scholarly journals Genetic and Physical Mapping of Avr1a in Phytophthora sojae

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 949-959 ◽  
Author(s):  
Terry MacGregor ◽  
Madan Bhattacharyya ◽  
Brett Tyler ◽  
Ravindra Bhat ◽  
August F Schmitthenner ◽  
...  
Keyword(s):  
Positional Cloning ◽  
Dna Marker ◽  
Physical Map ◽  
Phytophthora Sojae ◽  
Distance Ratio ◽  
Bac Contig ◽  
F2 Population ◽  
Genetic Linkage Maps ◽  
F2 Progeny ◽  
Avr Genes

Abstract The interaction between soybean and the phytopathogenic oomycete Phytophthora sojae is controlled by host resistance (Rps) genes and pathogen avirulence (Avr) genes. We have mapped the Avr1a locus in F2 populations derived from four different P. sojae races. Four RAPD and nine AFLP markers linked to Avr1a were initially identified. Nine markers were used to compare genetic linkage maps of the Avr1a locus in two distinct F2 populations. Distorted segregation ratios favoring homozygous genotypes were noted in both crosses. Segregation analysis of all the markers in one F2 population of 90 progeny generated a map of 113.2 cM encompassing Avr1a, with one marker cosegregating with the gene. The cosegregating DNA marker was used to isolate P. sojae BAC clones and construct a physical map covering 170 kb, from which additional DNA markers were developed. Three markers occurring within the BAC contig were mapped in an enlarged population of 486 F2 progeny. Avr1a was localized to a 114-kb interval, and an average physical to genetic distance ratio of 391 kb/cM was calculated for this region. This work provides a basis for the positional cloning of Avr1a.

scholarly journals A4Mb High Resolution BAC Contig on Bovine Chromosome1q12and Comparative Analysis With Human Chromosome21q22

2005 ◽  
Vol 6 (4) ◽  
pp. 194-203 ◽  
Author(s):  
Cord Drögemüller ◽  
Anne Wöhlke ◽  
Tosso Leeb ◽  
Ottmar Distl
Keyword(s):  
Positional Cloning ◽  
Physical Map ◽  
Dominant Gene ◽  
Bac Library ◽  
Exact Order ◽  
Bac Contig ◽  
Nucleotide Sequence Data ◽  
New Genes ◽  
Human Genes ◽  
First Time

The bovine RPCI-42 BAC library was screened to construct a sequence-ready ~4 Mb single contig of 92 BAC clones on BTA 1q12. The contig covers the region between the genesKRTAP8P1andCLIC6. This genomic segment in cattle is of special interest as it contains the dominant gene responsible for the hornless or polled phenotype in cattle. The construction of the BAC contig was initiated by screening the bovine BAC library with heterologous cDNA probes derived from 12 human genes of the syntenic region on HSA 21q22. Contig building was facilitated by BAC end sequencing and chromosome walking. During the construction of the contig, 165 BAC end sequences and 109 single-copy STS markers were generated. For comparative mapping of 25 HSA 21q22 genes, genomic PCR primers were designed from bovine EST sequences and the gene-associated STSs mapped on the contig. Furthermore, bovine BAC end sequence comparisons against the human genome sequence revealed significant matches to HSA 21q22 and allowed thein silicomapping of two new genes in cattle. In total, 31 orthologues of human genes located on HSA 21q22 were directly mapped within the bovine BAC contig, of which 16 genes have been cloned and mapped for the first time in cattle. In contrast to the existing comparative bovine–human RH maps of this region, these results provide a better alignment and reveal a completely conserved gene order in this 4 Mb segment between cattle, human and mouse. The mapping of known polled linked BTA 1q12 microsatellite markers allowed the integration of the physical contig map with existing linkage maps of this region and also determined the exact order of these markers for the first time. Our physical map and transcript map may be useful for positional cloning of the putative polled gene in cattle. The nucleotide sequence data reported in this paper have been submitted to EMBL and have been assigned Accession Numbers AJ698510–AJ698674.

Resolving the aphid resistance locus Sd-1 on a BAC contig within a sub-telomeric region of Malus linkage group 7

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 939-945 ◽  
Author(s):  
Volkan Cevik ◽  
Graham J King
Keyword(s):  
Linkage Group ◽  
Physical Map ◽  
Aphid Resistance ◽  
Economic Damage ◽  
Telomeric Region ◽  
Resistance Locus ◽  
Average Insert Size ◽  
Distance Ratio ◽  
Bac Contig ◽  
Bac Clones

Aphids cause serious physical and economic damage to most major crops throughout the world, and there is a pressing requirement to isolate genes conferring aphid resistance. The Sd-1 locus in Malus spp. (apple) confers resistance against the rosy leaf-curling aphid (Dysaphis devecta Wlk.), and was recently positioned within a 1.3-cM region on linkage group 7, flanked by molecular markers. These markers were used as a basis for development of a BAC contig spanning the locus, together with adapter-mediated amplification of flanking sequences to obtain BAC insert-end sequences, and fingerprinting of BAC clones. Approximately 800 kb of the Sd-1 genomic region was covered by 19 overlapping BACs, with an average insert size of 75–150 kb. The physical – genetic distance ratio was estimated at 460 kb/cM, although the distribution of recombination events was irregular with respect to estimated physical distance. Recombinant analysis and development of new markers allowed Sd-1 to be positioned within an interval of approximately 180 kb located on either of two overlapping BACs. From one of these, an insert end sequence showed a significant degree of similarity to nucleotide binding site – leucine rich repeat (NBS–LRR) resistance genes. Fluorescent in situ hybridization (FISH) of BAC clones within the contig enabled positioning and orientation of the locus within a euchromatic region, very close to the telomere of linkage group 7.Key words: aphid, resistance gene, apple, Malus, physical map.

scholarly journals Saturation Mapping of a Gene-Rich Recombination Hot Spot Region in Wheat

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 823-835 ◽  
Author(s):  
Justin D Faris ◽  
Karri M Haen ◽  
Bikram S Gill
Keyword(s):  
Positional Cloning ◽  
Physical Map ◽  
Hot Spot ◽  
Chromosome Breakage ◽  
Small Chromosome ◽  
Gene Density ◽  
Chromosome 5B ◽  
High Gene ◽  
The Many ◽  
Recombination Hot Spots

AbstractPhysical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.

scholarly journals Seleksi Berbasis Marka Molekuler pada Padi Generasi F2 Guna Merakit Galur Padi Harapan Tahan Wereng Coklat

Agrikultura ◽  
2016 ◽  
Vol 27 (1) ◽  
Author(s):  
Nono Carsono ◽  
Gigih Ibnu Prayoga ◽  
Neni Rostini ◽  
Danar Dono
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Yield Loss ◽  
Insect Pest ◽  
Brown Planthopper ◽  
F2 Population ◽  
Significant Yield ◽  
F2 Generation ◽  
F2 Progeny ◽  
Simple Sequence

ABSTRACTMolecular Marker-based Selection on F2 Progeny for Development of Promising Rice Lines Resistant to Brown PlanthopperBrown planthopper (BPH) is the major insect pest of rice and accounts for significant yield loss. This experiment was aimed to develop BC1F1 and F3 brown planthopper resistant rice lines. Selection on the basis of SSR markers can be done by using two polymorphic SSR markers, i.e., RM586 dan RM8213, which screened from eight SSR markers for BPH resistant. Sixty-three F2 genotypes from IP-1 (derived from IR-64 x PTB-33) population and twenty F2 genotypes from PP-11 (derived from Pandan Wangi x PTB-33) population were selected and will be used for further research by selfed and backcrossed to recipient parents. Chi-squares test for segregation of DNA bands in F2 generation showed that RM8213 fitted with 1:2:1 Mendelian ratio for controlling photosynthetic rates and trichomes length in IP-1 population. This information could be used in programs to develop a durable brown planthopper resistant rice cultivar.Keywords: BPH, F2 population, Moleculer marker, SSRABSTRAKWereng coklat merupakan salah satu hama utama pada tanaman padi yang mampu menurunkan produksi padi secara nyata. Penelitian ini bertujuan untuk memperoleh galur-galur padi F2 yang memiliki marka-marka yang berasosisasi dengan ketahanannya terhadap wereng coklat. Seleksi pada galur padi F2 hasil persilangan telah dilakukan melalui teknik marka molekuler Simple Sequence Repeat (SSR) menggunakan dua marka SSR yang menunjukkan polimorphisme yaitu RM586 dan RM8213 dari delapan marka yang diskrining. Sebanyak 63 genotip dari populasi IP-1 (hasil persilangan IR-64 x PTB-33) dan 20 genotip dari populasi PP-11 (hasil persilangan Pandan Wangi x PTB-33) untuk disilangkan sendiri maupun disilang balik dengan tetua recipient. Selain itu, hasil analisis Chi-Kuadrat untuk segregasi pita DNA menunjukkan bahwa primer RM8213 memiliki rasio 1:2:1 (dominasi tidak sempurna) dalam mengontrol karakter laju fotosintesis dan panjang trikoma terhadap wereng coklat pada populasi IP-1. Informasi yang diperoleh dari penelitian ini nantinya dapat digunakan untuk program perakitan kultivar padi tahan wereng coklat yang durable.Kata Kunci: Marka molekuler, Populasi F2, SSR, Wereng coklat

scholarly journals The Avr1b Locus of Phytophthora sojae Encodes an Elicitor and a Regulator Required for Avirulence on Soybean Plants Carrying Resistance Gene Rps1b

2004 ◽  
Vol 17 (4) ◽  
pp. 394-403 ◽  
Author(s):  
Weixing Shan ◽  
Minh Cao ◽  
Dan Leung ◽  
Brett M. Tyler
Keyword(s):  
Resistance Gene ◽  
Artificial Chromosome ◽  
Phytophthora Sojae ◽  
Secreted Protein ◽  
Bac Clone ◽  
Bac Contig ◽  
Soybean Plants ◽  
Substitution Mutations ◽  
Race 2 ◽  
Soybean Leaves

We have used map-based approaches to clone a locus containing two genes, Avr1b-1 and Avr1b-2, required for avirulence of the oomycete pathogen Phytophthora sojae (Kaufmann & Gerdemann) on soybean plants carrying resistance gene Rps1b. Avr1b-1 was localized to a single 60-kb bacterial artificial chromosome (BAC) clone by fine-structure genetic mapping. Avr1b-1 was localized within the 60-kb region by identification of an mRNA that is expressed in a race-specific and infection-specific manner and that encodes a small secreted protein. When the Avr1b-1 protein was synthesized in the yeast Pichia pastoris and the secreted protein infiltrated into soybean leaves, it triggered a hypersensitive response specifically in host plants carrying the Rps1b resistance gene. This response eventually spread to the entire inoculated plant. In some isolates of P. sojae virulent on Rps1b-containing cultivars, such as P7081 (race 25) and P7076 (race 19), the Avr1b-1 gene had numerous substitution mutations indicative of strong divergent selection. In other isolates, such as P6497 (race 2) and P9073 (race 25), there were no substitutions in Avr1b-1, but Avr1b-1 mRNA did not accumulate. Genetic complementation experiments with P6497 revealed the presence of a second gene, Avr1b-2, required for the accumulation of Avr1b-1 mRNA. Avr1b-2 was genetically mapped to the same BAC contig as Avr1b-1, using a cross between P7064 (race 7) and P6497. The Avr1k gene, required for avirulence on soybean cultivars containing Rps1k, was mapped to the same interval as Avr1b-1.

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.

scholarly journals Development of a sequence-based reference physical map of pea (Pisum sativum L.)

2019 ◽  
Author(s):  
Krishna Kishore Gali ◽  
Bunyamin Tar’an ◽  
Mohammed-Amin Madoui ◽  
Edwin van der Vossen ◽  
Jan van Oeveren ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Physical Map ◽  
Repetitive Sequences ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Bac Clones ◽  
Pooled Dna ◽  
Mapping Technology ◽  
Generation Sequencing

AbstractWhole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

scholarly journals An Integrated BAC and Genome Sequence Physical Map of Phytophthora sojae

2006 ◽  
Vol 19 (12) ◽  
pp. 1302-1310 ◽  
Author(s):  
Xuemin Zhang ◽  
Chantel Scheuring ◽  
Sucheta Tripathy ◽  
Zhanyou Xu ◽  
Chengcang Wu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Physical Map ◽  
Draft Genome ◽  
Restriction Enzymes ◽  
Artificial Chromosome ◽  
Phytophthora Sojae ◽  
Data Sets ◽  
Contig Assembly ◽  
Data Set ◽  
Phytophthora Spp

Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.

Genetics of resistance to Mycosphaerella pinodes in Lathyrus sativus

2004 ◽  
Vol 55 (9) ◽  
pp. 953 ◽  
Author(s):  
B. Skiba ◽  
R. Ford ◽  
E. C. K. Pang
Keyword(s):  
Confidence Intervals ◽  
Lathyrus Sativus ◽  
Mycosphaerella Pinodes ◽  
Genetics Of Resistance ◽  
Mendelian Segregation ◽  
Disease Symptoms ◽  
Segregation Data ◽  
Stem Lesion ◽  
F2 Population ◽  
F2 Progeny

Three Lathyrus sativus accessions were screened for their reaction to Mycosphaerella pinodes infection. Accession ATC 80878 displayed the lowest percentage stem lesion values (%SL) and was significantly more resistant to M. pinodes than ATC 80407 and ATC 80053. Accession ATC 80407 was the most susceptible, displaying the severest disease symptoms. A backcross and an F2 population were generated using accessions ATC 80878 and ATC 80407 as the resistant and susceptible parents, respectively. The backcross and F2 progeny segregated in a 3 : 1 and 7 : 9 ratio, respectively, for resistance/susceptibility, using the 99% confidence intervals for the means of the parental controls in each assay to determine the point of discontinuity. The segregation data from both populations fitted a Mendelian segregation model that suggested that resistance in the L. sativus accession ATC 80878 may be controlled by 2 independently segregating genes, operating in a complementary epistatic manner.

Detached-petiole inoculation method to evaluate Phytophthora root rot resistance in soybean plants

2017 ◽  
Vol 68 (6) ◽  
pp. 555
Author(s):  
Yinping Li ◽  
Suli Sun ◽  
Chao Zhong ◽  
Zhendong Zhu
Keyword(s):  
Root Rot ◽  
Dominant Gene ◽  
Phytophthora Sojae ◽  
Single Dominant Gene ◽  
Phytophthora Root Rot ◽  
Inoculation Methods ◽  
Inoculation Technique ◽  
Soybean Cultivars ◽  
F2 Population ◽  
Soybean Resistance

Phytophthora root rot (PRR) caused by Phytophthora sojae, is one of the most destructive soybean diseases. The deployment of resistant cultivars is an important disease management strategy. To this aim, the development of a fast and effective method to evaluate soybean resistance to P. sojae is strategic. In this study, a detached-petiole inoculation technique was developed and its reliability was verified in soybean cultivars and segregant populations for PRR resistance. The detached-petiole and hypocotyl inoculation methods were used to assess the resistance of soybean cultivars, the F2 population of a Zhonghuang47 × Xiu94-11 cross, and the derived F2:3 population. The reactions of 13 analysed cultivars to three P. sojae isolates were consistent between the two inoculation techniques. The reactions of the F2 and F2:3 populations to isolate PsMC1 were 95.20% similar between the two inoculation methods. The segregation of the resistance and susceptibility fit a 3 : 1 ratio. Our results suggest that the detached-petiole technique is a reliable method, and reveal that the PRR resistance in Xiu94-11 is controlled by a single dominant gene. The phenotypic ratios of the tested Jikedou2 × Qichadou1 F2 population using the detached-petiole inoculation technique fit a 3 : 1 ratio (Resistance : Susceptibility). This demonstrated that Qichadou1 contains a single dominant gene conferring resistance to P. sojae. Our new detached-petiole inoculation technique is effective, reliable, non-destructive to the plant, and does not require an excessive amount of seeds. It may be suitable for the largescale screening of soybean resistance to multiple P. sojae isolates.

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