Bacterial Blight Resistance Genes Research Articles

Introgression and Mapping of a Novel Bacterial Blight Resistance Gene xa49(t) from Oryza rufipogon acc. CR100098A into O. sativa.

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is one of the epidemic diseases in rice. Rapid changes in the pathogenicity of the X.oryzae pv. oryzae pathogen demand the identification and characterization of novel BB resistance genes. Here, we report the transfer and mapping of a new BB resistance gene from Oryza rufipogon acc. CR100098A. Inheritance studies on the BC2F2 population, BC2F3 progenies, and backcross-derived recombinant inbred lines derived from a cross between Pusa44/O. rufipogon acc. CR100098A//2*PR114 showed that a single recessive gene confers resistance in O. rufipogon acc. CR100098A. Bulked segregant analysis using 203 simple sequence repeat (SSR) markers localized the BB resistance gene on chromosome 11 bracketed between two SSR markers, RM27235 and RM2136. Using PR114 and O. rufipogon acc. CR100098A genotyping by sequencing data, 86 KASP markers within the bracketed region were designed and tested for bulked segregant analysis. Only five KASP markers showed polymorphism between parents, and three were associated with the target gene. Seventy-seven new SSR markers were designed from the same interval. A total of 33 polymorphic markers were analyzed on the whole population and mapped the BB gene in an interval of 2.8 cM flanked by SSR markers PAU11_65 and PAU11_44 within a physical distance of 376.3 kb. The BB resistance gene mapped in this study is putatively new and designated as xa49(t). Fourteen putative candidate genes were identified within the xa49(t) region having a role in biotic stress resistance. The linked markers to the xa49(t) gene were validated in other rice cultivars for its successful deployment in BB resistance breeding.

Pyramiding of multiple resistant genes of blast and bacterial blight diseases in the background of rice (Oryza sativa) mega variety BRRI dhan29

Blast and bacterial blight (BB) are the two major rice diseases in the world including Bangladesh. In this study, BB resistance genes (Xa21 and xa13) and blast resistance (Pi9 and Pb1) genes were pyramided into a mega variety, BRRI dhan29 through marker-assisted backcross breeding. IRBB58 was used as a BB-resistant donor and Pi9-US2, and Pb1-US2 were used as blast-resistant donors. Backcross was done between BRRI dhan29 and donor parents to develop BC3F1 population and then selfing was done to develop BC3F6 population. BC3F2 population was genotyped and phenotyped for segregation analysis and BC3F6 was evaluated for genotyping, phenotyping and morphological traits and yields. Chi-square analysis of BC3F2 data revealed that blast and BB resistance followed the single gene mendelian fashion (1:2:1 and 3:1). Two to four gene combinations were found in the advanced lines of the BC3F6 population. The yield of the advanced lines ranged from 6.42 (t ha−1) to 9.5 (t ha−1) and they showed resistant against blast and BB with mean disease scores ranging from 0.67 to 2.33 and 0.33–2.33, respectively. Finally, eight lines having four genes (xa13, Xa21, Pi9 and Pb1) were selected for multilocational (five locations) trials for yield performance and disease reaction. Mean yield data of eight advanced lines of all locations were varied from 6.48±0.15–8.38±0.11 t ha−1 and all the lines showed resistant reactions against blast (score 0.53–1) and BB (score 0.6–0.87) disease. The highest yield was found in BR (Path) 13800-BC3–224–12 (G28, 8.38±0.11 t ha−1) followed by BR (Path) 13800-BC3–134–252 (G26, 8.28±0.08 t ha−1) and BR (Path) 13800-BC3–136–115 (G12, 8.24±0.07 t ha−1). Pyramided advanced lines of this study could be released as BB and blast-resistant varieties or could be utilized as donor parents in resistant breeding.

Development and Validation of an SNP Marker for Identifying Xanthomonas oryzae pv. oryzae Thai Isolates That Break xa5-Mediated Bacterial Blight Resistance in Rice.

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogenic bacterium responsible for bacterial blight (BB) disease in rice, primarily mediated by the interaction between the plant and pathogen. The virulence mechanism involves the activation of the Sugars Will Eventually be Exported Transporter (SWEET) gene family in rice by transcription activator-like effectors derived from Xoo. The BB resistance gene xa5 has been identified as one of the most effective genes against Thai Xoo isolates, but xa5-mediated resistance-breaking Xoo strains have emerged. This study aimed to develop a single nucleotide polymorphism (SNP) marker for precise identification of xa5-mediated resistance-breaking Xoo. Comparative genomics of Thai Xoo isolates Xoo16PK001 and Xoo16PK002, which were incompatible and compatible with rice variety IRBB5 carrying xa5, respectively, identified eight SNP positions for the development of an SNP marker. The SNP marker XooE6 yields a specific 1,143 bp PCR product unique to Xoo16PK002. Screening 61 Thai isolates using XooE6 identified two positives: Xoo20PL010 and Xoo20UT002. Inoculation tests on rice varieties IRBB5 and IRBB13 demonstrated compatibility with IRBB5 and incompatibility with IRBB13, which bears Xa5 and xa13. Xoo16PK001 (XooE6-negative) showed different virulence. Inoculation on IRBB21 harboring Xa5, Xa13, and Xa21 resulted in partial resistance to both XooE6-positive and -negative strains. XooE6-positive strains up-regulated SWEET11 and suppressed SWEET14 in IRBB5, while Xoo16PK001 slightly induced SWEET11 but activated SWEET14 in IRBB13. This highlights the potential of XooE6 to identify xa5-mediated resistance-breaking Xoo strains and elucidate their pathogenic mechanisms through the upregulation of SWEET11.

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Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance

The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.

Association between molecular markers and resistance to bacterial blight using binary logistic analysis

The most effective strategy for managing wheat bacterial blight caused by Pseudomonas syringae pv. syringae is believed to be the use of resistant cultivars. Researching the correlation between molecular markers and stress resistance can expedite the plant breeding process. The current study aims to evaluate the response of 27 bread wheat cultivars to bacterial blight disease in order to identify resistant and susceptible cultivars and to pinpoint ISSR molecular markers associated with bacterial blight resistance genes. ISSR markers are recommended for assessing a plant's disease resistance. This experiment is focused on identifying ISSR molecular markers linked to bacterial blight resistance. After applying the bacterial solution to the leaves, we performed sampling to determine the infection percentage in the leaves at different intervals (7, 14, and 18 days after spraying). In most cultivars, the average leaf infection percentage decreased 18 days after spraying on young leaves. However, in some cultivars such as Niknegad, Darab2, and Zarin, leaf infection increased in older leaves and reached up to 100% necrosis. In our study, 12 ISSR primers generated a total of 170 bands, with 156 being polymorphic. The primers F10 and F5 showed the highest polymorphism, while the F7 primer exhibited the lowest polymorphism. Cluster analysis grouped these cultivars into four categories. The resistant group included Qods, Omid, and Atrak cultivars, while the semi-resistant and susceptible groups comprised the rest of the cultivars. Through binary logistic analysis, we identified three Super oxide dismutase-related genes that contribute to plant resistance to bacterial blight. These genes were linked to the F3, F5, and F12 primers in regions I (1500 bp), T (1000 bp), and G (850 bp), respectively. We also identified seven susceptibility-associated genes. Atrak, Omid, and Qods cultivars exhibited resistance against bacterial blight, and three genes associated with this resistance were linked to the F3, F5, and F12 primers. These markers can be used for screening or transferring tolerance to other wheat cultivars in breeding programs.

Pyramiding of bacterial blight resistance genes into promising restorer BRRI31R line through marker-assisted backcross breeding and evaluation of agro-morphological and physiochemical characteristics of developed resistant restorer lines.

BRRI31R is one of the Bangladesh's most promising restorer lines due to its abundant pollen producing capacity, strong restoring ability, good combining ability, high outcrossing rate and genetically diverse from cytoplasmic male sterile (CMS) line. But the drawback of this line is that it is highly susceptible to bacterial blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae. The present study highlighted the pyramiding of effective BB resistance genes (xa5, xa13 and Xa21) into the background of BRRI31R, through marker-assisted backcrossing (MABC). Backcross progenies were confirmed and advanced based on the foreground selection of target genes. Pyramided lines were used for pathogenicity test against five Bangladeshi Xanthomonas oryzae (BXo) races (BXo93, BXo220, BXo822, BXo826, BXo887) and confirmed the dominant fertility restore genes, Rf3 and Rf4 and further validated against SNP markers for more confirmation of target resistance genes. All pyramided restorer lines consisted of Xa4 (in built), xa5, xa13, Xa21, and Chalk5 with two fertility restorer genes, Rf3, Rf4. and these restorer lines showed intermediate amylose content (<25%). Restorer lines BRRI31R-MASP3 and BRRI31R-MASP4 showed high levels of resistance against five virulent BXo races and SNP genotyping revealed that these lines also contained a blast resistance gene Pita races. Gene pyramided restorer lines, BRRI31R-MASP3 and BRRI31R-MASP4 can directly be used as a male parent for the development of new BB resistant hybrid rice variety or could be used as a replacement of restorer line of BRRI hybrid dhan5 and 7 to enhance the quality of hybrid seeds as well as rice production in Bangladesh.

Precision mapping and expression analysis of recessive bacterial blight resistance gene xa-45(t) from Oryza glaberrima.

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of rice leading to huge yield losses in Southeast Asia. The recessive resistance gene xa-45(t) from Oryza glaberrima IRGC102600B, mapped on rice chromosome 8, spans 80Kb with 9 candidate genes on Nipponbare reference genome IRGSP-1.0. The xa-45(t) gene provides durable resistance against all the ten Xanthomonas pathotypes of Northern India, thus aiding in the expansion of recessive bacterial blight resistance gene pool. Punjab Rice PR127, carrying xa-45(t), was released for wider use in breeding programs. This study aims to precisely locate the target gene among the 9 candidates conferring resistance to bacterial blight disease. Sanger sequencing of all nine candidate genes revealed seven SNPs and an Indel between the susceptible parent Pusa 44 and the resistant introgression line IL274. The genotyping with polymorphic markers identified three recombinant breakpoints for LOC_Os08g42370, and LOC_Os08g42400, 15 recombinants for LOC_Os08g423420 and 26 for LOC_Os08g42440 out of 190 individuals. Relative expression analysis across six time intervals (0, 8, 24, 48, 72, and 96h) after bacterial blight infection showed over expression of LOC_Os08g42410-specific transcripts in IL274 compared to Pusa 44, with a significant 4.46-fold increase observed at 72h post-inoculation. The Indel marker at the locus LOC_Os08g42410 was found co-segregating with the phenotype, suggesting its candidacy towards xa-45(t). The transcript abundance assay provides strong evidence for the involvement of LOC_Os08g42410 in the resistance conferred by the bacterial blight gene xa-45(t).

Understanding the nature of blast resistance in combined bacterial leaf blight and blast gene pyramided lines of rice variety tellahamsa.

Rice blast and bacterial leaf blight (BLB) are the most limiting factors for rice production in the world which cause yield losses typically ranging from 20 to 30% and can be as high as 50% in some areas of Asia especially India under severe infection conditions. An improved line of Tellahamsa, TH-625-491 having two BLB resistance genes (xa13 and Xa21) and two blast resistance genes (Pi54 and Pi1) with 95% Tellahamsa genome was used in the present study. TH-625-491 was validated for all four target genes and was used for backcrossing with Tellahamsa. Seventeen IBC1F1 plants heterozygous for all four target genes, 19 IBC1F2 plants homozygous for four, three and two gene combinations and 19 IBC1F2:3 plants also homozygous for four, three and two gene combinations were observed. Among seventeen IBC1F1 plants, IBC1F1-62 plant recorded highest recurrent parent genome (97.5%) covering 75 polymorphic markers. Out of the total of 920 IBC1F2 plants screened, 19 homozygous plants were homozygous for four, three and two target genes along with bacterial blight resistance. Background analysis was done in all 19 homozygous IBC1F2 plants possessing BLB resistance (possessing xa13, Xa21, Pi54 and Pi1 in different combinations) with five parental polymorphic SSR markers. IBC1F2-62-515 recovered 98.5% recurrent parent genome. The four, three and two gene pyramided lines of Tellahamsa exhibited varying resistance to blast. Results show that there might be presence of antagonistic effect between bacterial blight and blast resistance genes since the lines with Pi54 and Pi1 combination are showing better resistance than the combinations with both bacterial blight and blast resistance genes.

Broad-Spectrum Resistance and Monogenic Inheritance of Bacterial Blight Resistance in an Indigenous Upland Rice Germplasm ULR207

Bacterial blight (BB) caused by Xanthomonas oryzae pv. Oryzae (Xoo) is a serious disease of rice worldwide that can reduce crop yield and affect food insecurity. A rice resistance variety is an alternate way to solve this problem. The broad-spectrum resistance (BSR) of ULR207 is important for durable resistance to several of the Xoo isolates. However, the inheritance of this resistance gene in ULR207 must be known before it can be utilized. Thus, this study aimed to survey the BB resistance gene with reference to the BB resistance gene for identification of non-analogous or analogous genes and confirmation of a broad-spectrum resistance, to investigate the gene effect, the number of genes, and the heritability of the BB resistance gene in the ULR207 variety. Six populations of two crosses (Maled Phai × ULR207 and RD6 × ULR207), i.e., ULR207 (Donor parent), Maled Phai and RD6 (Recurrent parent), F1, F2, BC1P1, and BC1P2 were constructed. These materials were evaluated for BB resistance by clipping methods under greenhouse conditions using a virulence isolate of a pathogen in Thailand. The results showed that ULR207 exhibited the strongest against BB with 0.8 of BSR with low area under the disease progress curve (AUDPC). Molecular screening for surveying of the BB resistance gene in ULR207 revealed a non-analogous resistance gene with resistance check varieties. The phenotype of the disease lesion length of F2 and BC1P2 populations exhibited a ratio of 1:3 and 1:1 (resistant: susceptible), respectively, revealing a single recessive gene in both crosses. The scaling test parameters A, B, and C were non-significant (p &lt; 0.01), indicating that variation in data was sufficiently explained by additive (d) and dominance (h) components. The gene action of ULR207 was controlled by additive gene action. Heritability of the two crosses, Maled Phai x ULR207 and RD6 x ULR207, exhibited high values with 0.817 and 0.716, whereas the numbers of the genes were 1.4 and 1.2, respectively. The result indicated that the breeding strategy could be employed in early generations when using ULR207 as a new source of bacterial blight resistance.

Screening for disease resistance and profiling the expression of defense-related genes contributing to resistance against bacterial blight (Xanthomonas oryzae pv. oryzae) in rice genotypes

Bacterial Bight profoundly affects global rice-growing regions. Breeding resistant cultivars is a reliable, effective, and eco-friendly way to control bacterial blight. The study was conducted during 2021–2022 to evaluate the resistance of rice genotypes to bacterial blight under glasshouse conditions. A total of 137 rice genotypes were screened for their resistance against two Xanthomonas oryzae pv. oryzae strains (TXO01 and TXO08) using the leaf clipping method. The results revealed diverse disease reactions among the genotypes, with some exhibiting high levels of resistance characterized by hypersensitive reactions and shorter lesion lengths. To further investigate the genetic basis of resistance, we screened moderately resistant and resistant genotypes for major bacterial blight resistance genes, including Xa21, xa5, and xa13, using gene-specific markers. Five genotypes viz., ADT55, CB MAS 13056, CB MAS 13060, CB MAS 13066, and ACM 18234 confirmed the presence of all R genes in a homozygous state, indicating a potentially robust resistance background. In addition, we examined the expression patterns of five defense-related genes involved in the salicylic acid (SA) and jasmonic acid (JA) signaling pathways using quantitative real-time PCR (qRT-PCR). The resistant genotypes exhibited significantly elevated expression levels of OsNPR1, OsWRKY45, OsPAL1, OsPR1a, and OsPR10a, ranging from 2 to 20-fold changes compared with the susceptible genotype. In conclusion, our findings suggest that the resistant genotypes not only harbor multiple bacterial blight resistance genes but also manifest up regulated defense responses against Xanthomonas oryzae pv. oryzae, possibly substantiating their elevated level of disease resistance.

Cost-effective multiplex PCR assay for simultaneous detection of bacterial leaf blight, blast and brown planthopper resistance genes in rice

Cost-effective multiplex PCR assay for simultaneous detection of bacterial leaf blight, blast and brown planthopper resistance genes in rice

Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach.

Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.

Pyramiding of blast and bacterial blight resistance genes in premium quality rice variety, BRRI dhan63 through marker-assisted breeding approach

Pyramiding of blast and bacterial blight resistance genes in premium quality rice variety, BRRI dhan63 through marker-assisted breeding approach

Genome Resource for the Highly Virulent Xanthomonas oryzae pv. oryzae Strain HN2011 from China

Xanthomonas oryzae pv. oryzae ( Xoo) is the causal bacterium of rice bacterial blight (BB), which is one of the most destructive bacterial diseases of rice worldwide. Although more than 40 BB resistance genes ( Xa genes) have been identified, only a few conferring broad resistance (e.g., Xa4 and Xa21) have been widely used for rice breeding in Asia. The narrow genetic basis for the BB resistance of rice cultivars has resulted in the emergence of new pathogenic strains that can overcome the resistance of commonly grown rice cultivars derived from breeding programs. For example, Xoo strain HN2011, which was isolated in Hainan (China), can overcome the resistance mediated by multiple BB resistance genes, including Xa4 and Xa21. We herein present the complete genome sequence of HN2011 generated by Nanopore sequencing. The genomic data will be useful for elucidating the genomic variations of Xoo and will contribute to clarifying the interaction between Xoo and rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding.

Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC3F1s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers.

Brown Planthopper, Nilaparvata lugens Stål Resistance in Backcross Derived Rice Lines

A prominent rice pest, brown planthopper (BPH) significantly reduces the grain yield in rice across the globe and employing chemical pesticides leads to unwarranted environmental issues. Breeding for BPH resistance is an essential strategy to mitigate the losses caused by them. Host plant resistance through marker assisted selection is a chief strategy to lessen harms caused by BPH and boost rice production. In this study, we have analyzed BPH resistance in the BC1F5 population, which is a backcross derivative of improved CO51 and Ptb33. Improved CO51 has already been introgressed with bacterial blight resistant genes xa5, xa13 and Xa21 and blast resistant gene Pi54 via marker assisted selection (MAS). Ptb33 was used as the donor parent to incorporate BPH resistant genes bph2 and Bph32 to this CO51 background. The genotypically and phenotypically selected 26 lines of BC1F5 generation were screened against BPH along with parents and checks. The bioassay of the population exhibited a range of variation for BPH resistance. Among the 26 near isogenic lines, 18 (2 resistant and 16 are moderately resistant) and eight showed susceptible to moderate susceptible reaction. The 18 resistant lines were further multiplied and are now in hot spot screening.

Multivariate analysis for morpho-physiological and milling traits along with molecular profiling of known bacterial blight resistance genes in advanced breeding lines of rice

Multivariate analysis for morpho-physiological and milling traits along with molecular profiling of known bacterial blight resistance genes in advanced breeding lines of rice

Efficient protein tagging and cis-regulatory element engineering via precise and directional oligonucleotide-based targeted insertion in plants.

Efficient and precise targeted insertion holds great promise but remains challenging in plant genome editing. An efficient non-homologous end-joining-mediated targeted insertion method was recently developed by combining CRISPR/SpCas9 gene editing with phosphorothioate modified double-stranded oligodeoxynucleotides (dsODNs). Yet this approach often leads to imprecise insertions with no control over the insertion direction. Here, we compared the influence of chemical protection of dsODNs on efficiency of targeted insertion. We observed that CRISPR/SpCas9 frequently induced staggered cleavages with 1-nucleotide 5´overhangs; we also evaluated the effect of donor end structures on the direction and precision of targeted insertions. We demonstrate that chemically protected dsODNs with 1-nucleotide 5´ overhangs significantly improved the precision and direction control of target insertions in all tested CRISPR targeted sites. We applied this method to endogenous gene tagging in green foxtail (Setaria viridis), and engineering of cis-regulatory elements for disease resistance in rice (Oryza sativa). We directionally inserted two distinct transcription activator-like effector binding elements into the promoter region of a recessive rice bacterial blight resistance gene with up to 24.4% efficiency. The resulting rice lines harboring heritable insertions exhibited strong resistance to infection by the pathogen Xanthomonas oryzae pv. oryzae in an inducible and strain-specific manner.

Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm.

Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.