Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz)

2004 ◽  
Vol 56 (4) ◽  
pp. 555-561 ◽  
Author(s):  
J. Tomkins ◽  
M. Fregene ◽  
D. Main ◽  
H. Kim ◽  
R. Wing ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Bacterial Artificial Chromosome ◽  
Resistance Genes ◽  
Manihot Esculenta ◽  
Positional Cloning ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Disease Resistance Genes ◽  
Manihot Esculenta Crantz ◽  
Library Resource

scholarly journals Construction and Characterization of a Bacterial Artificial Chromosome Library for the Hexaploid Wheat Line 92R137

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Qingdong Zeng ◽  
Fengping Yuan ◽  
Xin Xu ◽  
Xue Shi ◽  
Xiaojun Nie ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Hexaploid Wheat ◽  
Positional Cloning ◽  
Bac Library ◽  
Restriction Enzymes ◽  
Artificial Chromosome ◽  
Stripe Rust Resistance ◽  
Wheat Line ◽  
Genomic Resource

For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymesHindIII andBamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from theHindIII digestion and 375,552 from theBamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from theHindIII sublibrary and 573 clones from theBamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, theHindIII sublibrary was estimated to have a 3.01-fold coverage and theBamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as geneYr26for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools withXwe173, a marker tightly linked toYr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning ofYr26and other genes of interest.

BAC contig development by fingerprint analysis in soybean

Genome ◽  
1997 ◽  
Vol 40 (4) ◽  
pp. 420-427 ◽  
Author(s):  
L. Fredrick Marek ◽  
R. C. Shoemaker
Keyword(s):  
Disease Resistance ◽  
Linkage Group ◽  
Bacterial Artificial Chromosome ◽  
Resistance Gene ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Disease Resistance Gene ◽  
Average Insert Size ◽  
Specific Sequence ◽  
Class 1

We constructed a soybean bacterial artificial chromosome (BAC) library suitable for map-based cloning and physical mapping in soybean. This library consists of approximately 40 000 clones (4–5 genome equivalents) stored individually in 384-well microtiter dishes. A random sampling of 224 clones yielded an average insert size of 150 kb, giving a 98% probability of recovering any specific sequence. We screened the library for seven single or very low copy genie or genomic sequences using the polymerase chain reaction (PCR) and found between one and seven BACs for each of the seven sequences. When testing the library with a portion of the soybean psbA chloroplast gene, we found less than 1% chloroplast DNA representation. We also screened the library for eight different classes of disease resistance gene analogs (RGAs) and identified BACs containing all RGAs except class 8. We arranged nine of the class 1 RGA BACs and six of the class 3 RGA BACs into individual contigs based on fingerprint patterns observed after Southern probing of restriction digests of the member BACs with a class-specific sequence. This resulted in the partial localization of the different multigene family sequences without precise definition of their exact positions. Using PCR-based end rescue techniques and RFLP mapping of BAC ends, we mapped individual BACs of each contig onto linkage group J of the soybean public map. The class 1 contig mapped to the region on linkage group J that contains several disease resistance genes. The class 1 contig extended approximately 400 kb. The arrangement of the BACs within this contig has been confirmed using PCR. One end of the class 1 contig core BAC mapped to two positions on linkage group J and cosegregated with two class 1 RGA loci, suggesting that this segment is within an area of regional duplication.Key words: bacterial artificial chromosome, BAC library, soybean, contig, resistance gene analog.

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.

Genome-Wide Analysis of NBS-Encoding Disease Resistance Genes in Maize Inbred Line B73

2009 ◽  
Vol 35 (3) ◽  
pp. 566-570 ◽  
Author(s):  
Jie-Ming WANG ◽  
Hai-Yang JIANG ◽  
Yang ZHAO ◽  
Yan XIANG ◽  
Su-Wen ZHU ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Inbred Line ◽  
Resistance Genes ◽  
Disease Resistance Genes ◽  
Maize Inbred Line ◽  
Genome Wide Analysis ◽  
Genome Wide

Comparative Mapping of Three Bacterial, Three Fungal, and One Virus Disease-resistance Genes in Common Bean

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 547a-547
Author(s):  
Geunhwa Jung ◽  
James Nienhuis ◽  
Dermot P. Coyne ◽  
H.M. Ariyarathne
Keyword(s):  
Disease Resistance ◽  
Common Bean ◽  
Pseudomonas Syringae ◽  
Resistance Genes ◽  
Fungal Pathogens ◽  
Xanthomonas Campestris ◽  
Virus Disease ◽  
Disease Resistance Genes ◽  
Brown Spot ◽  
Viral Pathogen

Common bacterial blight (CBB), bacterial brown spot (BBS), and halo blight (HB), incited by the bacterial pathogens Xanthomonas campestris pv. phaseoli (Smith) Dye, Pseodomonas syringae pv. syringa, and Pseudomonas syringae pv. phaseolicola, respectively are important diseases of common bean. In addition three fungal pathogens, web blight (WB) Thanatephorus cucumeris, rust Uromyces appendiculatus, and white mold (WM) Sclerotinia sclerotiorum, are also destructive diseases attacking common bean. Bean common mosaic virus is also one of most major virus disease. Resistance genes (QTLs and major genes) to three bacterial (CBB, BBS, and HB), three fungal (WB, rust, and WM), and one viral pathogen (BCMV) were previously mapped in two common bean populations (BAC 6 × HT 7719 and Belneb RR-1 × A55). The objective of this research was to use an integrated RAPD map of the two populations to compare the positions and effect of resistance QTL in common bean. Results indicate that two chromosomal regions associated with QTL for CBB resistance mapped in both populations. The same chromosomal regions associated with QTL for disease resistance to different pathogens or same pathogens were detected in the integrated population.

scholarly journals Identification of Three Putative Signal Transduction Genes Involved in R Gene-Specified Disease Resistance in Arabidopsis

Genetics ◽  
1999 ◽  
Vol 152 (1) ◽  
pp. 401-412 ◽  
Author(s):  
Randall F Warren ◽  
Peter M Merritt ◽  
Eric Holub ◽  
Roger W Innes
Keyword(s):  
Disease Resistance ◽  
Pseudomonas Syringae ◽  
Resistance Genes ◽  
Virulent Strain ◽  
Disease Resistance Genes ◽  
Avirulence Gene ◽  
Detectable Effect ◽  
Disease Resistance Gene ◽  
Protein Functions ◽  
Signal Transduction Genes

Abstract The RPS5 disease resistance gene of Arabidopsis mediates recognition of Pseudomonas syringae strains that possess the avirulence gene avrPphB. By screening for loss of RPS5-specified resistance, we identified five pbs (avrPphB susceptible) mutants that represent three different genes. Mutations in PBS1 completely blocked RPS5-mediated resistance, but had little to no effect on resistance specified by other disease resistance genes, suggesting that PBS1 facilitates recognition of the avrPphB protein. The pbs2 mutation dramatically reduced resistance mediated by the RPS5 and RPM1 resistance genes, but had no detectable effect on resistance mediated by RPS4 and had an intermediate effect on RPS2-mediated resistance. The pbs2 mutation also had varying effects on resistance mediated by seven different RPP (recognition of Peronospora parasitica) genes. These data indicate that the PBS2 protein functions in a pathway that is important only to a subset of disease-resistance genes. The pbs3 mutation partially suppressed all four P. syringae-resistance genes (RPS5, RPM1, RPS2, and RPS4), and it had weak-to-intermediate effects on the RPP genes. In addition, the pbs3 mutant allowed higher bacterial growth in response to a virulent strain of P. syringae, indicating that the PBS3 gene product functions in a pathway involved in restricting the spread of both virulent and avirulent pathogens. The pbs mutations are recessive and have been mapped to chromosomes I (pbs2) and V (pbs1 and pbs3).

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1961-1977
Author(s):  
Michelle A Graham ◽  
Laura Fredrick Marek ◽  
Randy C Shoemaker
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Developmental Stages ◽  
Gene Evolution ◽  
Pcr Amplification ◽  
Disease Resistance Genes ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

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