Panicle blast 1 (Pb1) resistance is dependent on at least four QTLs in the rice genome
© The Author(s). 2017
Received: 30 March 2017
Accepted: 21 July 2017
Published: 1 August 2017
Rice blast is the most serious disease afflicting rice and there is an urgent need for the use of disease resistance (R) genes in blast tolerance breeding programs. Pb1 is classified as a quantitative resistance gene and it does not have fungal specificity. Pb1-mediated resistance develops in the latter stages of growth. However, some cultivars, such as Kanto209 (K209), cultivar name Satojiman, despite possessing Pb1, do not exert resistance to rice blast during the reproductive stage.
We found that the expression of WRKY45 gene downstream of Pb1 was weakly induced by rice blast inoculation at the full heading stage in K209. Genetic analysis using the SNP-based Golden Gate assay of K209 crossing with Koshihikari Aichi SBL (KASBL) found at least four regions related to the resistance in the rice genome (Chr8, Chr9, Chr7, Chr11). Mapping of QTL related to Chr7 confirmed the existence of factors that were required for the resistance of Pb1 in the 22 to 23 Mbp region of the rice genome.
We clarified how the K209 cultivar is vulnerable to the blast disease despite possessing Pb1 and found the DNA marker responsible for the quantitative resistance of Pb1. We identified the QTL loci required for Pb1-mediated resistance to rice panicle blast. Pb1 was negatively dependent on at least three QTLs, 7, 9 and 11, and positively dependent on one, QTL 8, in the K209 genome. This finding paves the way for creating a line to select optimal QTLs in order to make use of Pb1-mediated resistance more effectively.
KeywordsOryza sativa Pyricularia oryzae Panicle blast QTL Salicylic acid Resistance gene
Rice blast is a pathogenicity that affects rice plants worldwide. In order to minimize the damage of rice blast, resistance (R)-gene cultivars are commonly used. The use of R genes to develop resistant cultivars has become an urgent goal in rice breeding programs. Several molecular approaches to study rice blast resistance genes have been developed during the last decade. So far, hundreds of blast R genes have been mapped in the rice genome. A large group of R genes is clustered in several genomic regions reviewed in (Liu et al. 2014). Most of the genes encode nucleotide-binding site (NBS) leucine-rich repeat (LRR) proteins that interact with pathogen effectors and trigger defense reactions following a gene-for-gene model of recognition (Bryan et al. 2000; Okuyama et al. 2011; Cesari et al. 2013). One of the plant defense mechanisms is the recognition of Microbe-Associated Molecular Patterns (MAMPs) by receptors, leading to generally weak defense responses called MAMP-Triggered Immunity (MTI). Some pathogens overcome the resistance by secreting effector proteins that interfere with host resistance and promote pathogenicity. Plants have evolved to recognize against the effectors through Effector-Triggered Immunity (ETI). True resistance genes are specific and provide strong resistance to the rice blast, but the effect of R genes decline after 2 or 3 years.
In contrast to MTI or ETI, the quantitative resistance genes are durable to the blast, but are less understood (Cook et al. 2015; Fukuoka et al. 2015). Recently, intensive genetic analyses of quantitative “leaf” blast resistance genes including pi21, Pi34, Pi35, Pi39 and Pi63 have been carried out (Nguyen et al. 2006; Zenbayashi-Sawata et al. 2007; Terashima et al. 2008; Fukuoka et al. 2009; Xu et al. 2014). In contrast to these leaf blast resistance genes, the panicle blast (Pb1) resistance gene has been used as the durable form that confers rice plants partial resistance to the rice blast with no fungal race specificity (Fujii et al. 2000). Pb1 gene has been introduced into rice cultivars in Korea (Lee et al. 2015). The cultivars have remained resistant to panicle blast for over 35 years. Cloning of Pb1 has identified that the resistance is weak on the early stage and gradually becomes strong for the reproductive stage of the plant, and is dependent on the Pb1 expression (Hayashi et al. 2010). After heading stage, the resistance of Pb1 cultivar is very strong to rice blast.
The resistance mechanism of Pb1 is attributed to its interaction with WRKY45 (Inoue et al. 2013), which plays a crucial role in the salicylic acid (SA) pathway in rice immunity (Shimono et al. 2007). WRKY45 is regulated by a ubiquitin-proteasome system in the rice nucleus (Matsushita et al. 2012). The Pb1 coiled-coil domain interacts with the nuclear-localized WRKY45 (Inoue et al. 2013), resulting in a Pb1-WKRY45 complex is a weaker target than WRKY45 for protein degradation. WRKY45 overexpressed transgenic rice plants have strong resistance not only to the leaf rice blast but also to the panicle blast (SHIMONO et al. 2011). The genes in the downstream pathway of WRKY45, including OsNAC4, OsHSF1, OsOPR4 (Nakayama et al. 2013), and diterpenoid phytoalexin (DP), a bHLH transcription factor (Yamamura et al. 2015), play a crucial role in disease resistance. Cytokinins (CKs) play a role in mediating the signal of Pyricularia oryzae infection to trigger the induction of DP biosynthetic genes in benzothiadiazole- (BTH) primed plants (AKAGI et al. 2014).
Kanto 209 (K209) cultivar is one of the cultivars harboring Pb1; however, the resistance of the cultivar is weak in comparison with other Pb1 cultivars. In the K209 cultivar of rice, the expression of WRKY45 is lower than that of Koshihikari Aichi SBL (KASBL). The lower expression of the gene might be due to the genotype of the cultivar. To identify the mechanism of this rice blast resistance, we crossed the K209 and KASBL cultivars. Genomic DNA of their F3progeny was subjected to SNP-based Golden Gate assay and we found at least four quantitative trail loci (QTL) to the panicle rice blast resistance. Among the four QTLs, we focused on QTL7, which was located on chromosome 7 and showed Pb1-dependent defense against panicle blast in field tests, and performed a map-based cloning.
K209 has other potential mutations for blast resistance
To study gene expression by quantitative PCR, total RNAs were extracted from the 25 days old leaf of KASBL and K209 after treatment with water (mock) or BTH for 2 or 4 days. Surprisingly, WRKY45, NH1 and PR1a expression was reduced by BTH treatment on both days (Fig. 2b). The transcript abundance for Pb1 was significantly reduced at 4 days after treatment with BTH (Fig. 2b). The concentrations of SA and total SA were not statistically different between K209 and KASBL plants (Fig. 2c).
K209 has at least four DNA mutations for blast resistance on its genome
Putative QTLs associated with panicle blast resistance in K209/KASBL F4 lines in 2010
Logarithm of odds
b297 = C7–14
b063 = C8–4
b586 = C9–7
b285 = C8–4
Eight genotypes defined by four QTLs for panicle blast resistance and their phenotypes
Leaf disease index
Panicle disease index
Days until heading
QTL7 was located within a 1.8 Mbp region on chromosome 7
Rice with enhanced Pb1-mediated resistance can be produced by using QTL Analyses
Pb1 is known as a durable blast-resistance gene consisting of a single dominant locus. Introduction of Pb1 gene into rice plants by marker selection breeding has been actively carried out. As a result, there are several Pb1 cultivars to panicle blast resistance of rice in Japan. Among them, K209 and its progeny cultivar Hoshijirushi have been found to exhibit weak resistance to rice panicle blast despite harboring Pb1. The loss of Pb1-mediated resistance over time has generated a negative impact for rice breeders for a long time. To this end, we attempted to identify the mechanism of the loss of Pb1-mediated blast resistance of Pb1 in K209. Traditionally, a functional gene region is introduced into a genomic fragment, so the gene can have a large additive effect in breeding. However, interactions with the genes in the background have been known to cause differential effects with respect to rice bacterial blight resistance (Sun et al. 2004; Cao et al. 2007; Iyer-Pascuzzi et al. 2008). In this study, we attempted to solve the conundrum of the absence of resistance to rice blast despite the presence of the resistance gene Pb1in the K209 line. Our studies revealed the exact locus in the gene responsible for rice blast resistance, underscoring the importance of this research in blast resistance breeding. Genetic analysis of KASBL and K209 revealed that the regions Chr8, Chr9, Chr7, and Chr11 were involved in rice blast resistance in at least four rice genomes (Fig. 4). Among them, three QTLs (Chr9, Chr7 and Chr11) negatively affected the resistance despite the presence of Pb1. Chr8, on the other hand, had a positive influence on signal transduction, so it is expected that these QTLs will specifically change Pb1-mediated resistance single handedly or in combination with others (Fig. 4). This paves the way for creating a line in future containing just the positively acting QTL and excluding the negatively affecting QTLs in order to make a more effective Pb1-mediated resistance. Therefore, this result is important in developing highly persistent blast resistance disease varieties by selection of markers.
Investigations into finding the factors responsible for resistance reveal the signal transduction of several factors interacting with each other to produce enhanced resistance to the blast. Although several causative genes have been identified as factors involved in highly quantitative resistance, detailed studies on downstream factors are lacking. Analyses of factors responsible for highly effective, true resistance to rice blast have, however, been progressing. For example, Pit resistance is a true blast resistance gene located downstream of OsRAC1 (Os01g0229400) (Kawasaki et al. 1999; Kawano et al. 2010), OsRAR1 (Os02g0535400) and OsSGT1 (Os01g0624500) (Wang et al. 2008). They are located outside of all the four QTLs loci. Other downstream pathways involved in basic resistance of the blast such as Rice Chitin Receptor CEBiP (Os03g0133400) (Kaku et al. 2006), Rice LysM receptor-like kinase, OsCERK1 (Os08g0538300) (Shimizu et al. 2010), cytoplasmic kinase, OsRLCK176 (Os05g0110900), OsRLCK185 (Os05g0372100), lysin motif-containing proteins, OsLYP6 (Os06g0208800) (Ao et al. 2014) have been shown. They all exist in different QTLs in rice genome. They all exist in different loci in rice genome, except OsLYP4 (Os09g0452200) that may be one of candidates for the QTL on Chr9 (Ao et al. 2014). Altogether, we found that the QTLs of Chr7 and Chr11 are new genes exhibiting resistance to blast disease and this will contribute toward the efforts to elucidate the network of genes responsible for rice blast resistance.
K209 exhibits lower induction of SA-responsive genes with blast infection compared to KASBL cultivar
When K209 and KASBL cultivars were inoculated with rice blast, we found that WRKY45 and NH1 were weakly induced in K209 (Figs. 2b and 3) and the SA concentration was similar to that of KASBL (Fig. 2c). This result indicates that the transport or perception of SA was defective in the K209 cultivar. In Arabidopsis, there there is evidence for SA reception by AtNPR proteins (Wu et al. 2012; Fu et al. 2012). Rice has orthologous NPR proteins in the genome, OsNPR1 (Os01g0194300), OsNPR2 (Os01g0767966) and OsNPR3 (Os03g0667100), but these genes did not correspond to the QTLs derived from qualitative reasoning in these experiments.
The mechanism of the induced resistance of WRKY45 depended on the resistance of Pb1, and could not be induced by inoculation with blast disease in this cultivar. The expression of WRKY45 in rice is induced by BTH by activating the SA pathway (Shimono et al. 2007). Therefore, we investigated whether the induction of WRKY45 by BTH still remained in these cultivars. In this experiment, the expression of WRKY45 in both genotypes was maintained normally, and the resistance induced by BTH was conserved (Fig. 2b). However, when treated with rice blast in KASBL and K209 in reproductive growth, the induction of WRKY45 expression was not observed only in the K209 varieties (Fig. 3). Therefore, it is highly probable that the upstream signaling pathway up to WRKY45 is compromised by some mutations in this cultivar for infection of rice blast. Little is known on the upstream signaling activation mechanism of WRKY45 in rice plants. WRKY45 is regulated by several enzymes, including mitogen-activated protein kinase kinase OsMKK10–2 and mitogen-activated protein kinase, some phosphorylation events such as OsMPK4 and OsMPK6 phosphorylation, and also dephosphorylation events such as the tyrosine dephosphorylation of MAPKs by PTPases (OsPTP1/2) in the SA pathway (Ueno et al. 2015). OsMKK10–2 is located on chromosome 3 (Hamel et al. 2006), and the loci of OsMPK4 (Chromosome 10), OsMPK6 (Chromosome 10), OsPTP1 (Chromosome 12) and OsPTP2 (Chromosome 11), were all different from the QTLs derived from qualitative reasoning in these experiments. The mechanism of WRKY45 activation against the rice panicle blast of Pb1-mediated resistance is still unknown.
In this report, we have identified the QTL loci of Pb1 based on the resistance to rice panicle blast with map-based screening. We found that Pb1 was negatively dependent at least on three QTLs, 7, 9 and 11, and positively on one, QTL 8. This understanding of the molecular mechanism of blast resistance paves the way for creating a line in future containing just the positively acting QTL in order to make a more effective Pb1-mediated resistance.
Kanto 209 and Koshihikari Aichi SBL are cultivars that are susceptible and resistant to panicle blast, respectively, despite possessing Pb1. 82 F3 plants derived from a cross between these cultivars developed by single seed descent method were used for DNA genotyping. The F4 lines derived from respective F3 plants were used for assessing resistance to panicle blast to detect putative QTLs. To confirm and delimit putative QTLs on chromosome 7, a total of 320 F4 or F5 lines whose QTL regions were fixed (except for that on chromosome 7) were used to select recombinant inbred plants on and around the putative QTL on chromosome 7. Selected progeny lines (F5 or F6) were subjected to field tests in 2014, 2015 and 2016.
To sequence Pb1 and WRKY45, we amplified the following regions from the K209 cultivar: for Pb1, we amplified both the Pb1 upstream sequence (−2200 to −1) and ORF region using the primers 5′-AAGGTGAGGTGAGTCATTAGTG-3′ and 5′-TCATGGTTCATTACATTTAA-3′. For WRKY45, we amplified both the upstream sequence (−1700 to −1) and ORF genomic region using the primers 5′-GCCCAATCGGCTGTAATAC-3′ and 5′- AGGCACGTGAAGCTATATGT-3′. The DNA fragments were purified by Nucleo Spin Gel and PCR clean-up kit (Machery-Nagel, Germany). Then, we performed DNA sequencing using BigDye terminator v3.1 Cycle Sequencing kit (ThermoFisher, Japan) with 3130 genetic Analyzer. The obtained sequences were aligned with Nipponbare genome by a plasmid editor software, APE version 2.04 (http://biologylabs.utah.edu/jorgensen/wayned/ape/).
Evaluation of panicle blast resistance
Panicle blast resistance was evaluated in an experimental paddy field at the Aichi Agricultural Research Center, Mountainous Resin Agricultural Research Institute, where the high pressure of blast disease and its progress are well controlled. Thirteen plants were transplanted for each line in early June. Disease severity was visually evaluated 2–3 weeks after the heading date, and scored from 0 (no diseased grain) to 10 (100% diseased grain) according to the report (Asaga 1981). Some varieties developed for the evaluation of partial resistance to panicle blast (Hayashi et al., 1993) were used for comparison.
Total RNA was isolated from rice tissue using Trizol (Invitrogen). For quantitative RT-PCR, total RNA was treated with DNA remover to remove contaminating genomic DNA. cDNA was synthesized using ReverTra Ace reverse transcriptase (Toyobo, Japan). To determine Pb1 expression, quantitative RT-PCRs were run on a Thermal Cycler Dice TP800 system (Takara Bio, Japan) as shown previously (Hayashi et al. 2010) using primers Pb1sp4Fw/Pb1s4Rv. Rice ubiquitin 1 (Rubq1; AK121590) was used as an internal standard. The primers used in quantitative RT-PCR were listed in Additional file 1: Table S1.
The measurement of SA and SAG content
The SNP genotyping
The genotypes of the F3 plants, (which we characterized by using 199 SNP markers), were determined by using 768-plex SNPs for the Illumina Golden Gate Bead Array technology platform (Illumina, Inc., San Diego, CA, USA) based on previously reported information (Ebana et al. 2010; Nagasaki et al. 2010). DNA was extracted from 50 mg of fresh rice leaves using the DNeasy 96 Plant Kit (Qiagen). The designed OPA and 250 ng of DNA were used for the preparation of bead chips according to the protocol for the Golden Gate Genotyping Assay.
QTL analysis and progeny tests
We constructed a genetic map using MAPMAKER/EXP v. 3.0 software (Lander et al. 1987). QTL analysis for grain length and grain width was performed using version 2.5 of QTL Cartographer software (Basten et al. 2005), and the threshold was obtained by using 1000 permutations. The progeny lines of F4 or F5 plants were grown to select recombinants within the QTL in order to develop inbred lines with recombinations within and around QTL7. Plants with independent recombination events were selected from on the basis of genotypes around the QTL region determined by using simple-sequence repeat (SSR) markers. The primers for SSR markers were listed in Additional file 1: Table S1.
The cultivar of K209, Kanto HD2 and Hoshijirushi were kindly gifted by Dr. Sato, NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan. The chemical analysis of SA by HPLC was performed by Dr. Shigemi Seo, NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan.
This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement, LCT-0013) and by JSPS KAKENHI Grant Number 17 K07678.
HI, NH designed research; HI, MN, TM, AT, SS, SF, NH performed research; HI, SF, and NH wrote the paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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