Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping

Madsen, Lene Heegaard; Collins, Nicholas C.; Rakwalska, Magdalena; Backes, Gunter; Sandal, Niels; Krusell, Lene; Jensen, J.; Waterman, E.; Jahoor, A.; Ayliffe, Michael; Pryor, A.; Langridge, Peter; Schulze‐Lefert, Paul; Stougaard, Jens

doi:10.1007/s00438-003-0823-5

Cited by 77 publications

(39 citation statements)

References 72 publications

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“…Similar correlation between disease resistance QTL and NBS resistance genes has been found in other plants [56]–[59], indicating that the association between disease resistance QTL and NBS genes might be common in crop species. Therefore, we may be able to integrate multi-disease-resistance genes together by developing molecular markers for NBS genes in order to develop a supper disease resistance cultivated cotton variety.…”

Section: Discussionsupporting

confidence: 77%

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

Wei

Sun

et al. 2013

PLoS ONE

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Plant disease resistance genes are a key component of defending plants from a range of pathogens. The majority of these resistance genes belong to the super-family that harbors a Nucleotide-binding site (NBS). A number of studies have focused on NBS-encoding genes in disease resistant breeding programs for diverse plants. However, little information has been reported with an emphasis on systematic analysis and comparison of NBS-encoding genes in cotton. To fill this gap of knowledge, in this study, we identified and investigated the NBS-encoding resistance genes in cotton using the whole genome sequence information of Gossypium raimondii. Totally, 355 NBS-encoding resistance genes were identified. Analyses of the conserved motifs and structural diversity showed that the most two distinct features for these genes are the high proportion of non-regular NBS genes and the high diversity of N-termini domains. Analyses of the physical locations and duplications of NBS-encoding genes showed that gene duplication of disease resistance genes could play an important role in cotton by leading to an increase in the functional diversity of the cotton NBS-encoding genes. Analyses of phylogenetic comparisons indicated that, in cotton, the NBS-encoding genes with TIR domain not only have their own evolution pattern different from those of genes without TIR domain, but also have their own species-specific pattern that differs from those of TIR genes in other plants. Analyses of the correlation between disease resistance QTL and NBS-encoding resistance genes showed that there could be more than half of the disease resistance QTL associated to the NBS-encoding genes in cotton, which agrees with previous studies establishing that more than half of plant resistance genes are NBS-encoding genes.

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Section: Discussionsupporting

confidence: 77%

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

Wei

Sun

et al. 2013

PLoS ONE

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“…7; Additional file 1: Table S14). An association analysis between disease resistance QTLs and NBS genes found that at least 32 NBS-encoding genes were adjacent to disease resistance QTLs in cotton [56], and there were similar results in other crops [56, 83–85]. Six of the VdRLs adjacent to Verticillium wilt resistance QTLs were located on the short region of Chr07 (Fig.…”

Section: Discussionmentioning

confidence: 71%

Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt

Chen

Huang

et al. 2015

BMC Plant Biol

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BackgroundGossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs.ResultsThe G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes.ConclusionsThe cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0508-3) contains supplementary material, which is available to authorized users.

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“…Genes encoding the α-gliadin storage, Lrk10 , viviparous, sucrose synthase, granule-bound starch synthase proteins were genetically mapped (Table 4) to positions similar to those reported previously (see GrainGenes database at wheat.pw.usda.gov). Seven PstI tags orthologous to barley RGA sequences (Madsen et al 2003) were mapped to chromosomes 2D, 3B, 4A, 5A, 5B, 5D, and 7B. Moreover, GBS markers matching the wheat RGA sequences were mapped to chromosomes 1D, 2A, 3A, 3D, 4B, 5D, and 7D.…”

Section: Resultsmentioning

confidence: 99%

Sequence-Based Mapping of the Polyploid Wheat Genome

Saintenac

Jiang

Wang

et al. 2013

G3 Genes|Genomes|Genetics

133

131

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The emergence of new sequencing technologies has provided fast and cost-efficient strategies for high-resolution mapping of complex genomes. Although these approaches hold great promise to accelerate genome analysis, their application in studying genetic variation in wheat has been hindered by the complexity of its polyploid genome. Here, we applied the next-generation sequencing of a wheat doubled-haploid mapping population for high-resolution gene mapping and tested its utility for ordering shotgun sequence contigs of a flow-sorted wheat chromosome. A bioinformatical pipeline was developed for reliable variant analysis of sequence data generated for polyploid wheat mapping populations. The results of variant mapping were consistent with the results obtained using the wheat 9000 SNP iSelect assay. A reference map of the wheat genome integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. By analyzing the sequenced megabase-size regions of the wheat genome we showed that mapped markers are located within 40−100 kb from genes providing a possibility for high-resolution mapping at the level of a single gene. In our population, gene loci controlling a seed color phenotype cosegregated with 2459 markers including one that was located within the red seed color gene. We demonstrate that the high-density reference map presented here is a useful resource for gene mapping and linking physical and genetic maps of the wheat genome.

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Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping

Cited by 77 publications

References 72 publications

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

Systematic Analysis and Comparison of Nucleotide-Binding Site Disease Resistance Genes in a Diploid Cotton Gossypium raimondii

Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt

Sequence-Based Mapping of the Polyploid Wheat Genome

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