Disease Resistance Gene Family Research Articles

Genome-Wide Identification and Expression Analysis of the TIR-NBS-LRR Gene Family and Its Response to Fungal Disease in Rose (Rosa chinensis).

Roses, which are one of the world's most important ornamental plants, are often damaged by pathogens, resulting in serious economic losses. As a subclass of the disease resistance gene family of plant nucleotide-binding oligomerization domain (NOD)-like receptors, TIR-NBS-LRR (TNL) genes play a vital role in identifying pathogen effectors and activating defense responses. However, a systematic analysis of the TNL gene family is rarely reported in roses. Herein, 96 intact TNL genes were identified in Rosa chinensis. Their phylogenies, physicochemical characteristics, gene structures, conserved domains and motifs, promoter cis-elements, microRNA binding sites, and intra- and interspecific collinearity relationships were analyzed. An expression analysis using transcriptome data revealed that RcTNL genes were dominantly expressed in leaves. Some RcTNL genes responded to gibberellin, jasmonic acid, salicylic acid, Botrytis cinerea, Podosphaera pannosa, and Marssonina rosae (M. rosae); the RcTNL23 gene responded significantly to three hormones and three pathogens, and exhibited an upregulated expression. Furthermore, the black spot pathogen was identified as M. rosae. After inoculating rose leaves, an expression pattern analysis of the RcTNL genes suggested that they act during different periods of pathogen infection. The present study lays the foundations for an in-depth investigation of the TNL gene function and the mining of disease resistance genes in roses.

Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp.

Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.

Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp.

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora, Coffea eugenioides and their interspecific hybrid Coffea arabica). A total of 1311 non-redundant NLR loci were identified in C. arabica, 927 in C. canephora, and 1079 in C. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. The C. arabica genome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, and C. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared between C. arabica and the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.

Genome-Wide Analysis of the LRR-RLP Gene Family in a Wild Banana (Musa acuminata ssp. malaccensis) Uncovers Multiple Fusarium Wilt Resistance Gene Candidates.

Banana is the most popular fruit in the world, with a relevant role in food security for more than 400 million people. However, fungal diseases cause substantial losses every year. A better understanding of the banana immune system should facilitate the development of new disease-resistant cultivars. In this study, we performed a genome-wide analysis of the leucine-rich repeat receptor-like protein (LRR-RLP) disease resistance gene family in a wild banana. We identified 78 LRR-RLP genes in the banana genome. Remarkably, seven MaLRR-RLPs formed a gene cluster in the distal part of chromosome 10, where resistance to Fusarium wilt caused by Foc race 1 has been previously mapped. Hence, we proposed these seven MaLRR-RLPs as resistance gene candidates (RGCs) for Fusarium wilt. We also identified seven other banana RGCs based on their close phylogenetic relationships with known LRR-RLP proteins. Moreover, phylogenetic analysis of the banana, rice, and Arabidopsis LRR-RLP families revealed five major phylogenetic clades shared by these plant species. Finally, transcriptomic analysis of the MaLRR-RLP gene family in plants treated with Foc race 1 or Foc TR4 showed the expression of several members of this family, and some of them were upregulated in response to these Foc races. Our study provides novel insights into the structure, distribution, evolution, and expression of the LRR-RLP gene family in bananas as well as valuable RGCs that will facilitate the identification of disease resistance genes for the genetic improvement of this crop.

A Review on Nucleotide Binding Site – Leucine Rich Repeats Disease Resistance Genes in legumes

The crop plants of the family Leguminosae are second to cereal crops of commercial importance on the basis of area harvested and total production worldwide. It is well known globally that many crops do not give good yield due to certain diseases existing in their plants. Nowadays, there is much emphasis on developing disease resistant varieties of crops and especially of commercial crops. Plants need to protect themselves against attack from viruses, microbes, invertebrates and even other plants. NBS-LRR (Nucleotide binding site-leucine rich repeats) genes belong to the largest plant disease resistance gene family and are responsible for plant resistance to pathogens. Studies of the NBS-LRR gene family in plants represent an intriguing challenge and can provide knowledge on the genomic and molecular mechanisms that form the basis of gene regulation and protein function. Their evolution at the gene and genomic level can be defined through ancient and numerous gene families. In the present study, beneficial concepts for generating basic and fundamental knowledge on the NBS-LRR plant disease resistance genes are discussed with emphasis on selected legume plants of commercial importance.

High Resolution Genetic and Physical Mapping of a Major Powdery Mildew Resistance Locus in Barley.

Powdery mildew caused by Blumeria graminis f. sp. hordei is a foliar disease with highly negative impact on yield and grain quality in barley. Thus, breeding for powdery mildew resistance is an important goal and requires constantly the discovery of new sources of natural resistance. Here, we report the high resolution genetic and physical mapping of a dominant race-specific powdery mildew resistance locus, originating from an Ethiopian spring barley accession ‘HOR2573,’ conferring resistance to several modern mildew isolates. High-resolution genetic mapping narrowed down the interval containing the resistance locus to a physical span of 850 kb. Four candidate genes with homology to known disease resistance gene families were identified. The mapped resistance locus coincides with a previously reported resistance locus from Hordeum laevigatum, suggesting allelism at the same locus in two different barley lines. Therefore, we named the newly mapped resistance locus from HOR2573 as MlLa-H. The reported co-segregating and flanking markers may provide new tools for marker-assisted selection of this resistance locus in barley breeding.

Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited.

Phytopathogens have a limited range of host plant species that they can successfully parasitise ie. that they are adapted for. Infection of plants by nonadapted pathogens often results in an active resistance response that is relatively poorly characterised because phenotypic variation in this response often does not exist within a plant species, or is too subtle for genetic dissection. In addition, complex polygenic inheritance often underlies these resistance phenotypes and mutagenesis often does not impact upon this resistance, presumably due to genetic or mechanistic redundancy. Here it is demonstrated that phenotypic differences in the resistance response of Brachypodium distachyon to the nonadapted wheat stripe rust pathogen Puccinia striiformis f. sp. tritici (Pst) are genetically tractable and simply inherited. Two dominant loci were identified on B. distachyon chromosome 4 that each reduce attempted Pst colonisation compared with sib and parent lines without these loci. One locus (Yrr1) is effective against diverse Australian Pst isolates and present in two B. distachyon mapping families as a conserved region that was reduced to 5 candidate genes by fine mapping. A second locus, Yrr2, shows Pst race-specificity and encodes a disease resistance gene family typically associated with host plant resistance. These data indicate that some components of resistance to nonadapted pathogens are genetically tractable in some instances and may mechanistically overlap with host plant resistance to avirulent adapted pathogens.

BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing.

Numerous genes that determine the outcome of plant-pathogen interactions are currently being discovered and include, for example, immune receptors, susceptibility factors and pathogen effectors and their host targets. Target enrichment sequencing provides a means to preferentially resequence these genes of interest without the need to first generate a genotype-specific genome assembly. The Basic Local Alignment Search Tool (BLAST), in combination with the here developed BLASTmap, can be used to design probes that specifically target such gene(s), either by using the target species or the closest related genus as a reference. BLAST is a ubiquitous tool in biological sequence analysis and a multitude of programs are available for the visualization of BLAST alignments. However, there are currently no dedicated programs for visual comparison of large-scale BLAST output attributes such as bit score. The need to quickly and efficiently compare many thousands of BLAST results led to the development of BLASTmap, an interactive web application created using the Shiny R package, customized for clustering and viewing BLAST results as an interactive heat map. Here we show an example of how BLASTmap was successfully applied to analyze custom DNA/RNA probe sequences and to visually determine that four probes are sufficient for the specific yet inclusive enrichment of the potato R2 disease resistance gene family.

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns.

Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes.

BackgroundIncreased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL.ResultsIn sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL.ConclusionsNBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0253-z) contains supplementary material, which is available to authorized users.

A novel blast resistance gene, Pi54rh cloned from wild species of rice, Oryza rhizomatis confers broad spectrum resistance to Magnaporthe oryzae

The dominant rice blast resistance gene, Pi54 confers resistance to Magnaporthe oryzae in different parts of India. In our effort to identify more effective forms of this gene, we isolated an orthologue of Pi54 named as Pi54rh from the blast-resistant wild species of rice, Oryza rhizomatis, using allele mining approach and validated by complementation. The Pi54rh belongs to CC-NBS-LRR family of disease resistance genes with a unique Zinc finger (C(3)H type) domain. The 1,447 bp Pi54rh transcript comprises of 101 bp 5'-UTR, 1,083 bp coding region and 263 bp 3'-UTR, driven by pathogen inducible promoter. We showed the extracellular localization of Pi54rh protein and the presence of glycosylation, myristoylation and phosphorylation sites which implicates its role in signal transduction process. This is in contrast to other blast resistance genes that are predicted to be intracellular NBS-LRR-type resistance proteins. The Pi54rh was found to express constitutively at basal level in the leaves, but upregulates 3.8-fold at 96 h post-inoculation with the pathogen. Functional validation of cloned Pi54rh gene using complementation test showed high degree of resistance to seven isolates of M. oryzae collected from different geographical locations of India. In this study, for the first time, we demonstrated that a rice blast resistance gene Pi54rh cloned from wild species of rice provides broad spectrum resistance to M. oryzae hence can be used in rice improvement breeding programme.

A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature

BackgroundRice Xa3/Xa26 disease-resistance gene encodes a leucine-rich repeat (LRR) receptor kinase-type protein against Xanthomonas oryzae pv. oryzae (Xoo) and belongs to a multigene family. However, the functions of most genes in this family are unknown.ResultsHere we report that two orthologs of this family, the NRKe from rice variety Nipponbare and 9RKe from variety 93-11 at the RKe locus, have similar functions although they encode different proteins. This pair of orthologs could not mediate resistance to Xoo, but they were transcriptionally induced by raised temperature. Transcriptional activation of NRKe or 9RKe resulted in the formation of temperature-sensitive lesion mimics, which were spots of dead cells associated with accumulation of superoxides, in different organs of the transgenic plants. These plants were more sensitive to high temperature shock than wild-type controls. Transgenic plants carrying a chimeric protein consisting of the LRR domain of NRKe and the kinase domain of Xa3/Xa26 developed the same lesion mimics as the NRKe-transgenic plants, whereas transgenic plants carrying another chimeric protein consisting of the LRR domain of Xa3/Xa26 and the kinase domain of NRKe were free of lesion mimic. All the transgenic plants carrying a chimeric protein were susceptible to Xoo.ConclusionThese results suggest that the RKe locus is involved in rice response to raised temperature. The LRR domain of RKe protein appears to be important to sense increased temperature. The RKe-involved temperature-related pathway and Xa3/Xa26-mediated disease-resistance pathway may partially overlap.

Identification, isolation and characterization of a CC-NBS-LRR candidate disease resistance gene family in grapevine

Plasmopara viticola causes downy mildew of grapevine, one of the most important diseases in viticulture. Resistance to this oomycete is present in American and Asian Vitis species, while traditional European Vitis vinifera cvs. for wine and table grape production are susceptible. Breeding aims to achieve resistance through introgression, but the molecular mechanisms are still unknown. Therefore, the differential display approach was used to detect grapevine genes involved in defense. P. viticola sporangia were applied to the lower leaf surface of in vitro plants of the resistant Vitis riparia selection ‘Gloire de Montpellier’ and susceptible cv. ‘Riesling’. Controls were treated with sterile water. Messenger RNAs extracted 12 h post infection were subjected to differential display. Seven transcripts appeared specifically induced during the incompatible interaction. Sequencing showed that they build three classes. One of them, named VRP1, represented by three transcripts of almost identical sequence but differing lengths, showed clear homology to resistance genes of the NBS-LRR type from other plants. Northern hybridizations confirmed its elevated expression in the resistant ‘Gloire de Montpellier’. Redundancy of VRP1 PCR products from V. riparia prevented PCR-walking, so the VRP1 genes were isolated from a BAC-library of the resistant cv. ‘Regent’. Three genes matching the original VRP1 sequences were found within a BAC clone carrying a 134,392 bp insertion. These were referred to as VRP1-1, 1-2 and 1-3. They encode proteins of 798, 811 resp. 813 amino acids and exhibit the structure of CC-NBS-LRR resistance genes. They were genetically mapped to linkage group 10.

Organization, expression and evolution of a disease resistance gene cluster in soybean.

PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar "Williams 82" [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca(2+)-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

The rice Rim2 transcript accumulates in response to Magnaporthe grisea and its predicted protein product shares similarity with TNP2-like proteins encoded by CACTA transposons.

A rice transcript, Rim2, was identified that accumulated in both incompatible and compatible interactions between rice and Magnaporthe grisea. The Rim2 transcript also accumulated in response to treatment with a cell wall elicitor derived from M. grisea. A 3.3-kb RIM2 cDNA clone was isolated and is predicted to encode a protein of 653 amino acids, which shares 32 55% identity with TNP2-like proteins encoded by CACTA transposons of other plants. A 1.05-kb segment of the Rim2 sequence shows 82% nucleotide sequence identity with sequences flanking the A1 and C members of the rice Xa21 disease resistance gene family. The 5'-upstream region of Rim2 was cloned and the transcriptional start sites were identified. The 5' and 3' noncoding termini of Rim2 are AT-rich. A cis-element showing similarity to a sequence that mediates defense-associated transcriptional activation of the tobacco retrotransposon Tnt1, and four motifs that fit the consensus sequence of the elicitor-responsive elements in the promoters of the parsley PR-1 genes were found in the 5'-upstream region. Four imperfect tandem repeats were identified in the 3' noncoding terminus. Southern analysis with genomic DNA from different rice species indicated that Rim2 is present in 3-4 copies per genome. These results suggest that Rim2 may be one component of a large CACTA-like element, whose transcript accumulates in response to attack by pathogens.

The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes.

Plant-disease resistance (R) genes mediate the specific recognition of invading pathogens carrying cognate avirulence (avr) determinants. RPS4 is a disease-resistance locus on chromosome 5 of Arabidopsis thaliana specifying resistance to strains of Pseudomonas syringae pv. tomato expressing avrRps4. We have isolated the RPS4 gene using a map-based cloning approach. RPS4 encodes a predicted protein of 1217 amino acids that contains an N-terminus with homology to the intracellular domains of the Drosophila Toll protein and the mammalian interleukin-1 receptor (TIR domain), a tripartite nucleotide-binding site (NBS), and leucine-rich repeats (LRR). Incomplete splicing of the RPS4 mRNA was observed, which may give rise to truncated protein products consisting mainly of the TIR and NBS domains. These features classify RPS4 as a member of the TIR-NBS-LRR R gene family founded by N, L6 and RPP5, which determine resistance to viral, fungal and oomycete pathogens, respectively. Previous work has shown that RPS4, like other Arabidopsis TIR-NBS-LRR R genes specifying resistance to oomycetes, is dependent on a functional EDS1 allele for disease-resistance signaling. The characterization of RPS4 presented here thus establishes a role for TIR-NBS-LRR R genes in resistance to bacterial pathogens, and provides evidence for the model that dependence of R genes on EDS1 is determined by R protein structure, and not by pathogen type. The cloning of RPS4 and the previous isolation of avrRps4 provide the molecular tools for a genetic and molecular dissection of the TIR-NBS-LRR R gene signaling pathway in Arabidopsis.

The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes

The Arabidopsis RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR family of disease-resistance genes

Recombination between diverged clusters of the tomato Cf-9 plant disease resistance gene family.

The tomato Cf-4 and Cf-9 genes are the founder members of a large gene family of homologues of Cladosporium fulvum resistance gene Cf-9 (Hcr9 genes), several of which confer resistance against C. fulvum through recognition of different pathogen-encoded avirulence determinants. Three loci of tandemly repeated Hcr9 genes-Southern Cross (SC), Milky Way (MW), and Northern Lights (NL)-are located on the short arm of tomato chromosome 1. Comparisons between 2 SC-Hcr9s, 11 from MW, and 5 from NL implicated sequence exchange between gene family members in their evolution. The extent to which novel variants can be generated by recombination depends on the degree of sequence polymorphism available within the gene family. Here we show that physical separation of Hcr9 genes can be associated with elevated sequence divergence. Two diverged subclasses of Hcr9s could be defined. These are physically separated from each other, with members of one class exclusively residing at Northern Lights. One exceptional Hcr9 at Northern Lights carried sequence features specific for Hcr9s at other loci, suggesting a recent transfer of this gene by an interlocus recombination event. As members of diverged subclasses are brought into physical vicinity within a tandem repeat, a larger spectrum of sequence variants can potentially be generated by subsequent interhomologue sequence exchange.

Identification and characterization of 14 transposon-like elements in the noncoding regions of members of the Xa21 family of disease resistance genes in rice.

The rice disease resistance gene Xa21, which encodes a receptor-like kinase, is a member of a multigene family. Based on comparisons of genomic sequences of seven family members, seventeen transposon-like elements were identified in the 5' and 3' flanking regions and introns of these genes. Sequence characterization revealed that these elements are diverse, showing similarity to maize Ds, CACTA and miniature inverted repeat-like elements, as well as novel elements. Only two elements were located in presumed coding regions, indicating that integration of transposable elements at the Xa21 disease resistance locus occurred preferentially in noncoding regions.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat.

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS-leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.