitate the integration of RFLP and FISH maps in other large-genome species.

Construction and characterization of bacterial artificial chromosomes containing HSV-1 strains 17 and KOS

2006 ◽  
Vol 135 (2) ◽  
pp. 197-206 ◽  
Author(s):  
William W. Gierasch ◽  
David L. Zimmerman ◽  
Stephen L. Ward ◽  
Tambryn K. VanHeyningen ◽  
Joseph D. Romine ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosomes ◽  
Artificial Chromosomes ◽  
Hsv 1
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