A highly conserved NB-LRR encoding gene cluster effective against Setosphaeria turcica in sorghum
The fungal pathogen Setosphaeria turcica causes turcicum or northern leaf blight disease on maize, sorghum and related grasses. A prevalent foliar disease found worldwide where the two host crops, maize and sorghum are grown. The aim of the present study was to find genes controlling the host defense response to this devastating plant pathogen. A cDNA-AFLP approach was taken to identify candidate sequences, which functions were further validated via virus induced gene silencing (VIGS), and real-time PCR analysis. Phylogenetic analysis was performed to address evolutionary events.
cDNA-AFLP analysis was run on susceptible and resistant sorghum and maize genotypes to identify resistance-related sequences. One CC-NB-LRR encoding gene GRMZM2G005347 was found among the up-regulated maize transcripts after fungal challenge. The new plant resistance gene was designated as St referring to S. turcica. Genome sequence comparison revealed that the CC-NB-LRR encoding St genes are located on chromosome 2 in maize, and on chromosome 5 in sorghum. The six St sorghum genes reside in three pairs in one locus. When the sorghum St genes were silenced via VIGS, the resistance was clearly compromised, an observation that was supported by real-time PCR. Database searches and phylogenetic analysis suggest that the St genes have a common ancestor present before the grass subfamily split 50-70 million years ago. Today, 6 genes are present in sorghum, 9 in rice and foxtail millet, respectively, 3 in maize and 4 in Brachypodium distachyon. The St gene homologs have all highly conserved sequences, and commonly reside as gene pairs in the grass genomes.
Resistance genes to S. turcica, with a CC-NB-LRR protein domain architecture, have been found in maize and sorghum. VIGS analysis revealed their importance in the surveillance to S. turcica in sorghum. The St genes are highly conserved in sorghum, rice, foxtail millet, maize and Brachypodium, suggesting an essential evolutionary function.
KeywordsFoxtail Millet Maize Genotype Fungal Inoculation Virus Induce Gene Silence Sorghum Plant
The immune system has developed in a stepwise manner by progressive sophistication of basic functions that helped ancestral organisms to survive in their hostile environment. Recognition of pathogens in a species-specific way results in the generation of a very robust mode of surveillance system in plants. This form of protection termed resistance (R) protein-mediated or effector-triggered immunity is induced when a plant encoded R protein "perceives" the presence of a pathogen-derived effector molecule, represented by specific avirulence (Avr) gene products . Following recognition of the pathogen, one or more signal transduction pathways are induced in the host plant and these lead to the prevention of colonization by the pathogen.
The majority of characterized R proteins encode a nucleotide-binding site (NB) and leucine-rich repeats (LRR). NB-LRR-encoding genes make up one of the largest and most variable gene families found in plants, with most plant genomes containing several hundred family members [2, 3, 4, 5, 6]. The N-terminal ends of R-proteins are predominantly composed of a TIR (Toll/Interleukin-1 Receptor) homologous domain or form a coiled-coil (CC) motif. Monocots in particular, have numerous CC-NB-LRR proteins in their genomes. Accumulating data suggest furthermore that N termini of R-proteins may interact with a range of pathogen-derived proteins. However, the LRR domain may determine the final outcome of this recognition, leading to downstream signaling and initiation of defense responses .
Many R-genes are located in clusters that either comprise several copies of homologous sequences arising from a single gene family or co-localized R-gene sequences derived from unrelated gene families [8, 9]. This genomic make-up assists multiple proteins to become modified via various genic and intergenic processes enabling rapid evolution and adaptation to changes in a pathogen genome . R-genes can also act in pairs [11, 12]. The R-gene pairs can differ in genomic location and protein domain structure but also to their interaction with different pathogen isolates.
The heterothallic ascomycete Setosphaeria turcica (Luttrell) Leonard & Suggs (anamorph: Exserohlium turcicum, former Helminthosporium turcicum) causes turcicum or northern leaf blight disease on maize. This fungal pathogen also attacks sorghum and related grass species, for example Johnson grass [13, 14]. Turcicum leaf blight is one of the most prevalent foliar diseases in most maize-growing regions of the world. The disease causes periodic epidemics associated with significant yield losses, particularly under conditions of moderate temperature and high humidity [15, 16, 17]. Resistance to S. turcica has mainly been characterized in maize. S. turcica was earlier named Helminthosporium turcicum and resistance has hitherto been designated Ht and conferred by major race-specific genes (Ht1, Ht2, Ht3 or HtN) or via partial resistance, reviewed by Welz and Geiger . In our work we designate the new resistance genes as St referring to Setosphaeria turcica.
Maize and sorghum are the most important staple cereals for sub-Saharan Africa (SSA). While maize is an introduced crop , sorghum is believed to have been domesticated in SSA particularly in the Nile basin or Ethiopia, as recently as 1000 BC . Sorghum like many other crop species experience large problems with plant pathogens, particularly fungal diseases. Turcicum leaf blight incited by S. turcica is one main problem . This disease has been considered as of minor importance in Uganda until 1988 when it caused extensive yield losses on maize . By introducing improved resistance in new varieties the threat posed by the disease was subsequently reduced. Severe and sporadic outbreaks of turcicum leaf blight have now reappeared in East Africa [23, 24, 25]. A change in the S. turcica population has been suggested to be the main cause of this shift in disease pattern. In order to detect potential new changes of the S. turcica pathogen and the turcicum leaf blight disease, a survey was undertaken in Uganda to examine the sorghum - S. turcica pathosystem in terms of disease severity and incidence, race patterns and new resistant resources . It can be concluded from those studies that fungal isolates from sorghum could infect maize. Upon cross inoculation on maize differential lines harboring different Ht genes, four S. turcica isolates were identified as race 1, two as race 2, and one isolate corresponded to race 0 and race 3, respectively, whereas 10 isolates were unclassified. Highly resistant sorghum accessions originating from a regional collection were also identified.
In this work, we used cDNA-amplified fragment length polymorphism (AFLP) on resistant and susceptible maize and sorghum genotypes to identify differentially expressed genes, when challenged with S. turcica. This was followed by functional assessment of selected gene candidates by virus-induced gene silencing (VIGS) using a Brome mosaic virus vector. We found one R-gene cluster, containing six CC-NB-LRR encoding genes residing as three pairs in the sorghum genome, of importance for defense to S. turcica. Genome data further showed that the St genes are highly conserved within monocots.
Identification of an up-regulated R-gene family in maize and sorghum in response to S. turcicainoculation
In order to identify important defense genes to S. turcica, cDNA-AFLP analysis was carried out on susceptible (S) and resistant (R) sorghum and maize genotypes following fungal infection. In our case, the Ugandan sorghum genotypes GA06/18 (R) and Sila (S) and the maize A619Ht1 (R) and A619 (S) lines were used. The sorghum material had earlier been evaluated on various agronomical traits including important fungal diseases. Apart from S. turcica responses, GA06/18 was found to be susceptible to Cercospora sorghi, and Colletotrichum sublineolum, whereas Sila was susceptible to C. sorghi and resistant to C. sublineolum.
In total, approximately 3000 transcript-derived fragments were monitored ranging from 50 to 600 bp in size using different primer combinations (Additional file 1). Unique, up- or down-regulated transcripts in the resistant genotypes compared to the susceptible, sampled at 24, 48 and 72 hours post inoculation (hpi) were excised, amplified, sequenced and analyzed for putative function. The final transcript-set comprised of 68 sorghum and 82 maize gene candidates. Among these genes, 11 and 13, respectively, were putative stress-related according to closest genes identified in other organisms using BLASTP.
The Stgenes are conserved among grasses
The six St genes in sorghum form three gene pairs in a cluster on chromosome 5 and share a common ancestor (Figure 1; Additional file 2; Additional file 3). St gene orthologs were also found in clusters when searching the rice, maize, foxtail millet and Brachypodium genome databases. The St gene encoded proteins from the other grass species, grouped with the sorghum St proteins with high edge support (100) (Additional file 2). The rice genome contains orthologs of sorghum St1A, St1B, St2A, St2B and an St3 gene (Figure 1A, B). This indicates that the ancestor of rice and sorghum likely had a copy of these genes. Sorghum St3A and St3B are likely a result of a more recent genome duplication event after the split between the rice and sorghum species (Figure 1G). The rice genome also contains multiple copies of St1A, St2A and St2B orthologs, likely produced from gene duplications after the species split from sorghum. Likewise, the Setaria italica (foxtail millet) genome contains orthologs of St1A, St1B, St2A and St2B, with seven of the nine genes found in a cluster within the same scaffold, as complete chromosome annotation have yet to be determined (Figure 1C). An St3 homolog was not found in millet. In addition to the maize gene pair identified in our cDNA-AFLP analysis, BLASTP and BLASTN searches revealed a third single gene homolog, GRMZM2G050959, St2A on maize chromosome 2 (Figure 1D). The model grass Brachypodium genome, on the other hand, has a gene pair orthologous to St1B on chromosome 4, and one to St2B on chromosome 5, but lacks all other gene homologs (Figure 1E). The St gene cluster is maintained between sorghum, rice and possibly millet genomes but is smaller in maize and Brachypodium with St genes located across or on different chromosomes.
Adapting the VIGS system on sorghum
Genetic transformation of sorghum and maize is possible but laborious and requires other genotypes than those used in this study to be successful [28, 29]. Hence, our candidate genes were further studied using virus induced gene silencing (VIGS) using the Brome mosaic virus (BMV) system, previously used to silence genes in monocots . VIGS was followed by fungal inoculation to assess the potential defense function of the St genes. In our hands, the VIGS procedure was not successful when applied to the A619Ht1 maize genotype. Because the St genes were up-regulated upon fungal inoculation with S. turcica in our sorghum GA06/18 genotype (Figure 2), we continued the studies on our sorghum materials.
Silencing of St genes increases S. turcicainfection in the resistant and susceptible sorghum genotypes
Taken together, as expected the resistant GA06/18 genotype showed a compromised defense response when inoculated with VIGS construct 1 or 2 prior fungal inoculation. Interestingly, we observed enhanced disease phenotypes on the susceptible Sila genotype upon corresponding VIGS treatments.
Sorghum [Sorghum bicolor (L.) Moench] serves as a major food staple and fodder resource especially in arid and semi-arid regions of the world . It is mainly a self-pollinating and diploid grass species (2n = 2x = 20), with a genome size of 1C = 730 Mbp, which is about 25% the size of the maize genome [4, 5]. In the sorghum genome, 211 NB-LRR encoding R-genes are present, which is approximately half the number found in rice and slightly more compared to Arabidopsis . The number of NB-LRR encoding genes in the small genome of the wild grass Brachypodium is estimated to 178 . But in the much larger maize genome, 95 NB-LRR encoding genes have up to now been identified . However, depending on search programs and threshold settings, slightly different R-gene numbers in each grass species are published.
It is postulated that the high numbers of R-genes in plant genomes and their large sequence diversity are essential evolutionary factors in the surveillance machinery to resist pathogen attacks. Resistance genes evolve through duplication, unequal crossing over, recombination and diversification leading to clusters of paralogous genes [10, 34]. The proliferation of R-genes is also coupled with rapid turnover of gene copies, eventually leading to deletion or expansion and thus dynamic R-gene clusters . Resistance gene clusters have also been found to be conserved between different species in Poaceae , although, such clusters are in the minority with 71.6% being specific to a species .
Whole genome duplications occurred when the grass subfamilies diverged from each other and genome data suggest further, that paleo-duplicated gene pairs in sorghum and rice remained extant in about 17% of the cases . Recent duplications of chromosomal segments are particularly found on rice chromosomes 11 and 12, and corresponding regions on chromosome 5 and 8 in sorghum. Chromosome 5, in the sequenced BTx623 sorghum genotype, where the St genes are located showed the highest abundance (62) of R-genes . Thirty-six of these NB-LRR encoding genes are affected by recent duplication events based on the bioinformatic analyses presented by Wang et al. , including St3A and St3B, which is in agreement with our results (Figure 1; Additional file 2). Interestingly, the rice genome contains orthologs of St1A, St1B, St2A, St2B and a single ortholog of the St3 genes, all in one single locus. This indicates that this gene cluster predates the species split of rice and sorghum. In the grass family, sorghum, maize and millets belong to the same sub-family (Panicoideae), whereas rice is located in Ehrhartoideae . It is estimated that these two subfamilies diverged from a common ancestor 50-70 million years ago together with Pooideae, the subfamily to which Brachypodium, wheat, and barley belong.
In a genome-wide comparison of Arabidopsis thaliana and A. lyrata, the evolutionary pattern of the R-genes could be divided into two distinct groups, the positively selected (> 50%) with high sequence divergence between the two species, or the stably selected genes (< 30%) . The remaining genes were only found in one genome and absent from the other. The St genes found in this work have experienced few sequence exchanges resulting in low divergence, and hence more resemble the description of stably selected genes, although the copy numbers vary between the five grass genomes compared (Figure 1). That NB-LRR encoded R-genes remain conserved between different grass species is presently believed to be a common phenomenon .
Sorghum plants, particularly genotypes with red seed color, accumulate a range of phenolic substances in response to pathogen attacks . Large amounts of red-pigmented flavonoids induced at the site of infection were also seen in our materials, particularly in the resistant genotype. Whether flavonoids contribute to the defense response against S. turcica is not elucidated but a genetic link has been found in the sorghum - C. sublineolum interaction, produced via the presence of 3-deoxyanthocyanidins . Reinforcement of plant cells via callose deposition upon pathogen attacks have been observed in many pathosystems. Enhanced callose deposition has also been reported as a resistance response to S. turcica in maize . Despite extensive staining efforts, no callose accumulation was seen in either of our sorghum genotypes (data not shown).
Furthermore, our gene silencing work resulted in an enhanced susceptible response in Sila, our susceptible sorghum cultivar. This observation may suggest that by targeting the St genes in this genomic background, effects on downstream signaling masked in the resistant sorghum genotype are revealed, and could potentially constitute a fraction of the quantitative traits earlier found . This hypothesis is speculative and remains to be included in future functional studies of the St genes. Future studies do also comprise a search for important effectors in the genome recently released from JGI http://www.jgi.doe.gov. In parallel, the sequence information from the St gene cluster is presently converted into molecular markers and used in germplasm assessments and breeding programs in East Africa, an important development to sustain sorghum and maize crop production in this part of the world.
Our cDNA-AFLP analysis on susceptible and resistance maize and sorghum genotypes challenged by S. turcica resulted in identification of a CC-NB-LRR encoding gene in maize. This gene resides in two loci on maize chromosome 2. In sorghum, 6 St orthologous genes are present in a cluster of three pairs, on chromosome 5. Upon gene-silencing of the sorghum St genes, the resistance was clearly compromised, an observation that was supported by real-time PCR analysis and fungal DNA quantification. Database searches and phylogenetic analysis suggest that the St genes have a common ancestor present before the subfamily split, 50-70 million years ago, and the genes are highly conserved in sorghum, rice, foxtail millet, maize and Brachypodium.
Plant and fungal materials
Resistant (R) and susceptible (S) Sorghum bicolor genotypes from Uganda, GA06/18 (R) and Sila (S), and maize lines A619Ht1 (R) and A619 (S) provided by USDA ARS, were used in the study. The plants were grown in a growth chamber (Percival) using a 12/12 h photoperiod at 22°C. A single spore isolate from S. turcica infected sorghum (Ig1), or infected maize (Mb1), collected from Iganga and Mbale, Uganda, was used for all sorghum and maize analysis, respectively. The fungal DNA was extracted using a modified CTAB method . DNA was analyzed by using S. turcica specific ITS1 and ITS2 primers (F -GCAACAGTGCTCTGCTGAAA and R-ATAAGACGGCCAACACCAAG). PCR was carried out using the following conditions: 10 ng of template DNA was added to a 24 μl mix consisting of H2O, 2.5 mM MgCl2, 2.5 μl Taq buffer (Fermentas, Helsingborg, Sweden) 0.2 mM of each dNTP, 0.25 μM of forward and reverse primers and 1 U of Taq polymerase (Fermentas) with: 3 min at 94°C, 35 cycles of (1 min at 94°C, 1 min at 60°C, and 1.5 min at 72°C), and final extension at 72°C for 10 min. The PCR products were separated on 1% agarose gels to confirm fragment size, (344 bp) followed by sequencing (Macrogen Inc., Seoul, Korea).
Fungal inoculation of plant material
Three-week old seedlings were inoculated on the third leaf whorl with 25 μl conidia suspension (5 × 105 conidia/ml) as described by Carson . Inoculated leaves from three to four plants were pooled and harvested at 24, 48, and 78 hours post inoculation (hpi) for cDNA-AFLP analysis. Water treated control samples were harvested at the same time-points.
RNA extraction and cDNA-AFLP analysis
Total RNA was isolated from the leaf samples using the BioRad RNA isolation kit (BioRad, California, USA) followed by mRNA preparation with the mRNA capture kit (Roche, California, USA). cDNA was synthesized with Oligo-dT primer and RevertAid™ H Minus M-MuLV Reverse Transcriptase (Fermentas). Second strand was synthesized using E. coli DNA Polymerase I (Fermentas). The double stranded cDNA was digested with BstY1 and Mse1 (Fermentas) and ligated to respective adaptors, pre-amplified and later selectively amplified using the BstYI +N (33P labeled) and MseI +N primers. Pre-amplification was carried out with the adapter-ligated cDNA, Taq DNA Polymerase (Fermentas) and the non-selective primers specific to the BstYI and MseI adapters using 25 cycles of 94°C for 30 s; 56°C for 1 min and 72°C for 1 min. The pre-amplified reaction mixture was diluted 600-fold and 5 μl was used for final selective amplification with 24 primer combinations, carried out with BstYI +N (33P labeled) primers (Additional file 1) and touchdown amplification . The selective amplification products were resolved on 6% polyacrimide gel run at 100 W until 4300 Vh was reached. Gels were dried and exposed to Kodak Biomax film (Amersham Pharmacia, California, USA) for 5-7 days.
Isolation and sequencing of transcripts
Approximately 150 transcripts (unique, up and down-regulated) from the resistant genotypes in relation to the susceptible genotypes, were excised from the dried PAGE gels, eluted in H2O and PCR amplified using the non-selective primers under the same conditions as earlier described in the pre-amplification step. The products were cloned into the pJET 1.2 blunt vector (CloneJET™ PC, Fermentas) and sequenced. The sequences were analyzed using the BLASTN and BLASTX programs  and compared with sequences deposited in NCBI, GRAMENE and PHYTOZOME databases. Identified fungal sequences were excluded.
Virus induced gene silencing (VIGS) in sorghum
The VIGS system used is based on the monocot-infecting Brome mosaic virus (BMV) as previously described  but pre-inoculation on barley was excluded. The BMV VIGS vector consists of three plasmids harboring BMV RNA1 (p1-1), RNA2 (p2-2) and RNA3 (pF13m, formally pF3-5/13A/G), respectively. To generate VIGS constructs, PCR fragments ranging from 246 to 253 bp in size were amplified from the sorghum candidate gene using genomic DNA of the resistant GA06/18 genotype and gene-specific primers harboring NcoI and AvrII restriction sites using the Primer 3 version 0.4.0 http://frodo.wi.mit.edu/primer3/ software (Additional file 6). Prior to PCR amplification, off-target gene searches were undertaken to design optimal VIGS constructs (Figure 4). After restriction, each fragment was cloned into the corresponding site of the pF13m plasmid. The identity of the inserts was verified by sequencing. P1-1, p2-2 and the pF13m containing different constructs were digested with SpeI, PshAI and PshAI, respectively. Infectious RNA transcripts were synthesized from linearized plasmids through in vitro transcription using T3 Polymerase (Fermentas), according to manufacturer instructions. 1 μl of the reaction product was run on a 1.5% agarose gel to confirm presence of a transcript.
Plant inoculation procedures were performed as described  with slight modifications. A 10 μl aliquot of the transcription mix from each of the plasmids p1-1, p2-2 and pF13m-insert was combined with 30 μl FES inoculation buffer and used directly to rub inoculate the second and third leaves of 3-week-old sorghum and maize plants. As a control, plants were inoculated in the same way with water or combined transcripts from p1-1, p2-2 and empty pF13m. Maize and sorghum plants were challenged with S. turcica as earlier described one week after viral inoculation (when faint chlorosis and vein clearing started to appear) to assess the effect of the different constructs. Plants were randomized and coded to reduce potential bias in the scoring of fungal colonization and growth.
Quantitative real-time PCR
Prior to fungal inoculation of the VIGS treated sorghum plants, approximated 3 cm of the second leaf above the VIGS inoculated leaf was collected from 3 independent plants in triplicates for each condition and used for RNA extraction as previously described. First strand-cDNA was synthesized from 1 μg of total RNA, with Oligo-dT primer and RevertAid™ H Minus M-MuLV Reverse Transcriptase (Fermentas) according to the manufacturer's instructions. Real-time PCR was carried out using the first strand cDNA in an iQ5 cycler (Bio-Rad). Maxima Sybr Green/Fluorescein qPCR Master Mix (Fermentas) was used for PCR amplification in a 20 μl total reaction volume consisting of 10 μl of SYBR Green qPCR Master Mix, 0.3 μM forward and reverse primers and 5 ng of cDNA template. All PCRs were performed in triplicate under the following amplification conditions; 10 min at 95°C followed by 40 cycles of 95°C, for 15 s, 60°C for 30 s, and 72°C for 30 s, followed 1 min at 95°C, and melt curve analysis. Primers sequences for St genes were designed using the Primer 3 version 0.4.0 http://frodo.wi.mit.edu/primer3/ software (Additional file 7). The sorghum elongation factor 1-alpha (Sb02g036420) and Actin (Sb01g010030) were used as reference genes and relative transcript values were calculated. All calculations and statistical analyses were performed as described in the ABI PRISM 7700 Sequence Detection System User Bulletin #2 (Applied Biosystems, USA) slightly modified by Vetukuri et al. . Quantification of S. turcica DNA on VIGS material 7 days post fungal inoculation was carried out as earlier described . Approximately 3 cm of leaf material from three plants was pooled and DNA extracted. Three biological samples per treatment were analyzed. Statistical significance was calculated using Student's t-test.
The amino acid sequences of St1A (Sb05g008280), St1B (Sb05g008140), St2A (Sb05g008350), St2B (Sb05g008030), St3A (Sb05g008250) and St3B (Sb05g008270) were aligned to sorghum, maize, millet, rice, Brachypodium and Arabidopsis genome databases using BLASTN and BLASTP (PHYTOZOME). Predicted domains were identified using coiled-coil prediction ), LRRfinder  and CD-Search . St-like gene loci were identified using Genomic Viewer (PHYTOZOME). Phylogenetic analysis was conducted using Treefinder and maximum likelihood and 10, 000 replicates . The JTT+G model  was found to best fit the data using ProtTest v2.4 . Confidences were calculated using local rearrangement of expected likelihood weights (LR-ELW) . Phylograms were drawn using Treeview 1.6.6 .
We greatly acknowledge B. Sarosh for assisting with the cDNA-AFLP work. This study was funded by the SIDA-SAREC grant for the East African Biotechnology Network (BIO-EARN), Sida SWE-2005-453, and the Swedish University of Agricultural Sciences.
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