Genome- Wide Analysis of the Nucleotide Binding Site Leucine-Rich Repeat Genes of Four Orchids Revealed Extremely Low Numbers of Disease Resistance Genes

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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Bioinformatic analysis of the nucleotide binding site-encoding disease-resistance genes in foxtail millet (Setaria italica (L.) Beauv.)

Genetics and Molecular Research ◽

10.4238/2014.august.28.5 ◽

2014 ◽

Vol 13 (3) ◽

pp. 6602-6609 ◽

Cited By ~ 1

Author(s):

Y.B. Zhu ◽

X.Q. Xie ◽

Z.Y. Li ◽

H. Bai ◽

L. Dong ◽

...

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Genes ◽

Foxtail Millet ◽

Nucleotide Binding ◽

Bioinformatic Analysis ◽

Nucleotide Binding Site ◽

Disease Resistance Genes ◽

Setaria Italica

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Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes inBrachypodium distachyon

Comparative and Functional Genomics ◽

10.1155/2012/418208 ◽

2012 ◽

Vol 2012 ◽

pp. 1-12 ◽

Cited By ~ 32

Author(s):

Shenglong Tan ◽

Song Wu

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Resistance Genes ◽

Brachypodium Distachyon ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Disease Resistance Genes ◽

Protein Motifs ◽

Wide Range ◽

Encoding Genes

Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes inBrachypodium distachyon. In this study, using computational analysis of theB. distachyongenome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (fromBrachypodiumdatabase) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes inBrachypodiumdatabase revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.

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Genome-Wide Analysis of Nucleotide-Binding Site (NBS) Disease Resistance (R) Genes in Sacred Lotus (Nelumbo nucifera Gaertn.) Reveals Their Transition Role During Early Evolution of Land Plants

Tropical Plant Biology ◽

10.1007/s12042-013-9122-4 ◽

2013 ◽

Vol 6 (2-3) ◽

pp. 98-116 ◽

Cited By ~ 4

Author(s):

Rui Zong Jia ◽

Ray Ming ◽

Yun J. Zhu

Keyword(s):

Disease Resistance ◽

Binding Site ◽

Nucleotide Binding ◽

Nucleotide Binding Site ◽

Nelumbo Nucifera ◽

Land Plants ◽

R Genes ◽

Genome Wide Analysis ◽

Sacred Lotus ◽

Genome Wide

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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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