Construction of a binary bacterial artificial chromosome library of Petunia inflata and the isolation of large genomic fragments linked to the self-incompatibility (S-) locus

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 820-826 ◽  
Author(s):  
Andrew G McCubbin ◽  
Carmen Zuniga ◽  
Teh-hui Kao
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bacterial Artificial Chromosome Library ◽  
Artificial Chromosome ◽  
Average Insert Size ◽  
Self Incompatibility ◽  
S Locus ◽  
Petunia Inflata ◽  
Insert Size ◽  
S Gene ◽  
Polymorphic Gene

The Solanaceae family of flowering plants possesses a type of self-incompatibility mechanism that enables the pistil to reject self pollen but accept non-self pollen for fertilization. The pistil function in this system has been shown to be controlled by a polymorphic gene at the S-locus, termed the S-RNase gene. The pollen function is believed to be controlled by another as yet unidentified polymorphic gene at the S-locus, termed the pollen S-gene. As a first step in using a functional genomic approach to identify the pollen S-gene, a genomic BAC (bacterial artificial chromosome) library of the S2S2 genotype of Petunia inflata, a self-incompatible solanaceous species, was constructed using a Ti-plasmid based BAC vector, BIBAC2. The average insert size was 136.4 kb and the entire library represented a 7.5-fold genome coverage. Screening of the library using cDNAs for the S2-RNase gene and 13 pollen-expressed genes that are linked to the S-locus yielded 51 positive clones, with at least one positive clone for each gene. Collectively, at least 2 Mb of the chromosomal region was spanned by these clones. Together, three clones that contained the S2-RNase gene spanned ~263 kb. How this BAC library and the clones identified could be used to identify the pollen S-gene and to study other aspects of self-incompatibility is discussed.Key words: bacterial artificial chromosome, Petunia inflata, pollen-pistil interactions, self-incompatibility, S-locus.

scholarly journals Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research

Genome ◽  
2009 ◽  
Vol 52 (1) ◽  
pp. 57-67 ◽  
Author(s):  
Brad S. Coates ◽  
Douglas V. Sumerford ◽  
Richard L. Hellmich ◽  
Leslie C. Lewis
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bacterial Artificial Chromosome Library ◽  
Ostrinia Nubilalis ◽  
European Corn Borer ◽  
Artificial Chromosome ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Average Insert Size ◽  
Corn Borer ◽  
Site Markers

The European corn borer, Ostrinia nubilalis , is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of ≥120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5′ ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.

scholarly journals Construction and Preliminary Characterization Analysis of Wuzhishan Miniature Pig Bacterial Artificial Chromosome Library with Approximately 8-Fold Genome Equivalent Coverage

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Changqing Liu ◽  
Yuo Guo ◽  
Taofeng Lu ◽  
Hongmei Wu ◽  
Risu Na ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Blood Cells ◽  
Large Scale ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Genetic Dissection ◽  
Average Insert Size ◽  
Miniature Pig ◽  
Insert Size ◽  
Statistical Probability

Bacterial artificial chromosome (BAC) libraries have been invaluable tools for the genome-wide genetic dissection of complex organisms. Here, we report the construction and characterization of a high-redundancy BAC library from a very valuable pig breed in China, Wuzhishan miniature pig (Sus scrofa), using its blood cells and fibroblasts, respectively. The library contains approximately 153,600 clones ordered in 40 superpools of 10 × 384-deep well microplates. The average insert size of BAC clones was estimated to be 152.3 kb, representing approximately 7.68 genome equivalents of the porcine haploid genome and a 99.93% statistical probability of obtaining at least one clone containing a unique DNA sequence in the library. 19 pairs of microsatellite marker primers covering porcine chromosomes were used for screening the BAC library, which showed that each of these markers was positive in the library; the positive clone number was 2 to 9, and the average number was 7.89, which was consistent with 7.68-fold coverage of the porcine genome. And there were no significant differences of genomic BAC library from blood cells and fibroblast cells. Therefore, we identified 19 microsatellite markers that could potentially be used as genetic markers. As a result, this BAC library will serve as a valuable resource for gene identification, physical mapping, and comparative genomics and large-scale genome sequencing in the porcine.

A bacterial artificial chromosome library for ‘Jefferson’ hazelnut and identification of clones associated with eastern filbert blight resistance and pollen–stigma incompatibility

Genome ◽  
2011 ◽  
Vol 54 (10) ◽  
pp. 862-867 ◽  
Author(s):  
Vidyasagar R. Sathuvalli ◽  
Shawn A. Mehlenbacher
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Random Amplified Polymorphic Dna ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Physical Distance ◽  
Resistance Locus ◽  
S Locus ◽  
Insert Size ◽  
Eastern Filbert Blight ◽  
Corylus Avellana L

European hazelnut ( Corylus avellana L.) is the only economically important nut crop in the family Betulaceae. Because of its small genome size (~385 Mb / 1C), relatively short life cycle, availability of a dense linkage map, and amenability to transformation by Agrobacterium, the European hazelnut could serve as a model plant for the Betulaceae. Here we report the construction of a bacterial artificial chromosome (BAC) library for ‘Jefferson’ hazelnut using the cloning enzyme MboI and the vector pECBAC1 (BamHI site). The library consists of 39 936 clones arrayed in 104 384-well microtitre plates with a mean insert size of 117 kb. The genomic coverage of the library is estimated to be about 12 genome equivalents. This library provides a valuable resource for the map-based cloning of two important genes, the resistance gene from ‘Gasaway’ that confers resistance to eastern filbert blight caused by the fungus Anisogramma anomala (Peck) E. Müller and the S locus that controls pollen–stigma incompatibility. Fine-resolution mapping near the two loci was carried out using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers. Fine mapping at the disease resistance locus showed that markers W07-375 and X01-825 flanked the resistance locus at distances of 0.06 and 0.05 cM, respectively. The S locus is flanked by markers 204-950 and KG819-200 at distances of 0.14 and 0.24 cM, respectively. Assuming that 1 cM corresponds to a physical distance of 430 kb, it will take approximately two to three chromosome walks to assemble BAC contigs that span both loci.

Construction and characterization of the first bacterial artificial chromosome library for the cotton species Gossypium barbadense L.

Genome ◽  
2006 ◽  
Vol 49 (11) ◽  
pp. 1393-1398 ◽  
Author(s):  
X.F. Wang ◽  
J. Ma ◽  
W.S. Wang ◽  
Y.M. Zheng ◽  
G.Y. Zhang ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Gossypium Barbadense ◽  
Average Insert Size ◽  
Insert Size ◽  
Breeding Programs ◽  
Fiber Properties ◽  
Cotton Species

As the second most widely cultivated cotton, Gossypium barbadense is well known for its superior fiber properties and its high levels of resistance to Fusarium and Verticillium wilts. To enhance our ability to exploit these properties in breeding programs, we constructed the first bacterial artificial chromosome (BAC) library for this species. The library contains 167 424 clones (49 920 BamHI and 117 504 HindIII clones), with an estimated average insert size of 130 kb. About 94.0% of the clones had inserts over 100 kb, and the empty clones accounted for less than 4.0%. Contamination of the library with chloroplast clones was very low (0.2%). Screening the library with locus-specific probes showed that BAC clones represent 6.5-fold genome equivalents. This high-quality library provides an additional asset with which to exploit genetic variation for cotton improvement.

Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 199-204 ◽  
Author(s):  
Junqi Song ◽  
Fenggao Dong ◽  
Jiming Jiang
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Physical Map ◽  
Molecular Cytogenetics ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Average Insert Size ◽  
Chromosome Identification ◽  
Insert Size ◽  
Potato Genome ◽  
Bac Clones

Lack of reliable techniques for chromosome identification is the major obstacle for cytogenetics research in plant species with large numbers of small chromosomes. To promote molecular cytogenetics research of potato (Solanum tuberosum, 2n = 4x = 48) we developed a bacterial artificial chromosome (BAC) library of a diploid potato species S. bulbocastanum. The library consists of 23 808 clones with an average insert size of 155 kb, and represents approximately 3.7 equivalents to the potato genome. The majority of the clones in the BAC library generated distinct signals on specific potato chromosomes using fluorescence in situ hybridization (FISH). The hybridization signals provide excellent cytological markers to tag individual potato chromosomes. We also demonstrated that the BAC clones can be mapped to specific positions on meiotic pachytene chromosomes. The excellent resolution of pachytene FISH can be used to construct a physical map of potato by mapping molecular marker-targeted BAC clones on pachytene chromosomes. Key words: potato, BAC library, chromosome identification, physical mapping, molecular cytogenetics.

scholarly journals Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1176-1182 ◽  
Author(s):  
D Lijavetzky ◽  
G Muzzi ◽  
T Wicker ◽  
B Keller ◽  
R Wing ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Repetitive Sequences ◽  
Bac Library ◽  
Artificial Chromosome ◽  
High Density ◽  
Triticum Monococcum ◽  
Average Insert Size ◽  
Insert Size ◽  
High Molecular Weight Dna ◽  
A Genome

A genomic bacterial artificial chromosome (BAC) library of the A genome of wheat has been constructed. Triticum monococcum accession DV92 was selected for this purpose because it is a cultivated diploid wheat and one of the parental lines used in the construction of a saturated genetic map. Leaves from this accession were used to isolate high-molecular-weight DNA from nuclei. This DNA was partially digested with restriction enzyme Hind III, subjected to double size selection, electroeluted and cloned into the pINDIGO451 BAC vector. The library consists of 276 480 clones with an average insert size of 115 kb. Excluding the 1.33% of empty clones and 0.14% of clones with chloroplast DNA, the coverage of this library is 5.6 genome equivalents. With this genome coverage the probability of having any DNA sequence represented in this library is higher than 99.6%. Clones were sorted in 720 384-well plates and blotted onto 15 high-density filters. High-density filters were screened with several single or low-copy clones and five positive BAC clones were selected for further analysis. Since most of the T. monococcum BAC ends included repetitive sequences, a modification was introduced into the classical end-isolation procedure to select low copy sequences for chromosome walking.Key words: bacterial artificial chromosome, BAC library, Triticum monococcum, wheat.

Construction of a marsupial bacterial artificial chromosome library from the model Australian marsupial, the tammar wallaby (Macropus eugenii)

2005 ◽  
Vol 53 (6) ◽  
pp. 389 ◽  
Author(s):  
Natasha Sankovic ◽  
Wayne Bawden ◽  
John Martyn ◽  
Jennifer A. M. Graves ◽  
Kurt Zuelke
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Positional Cloning ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Single Copy ◽  
Tammar Wallaby ◽  
Average Insert Size ◽  
Insert Size ◽  
Macropus Eugenii ◽  
Australian Marsupial

With the accelerating recognition of the power of comparative genomics, there is now enormous interest in sequencing the genomes of a broad range of species. Marsupials diverged at an important evolutionary time. The model Australian marsupial, the tammar wallaby (Macropus eugenii), has long been a resource for biological and genetic studies of marsupials, and the availability of a bacterial artificial chromosome (BAC) library will be a valuable resource in these studies. A tammar wallaby BAC library was constructed using pRazorBAC vector. It contains 55 296 clones with an average insert size of 108 kb, representing 2.2 times coverage of the wallaby genome (based on an estimated 2.7 × 109 bp haploid genome size). The library was arrayed in 384-well plates, and spotted in duplicate onto nylon membranes. Screening these membranes has yielded clones containing 34 single-copy genes distributed over the genome, while it failed for only one gene. Each probe isolated 1–12 BAC clones and, to date, no chimeric clones have been found. This BAC library will constitute an invaluable resource for creating physical maps, positional cloning of genes and other sequences in the tammar wallaby, as well as comparative mapping studies in mammals.

scholarly journals Construction of a Llama Bacterial Artificial Chromosome Library with Approximately 9-Fold Genome Equivalent Coverage

2012 ◽  
Vol 2012 ◽  
pp. 1-4 ◽  
Author(s):  
K. W. Airmet ◽  
J. D. Hinckley ◽  
L. T. Tree ◽  
M. Moss ◽  
S. Blumell ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bac Library ◽  
Artificial Chromosome ◽  
The United States ◽  
Modern Technology ◽  
Average Insert Size ◽  
Genome Equivalent ◽  
Insert Size ◽  
Genome Coverage ◽  
Genomic Studies

The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be2.4×109 bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.

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