Isolation and diversity analysis of resistance gene analogues (RGAs) from cultivated and wild strawberries

A haplotype-phased genome characterizes the genomic architecture and causal variants for RXf1 conferring resistance to Xanthomonas fragariae in strawberry (F. × ananassa)

BACKGROUND

Cultivated octoploid strawberry (Fragaria × ananassa) is one of the most economically important fruits worldwide due to its flavor, texture, and health benefits. However, bacterial angular leaf spot (ALS) causes economic losses in fruit production and plant nurseries. All commercial strawberry varieties are susceptible to ALS. A major resistance locus, RXf1, has been reported, but the genomic structure and candidate genes underlying this resistance remain known.

RESULTS

Fine-mapping was performed using three segregating populations containing 663 individuals that were genotyped with subgenome specific seven high-resolution melting (HRM) markers to narrow the RXf1 region to a 486-kb interval on chromosome 6C. We assembled a haplotype-phased chromosome-scale genome of ALS-resistant breeding selection FL17.68-110 using highly accurate long-read sequencing and trio-binning with parental short reads. The 1.62 Gbp genome containing two haplotypes, 56 chromosomes and 193,072 annotated genes. Transcriptome analysis in response to the ALS pathogen identified a candidate gene, Resistance gene analogue 3 (RGA3), associated with the RXf1 resistance. The gene structure and sequence variations within FaRGA3 were identified between resistant and susceptible genotypes.

CONCLUSIONS

Our results narrowed the RXf1 region, identified structural variations within this locus and pointed to FaRGA3 as a promising candidate gene. This information will be useful for breeders toward developing ALS-resistant strawberry varieties, and the high-quality genome will be a valuable resource for further genomics research in octoploid strawberry.

The devastating oomycete phytopathogen Phytophthora cactorum: Insights into its biology and molecular features

Phytophthora cactorum is one of the most economically important soilborne oomycete pathogens in the world. It infects more than 200 plant species spanning 54 families, most of which are herbaceous and woody species. Although traditionally considered to be a generalist, marked differences of P. cactorum isolates occur in degree of pathogenicity to different hosts. As the impact of crop loss caused by this species has increased recently, there has been a tremendous increase in the development of new tools, resources, and management strategies to study and combat this devastating pathogen. This review aims to integrate recent molecular biology analyses of P. cactorum with the current knowledge of the cellular and genetic basis of its growth, development, and host infection. The goal is to provide a framework for further studies of P. cactorum by highlighting important biological and molecular features, shedding light on the functions of pathogenicity factors, and developing effective control measures.

TAXONOMY

P. cactorum (Leb. & Cohn) Schröeter: kingdom Chromista; phylum Oomycota; class Oomycetes; order Peronosporales; family Peronosporaceae; genus Phytophthora.

HOST RANGE

Infects about 200 plant species in 154 genera representing 54 families. Economically important host plants include strawberry, apple, pear, Panax spp., and walnut.

DISEASE SYMPTOMS

The soilborne pathogen often causes root, stem, collar, crown, and fruit rots, as well as foliar infection, stem canker, and seedling damping off.

Expression of resistance gene analogs in woodland strawberry (Fragaria vesca) during infection with Phytophthora cactorum

Important losses in strawberry production are often caused by the oomycete Phytophthora cactorum, the causal agent of crown rot. However, very limited studies at molecular levels exist of the mechanisms related to strawberry resistance against this pathogen. To begin to rectify this situation, a PCR-based approach (NBS profiling) was used to isolate strawberry resistance gene analogs (RGAs) with altered expression in response to P. cactorum during a time course (2, 4, 6, 24, 48, 96 and 192 h post-infection). Twenty-three distinct RGA fragments of the NB-LRR type were identified from a resistance genotype (Bukammen) of the wild species Fragaria vesca. The gene transcriptional profiles after infection showed that the response of most RGAs was quicker and stronger in the resistance genotype (Bukammen) than in the susceptible one (FDP821) during the early infection stage. The transcriptional patterns of one RGA (RGA109) were further monitored and compared during the P. cactorum infection of two pairs of resistant and susceptible genotype combinations (Bukammen/FDP821 and FDR1218/1603). The 5′ end sequence was cloned, and its putative protein was characteristic of NBS-LRR R protein. Our results yielded a first insight into the strawberry RGAs responding to P. cactorum infection at molecular level.

Identifying and Analyzing the Diversity of Resistance Gene Analogs in Colombian Rubus Genotypes

Five Andean blackberry Rubus genotypes, three resistant and two susceptible to anthracnose, were used to identify regions in the Rubus genome with homology to disease-resistance genes found in other plant species. Polymerase chain reaction amplification with 12 pairs of primers and fragment cloning yielded 520 clones, of which 151 showed inserts between 500 and 700 bp long. When sequenced, 47 clones showed homology with two types of resistance genes, non-Toll/interleukin-1 receptor (TIR) nucleotide binding site (NBS) leucine-rich repeat (LRR) and TIR-NBS-LRR, thereby confirming their designation as resistance gene analogs (RGAs). The number of RGAs detected per Rubus genotype ranged from 7 to 11, with the highest in a wild resistant and a cultivated susceptible genotype. Rubus RGAs were also homologous with several non-TIR- and TIR-type RGAs found in other members of the Rosaceae family (Rosa hybrid cultivar, Rosa roxburghii, Malus × domestica, M. prunifolia, M. baccata, M. floribunda, Pyrus communis, Prunus persica, P. kansuensis, P. avium, and Fragaria vesca). Three RGAs shared identity with two Rosaceae RGAs associated with the CRPM1 locus for powdery mildew resistance in R. roxburghii and the Rosa hybrid cultivar. This is the first report on RGAs present in the Andean blackberry in Colombia.

Identification and phylogenetic analysis of a CC-NBS-LRR encoding gene assigned on chromosome 7B of wheat

Hexaploid wheat displays limited genetic variation. As a direct A and B genome donor of hexaploid wheat, tetraploid wheat represents an important gene pool for cultivated bread wheat. Many disease resistant genes express conserved domains of the nucleotide-binding site and leucine-rich repeats (NBS-LRR). In this study, we isolated a CC-NBS-LRR gene locating on chromosome 7B from durum wheat variety Italy 363, and designated it TdRGA-7Ba. Its open reading frame was 4014 bp, encoding a 1337 amino acid protein with a complete NBS domain and 18 LRR repeats, sharing 44.7% identity with the PM3B protein. TdRGA-7Ba expression was continuously seen at low levels and was highest in leaves. TdRGA-7Ba has another allele TdRGA-7Bb with a 4 bp deletion at position +1892 in other cultivars of tetraploid wheat. In Ae. speltoides, as a B genome progenitor, both TdRGA-7Ba and TdRGA-7Bb were detected. In all six species of hexaploid wheats (AABBDD), only TdRGA-7Bb existed. Phylogenic analysis showed that all TdRGA-7Bb type genes were grouped in one sub-branch. We speculate that TdRGA-7Bb was derived from a TdRGA-7Ba mutation, and it happened in Ae. speltoides. Both types of TdRGA-7B participated in tetraploid wheat formation. However, only the TdRGA-7Bb was retained in hexaploid wheat.

Genome-wide identification and comparative expression analysis of NBS-LRR-encoding genes upon Colletotrichum gloeosporioides infection in two ecotypes of Fragaria vesca

Anthracnose caused by Colletotrichum spp. is one of the most destructive diseases of cultivated strawberry (Fragaria×ananassa Duchesne) worldwide. The correlation between NBS-LRR genes, the largest class of known resistance genes, and strawberry anthracnose resistance has been elusive. BLAST search in NCBI identified 94 FvNBSs in the diploid genome of strawberry Fragaria vesca, with 67 of the TIR-NBS-LRR type. At least 36 FvNBSs were expressed, with 25% being non-coding genes. Two F. vesca ecotypes, HLJ and YW, showed great variations in both morphological and physiological responses upon C. gloeosporioides infection. qRT-PCR revealed that 5 of the 12 leaf-expressed FvNBSs displaying opposite transcription responses to C. gloeosporioides infection in two ecotypes. These results showed that the transcriptional responses of several FvNBSs were involved in the ecotype-specific responses to C. gloeosporioides in F. vesca. These FvNBSs hold potential in characterizing molecular components and developing novel markers associated with anthracnose resistance in strawberry.

Molecular characterization of ZzR1 resistance gene from Zingiber zerumbet with potential for imparting Pythium aphanidermatum resistance in ginger

Soft rot disease caused by the oomycete Pythium aphanidermatum (Edson) Fitzp. is the most economically significant disease of ginger (Zingiber officinale Rosc.) in tropical countries. All available ginger cultivars are susceptible to this pathogen. However a wild ginger relative viz., Zingiber zerumbet L. Smith, was identified as a potential soft rot resistance donor. In the present study, a putative resistance (R) gene designated, ZzR1 was isolated and characterized from Z. zerumbet using sequence information from Zingiber RGCs identified in our earlier experiments. Analysis of the 2280 bp segment revealed a 2157 bp open reading frame (ORF) encoding a putative cytoplasmically localized protein. The deduced ZzR1 protein shared high homology with other known R-genes belonging to the CC-NBS-LRR (coiled coil-nucleotide binding site-leucine rich repeat) class and had a calculated molecular weight of 84.61kDa. Real-time PCR analysis of ZzR1 transcription in Z. zerumbet following pathogen infection demonstrated activation at 3 hpi thus suggesting an involvement of ZzR1 in Z. zerumbet defense mechanism. Although many R-genes have been characterized from different taxa, none of them will help in the development of resistant ginger cultivars owing to the phenomenon of "Restricted Taxonomic Functionality" (RTF). Thus ZzR1 gene characterized from the resistant wild Zingiber accession represents a valuable genomic resource for ginger improvement programs. This first report on R-gene isolation from the Zingiber secondary gene pool is pivotal in designing strategies for engineering resistance in ginger, which is otherwise not amenable to conventional improvement programs owing to sexual reproduction barriers.

Identification of resistance gene analogs in Korean wild apple germplasm collections

Several plant disease resistance gene (R-gene) classes have been identified on the basis of specific conserved functional domains. Cloning of disease-resistance apple genes would be useful for breeding programs and for studying resistance mechanisms. We used a PCR approach with degenerate primers designed from conserved NBS-LRR (nucleotide binding site-leucine-rich repeat) regions of known R-genes to amplify and clone homologous sequences from six Korean wild apple germplasm collections and an individual plant of the Siberian wild apple, Malus baccata. One hundred and twenty-four sequenced clones showed high similarity at multiple NBS motifs with the R-genes of other plants. The clones OLE 2-9, BP 6-11, OLE 1-22, and OLE 5-13 shared 45% identity with the R-gene of other plants. The conserved sequence, which plays an important role in resistance, was found in our isolated resistance gene analogs (RGAs). The sequences of isolated apple RGAs showed more similarity to Toll/interleukin-1 receptor (TIR)-NBS-LRR than non-TIR-NBS-LRR. We suggest using a marker for this resistance gene region as well as for identifying potential material for disease-resistant breeding among Korea wild apple germplasms. This is the first step in preparing a comprehensive analysis of the RGAs in Korean wild apple germplasm.

Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops

BACKGROUND

Plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber genome was performed, and the phylogenetic relationships of NBS-encoding resistance gene homologues (RGHs) belonging to six species in five genera of Cucurbitaceae crops were compared.

RESULTS

Cucumber has relatively few NBS-encoding genes. Nevertheless, cucumber maintains genes belonging to both Toll/interleukine-1 receptor (TIR) and CC (coiled-coil) families. Eight commonly conserved motifs have been established in these two families which support the grouping into TIR and CC families. Moreover, three additional conserved motifs, namely, CNBS-1, CNBS-2 and TNBS-1, have been identified in sequences from CC and TIR families. Analyses of exon/intron configurations revealed that some intron loss or gain events occurred during the structural evolution between the two families. Phylogenetic analyses revealed that gene duplication, sequence divergence, and gene loss were proposed as the major modes of evolution of NBS-encoding genes in Cucurbitaceae species. Compared with NBS-encoding sequences from the Arabidopsis thaliana genome, the remaining seven TIR familes of NBS proteins and RGHs from Cucurbitaceae species have been shown to be phylogenetically distinct from the TIR family of NBS-encoding genes in Arabidopsis, except for two subfamilies (TIR4 and TIR9). On the other hand, in the CC-NBS family, they grouped closely with the CC family of NBS-encoding genes in Arabidopsis. Thus, the NBS-encoding genes in Cucurbitaceae crops are shown to be ancient, and NBS-encoding gene expansions (especially the TIR family) may have occurred before the divergence of Cucurbitaceae and Arabidopsis.

CONCLUSION

The results of this paper will provide a genomic framework for the further isolation of candidate disease resistance NBS-encoding genes in cucumber, and contribute to the understanding of the evolutionary mode of NBS-encoding genes in Cucurbitaceae crops.

Identification and characterisation of a novel class I endo-β-1,3-glucanase regulated by salicylic acid, ethylene and fungal pathogens in strawberry

The identification of a full length cDNA encoding an endo-β-1,3-glucanase (FaOGBG-5) from strawberry (Fragaria×ananassa Duch) is reported. The analysis of the deduced amino acid sequence of FaOGBG-5 showed that it shares typical structural features and a high degree of identity with other plant β-1,3-glucanases of the class I. The expression of FaOGBG-5 in plants infected with a virulent isolate of Colletotrichum acutatum and an avirulent isolate of Colletotrichum fragariae was examined. Induction of expression was observed with both pathogens but exhibited a delayed high expression with the virulent one. Additionally, the accumulation of FaOGBG-5 transcripts was also observed after treatments with the stress related hormones salicylic acid and ethylene. Results obtained suggest that the β-1,3-glucanase encoded by FaOGBG-5 may be implicated in plant defence against biotic and abiotic stress.

Phylogenetic and evolutionary analysis of NBS-encoding genes in Rutaceae fruit crops

The nucleotide-binding site leucine-rich repeat (NBS-LRR) genes are the largest class of disease resistance genes in plants. However, our understanding of the evolution of NBS-LRR genes in Rutaceae fruit crops is rather limited. We report an evolutionary study of 103 NBS-encoding genes isolated from Poncirus trifoliata (trifoliate orange), Citrus reticulata (tangerine) and their F(1) progeny. In all, 58 of the sequences contained a continuous open reading frame. Phylogenetic analysis classified the 58 NBS genes into nine clades, eight of which were genus specific. This was taken to imply that most of the ancestors of these NBS genes evolved after the genus split. The motif pattern of the 58 NBS-encoding genes was consistent with their phylogenetic profile. An extended phylogenetic analysis, incorporating citrus NBS genes from the public database, classified 95 citrus NBS genes into six clades, half of which were genus specific. RFLP analysis showed that citrus NBS-encoding genes have been evolving rapidly, and that they are unstable when passed through an intergeneric cross. Of 32 NBS-encoding genes tracked by gene-specific PCR, 24 showed segregation distortion among a set of 94 F(1) individuals. This study provides new insight into the evolution of Rutaceae NBS genes and their behaviour following an intergeneric cross.

Identification and characterization of potential NBS-encoding resistance genes and induction kinetics of a putative candidate gene associated with downy mildew resistance in Cucumis

BACKGROUND

Due to the variation and mutation of the races of Pseudoperonospora cubensis, downy mildew has in recent years become the most devastating leaf disease of cucumber worldwide. Novel resistance to downy mildew has been identified in the wild Cucumis species, C. hystrix Chakr. After the successful hybridization between C. hystrix and cultivated cucumber (C. sativus L.), an introgression line (IL5211S) was identified as highly resistant to downy mildew. Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes are the largest class of disease resistance genes cloned from plant with highly conserved domains, which can be used to facilitate the isolation of candidate genes associated with downy mildew resistance in IL5211S.

RESULTS

Degenerate primers that were designed based on the conserved motifs in the NBS domain of resistance (R) proteins were used to isolate NBS-type sequences from IL5211S. A total of 28 sequences were identified and named as cucumber (C. sativus = CS) resistance gene analogs as CSRGAs. Polygenetic analyses separated these sequences into four different classes. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that these CSRGAs expressed at different levels in leaves, roots, and stems. In addition, introgression from C. hystrix induced expression of the partial CSRGAs in cultivated cucumber, especially CSRGA23, increased four-fold when compared to the backcross parent CC3. Furthermore, the expression of CSRGA23 under P. cubensis infection and abiotic stresses was also analyzed at different time points. Results showed that the P. cubensis treatment and four tested abiotic stimuli, MeJA, SA, ABA, and H2O2, triggered a significant induction of CSRGA23 within 72 h of inoculation. The results indicate that CSRGA23 may play a critical role in protecting cucumber against P. cubensis through a signaling the pathway triggered by these molecules.

CONCLUSIONS

Four classes of NBS-type RGAs were successfully isolated from IL5211S, and the possible involvement of CSRGA23 in the active defense response to P. cubensis was demonstrated. These results will contribute to develop analog-based markers related to downy mildew resistance gene and elucidate the molecular mechanisms causing resistance in IL5211S in the future.

An examination of targeted gene neighborhoods in strawberry

BACKGROUND

Strawberry (Fragaria spp.) is the familiar name of a group of economically important crop plants and wild relatives that also represent an emerging system for the study of gene and genome evolution. Its small stature, rapid seed-to-seed cycle, transformability and miniscule basic genome make strawberry an attractive system to study processes related to plant physiology, development and crop production; yet it lacks substantial genomics-level resources. This report addresses this deficiency by characterizing 0.71 Mbp of gene space from a diploid species (F. vesca). The twenty large genomic tracks (30-52 kb) captured as fosmid inserts comprise gene regions with roles in flowering, disease resistance, and metabolism.

RESULTS

A detailed description of the studied regions reveals 131 Blastx-supported gene sites and eight additional EST-supported gene sites. Only 15 genes have complete EST coverage, enabling gene modelling, while 76 lack EST support. Instances of microcolinearity with Arabidopsis thaliana were identified in twelve inserts. A relatively high portion (25%) of targeted genes were found in unanticipated tandem duplications. The effectiveness of six FGENESH training models was assessed via comparisons among ab initio predictions and homology-based gene and start/stop codon identifications. Fourteen transposable-element-related sequences and 158 simple sequence repeat loci were delineated.

CONCLUSIONS

This report details the structure and content of targeted regions of the strawberry genome. The data indicate that the strawberry genome is gene-dense, with an average of one protein-encoding gene or pseudogene per 5.9 kb. Current overall EST coverage is sparse. The unexpected gene duplications and their differential patterns of EST support suggest possible subfunctionalization or pseudogenization of these sequences. This report provides a high-resolution depiction of targeted gene neighborhoods that will aid whole-genome sequence assembly, provide valuable tools for plant breeders and advance the understanding of strawberry genome evolution.

Genetic diversity of Pto-like serine/threonine kinase disease resistance genes in cultivated and wild strawberries

Degenerate oligonucleotide primers, designed based on conserved regions of several serine-threonine kinases (STK) previously cloned in tomato and Arabidopsis, were used to isolate STK candidates in wild and cultivated strawberries. Seven distinct classes of STKs were identified from three related wild species, i.e., Fragaria vesca, Fragaria chiloensis, and Potentilla tucumanensis, and seven different Fragaria x ananassa cultivars. Alignment of the deduced amino acid sequences and the Pto R protein from tomato revealed the presence of characteristic subdomains and conservation of the plant STK consensus and other residues that are crucial for Pto function. Based on identity scores and clustering in phylogenetic trees, five groups were recognized as Pto-like kinases. Strawberry Pto-like clones presented sequences that were clearly identified as the activation segments contained in the Pto, and some of them showed residues previously identified as being required for binding to AvrPto. Some of the non-Pto-like kinases presented a high degree of identity and grouped together with B-lectin receptor kinases that are also involved in disease resistance. Statistical studies carried out to evaluate departure from the neutral theory and nonsynonymous/synonymous substitutions suggest that the evolution of STK-encoding sequences in strawberries is subjected mainly to a purifying selection process. These results represent the first report of Pto-like STKs in strawberry.

Genomic organization, rapid evolution and meiotic instability of nucleotide-binding-site-encoding genes in a new fruit crop, "chestnut rose"

From chestnut rose, a promising fruit crop of the Rosa genus, powdery mildew disease-resistant and susceptible genotypes and their F(1) progeny were used to isolate nucleotide-binding-site (NBS)-encoding genes using 19 degenerate primer pairs and an additional cloning method called overlapping extension amplification. A total of 126 genes were harvested; of these, 38 were from a resistant parent, 37 from a susceptible parent, and 51 from F(1) progeny. A phylogenetic tree was constructed, which revealed that NBS sequences from parents and F(1) progeny tend to form a mixture and are well distributed among the branches of the tree. Mapping of these NBS genes suggested that their organization in the genome is a "tandem duplicated cluster" and, to a lesser extent, a "heterogeneous cluster." Intraspecific polymorphisms and interspecific divergence were detected by Southern blotting with NBS-encoding genes as probes. Sequencing on the nucleotide level revealed even more intraspecific variation: for the R4 gene, 9.81% of the nucleotides are polymorphic. Amino acid sites under positive selection were detected in the NBS region. Some NBS-encoding genes were meiotically unstable, which may due to recombination and deletion events. Moreover, a transposon-like element was isolated in the flanking region of NBS genes, implying a possible role for transposon in the evolutionary history of resistance genes.

Diversity and evolutionary relationship of nucleotide binding site-encoding disease-resistance gene analogues in sweet potato (Ipomoea batatas Lam.)

Most plant disease-resistance genes (R-genes) isolated so far encode proteins with a nucleotide binding site (NBS) domain and belong to a superfamily. NBS domains related to R-genes show a highly conserved backbone of an amino acid motif, which makes it possible to isolate resistance gene analogues (RGAs) by degenerate primers. Degenerate primers based on the conserved motif (P-loop and GLPL) of the NBS domain from R -genes were used to isolate RGAs from the genomic DNA of sweet potato cultivar Qingnong no.2. Five distinct clusters of RGAs (22 sequences) with the characteristic NBS representing a highly diverse sample were identified in sweet potato genomic DNA. Sequence identity among the 22 RGA nucleotide sequences ranged from 41.2% to 99.4%, while the deduced amino acid sequence identity from the 22 RGAs ranged from 20.6%to 100%. The analysis of sweet potato RGA sequences suggested mutation as the primary source of diversity. The phylogenetic analyses for RGA nucleotide sequences and deduced amino acids showed that RGAs from sweet potato were classified into two distinct groups--toll and interleukin receptor-1 (TIR)-NBS-LRR and non-TIR-NBS-LRR. The high degree of similarity between sweet potato RGAs and NBS sequences derived from R-genes cloned from tomato, tobacco, flax and potato suggest an ancestral relationship. Further studies showed that the ratio of non-synonymous to synonymous substitution within families was low. These data obtained from sweet potato suggest that the evolution of NBS-encoding sequences in sweet potato occur by the gradual accumulation of mutations leading to purifying selection and slow rates of divergence within distinct R-gene families.

Characterization of major enzymes and genes involved in flavonoid and proanthocyanidin biosynthesis during fruit development in strawberry (Fragaria ×ananassa)

The biosynthesis of flavonoids and proanthocyanidins was studied in cultivated strawberry (Fragaria xananassa) by combining biochemical and molecular approaches. Chemical analyses showed that ripe strawberries accumulate high amounts of pelargonidin-derived anthocyanins, and a larger pool of 3',4'-hydroxylated proanthocyanidins. Activities and properties of major recombinant enzymes were demonstrated by means of in vitro assays, with special emphasis on specificity for the biologically relevant 4'- and 3',4'-hydroxylated compounds. Only leucoanthocyanidin reductase showed a strict specificity for the 3',4'-hydroxylated leucocyanidin, while other enzymes accepted either hydroxylated substrate with different relative activity rates. The structure of late flavonoid pathway genes, leading to the synthesis of major compounds in ripe fruits, was elucidated. Complex developmental and spatial expression patterns were shown for phenylpropanoid and flavonoid genes in fruits throughout ripening as well as in leaves, petals and roots. Presented results elucidate key steps in the biosynthesis of strawberry flavonoid end products.

Structural and phylogenetic analysis of Pto-type disease resistance gene candidates in banana

The tomato Pto gene encodes a serine/threonine kinase (STK) whose molecular characterization has provided valuable insights into the disease resistance mechanism of tomato and it is considered as a promising candidate for engineering broad-spectrum pathogen resistance in this crop. In this study, a pair of degenerate primers based on conserved subdomains of plant STKs similar to the tomato Pto protein was used to amplify similar sequences in banana. A fragment of approximately 550 bp was amplified, cloned and sequenced. The sequence analysis of several clones revealed 13 distinct sequences highly similar to STKs. Based on their significant similarity with the tomato Pto protein (BLASTX E value <3e-53), seven of them were classified as Pto resistance gene candidates (Pto-RGCs). Multiple sequence alignment of the banana Pto-RGC products revealed that these sequences contain several conserved subdomains present in most STKs and also several conserved residues that are crucial for Pto function. Moreover, the phylogenetic analysis showed that the banana Pto-RGCs were clustered with Pto suggesting a common evolutionary origin with this R gene. The Pto-RGCs isolated in this study represent a valuable sequence resource that could assist in the development of disease resistance in banana.

Identification and characterization of NBS-LRR class resistance gene analogs in faba bean (Vicia faba L.) and chickpea (Cicer arietinum L.)

A PCR approach with degenerate primers designed from conserved NBS-LRR (nucleotide binding site-leucine-rich repeat) regions of known disease-resistance (R) genes was used to amplify and clone homologous sequences from 5 faba bean (Vicia faba) lines and 2 chickpea (Cicer arietinum) accessions. Sixty-nine sequenced clones showed homologies to various R genes deposited in the GenBank database. The presence of internal kinase-2 and kinase-3a motifs in all the sequences isolated confirm that these clones correspond to NBS-containing genes. Using an amino-acid sequence identity of 70% as a threshold value, the clones were grouped into 10 classes of resistance-gene analogs (RGA01 to RGA10). The number of clones per class varied from 1 to 30. RGA classes 1, 6, 8, and 9 were comprised solely of clones isolated from faba bean, whereas classes 2, 3, 4, 5, and 7 included only chickpea clones. RGA10, showing a within-class identity of 99%, was the only class consisting of both faba bean and chickpea clones. A phylogenetic tree, based on the deduced amino-acid sequences of 12 representative clones from the 10 RGA classes and the NBS domains of 6 known R genes (I2 and Prf from tomato, RPP13 from Arabidopsis, Gro1-4 from potato, N from tobacco, L6 from flax), clearly indicated the separation between TIR (Toll/interleukin-1 receptor homology: Gro1-4, L6, N, RGA05 to RGA10)- and non-TIR (I2, Prf, RPP13, RGA01 to RGA04)-type NBS-LRR sequences. The development of suitable polymorphic markers based on cloned RGA sequences to be used in genetic mapping will facilitate the assessment of their potential linkage relationships with disease-resistance genes in faba bean and chickpea. This work is the first to report on faba bean RGAs.

Phylogenetic and evolutionary analysis of NBS-encoding genes in Rosaceae fruit crops

Phylogenetic relationships of the nucleotide binding site (NBS)-encoding resistance gene homologues (RGHs) among 12 species in five genera of Rosaceae fruit crops were evaluated. A total of 228 Rosaceous RGHs were deeply separated into two distinct clades, designated as TIR (sequences within this clade containing a Toll Interleukin-1 Receptor domain) and NonTIR (sequences lacking a TIR domain). Most Rosaceous RGH genes were phylogenetically distinct from Arabidopsis, Rice or Pine genes, except for a few Rosaceous members which grouped closely with Arabidopsis genes. Within Rosaceae, sequences from multiple species were often phylogenetically clustered together, forming heterogenous groups, however, apple- and chestnut rose-specific groups really exist. Gene duplication followed by sequence divergence were proposed as the mode for the evolution of a large number of distantly or closely related RGH genes in Rosaceae, and this mode may play a role in the generation of new resistance specificity. Positively selected sites within NBS-coding region were detected and thus nucleotide variation within NBS domain may function in determining disease resistance specificity. This study also discusses the synteny of a genomic region that encompass powdery mildew resistance locus among Malus, Prunus and Rosa, which may have potential use for fruit tree disease breeding and important gene cloning.

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

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.

Characterization and mapping of NBS-LRR resistance gene analogs in apricot (Prunus armeniaca L.)

Genomic DNA sequences sharing homology with the NBS-LRR (nucleotide binding site-leucine-rich repeat) resistance genes were isolated and cloned from apricot (Prunus armeniaca L.) using a PCR approach with degenerate primers designed from conserved regions of the NBS domain. Restriction digestion and sequence analyses of the amplified fragments led to the identification of 43 unique amino acid sequences grouped into six families of resistance gene analogs (RGAs). All of the RGAs identified belong to the Toll-Interleukin receptor (TIR) group of the plant disease resistance genes (R-genes). RGA-specific primers based on non-conserved regions of the NBS domain were developed from the consensus sequences of each RGA family. These primers were used to develop amplified fragment length polymorphism (AFLP)-RGA markers by means of an AFLP-modified procedure where one standard primer is substituted by an RGA-specific primer. Using this method, 27 polymorphic markers, six of which shared homology with the TIR class of the NBS-LRR R-genes, were obtained from 17 different primer combinations. Of these 27 markers, 16 mapped in an apricot genetic map previously constructed from the self-pollination of the cultivar Lito. The development of AFLP-RGA markers may prove to be useful for marker-assisted selection and map-based cloning of R-genes in apricot.