Isolation and Characterization of Nucleotide-Binding Site Resistance Gene Homologues in Common Bean (Phaseolus vulgaris)

Common bean production is constrained by many fungal, viral, and bacterial pathogens. Thus, the identification of resistance (R) genes is an important focal point of common bean research. The main goal of our study was to identify resistance gene homologues (RGH) in the crop, using degenerate primers designed from conserved sequences in the nucleotide-binding site (NBS) domains of R-genes from the model legume Medicago truncatula. Total DNA of the Andean common bean genotype G19833 was used for amplification of over 500 primer combinations. Sequencing of amplicons showed that 403 cloned fragments had uninterrupted open reading frames and were considered representative of functional RGH genes. The sequences were grouped at two levels of nucleotide identity (90 and 80%) and representative sequences of each group were used for phylogenetic analyses. The RGH sequence diversity of common bean was divided into TIR and non-TIR families, each with different clusters. The TIR sequences grouped into 14 clades while non-TIR sequences grouped into seven clades. Pairwise comparisons showed purifying selection, although some sequences may have been the result of diversifying selection. Knowledge about RGH genes in common bean can allow the design of molecular markers for pyramiding of resistance genes against various pathogens.

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Isolation, Characterization and Phylogenetic Analysis of Nucleotide Binding Site-encoding Disease-resistance Gene Analogues from European Aspen (Populus tremula)

Silvae Genetica ◽

10.1515/sg-2010-0009 ◽

2010 ◽

Vol 59 (1-6) ◽

pp. 68-77 ◽

Cited By ~ 1

Author(s):

Yong Zhang ◽

Shougong Zhang ◽

Liwang Qi ◽

Tao Zhang ◽

Chunguo Wang ◽

...

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Gene ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Populus Tremula ◽

R Gene ◽

R Genes ◽

Degenerate Primers ◽

European Aspen

Abstract The majority of verified plant disease resistance genes (R genes) isolated to date was of the nucleotide binding site-leucine rich repeat (NBS-LRR) class. The conservation between different NBS-LRR R genes opens the avenue for the use of PCR based strategies in isolating and cloning other R gene family members or analogs (resistance gene analogue, RGA) using degenerate primers for these conserved regions. In this study, to better understand the R gene in European aspen (Populus tremula), a perennial tree, we used degenerate primers to amplify RGA sequences from European aspen. Cloning and sequence characterization identified 37 European aspen RGAs, which could be phylogenetically classified into seven subfamilies. Deduced amino acid sequences of European aspen RGAs showed strong identity, ranging from 30.41 to 46.63%, to toll interleukin receptor (TIR) R gene subfamily. BLAST searches with reference to the genomic sequence of P. trichocarpa found 209 highly homologous regions distributed in 28 genomic loci, suggesting the abundance and divergence of NBS-encoding R genes in European aspen genome. Although, numerous studies have reported that plant R genes are under diversifying selection for specificity to evolving pathogens, non-synonymous to synonymous nucleotide substitution (dN/dS) ratio were <1 for NBS domains of European aspen RGA, showing the evidence of purifying selection in this perennial tree. In further analysis, many intergenic exchanges were also detected among these RGAs, indicating a probable role in homogenising NBS domains. The present study permits insights into the origin, diversification, evolution and function of NBS-LRR R genes in perennial species like European aspen and will be useful for further R gene isolation and exploitation.

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Isolation and characterization of nucleotide-binding site and C-terminal leucine-rich repeat-resistance gene candidates in bananas

Genetics and Molecular Research ◽

10.4238/2011.december.15.1 ◽

2011 ◽

Vol 10 (4) ◽

pp. 3098-3108 ◽

Cited By ~ 4

Author(s):

Y. Lu ◽

W.H. Xu ◽

Y.X. Xie ◽

X. Zhang ◽

J.J. Pu ◽

...

Keyword(s):

Binding Site ◽

Resistance Gene ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Leucine Rich Repeat ◽

Isolation And Characterization ◽

Resistance Gene Candidates

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Isolation of a family of resistance gene analogue sequences of the nucleotide binding site (NBS) type fromLensspecies

Genome ◽

10.1139/g04-027 ◽

2004 ◽

Vol 47 (4) ◽

pp. 650-659 ◽

Cited By ~ 33

Author(s):

M W.F Yaish ◽

L E Sáenz de Miera ◽

M Pérez de la Vega

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Gene ◽

Resistance Genes ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Disease Resistance Genes ◽

Nucleotide Sequence Analysis ◽

Degenerate Primers ◽

Conserved Motifs

Most known plant disease-resistance genes (R genes) include in their encoded products domains such as a nucleotide-binding site (NBS) or leucine-rich repeats (LRRs). Sequences with unknown function, but encoding these conserved domains, have been defined as resistance gene analogues (RGAs). The conserved motifs within plant NBS domains make it possible to use degenerate primers and PCR to isolate RGAs. We used degenerate primers deduced from conserved motifs in the NBS domain of NBS-LRR resistance proteins to amplify genomic sequences from Lens species. Fragments from approximately 500-850 bp were obtained. The nucleotide sequence analysis of these fragments revealed 32 different RGA sequences in Lens species with a high similarity (up to 91%) to RGAs from other plants. The predicted amino acid sequences showed that lentil sequences contain all the conserved motifs (P-loop, kinase-2, kinase-3a, GLPL, and MHD) present in the majority of other known plant NBSLRR resistance genes. Phylogenetic analyses grouped the Lens NBS sequences with the Toll and interleukin-1 receptor (TIR) subclass of NBSLRR genes, as well as with RGA sequences isolated from other legume species. Using inverse PCR on one putative RGA of lentil, we were able to amplify the flanking regions of this sequence, which contained features found in R proteins.Key words: disease resistance genes, comparative analysis, lentils, TIR, LRR.

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A superfamily of disease resistance gene analogs is located on all homoeologous chromosome groups of wheat (Triticum aestivum)

Genome ◽

10.1139/g98-083 ◽

1998 ◽

Vol 41 (6) ◽

pp. 782-788 ◽

Cited By ~ 11

Author(s):

W Spielmeyer ◽

M Robertson ◽

N Collins ◽

D Leister ◽

P Schulze-Lefert ◽

...

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Gene ◽

Resistance Genes ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Resistance Gene Analogs ◽

Leucine Rich Repeat ◽

Homoeologous Chromosome ◽

Entry Points

In this study, resistance gene analogs (RGAs) which were isolated from monocot crop species (wheat, barley, maize and rice) and contained conserved sequence motifs found within the nucleotide binding site - leucine rich repeat (NBS-LRR) class of resistance genes, were used to assess their distribution in the wheat genome. The RGAs showed 30-70% amino acid identity to a previously isolated monocot NBS-LRR sequence from the Cre3 locus for cereal cyst nematode (CCN) resistance in wheat. We used the RGAs as probes to identify and map loci in wheat using recombinant inbred lines of an international Triticeae mapping family. RGA loci mapped across all seven homoeologous chromosome groups of wheat. This study demonstrated that the RGA mapping approach provides potential entry points toward identifying resistance gene candidates in wheat.Key words: wheat, disease resistance genes, nucleotide binding site, leucine rich repeat, resistance gene analogs.

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Isolation and characterization of a set of disease resistance-gene analogs (RGAs) from wild rice, Zizania latifolia Griseb. I. Introgression, copy number lability, sequence change, and DNA methylation alteration in several rice–Zizania introgression lines

Genome ◽

10.1139/g05-097 ◽

2006 ◽

Vol 49 (2) ◽

pp. 150-158 ◽

Cited By ~ 8

Author(s):

Yu Chen ◽

Likun Long ◽

Xiuyun Lin ◽

Wanli Guo ◽

Bao Liu

Keyword(s):

Dna Methylation ◽

Binding Site ◽

Resistance Gene ◽

Wild Rice ◽

Copy Number ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Amino Acid Sequence Similarity ◽

Resistance Gene Analogs ◽

Zizania Latifolia

Eight resistance-gene analogs (RGAs) were isolated from wild rice, Zizania latifolia Griseb., by degenerate primers designed according to conserved motifs at or around the nucleotide-binding site (NBS) of known NBS-containing plant resistance genes. The 8 RGAs were classified into 6 distinct groups based on their deduced amino acid sequence similarity of 60% or greater. Gel-blot hybridization of each of the RGAs to 4 rice – Z. latifolia intro gression lines indicated an array of changes at either introgressed Zizania RGAs or, more likely, their rice homologs. The changes included dramatic increase in copy number, modification at the primary DNA sequence, and alteration in DNA methylation patterns.Key words: resistance gene analogs (RGAs), Zizania, introgression, nucleotide-binding site (NBS), leucine-rich repeat (LRR), genetic and epigenetic changes.

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Mutational Analysis of the Arabidopsis Nucleotide Binding Site–Leucine-Rich Repeat Resistance Gene RPS2

The Plant Cell ◽

10.1105/tpc.12.12.2541 ◽

2000 ◽

Vol 12 (12) ◽

pp. 2541-2554 ◽

Cited By ~ 55

Author(s):

Yi Tao ◽

Fenghua Yuan ◽

R. Todd Leister ◽

Frederick M. Ausubel ◽

Fumiaki Katagiri

Keyword(s):

Binding Site ◽

Resistance Gene ◽

Mutational Analysis ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Leucine Rich Repeat

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Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

10.1101/2020.02.08.939736 ◽

2020 ◽

Author(s):

Darlon V. Lantican ◽

Cris Q. Cortaga ◽

Anand Noel C. Manohar ◽

Fe M. dela Cueva ◽

Maria Luz J. Sison

Keyword(s):

Binding Site ◽

Resistance Gene ◽

De Novo ◽

Insect Pests ◽

Expression Profiles ◽

Interleukin 1 ◽

Coiled Coil ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Resistance Gene Analogs

AbstractMango is an economically important fruit crop largely cultivated in the (sub)tropics and thus, is constantly challenged by a myriad of insect pests and diseases. Here, we identified and characterized the resistance gene analogs (RGAs) of mango from de novo assembly of transcriptomic sequences. A core RGA database of mango with 747 protein models was established and classified based on conserved domains and motifs: 53 nucleotide binding site proteins (NBS); 27 nucleotide binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein (TM-CC), and 6 NBS-encoding proteins with other domains. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their expression profiles across different mango varieties were also determined. Phylogenetic analysis broadly clustered the core RGAs into 6 major clades based on their domain classification, while TM-CC proteins formed subclades all across the tree. The phylogenetic results suggest highly divergent functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms race. From the mango RGA transcripts, 134 unique EST-SSR loci were identified, and primers were designed targeting these potential markers. To date, this is the most comprehensive analysis of mango RGAs which offer a trove of markers for utilization in resistance breeding of mango.

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Identifying Resistance Gene Analogs Associated With Resistances to Different Pathogens in Common Bean

Phytopathology ◽

10.1094/phyto.2003.93.1.88 ◽

2003 ◽

Vol 93 (1) ◽

pp. 88-95 ◽

Cited By ~ 74

Author(s):

Camilo E. López ◽

Iván F. Acosta ◽

Carlos Jara ◽

Fabio Pedraza ◽

Eliana Gaitán-Solís ◽

...

Keyword(s):

Common Bean ◽

Resistance Gene ◽

Plant Disease Resistance ◽

Amino Acid Sequences ◽

Yellow Mosaic Virus ◽

Resistance Gene Analogs ◽

R Genes ◽

Degenerate Primers ◽

Golden Yellow ◽

Major Cluster

A polymerase chain reaction approach using degenerate primers that targeted the conserved domains of cloned plant disease resistance genes (R genes) was used to isolate a set of 15 resistance gene analogs (RGAs) from common bean (Phaseolus vulgaris). Eight different classes of RGAs were obtained from nucleotide binding site (NBS)-based primers and seven from not previously described Toll/Interleukin-1 receptor-like (TIR)-based primers. Putative amino acid sequences of RGAs were significantly similar to R genes and contained additional conserved motifs. The NBS-type RGAs were classified in two subgroups according to the expected final residue in the kinase-2 motif. Eleven RGAs were mapped at 19 loci on eight linkage groups of the common bean genetic map constructed at Centro Internacional de Agricultura Tropical. Genetic linkage was shown for eight RGAs with partial resistance to anthracnose, angular leaf spot (ALS) and Bean golden yellow mosaic virus (BGYMV). RGA1 and RGA2 were associated with resistance loci to anthracnose and BGYMV and were part of two clusters of R genes previously described. A new major cluster was detected by RGA7 and explained up to 63.9% of resistance to ALS and has a putative contribution to anthracnose resistance. These results show the usefulness of RGAs as candidate genes to detect and eventually isolate numerous R genes in common bean.

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