Transcriptome profiling of Gossypium barbadense inoculated with Verticillium dahliae provides a resource for cotton improvement
- Yan Zhang†1,
- Xing Fen Wang†1,
- Ze Guo Ding1,
- Qing Ma1,
- Gui Rong Zhang1,
- Shu Ling Zhang1,
- Zhi Kun Li1,
- Li Qiang Wu1,
- Gui Yin Zhang1 and
- Zhi Ying Ma1Email author
© Zhang et al.; licensee BioMed Central Ltd. 2013
Received: 9 March 2013
Accepted: 13 September 2013
Published: 22 September 2013
Verticillium wilt, caused by the fungal pathogen Verticillium dahliae, is the most severe disease in cotton (Gossypium spp.), causing great lint losses worldwide. Disease management could be achieved in the field if genetically improved, resistant plants were used. However, the interaction between V. dahliae and cotton is a complicated process, and its molecular mechanism remains obscure. To understand better the defense response to this pathogen as a means for obtaining more tolerant cultivars, we monitored the transcriptome profiles of roots from resistant plants of G. barbadense cv. Pima90-53 that were challenged with V. dahliae.
In all, 46,192 high-quality expressed sequence tags (ESTs) were generated from a full-length cDNA library of G. barbadense. They were clustered and assembled into 23126 unigenes that comprised 2661 contigs and 20465 singletons. Those unigenes were assigned Gene Ontology terms and mapped to 289 KEGG pathways. A total of 3027 unigenes were found to be homologous to known defense-related genes in other plants. They were assigned to the functional classification of plant–pathogen interactions, including disease defenses and signal transduction. The branch of "SA→NPR1→TGA→PR-1→Disease resistance" was first discovered in the interaction of cotton–V. dahliae, indicating that this wilt process includes both biotrophic and necrotrophic stages. In all, 4936 genes coding for putative transcription factors (TF) were identified in our library. The most abundant TF family was the NAC group (527), followed by G2-like (440), MYB (372), BHLH (331), bZIP (271) ERF, C3H, and WRKY. We also analyzed the expression of genes involved in pathogen-associated molecular pattern (PAMP) recognition, the activation of effector-triggered immunity, TFs, and hormone biosynthesis, as well as genes that are pathogenesis-related, or have roles in signaling/regulatory functions and cell wall modification. Their differential expression patterns were compared among mock-/inoculated- and resistant/susceptible cotton. Our results suggest that the cotton defense response has significant transcriptional complexity and that large accumulations of defense-related transcripts may contribute to V. dahliae resistance in cotton. Therefore, these data provide a resource for cotton improvement through molecular breeding approaches.
This study generated a substantial amount of cotton transcript sequences that are related to defense responses against V. dahliae. These genomics resources and knowledge of important related genes contribute to our understanding of host–pathogen interactions and the defense mechanisms utilized by G. barbadense, a non-model plant system. These tools can be applied in establishing a modern breeding program that uses marker-assisted selections and oligonucleotide arrays to identify candidate genes that can be linked to valuable agronomic traits in cotton, including disease resistance.
Cotton (Gossypium spp.) is widely cultivated because of its economically valuable fibers and oil seeds. During a plant’s life cycle, it is continuously threatened by Verticillium wilt, one of the most destructive diseases. The fungal pathogen, Verticillium dahliae, is extremely persistent in the soil and has a broad host range (Klosterman et al., ). It infects cotton roots and colonizes and occludes the xylem vessels, resulting in leaf curl, necrosis, defoliation, vascular tissue wilt, and discoloration (Additional file 1; Figure S1; Sink and Grey, ). A severe outbreak of this disease can reduce fiber quality and cause significant losses in yield. Between 2009 and 2010, 5.0 to 6.6 million acres, or more than 50% of the area in which cotton is grown in China, was affected (National Cotton Council of America–Disease Database).
No fungicides or other chemical means have proven effective for combating this disease. Although cultural practices such as appropriate seeding, irrigation, fertilization, and crop rotation can influence the development of this disease, none can efficiently control Verticillium wilt (Kamal, ). Genetic resistance is considered the most effective and sustainable management option, but has received little attention. Many crosses within certain lines of G. hirsutum can be readily made and multiple generations can be easily produced each year (Wang et al., ). However, a lack of genetics resources within such conventional breeding programs has meant that attempts to improve tolerance to Verticillium wilt have not been successful with this particular species, which accounts for >90% of the total acreage used for cotton production worldwide (Cai et al., ). However, plants of G. barbadense display high levels of wilt resistance, and could provide a good opportunity for genetically enhancing G. hirsutum. Despite this possibility, crosses between those species have historically resulted in abnormal separations, linkage drag, or hybrid dysgenesis. In addition, incorporating such materials from G. barbadense via molecular breeding techniques has been limited by a paucity of resistance genes and a lack of information about potential molecular markers. Therefore, the ability to explore functional genes or markers would be beneficial to researchers who are trying to introduce varieties with excellent wilt resistance.
Progress has been made in investigations of defense mechanisms by cotton against V. dahliae infection. For example, the cotton terpenoid pathway has been elucidated as an important contributor to the pathogen response by these plants (Tan et al., ; Luo et al., ; Xu et al., ). The phenylpropanoid pathway also has a critical protective role (Smit and Dubery, ; Pomar et al., ; Gayoso et al., ; Xu et al., ). Defense-responsive genes have been identified for the 14-3-3-like protein, PR10, anti-apoptosis (p35), HR-induced Hpa1Xoo, a thaumatin-like protein, major latex protein (MLP), and GbVe (Hill et al., ; Zhou et al., ; Wang et al., ; Chen and Dai, ; Munis et al., ; Tian et al., ; Zhang et al., a). In addition, the transcriptional activator ethylene-responsive element binding factor gene (Qin et al., ), the oxygen transporter non-symbiotic hemoglobin gene (Qu et al., ), NDR1, and MAP kinase kinase (Gao et al., ) are associated with resistance to Verticillium. All of these findings indicate that various defense pathways are activated during the complicated response to V. dahliae by cotton. Nevertheless, although some defense-related genes have been identified from G. hirsutum, their molecular mechanisms remain obscure.
Several transcriptome analyses have been reported, such as from a drought-related cDNA library (Zhang et al., ) and an SSH library from cotton plants inoculated by V. dahliae (Zhang et al., b). However, few studies of transcription have been described for G. barbadense. Although the D genome of cotton has recently been sequenced (Wang et al., ), its complexity means that publicly available data sets are of limited use for future research, including examinations of its entire transcriptome at specific developmental states or under certain stress conditions, as well as the elucidation of molecular mechanisms for the cotton defense response to V. dahliae. Such efforts would provide information on gene expression and regulation, and the amino acid content of proteins. Therefore, a thorough transcriptome analysis is essential for interpreting the functional elements of the genome and revealing the molecular constituents of cells and tissues. Extensive transcriptomic data would aid in our discovery of genes related to Verticillium wilt resistance, and would enable us to construct high density microarrays for further characterization of gene expression profiles during the cotton–V. dahliae interaction.
The technology used with full-length cDNA clones involves capturing mRNA via the 5’-end and stabilizing the full transcript when ligating into an appropriate vector and during reverse-transcription from the poly A tail (Carninci et al., ; Seki and Shinozaki, ). Therefore, full-length cDNA libraries can represent entire transcription units rather than partial gene sequences, making them extremely useful for transcriptome analysis and comparative genomics work (Seki et al., ). Such libraries also contain the transcriptional start site for most genes, and EST sequencing of the 5’-ends can reveal the untranslated region, methionine-encoding ATG codon, and translational start signal. Some researchers have used cDNA clones to construct microarrays for characterizing the binding of transcription factors (TFs) to promoter elements within the 5’-UTRs (Seki et al., ). Full-length cDNA clones also have a role in characterizing genetic structures in different species (Sakurai et al., ). Finally, as with other kinds of ESTs, results from the sequencing of such cDNA clones can be used for developing many types of genetic markers, including SSR (simple sequence repeat) and SNP (single nucleotide polymorphism) markers (Kofler et al., ; Galeano et al., ).
Because not enough genes/ESTs for G. barbadense are available in the public databases, and because the 'Pima90-53’ cultivar of this species shows significant advantages over G. hirsutum in both Verticillium wilt resistance and fiber quality, we decided to use full-length cDNA library construction and sequencing analysis to conduct an initial global analysis of the defense transcriptome dynamics in G. barbadense. Our study objectives were to create full-length cDNA libraries that would be useful for gene discovery in cotton, as well as for genome annotation and global investigations of the pathogen–plant interaction. We also proposed that the results would provide novel insights into the molecular mechanisms involved in defense processes by cotton. In doing so, we could obtain valuable resources for the development of molecular markers to study Upland cotton with recently published sequencing data for the D genome.
Fungal strain and inoculum preparation
The highly aggressive defoliating Verticillium dahliae fungal strain T5, isolated from an infected Upland cotton variety, was used for inoculation. To produce conidia, we took this strain from potato dextrose agar (PDA) plates and sub-cultured it onto Czapek’s medium (2 g of NaNO3, 1 g of K2HPO4, 1 g of MgSO4.7H2O, 1 g of KCl, 2 mg of FeSO4.7H2O, and 30 g L-1 sucrose) and incubated it at 25°C for 3 to 5 d. The resultant fungal cultures were filtered through sterile gauze to retain the mycelia. For root-dip inoculations, a conidial suspension (107 mL-1) was prepared.
Plant cultivation and inoculation
Seeds of cotton (Gossypium barbadense cv. Pima90–53) were surface-sterilized, then incubated on Petri dishes between sheets of moist filter paper for 48 h at 28°C. The new seedlings were transferred to tissue culture pots containing an MS medium (pH 6.0) supplemented with 10 g L-1 sucrose and 2 g L-1 Phytagel (Sangon Biotech Co., Ltd., Shanghai, China). They were then incubated for another 5 d at 28/25°C (day/night). Afterward, the seedlings were removed from the pots and inoculated via root-dipping for 30 s into either sterile water (for mock inoculation) or a conidial suspension of V. dahliae. They were transferred to fresh pots containing the same MS medium and incubated in a growth room at 25°C. The mock-inoculated and fungal-inoculated pots were placed in pairs, adjacent to each other, to minimize the effects of different microenvironments. Roots were harvested at 0, 1, 2, 4, 6, 8, 12, 24, 36, 48, 72, 96, and 120 hours post-inoculation (hpi). The treated tissues were quickly frozen in liquid nitrogen and stored at –80°C. As much mycelia as possible was removed from the roots.
Sections (approximately 0.5 mm) were cut from the surface-sterilized roots and stems of 10 seedlings per sampling time point. They were transferred to plates containing 25% PDA and incubated at 25°C for at least 2 d. They were then examined for the presence of mycelial growth from the vascular tissue; the percentage of sections showing such growth was recorded for each sample.
Extraction and purification of total RNA
Frozen tissues were ground mechanically to a fine powder in liquid nitrogen. Total RNA was isolated with TRIzol® reagent (Invitrogen), according to the manufacturer’s guidelines. Remaining traces of genomic DNA were removed by DNase after a purification step with the CleanUp protocol of the RNeasy Plant Mini kit (Qiagen). Pellets of total RNA were re-suspended in RNAse-free water and quantified spectrophotometrically. Quality was determined via denaturing agarose gels (1.5%) that contained formaldehyde and were stained with ethidium bromide. Equal amounts of total RNA from each sampling event were pooled. The mRNA was further isolated with the PolyATract mRNA Isolation System (Promega, Madison, WI, USA).
Library construction and EST sequencing
The cDNA was synthesized from 100 ng of mRNA with the Clontech Creator SMART cDNA synthesis system. It was recovered in autonomously replicating pSMART2IFD, using an in vivo fusion protocol provided by the manufacturer. Plasmid DNA was excised in Escherichia coli strain DH10B. Clones were picked randomly and transferred into 384-well plates. Single-pass sequencing from the 5’-end was carried out using a universal primer and BigDye Terminator, on an ABI 3730 automatic DNA sequencer (Sangon).
Pre-processing and assembly of ESTs
All sequences were processed to remove low-quality regions and adaptor sequences, using the LUCY programs (Chou and Holmes, ). This step was followed by SeqClean to shorten the Poly-A/T (http://compbio.dfci.harvard.edu/tgi/software). To remove possible contamination, we screened the resulting sequences against the National Center for Biotechnology Information (NCBI) UniVec database, E. coli genome sequences, and Gossypium on ribosomal RNA sequences. EST sequences longer than 100 bp after trimming were clustered and assembled into contigs and singletons (unisequences) via EST Clustering, which was designed based on the MegaBlast and CAP3 programs (Huang and Madan, ; Zhang et al., ).
After clustering and assembly, the NCBI BLAST program version 2.2.6 (Altschul et al., ) was used to identify similarities between the ESTs and sequences deposited in public databases. We compared them against the GenBank non-redundant protein (Nr) and UniProt (TrEMBL and SwissProt) databases, using a cutoff E-value of 1e-5. The unigene sequences were also translated into proteins via ESTScan (Iseli et al., ). Translated protein sequences were then compared with information from pfam domain databases. Our Gene Ontology (GO) annotation (Harris et al., ) was performed with BLAST2GO (Conesa et al., ; Götz et al., ), based on sequence similarity in the UniProt databases and domains in the pfam database. WEGO (Ye et al., ) was used for GO functional classification of all unigenes and to plot the distribution of those same gene functions. The unigene sequences were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify functions. Pathway assignments were made based on information from the KEGG database (Kanehisa and Goto, ).
Quantitative real-time PCR
For selected genes, differential gene expression was verified by Q-PCR. The roots from triplicate samples (n=3 seedlings) were collected at each time point. Gene expression analysis was performed with three biological replicates and three technical replicates. First-strand cDNA was generated from 1 μg of total RNA isolated from the roots of both mock- and Verticillium-inoculated G. barbadense 'Pima90-53’ (resistant) and G. hirsutum 'Han208’ (susceptible), using the Superscript First-strand Synthesis System (Invitrogen). Primers for Q-PCR were designed according to the parameters of an optimum GC content of 50%, Tm>55 to 65°C, length 18 to 30 nucleotides, and an expected amplified fragment size of 80 to 200 bp. For qPCR, 20-μL samples were run in three technical replicates on a LightCycler® Real Time PCR System (Roche Germany), using 2 μL of first-strand cDNA and SYBR Green PCR Master Mix (Takara). Amplification conditions included the following: one cycle at 94°C for 15 s; then 40 cycles at 94°C for 10 s, 59°C for 10 s, and 72°C for 15 s. Afterward, all products were subjected to melt curve analysis. A negative control without a cDNA template was run with each analysis to evaluate the overall specificity. Both GhUBQ14 (GenBank: DW505546) and cotton actin (AF059484) were used as reference genes to normalize the total amount of cDNA in each reaction (Artico et al., ; Zhang et al., b). A mean normalization from two reference genes was used to analyze the level of expression for each gene. Data from each biological replicate were given as the mean of three technical replicates. Each bar in the column chart represented the mean of three biological replicate experiments (n=3); vertical bars indicated standard errors. Relative fold-changes were calculated per the 2-△△Ct method, as described by Livak and Schmittgen . All of the selected genes and primers are listed in Additional file 2: Table S1.
Transcription factor analysis
We used BLAST results for unique cotton sequences against Arabidopsis proteins to identify cotton sequences homologous to Arabidopsis TFs. The comprehensive Plant Transcription Factor Database was searched (PlantTFDB; http://planttfdb.cbi.pku.edu.cn) (Guo et al., ; Zhang et al., a).
Analysis of microsatellite repeats
The EST-SSRs in unigene sequences were identified by the MISA program (http://pgrc.ipk-gatersleben.de/misa), a powerful pipeline for SSR detection. The minimum repeat number was six for dinucleotides and five for tri-, tetra-, penta-, or hexanucleotides.
Establishment of experimental system
To obtain a global overview of the cotton transcriptome and gene activity at nucleotide resolution, we thoroughly mixed RNA that was extracted at 1, 2, 4, 6, 8, 12, 24, 36, 48, 72, 96, or 120 hpi. To minimize any systematic bias from transcriptome sampling, and to improve our accuracy in detecting low-abundance transcripts, we constructed and sequenced three cDNA libraries from the same pooled RNA sample.
EST sequencing and assembly
Functional annotation of the cotton unigene dataset
A sequence similarity search was conducted against the NCBI, Nr, and SwissProt databases, using BLASTx and tBLASTn algorithms that specified E-values of less than 10-5. This analysis revealed that 22,446 unigenes had significant hits in the Nr database. However, of these, only 10,060 unigenes showed similarities to proteins of known function, 12,386 had similarities to predicted proteins of unknown function, and 680 unigenes had no significant similarity to any sequences contained in that database. This indicated that most of the unigenes could be assigned a known or putative function. Those without database hits were likely to include non-coding RNAs, genes whose sequences did not capture regions that contained conserved functional domains, or protein-coding genes that were novel in the database and/or cotton-specific.
GO enrichment analysis
Based on our BLAST and SwissProt results, we further annotated the cotton unigenes with GO terms. In all, 20,397 (72.0%) could be assigned at least one term. Among them, 6,893 were placed in the category of biological processes, 8,383 in molecular functions, 11305 in cellular components, and 6184 in all three categories.
Pathway classification of transcripts
Distribution of functions in the KEGG pathway
Metabolism (8017, 38.75%)
Metabolism of other amino acids
Xenobiotic biodegradation and metabolism
Terpenoid and polyketide metabolism
Biosynthesis of other secondary metabolites
Amino acid metabolism
Glycan biosynthesis and metabolism
Cofactor and vitamin metabolism
GIP (2354, 6.68%)
Folding, sorting, and degradation
Replication and repair
EIP (773, 2.91%)
Signaling molecules and interactions
CP (1077, 4.05%)
Cell growth and death
Transport and catabolism
OS (1901, 7.05%)
Comparisons of unigenes from other species of cotton and model plants
Disease resistance-related protein families
Known unigenes expressed in response to V. dahliae infection in resistant G. barbadense
Perception of PAMPs by PRRs
Chitin elicitor receptor kinase (CERK1)
Chitin elicitor signaling
Elicitor-responsive proteins (ERG)
Plant defense signaling
Proline-rich extensin-like receptor kinases (PERKs)
Perception of PAMPs and induction of defense responses
BRI1-associated receptor kinase 1 (BAK1)
Perception of PAMPs and induction of defense responses
Somatic embryogenesis receptor-like kinases (SERKs)
Plant immune responses to pathogen attack
Plant receptor-like kinases (RLKs)
Perception of PAMPs and induction of defense responses
Mitogen-activated protein kinase (MAPK)
Downstream components in PTI
CC-NBS-LRR resistance protein (RPM1)
Manages of signaling potential via intra-molecular negative regulation
Effector-triggered immunity (ETI)
TMV resistance protein
TMV-N mediated signal transduction pathway
Disease resistance protein (RPS2)
Specifically recognizes effector protein from pathogen
NBS-LRR resistance gene (RPP8)
Specifically recognizes effector protein from pathogen
RPM1 Interacting Protein 4 (RIN4)
Negatively regulates disease resistance mediated by RPS2
Calcium signal transducer
Plant cyclic nucleotide gated channels (CNGCs)
Facilitates Ca2+ uptake into the cytosol in response to PAMP
Calcium signal transducer
Calcium binding protein
Calcium signal transducer
Calmodulin-like protein (CML)
Calcium signal transducer
Calcineurin B-like proteins (CBL)
Decoding of calcium transients
Transcription factors (TFs)
Binding ethylene-responsive element
Regulates signaling and transcriptional reprogramming associated with plant defense responses
Regulates signaling and transcriptional reprogramming associated with plant defense responses
Histone promoter-binding protein (HBP)-1a
Negatively regulates defense response
NADPH oxidase or respiratory burst oxidase
Generation of superoxide
Reduces various peroxides
Glutathione peroxidases (GPXs)
Reduces H2O2, organic hydroperoxidases, and lipid peroxides
Causes a disease resistance response
Protein disulfide-isomerase (PDI)
Ubiquitous redox protein
Decomposition of hydrogen peroxide to water and oxygen
Confers resistance to pathogen and hallmarks of defense pathways
Pathogenesis-related (PR) proteins
Beta-1,3-glucanase-like genes (PR2 homologs)
Lyses cell walls of fungal pathogens
Confers resistance to pathogen and hallmarks of defense pathways
Chitinase (PR3 and 8 homologs)
Lyses cell walls of fungal pathogens
Thaumatin-like protein (PR5)
Inhibits hyphal growth and sporulation by various fungi
BAG-like genes: BCL-2-associated athanogenes
Dynamin-related proteins (DRP)
Key regulators of PCD
Programmed cell death (PCD)
Apoptosis Inducing Factor homolog (AIF)
Chromatin condensation and DNA degradation
Nitric oxide synthase
Catalyzes arginine to produce nitric oxide
Enhanced Disease Susceptibility 1(EDS1)
Catalyzes arginine to produce nitric oxide
Non-expression of PR gene 1 (NPR1)
Regulatory component in SA signaling
Pathogen-inducible salicylic acid glucosyltransferase (SGT1)
Involved in the early disease response and the accumulation of glucosyl SA during pathogenesis
Phenylalanine ammonia lyase (PAL)
Key enzyme in SA biosynthesis
Isochorismate synthase (ICS)
Key enzyme in SA biosynthesis
Key enzyme in jasmonic acid (JA) biosynthesis
Allene oxide synthase (AOS)
Key enzyme in jasmonic acid biosynthesis
Jasmonate ZIM-motif (JAZ) proteins (TIFY10B)
1-aminocyclopropane-1-carboxylic acid oxidase (ACO)
Key enzyme in ethylene biosynthesis
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
Biosynthesis of derived secondary metabolites
Cell wall modification
Oxidation of phenol compounds
Conjugates electrophilic molecules to glutathione (GSH)
Caffeic acid 3-O-methyltransferase
Inhibits pathogen invasion
UDP-glucuronic acid decarboxylase 1
Key factor in xylose formation
Most frequent families found in the cotton library
PR protein class 10
glutathione S-transferase (Tau class)
meloidogyne-induced cotton protein
short chain alcohol dehydrogenase
glutathione S-transferase omega
metallothionein-like type 1 protein
Differential expression analysis of unigenes after V. dahliae inoculation
We subjected a subset of genes to qPCR analysis during the interactions between V. dahliae and the two species. The transcriptomes were compared for differentially expressed AOS, MPK4, CYS, and RPP8. After inoculation occurred, expressions were either reduced or showed delays in their upregulation in tissues from the susceptible 'Han208’ when compared with the more resistant 'Pima90-53’ (Figure 8).
Identification of putative transcription factors
The most abundant putative transcriptional factors (TFs) in cotton resistant to Verticillium infection
No apical meristem (NAM) protein
Golden 2-like (GLK)
Myb-like DNA-binding domain
Basic leucine zipper (bZIP) motif
Single AP2/ERF domain
Zinc finger, C-x8-C-x5-C-x3-H type
WRKY DNA-binding domain
Zinc finger, C2H2 type
DNA binding with one zinc finger
Auxin response factor
Three initially identified members GAI, RGA, and SCR
Trihelix DNA-binding domain
Far-red-impaired Response 1
HD domain with leucine zipper motif
MADS-box transcription factors
Binds to DNA sequence "GATA"
Lateral organ boundary domain (LBD) gene family
Non-canonical basic-Helix-Loop-Helix (bHLH) structure
Identification of EST-SSRs
Molecular markers are valuable resources for constructing high-density genetics maps, facilitating crop breeding, and identifying traits of interest. Special EST-SSRs have high efficiency and incur a low cost, making them one of the best genetic markers for such systems. Here, 1212 SSRs were identified in 1169 (4.3%) unigenes. Among the repeat types, trinucleotide repeats were the most abundant SSRs (760, or 62.7% of the EST-SSRs), followed by dimeric SSRs (311; 25.7%), and tetrameric SSRs (98; 8.1%) (Additional file 5: Table S4). We previously reported the construction of a genome-wide map for cotton, in which these SSRs were used to add to the map density (Yang et al., ).
Because allotetraploid cotton has a large and complex genome, researchers had not previously elucidated any comprehensive sequence information to describe the transcriptome related to defense responses against Verticillium dahliae. Here, we investigated such responses through full-length cDNA library construction and EST sequencing. Although two tetraploid species, G. hirsutum and G. barbadense, exist, few examinations of the latter have been made because it is less commonly cultivated. However, because it is more resistant to this wilt pathogen (Zhang et al., d), we used G. barbadense 'Pima90-53’ in our tests. As an American type of Pima, this cultivar has proven to be a better germplasm resource than other available types (i.e., Egyptian or Mid-Asian types of G. barbadense) because of its desirable traits for immunity to Verticillium, fiber quality, and greater yield (Ma et al., , Wang et al., ). Its resistance and phenotypic characters have long been recognized in both field and greenhouse settings. Moreover, we have previously cloned several functional genes related to resistance and/or fiber quality from 'Pima90-53’, e.g., GbVe, GbWRKY1, and ADF1 (Chi et al., [53, 54]; Liu et al., ; Pan et al., ; Zhang et al., b; Zhang et al., a; Zhang et al., d). Therefore, we chose this specific Pima cotton for profiling the G. barbadense transcriptome. Our goal was to mine those genes for economically important traits so that we might potentially improve those traits in the Upland cotton G. hirsutum.
Infections with V. dahliae progress throughout the roots and into the rest of the plant, causing serious losses in both yield and quality. Because the root is the first barrier against such an attack, we selected this particular tissue for analysis. Fungal spores germinate and epidermal cells are often penetrated within the first 12 h (Fradin and Thomma, ). Complex perception, transduction, and exchange of signals usually occurs in the early stages of infection (Zhang and Klessig, ; Kunkel and Brooks, ; Jones and Dangl, ). Therefore, we sampled at 1, 2, 4, 6, 8, 12, 24, 36, 48, 72, 96, and 120 hpi to coincide with those crucial stages and to isolate early pathogen-responsive genes. We also utilized an experimental system that allowed for tight control of environmental conditions so that gene expression was not altered by any factors other than the pathogen. This enabled us to identify and monitor as many genes as possible from our library.
More than 46,192 high-quality ESTs were generated from our root cDNA library of Verticillium-infected G. barbadense seedlings. These ESTs were assembled into 23,126 unigenes. Annotation results showed that this library contained many previously reported key response genes, such as for PR protein, chitinase, members of the GST gene family, PAL, CYP, and NDR1 (McFadden et al., ; Li et al., ; Gao et al., ; Xu et al., ; Zhu et al., ; Ahmed et al., ). Our library also included several genes that function in the development of cotton fibers, e.g., SusA1, CesAs, UXS1, ADF1, tubulin, and aquaporin (Pan et al., ; Yuan et al., ; Jiang et al., ; Kim et al., ; Chi et al., ). Our findings suggested that defense-related genes were abundant in our library, and that genes contributing to fiber formation might also function in protecting G. barbadense against infection by V. dahliae. Therefore, this library is an important genomics resource for isolating genes with novel roles. We also demonstrated the importance of identify critical genes that code for different phenotypes, such as stress resistance or fiber quality. That is, researchers can now construct a subtracted library to find genes that are preferentially expressed in resistant lines. We previously completed an SSH library that used a resistant G. hirsutum cultivar and contained more than 200 genes that are differentially expressed between it and susceptible cultivars (Zhang et al. ). Future studies will incorporate microarrays to achieve this goal in related experiments.
When exposed to various environmental stimuli, plants utilize elaborate mechanisms to regulate cellular and molecular events so they can protect themselves with pre-formed defense barriers and induce appropriate responses. For example, pathogen-triggered immunity (PTI) constitutes the first layer of that response, restricting pathogen activity by blocking further colonization (Zhang et al., ). A second layer, ETI, specifically recognizes the effector by one of its NB-LRR proteins (Nürnberger et al., ). ETI is an accelerated response while PTI is amplified, resulting in disease resistance and, usually, a hypersensitive cell death response at the infection site. In our full-length cDNA library, groups such as LRR-RLKs, signalling-related genes, and TFs were expressed during the cotton defense response. All of them possibly contribute to these PTI- or ETI-related systems.
Most PTI-associated genes were obtained in our library, including the chitin elicitor receptor kinase (CERK1), which recognizes chitin oligosaccharides during plant–pathogen interactions. It acts as a representative general elicitor to induce defense responses in a wide range of plant cells (Kaku et al., ). We also identified chitinases, which, as PR proteins, play important roles in enhancing stress resistance in a variety of plants. These chitin-degrading enzymes hydrolyze b-(1, 4) linkages and are capable of degrading the cell walls of plant pathogenic fungi (Adams, ; Cheng et al., ; Lawrence and Novak, ) while releasing elicitors of defense reactions. Therefore, chitinases are thought to have crucial roles in plant defenses against biotic stresses. Based on this, we might conclude that chitinases and their elicitors confer pathogen resistance in cotton by hydrolyzing the cell walls of V. dahliae.
Another important PTI-related gene, Brassinosteroid Insensitive 1-Associated Kinase 1, or BAK1, was isolated here. Known as Somatic Embryo Genesis Receptor-Like Kinase 3 (SERK3), it is required by PRRs (Heese et al., ; Dodds and Rathjen, ). SERK3/BAK1 not only interacts with BRI1, which is involved in brassinosteroid signal transduction, but it also rapidly forms a complex with FLS2, which functions in reactions for plant disease resistance. For example, the BAK1/SERK4 homolog in Nicotiana has a direct role in elicitor perception of bacterial cold shock protein, flagellin, and elicitin, but not chitin (Heese et al., ). However, we must still investigate whether similar elicitors exist in V. dahliae and how the FLS2–BAK1 complex acts to confer pathogen immunity in resistant cotton plants.
In addition to the genes already mentioned, we obtained another important clue regarding wilt resistance in cotton. The major pollen allergen (Bet v1) family protein was one of the most abundant in our library. Proteins in this family have previously been identified under various biotic and abiotic stresses in birch, potato, pea, soybean, and cotton (Breiteneder et al., ; Matton and Brisson, ; Barratt and Clark, ; Crowell et al., ; Cheng et al., ). Family members may also have essential roles in the defense response by Sea Island cotton to Verticillium wilt (Chen et al., ). The mRNA transcripts examined in our study demonstrated that Bet v1 family genes were more abundant than any others, suggesting that this family is a vital component of the cotton response to Verticillium infection.
With critical roles in complex signaling cascades, phytohormones have been integrated into current models for defense responses (Bari and Jones, ; Grant and Jones, ). For example, the pathways for salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and brassinosteroids are important regulators of expression by defense-related genes (Bari and Jones, ). In general, SA induces systemically acquired resistance and is implicated in plant tolerance to biotrophic pathogens (Spoel and Dong, ; Leon-Reyes et al., ). Both ET and JA are typically associated with defense responses to necrotrophic pathogens (Spoel et al., ; Bari and Jones, ). Cross-talk can occur between those SA- and JA/ET-mediated defense reactions to abiotic- and biotic-stress stimuli (Grant and Jones, ). Results from our Q-PCR analysis showed that expression patterns were the same for EDS1 and PAD4. Both genes were up-regulated upon inoculation, and their transcript levels were several-fold higher than that of the mock. This implied that the EDS1–PAD4 complex interferes with activation of innate cotton immunity. In addition, while identifying the biochemical pathways that were active during the response to V. dahliae inoculation, we discovered a plant hormone signal transduction pathway, within which exists an important branch: "SA→NPR1→TGA→PR-1→Disease resistance". The presence of this branch might suggest its role in the resistance response. However, in contrast to earlier conclusions (Leon-Reyes et al., ), we determined that SA is not involved in resistance to necrotrophic pathogens, such as V. dahliae. Therefore, we deduced that the process by which cotton becomes infected by Verticillium involves both biotrophic and necrotrophic stages.
The plant cell wall serves not only as a physical barrier, but as a defense barrier against pathogen penetration. Secondary metabolites play a fundamental role in the plant’s ability to fight against invading pathogens (Dubery and Smit, ; Naoumkina et al., ). That capacity is derived through multiple pathways, including those for the biosynthesis of phenylpropanoids, terpenoids, and cellulose. Most of the genes associated with those pathways, e.g., genes for caffeic acid, 3-O-methyltransferase, glutathione S–transferase, 4-coumarate:CoA ligase, UDP-glucuronic acid decarboxylase, cellulose synthase, and sucrose synthase. In this study, we detected a large phenylpropanoid pathway that encompassed those for flavonoid and lignin biosynthesis. We also obtained most of the genes that encode enzymes involved in the lignin pathway. For example, PAL, located in the core and entry of the phenylpropanoid pathway, is responsive to both biotic and abiotic stresses, including pathogen attack, and wounding (Huang et al., ). Likewise, POD has a role in reinforcing cell walls against the effects of pathogens or wounding through the polymerization of monolignols into lignin (Marjamaa et al., ). In Arabidopsis, Laccase4 and Laccase17 contribute to the constitutive lignification of stems, with the latter being involved in the deposition of G lignin units in fibers (Berthet et al., ). Therefore, all of these findings demonstrate that the phenylpropanoid pathway has an essential role in preventing the invasion or expansion of pathogens by reinforcing the cell wall. Nonetheless, future research should focus on the exact function of related genes within the phenylpropanoid pathway. Further characterization of those genes may provide valuable candidates for efforts toward the genetic improvement of cotton.
In this study, we characterized the root transcriptome of G. barbadense and provided gene resource that related to defense responses against V. dahliae. These findings provide a substantial contribution to existing sequence resources for cotton, and a strong basis for future genomic research. The putative signaling pathways generated in the present study revealed that the defense system of cotton may be a complex process. The findings of this study will hopefully accelerate research on resistance in cotton to V. dahliae and contribute to a better understanding of the cotton defense response to plant pathogens. Besides, the spatial and temporal expressions of defense-related genes require further study.
This study was supported by funds for the early-stage basic research key project (No. 2011CB111609) and for the 863 project of China (No. 2013AA102601-5). The authors are grateful to Priscilla Licht for critical reading of the manuscript.
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