The resistance investigation of the top 20 rice cultivars grown in Taiwan.
Rice bacterial blight disease (BBD), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the serious diseases in most rice production regions. In this report, we screened for resistance mutants from the mutation pool of TNG67 variety derived by sodium azide (SA) mutagenesis with phenotype investigation and assisted with fluorescent detection. SA0423 is a mutant of broad range resistance against Xoo for many years; the resistance was studied following the concept of central dogma. The inheritance of resistance was characterized, and three QTLs were mapped onto the genome of SA0423 using simple sequence repeat (SSR) markers and R/qtl by genomic approach. In transcriptomic approach, only one differential expression QTLs (eQTLs) were identified; two differentially expressed proteins (pQTLs) were identified and genetically characterized by proteomics after Xoo challenged in SA0423 mutant. To improve the bacterial blight resistance, makers are developed from QTLs, eQTLs and pQTLs to pyramid the resistance genes through marker-assisted breeding in our rice breeding programs.
- bacterial blight disease (BBD)
- marker-assisted breeding (MAB)
Rice is a staple food crop and provides more than one-fifth of the calories to humans . However, rice production is often challenged by bacterial blight disease (BBD), which is one of the most destructive diseases caused by
The existing prevention of BBD includes field management, fertilizer control, pesticide application and resistance varieties with the major resistance gene (
Previous studies demonstrated that climate change has been proposed to affect the microflora of
|Planting area during 2010–2015||Variety||Response for |
|1||484,063||Tai Nan No. 11||7||7|
|2||142,132||Taikeng No. 8||7||7|
|3||119,641||Taikeng No. 14||7||9|
|4||98,404||Taikeng No. 16||7||9|
|5||47,139||Taikeng No. 9||9||9|
|6||46,204||Taichung-Hsien No. 10||9||9|
|7||41,424||Taikeng No. 2||7||9|
|9||39,149||Taikeng No. 11||9||7|
|10||23,767||Taichung-Hsien No. 1||7||9|
|12||19,357||Taikeng No. 4||7||7|
|13||19,108||Tail Nung No. 71||5||7|
|14||13,989||Tail Nung No. 67||9||9|
|15||13,867||Taikeng No. 5||7||9|
|16||9341||Tai Tung No. 30||9||7|
|18||7318||Taoyuan No. 1||5||7|
|20||5660||Taichung-Hsien No. 17||9||9|
The availability of resistant sources is the major limitation in breeding. A series of near isogenic lines (NILs) harboured various
2. Mutant screening
Sodium azide (NaN3, SA) induced mutants can be applied to any rice breeding program at any facility, while genetically modified mutants can only be handled in the isolating facilities under the governmental regulation. A TNG67 mutant pool was developed by SA mutagenesis at the Taiwan Agricultural Research Institute (TARI) in our previous breeding program. All the mutants were screened and purified according to their morphological traits by at least 10 generations of self-crossing, selection and purification following pedigree procedures. Over 3000 pure line mutants on the same genetic background of TNG67 variety were maintained in the pool . The genetic diversity of mutant lines in this pool includes disease resistance (blast, bacterial blight and sheath blight) , pest resistance (brown planthopper, white backed planthopper and leafroller) , herbicide resistance (bentazon, glufosinate and glyphosate)  and many agronomic traits; grain quality and morphology diversities seldom found in rice cultivars. These results suggested that the TNG67 mutant pool should have high potential in basic research as well as variety improvement .
To improve the bacterial blight resistance for local rice varieties, we attempted to obtain the local resistant germplasms from the selection of TNG67 mutant pool . So far, at least 50 bacterial blight-resistant mutants have been selected from the mutant pool (Figure 2). These mutants might carry various genotypes of resistance and participate in the resistant pathway. Among them, SA0423 and SA0424 showed stable resistances against various
3. Genetic and mapping of resistant genes
At present, planting resistant varieties is accepted as the most efficient, reliable and economic strategy against bacterial blight. It has been proposed that the durable and broad spectrum resistance of plants was usually governed by multiple genes or quantitative trait loci (QTLs) . Therefore, the discovery of novel resistance genes against
Near isogenic lines (NILs) with various
Among the previously selected resistant mutants, SA0423 shows a stable resistance to Taiwan local pathogens for years. Hence, their genetic properties and BBD resistance genes were characterized in our team. Except for the bacterial blight resistance, SA0423 also has thinner leaf blades, shorter plants, more erect plant type and less tiller number than its mutagenesis parent, TNG67 (Figure 3). A strong and stable Taiwanese epidemic pathogen,
A linkage map covering 12 chromosomes with an average distance of 11.2 cM was constructed and applied to map the resistance of SA0423 using 361 TN1/SA0423 F2 individuals . QTL analysis was performed using the R program language platform (version 3.1.0; http://www.r-progect.org/) with an add-on package, qtl [46, 47]. Three QTLs are detected on chromosomes 11, 8 and 6 and account for 21.1, 11 and 9.6% of the observed phenotypic variance, respectively (Table 2 and Figure 6). Three QTLs are localized to 6, 7 and 14 cM intervals, respectively; they contribute to approximately 47% of the total phenotypic variation (resistance) and no epistatic effect could be detected among them .
|QTL||Chr.||QTL (Confidence interval) (cM)||LOD||Phenotyping variance (%)||Additive effect||Dominance effect|
|qBBR11.1 (Q1)||11||124 (121–127)||26.60||21.10||–1.64||–0.44|
|qBBR08.1 (Q2)||8||39 (34–41)||15.04||11.04||–1.20||–0.82|
|qBBR06.1 (Q3)||6||120 (111–125)||13.20||9.58||–1.13||0.79|
4. Transcriptomic studies
According to QTL analysis, all the three identified QTLs contribute to 47% of the resistance indicating that other resistance genes may exist in SA0423 . Therefore, the transcriptomes of TNG67 and SA0423 were determined by microarray technologies to explore the bacterial-resistant genes in SA0423.
For a precise and non-destructive investigation in the infection process of bacterial blight pathogen after inoculation, a
After the infection of
|Gene name||Gene ontology|
Ankyrin repeat-rich protein
|BP||Cellular process, biosynthetic process, protein modification process, post-embryonic development, anatomical structure morphogenesis, response to endogenous stimulus|
|MF||Binding, protein binding, catalytic activity,|
|BP||Cellular process, cellular component organization, protein modification process|
|BP||Biological process, response to abiotic stimulus, post-embryonic development, signal transduction|
|MF||Binding, protein binding|
|BP||Biological process, response to abiotic stimulus, post-embryonic development, signal transduction|
|MF||Binding, protein binding|
EF hand family protein
|BP||Protein modification process, biosynthetic process|
|MF||Signal transducer activity, binding, protein binding|
Immediate-early fungal elicitor protein CMPG1
|BP||Protein modification process, biological process|
|MF||Catalytic activity, binding|
Domain of Unknown
|BP||Protein modification process, cellular process, metabolic process|
|MF||kinase activity, protein binding, cellular process,|
Flavin-containing monooxygenase family protein
|BP||Cell death, signal transduction, metabolic process, response to biotic stimulus, cellular process, response to stress|
|CC||Endoplasmic reticulum, membrane, cell|
|MF||Nucleotide binding, catalytic activity, binding|
|BP||Multicellular organismal development, cellular process, metabolic process|
|MF||Binding, protein binding, transferase activity|
SAM dependent carboxyl methyltransferase
|BP||Biological process, cellular process, metabolic process|
SNARE associated Golgi
Ubiquitin family protein
OsSAUR21—Auxin-responsive SAUR gene family member
|BP||Response to endogenous stimulus|
Nodulin MtN3 family protein
|BP||Biological process, cellular process, transport|
|CC||Plasma membrane, membrane, cell|
Transcription initiation factor IIA gamma chain
|BP||Biosynthetic process, nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|
To confirm the function of the identified genes from transcriptomic analysis, the SSR markers flanking in 5 cM region of these genes were retrieved from GRAME web site, screened for the polymorphic markers between TN1 (the susceptible parent) and SA0423 (the resistant parent), and then genotyping was performed in the F2 population . Simultaneously, the disease lesion of F2 individuals was investigated to represent the resistance phenotype after the inoculation of
5. Proteomics study
Proteomics technology provides a direct investigation of proteins which may participate in rice disease resistance. In previous studies, plasma membrane (PM) proteomic analysis of the genetically modified rice suspension cells with
A comparative proteomics analysis was conducted to characterize the proteomic profiling in leaves of TN1 (as a susceptible control), TNG67 and SA0423 after the infection of
|L-ascorbate peroxidase 1, cytosolic (APX1)||RM7197||30||35||29||94||6.56||8.28||7.57||0.05||0.862||0.15158||0.18||2.5||0.08795|
|Putative 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (BIPM)||RM5970||16||28||50||94||8.29||8.841||6.52||0.12||0.276||–2.04831||7.41||6.05||0.00337||* *|
|Glyceraldehyde-3-phosphate dehydrogenase, putative, expressed (G3PD)||RM14336||23||23||40||86||6.75||7.833||7.4||0.02||0.539||0.10949||0.2||0.77||0.46538|
|Aspartate aminotransferase (AST)||RM14099||42||22||14||78||6.61||9.433||7.29||0.14||1.412||–0.73185||0.52||6.34||0.00281||**|
|2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative, expressed (BIPME)||RM8084||24||52||18||94||6.74||8.134||6.73||0.05||0.695||–0.70982||1.02||2.34||0.10172|
|Triosephosphate isomerase (TRI)||RM24714||16||33||45||94||7.43||8.23||7.01||0.03||0.401||–0.81535||2.03||1.44||0.24307|
|30S ribosomal protein S4, chloroplastic (RP30S)||RM5579a||18||36||40||94||6.59||8.479||7.05||0.06||0.943||–0.48336||0.51||3||0.05439|
|Fructose-bisphosphate aldolase, chloroplastic (FBPA)||RM26143||10||46||35||91||8.09||7.596||7.31||0.01||–0.247||–0.53336||2.16||0.24||0.78348|
|Cysteine synthase (CYS1)||RM520||23||28||43||94||7.8||6.835||7.8||0.02||–0.483||0.47717||0.99||0.91||0.40443|
The candidate genes identified from proteomics approach were genetically confirmed as previously described, the SSR markers flanking in 5 cM region of them were retrieved from GRAMENE web site, and screened for polymorphism TN1 (the susceptible parent) and SA0423 (the resistant parent). Genotyping analysis was performed in 94 TN1/SA0423 F2 individuals using the polymorphic markers. The lesion of these F2 individuals was investigated after the inoculation of
Breeding resistance variety is the best strategy to overcome the bacterial blight disease damage in rice and is a very challengeable work. Availability of resistant genotype is the major limitation to the resistance improvement. However, plant disease resistance is a complex trait usually regulated by QTLs, epistatic effect, and influenced by the interactions among pathogen, host and environment.
In this review, a durable resistance mutant, SA0423, was firstly obtained from screening a sodium azide-induced mutation pool on the genetic background of TNG67 rice variety. The genomic approaches and technologies were conducted according to the concept and flow of Central Dogma. In the genomic study, the inheritance and gene corresponding to the BBD resistance of SA0423 was conducted. Linkage maps were constructed, and three QTLs (qBBR06.1, qBBR08.1 and qBBR11.1) for resistance were identified from SA0423. Meanwhile, the linkage markers for each QTL were developed according to the linkage map for marker-assisted breeding.
The transcriptomics and proteomics technologies were applied to identify the expressed genes and proteins corresponding to the pathogen inoculation for BBD resistance on SA0423. The differential displayed genes (or proteins) were annotated by blast with the gene database (NCBI and GRAMENE websites), and then their putative biological functions or the participating pathways were predicted by GO analysis. Besides, they were compared with the published resistance genes in
Phenomics or phenotype can provide the solid evidence for gene function. Our previous findings were tested through transgenic approach as well as marker-assisted backcrossing (MABC). The transgenic rice plants with less expression of
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