Development of Clustered Resistance Gene Analogs-Based Markers of Resistance toPhytophthora capsiciin Chili Pepper

The soil-borne pathogenPhytophthora capsicicauses severe destruction ofCapsicumspp. Resistance inCapsicumagainstP. capsiciis controlled by numerous minor quantitative trait loci (QTLs) and a consistent major QTL on chromosome 5. Molecular markers onCapsicumchromosome 5 have been developed to identify the predominant genetic contributor to resistance but have achieved little success. In this study, previously reported molecular markers were used to reanalyze the major QTL region on chromosome 5 (6.2 Mbp to 139.2 Mbp). Candidate resistance gene analogs (RGAs) were identified in the extended major QTL region including 14 nucleotide binding site leucine-rich repeats, 3 receptor-like kinases, and 1 receptor-like protein. Sequence comparison of the candidate RGAs was performed between twoCapsicumgermplasms that are resistant and susceptible, respectively, toP. capsici.11 novel RGA-based markers were developed through high-resolution melting analysis which were closely linked to the major QTL forP. capsiciresistance. Among the markers, CaNB-5480 showed the highest cosegregation rate at 86.9% and can be applied to genotyping of the germplasms that were not amenable by previous markers. With combination of three markers such as CaNB-5480, CaRP-5130 and CaNB-5330 increased genotyping accuracy for 61Capsicumaccessions. These could be useful to facilitate high-throughput germplasm screening and further characterize resistance genes againstP. capsiciin pepper.

Download Full-text

Cloning of apricot RGAs (Resistance Gene Analogs) and development of molecular markers associated with Sharka (PPV) resistance

The Journal of Horticultural Science and Biotechnology ◽

10.1080/14620316.2004.11511834 ◽

2004 ◽

Vol 79 (5) ◽

pp. 729-734 ◽

Cited By ~ 8

Author(s):

L. Dondini ◽

F. Costa ◽

G. Tataranni ◽

S. Tartarini ◽

S. Sansavini

Keyword(s):

Molecular Markers ◽

Resistance Gene ◽

Resistance Gene Analogs ◽

Ppv Resistance

Download Full-text

The Isolation and Mapping of Disease Resistance Gene Analogs in Maize

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.1998.11.10.968 ◽

1998 ◽

Vol 11 (10) ◽

pp. 968-978 ◽

Cited By ~ 143

Author(s):

N. C. Collins ◽

C. A. Webb ◽

S. Seah ◽

J. G. Ellis ◽

S. H. Hulbert ◽

...

Keyword(s):

Disease Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Plant Disease Resistance ◽

Amino Acid Identity ◽

Disease Resistance Gene ◽

Resistance Gene Analogs ◽

Resistance Proteins ◽

Genomic Regions ◽

Leucine Rich Repeats

Many of the plant disease resistance genes that have been isolated encode proteins with a putative nucleotide binding site and leucine-rich repeats (NBS-LRR resistance genes). Oligonucleotide primers based on conserved motifs in and around the NBS of known NBS-LRR resistance proteins were used to amplify sequences from maize genomic DNA by polymerase chain reaction (PCR). Eleven classes of non-cross-hybridizing sequences were obtained that had predicted products with high levels of amino acid identity to NBS-LRR resistance proteins. These maize resistance gene analogs (RGAs) and one RGA clone obtained previously from wheat were used as probes to map 20 restriction fragment length polymorphism (RFLP) loci in maize. Some RFLPs were shown to map to genomic regions containing virus and fungus resistance genes. Perfect co-segregation was observed between RGA loci and the rust resistance loci rp1 and rp3. The RGA probe associated with rp1 also detected deletion events in several rp1 mutants. These data strongly suggest that some of the RGA clones may hybridize to resistance genes.

Download Full-text

Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype

BMC Genomics ◽

10.1186/s12864-019-6207-y ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Hugo V. S. Rody ◽

Renato G. H. Bombardelli ◽

Silvana Creste ◽

Luís E. A. Camargo ◽

Marie-Anne Van Sluys ◽

...

Keyword(s):

Immune System ◽

Resistance Gene ◽

Innate Immune System ◽

De Novo ◽

Innate Immune ◽

Differentially Expressed ◽

Resistance Gene Analogs ◽

Chromosome 5 ◽

Resistant Genotype ◽

Genomic Features

Abstract Background Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging. Results We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs. Conclusions Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.

Download Full-text

Genetic variation of populations of Pinus oocarpa revealed by resistance gene analog polymorphism (RGAP)

Genome ◽

10.1139/g03-023 ◽

2003 ◽

Vol 46 (3) ◽

pp. 404-410 ◽

Cited By ~ 7

Author(s):

V Díaz ◽

E Ferrer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Resistance Gene ◽

Population Diversity ◽

Resistance Gene Analog ◽

Resistance Gene Analogs ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Pinus Oocarpa

Primers based on conserved motifs of plant resistance genes were used to generate multilocus molecular markers referred to as resistance gene analog polymorphisms (RGAPs) in Pinus oocarpa subsp. oocarpa. Ten populations from three regions of Nicaragua were analyzed with 53 RGAPs. The aim of this study was to determine the levels of within- and between-population diversity with this kind of marker, and to compare estimates with previously obtained results based on RAPD and AFLP. All populations showed high levels of diversity. GST values and the analysis of molecular variance (AMOVA) revealed most variation to be within populations, although significant differences between populations and regions were also detected. This pattern of genetic diversity was similar to that obtained for RAPD and AFLP, which suggests that variation at RGAP loci as detected in this work is mostly influence by non-selective forces.Key words: resistance gene analogs, molecular markers, genetic diversity, population structure, Pinus oocarpa.

Download Full-text

Identification of resistance gene analogs involved in Phytophthora capsici recognition in black pepper (Piper nigrum L.)

Journal of Plant Pathology ◽

10.1007/s42161-020-00586-3 ◽

2020 ◽

Vol 102 (4) ◽

pp. 1121-1131

Author(s):

Erinjery Jose Suraby ◽

Duraiswami Prasath ◽

Kantipudi Nirmal Babu ◽

Muthuswamy Anandaraj

Keyword(s):

Resistance Gene ◽

Phytophthora Capsici ◽

Black Pepper ◽

Piper Nigrum ◽

Resistance Gene Analogs

Download Full-text

Genetic Analysis of Resistance to Multiple Isolates of Phytophthora capsici and Linkage to Horticultural Traits in Bell Pepper

HortScience ◽

10.21273/hortsci13359-18 ◽

2019 ◽

Vol 54 (7) ◽

pp. 1143-1148

Author(s):

Jareerat Chunthawodtiporn ◽

Theresa Hill ◽

Kevin Stoffel ◽

Allen Van Deynze

Keyword(s):

Candidate Genes ◽

Gene Annotation ◽

Phytophthora Capsici ◽

Genetic Resistance ◽

Bell Pepper ◽

Chromosome 5 ◽

Horticultural Traits ◽

Trait Locus ◽

High Level ◽

Major Qtl

Phytophthora capsici is one of the major pathogens found in pepper production, especially in bell pepper. Due to the high level of genetic diversity of the pathogen, bell pepper varieties with broad genetic resistance are essential for disease management. Criollo de Morelos – 334 (CM334), a landrace that has a high level of genetic resistance to P. capsici, has been used as the resistant source for P. capsici to generate a recombinant inbred line (RIL) population with the susceptible bell pepper cultivar Maor. From the resulting population, quantitative trait locus (QTL) models explaining resistance to each of four isolates of P. capsici were derived from QTL regions on three chromosomes using stepwiseqtl in R/qtl. A single region of chromosome 5 contained major QTL for resistance to each of the four isolates. Two isolate-specific QTL conferring resistance to isolates PWB53 and PWB106 were located on chromosomes 10 and 11, respectively. Both isolate-specific QTL had epistatic interactions with a major QTL on chromosome 5. Using the pepper reference genome and gene annotation, candidate genes for P. capsici resistance within 1.5-logarithm of odds (LOD) interval were identified. Based on functional annotations derived from Arabidopsis thaliana and solanaceous crop databases, multiple candidate genes related to resistance (R) gene complexes or to plant immune system were found under the QTL on all three chromosomes. A comparison of the locations of resistance QTL and previously identified horticultural QTL using the same population revealed tight linkage between resistance to P. capsici and a stem pubescence QTL o chromosome 10. Both candidate genes for P. capsici resistance and the linkages between resistance and horticultural traits could be applied for selection to broad resistance to P. capsici in bell pepper–breeding programs.

Download Full-text