Bacterial Leaf Blight Resistance Genes Research Articles

Insights into the virulence profiles and molecular diversity of Xanthomonas oryzae pv. oryzae isolates associated with bacterial blight of rice in major districts of Karnataka, India

Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating disease affecting rice worldwide. In this study, to characterize Xoo isolates and evaluate the effectiveness of various BLB-resistant genes in rice, a set of 29 rice differentials each carrying, single or combinations of BLB resistant genes were used for characterizing Xoo isolates under glasshouse condition. None of the tested isolates were able to show complete virulence across all Near Isogenic Lines (NILs). All isolates varied with degrees of resistance and susceptibility. Notably, isolate KXo-3 exhibited high virulence. Among single BLB resistant genes, IRBB-8 (xa8) and IRBB-13 (xa13) were found highly promising while among two gene combinations, IRBB-51 (Xa4+xa13), IRBB-52 (Xa4+Xa21) and IRBB-53 (xa5+xa13). Among three and four gene combination of BB resistant genes, IRBB-56 (Xa4+xa5+xa13), IRBB-57 (Xa4+xa5+Xa21), IRBB-58 (Xa4+xa13+Xa21), IRBB-59 (Xa5+xa13+Xa21), IRBB-60 (Xa4+xa5+xa13+Xa21), IRBB-63 (xa5+Xa7+xa13) and IRBB-65 (Xa4+Xa7+xa13+Xa21) were resistant against almost all the Xoo isolates. Based on disease reactions, Xoo isolates were grouped into 6 pathotypes, as IXoPt # 1, 2, 4, 5, 17 and 22. IXoPt-22 was highly virulent and IXoPt-1 was least virulent. IXoPt-2 was widely distributed with the maximum distribution frequency of 23.8. Molecular diversity using IS1112 repetitive elements showed that the Xoo isolates were genetically very diverse with three major clusters, I, II and III. The haplotype diversity resulted in 27 haplotypes generation. The isolates of Belagavi, Haveri and Davanagere were very diverse with distinct haplotypes. These findings enhance our understanding of BLB resistance mechanisms and Xoo population diversity, aiding in the development of effective disease management strategies in rice cultivation.

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.

Genetic Enhancement of Blast and Bacterial Leaf Blight Resistance in Rice Variety CO 51 through Marker-Assisted Selection

The increased use of chemicals in rice farming poses significant issues regarding the emergence of pesticide/fungicide resistance and environmental sustainability concerns. This study was aimed at the genetic improvement of blast, bacterial leaf blight (BB) and gall midge resistance in a popular rice variety CO 51 which already harbours a blast resistance gene Pi54. Efforts were made to pyramid an additional blast resistance gene Pi9 along with two BB resistance genes (xa13 and Xa21) and two gall midge resistance genes (Gm1 and Gm4) into an elite rice variety CO 51 to enhance the resistance level to biotic stresses. The superior lines were selected using functional markers conferring resistance to blast (NBS4 and Pi54MAS linked to Pi9 and Pi54 genes, respectively) and BB [(xa13Prom (xa13) and pTA248 (Xa21)] and SSR markers linked to Gm1 (RM1328) and Gm4 (RM22550) for phenotypic screening and agronomic evaluation. The genotyping and phenotyping of F6 and BC2F6 progenies of CO 51 X 562-4, for agronomic traits and resistance to BB and blast, identified ten superior progenies in F6 and five superior progenies in BC2F6. The breeding lines harbouring both xa13+Xa21 exhibited high levels of resistance to BB (score ≤ 1 cm) and Pi9+Pi54 exhibited strong resistance to blast (score ≤ 2). Identified lines can be evaluated further for varietal improvement or utilised as genetic stocks in breeding programs.

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 resistance genes for bacterial leaf blight (Xanthomonas oryzae pv. Oryzae) into the popular rice variety, Pratikshya through marker assisted backcrossing.

Bacterial leaf blight (BLB) is one of the major biotic stress in rice cultivation. Management techniques, such as the development of BLB-resistant cultivars, are required to lessen the severity of the disease attack and yield losses. Pratikshya was selected in the present investigation as the recipient parent, as it is one of the popular high-yielding rice varieties of Odisha, India, which is having excellent grain as well as cooking quality. However, Pratikshya is highly susceptible to BLB which is prevalent in Eastern Indian region. Three major BLB resistance genes xa5, xa13, and Xa21 from the donor source Swarna MAS (CR Dhan 800) were attempted to introduce into Pratikshya through a marker-assisted backcross breeding program. Those markers closely linked to the target genes were employed for foreground selection in the segregating generations till BC2F3. In each backcross generation, progenies containing all three targeted resistance genes and phenotypically more similar to the recipient parent, Pratikshya were selected and backcrossed. Screening of 1,598 plants of the BC2F2 population was conducted against BLB using Xoo inoculum and 35 resistant plants similar to Pratikshya were carried forward to the next generation. In the BC2F3 generation, 31 plants were found to possess all the three resistance genes. For background selection of plants carrying resistance genes 45 polymorphic SSR markers were employed. Evaluation of the pyramided lines at BC2F4 generation exhibited that, most pyramided lines were similar to Pratikshya in terms of morphological features and yield parameters, and some lines were superior to the recurrent parent in terms of morphological features and yield parameters. The three-gene pyramided lines showed a high level of resistance to BLB infection and are anticipated to offer a significant yield advantage over the recipient parent Pratikshya.The pyramided lines can further be used for multi-location trial, so as to be released as a variety or can be used as a potential donor for BLB resistance genes.

Genome-Wide Association Study Using Genotyping by Sequencing for Bacterial Leaf Blight Resistance Loci in Local Thai Indica Rice

Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genome-wide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify candidate single nucleotide polymorphisms (SNPs) associated with BLB resistance genes. The study utilized 200 indica rice accessions inoculated with seven distinct Xoo isolates and filtered highly significant SNPs using a minor allele frequency (MAF) of >5% and a call rate of 75%. Four statistical models were used to explore potential SNPs associated with BLB resistance, resulting in the identification of 32 significant SNPs on chromosomes 1–8 and 12 in the rice genome. Additionally, 179 genes were located within ±100 kb of the SNP region, of which 49 were selected as candidate genes based on their known functions in plant defense mechanisms. Several candidate genes were identified, including two genes in the same linkage disequilibrium (LD) decay as the well-known BLB resistance gene (Xa1). These findings represent a valuable resource for conducting further functional studies and developing novel breeding strategies to enhance the crop’s resistance to this disease.

Pheno-Genotypic Screening of Medium Slender Rice Genotypes for Bacterial Leaf Blight (BLB) Disease Resistance

The bacterial leaf blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is an economically important and one of the most destructive disease of rice in both irrigated and rainfed environments in Asia. In particular, in recent years, the occurrence of abnormal climate and warming phenomena has produced a good environment for bacterial leaf blight. The rice yield continues to decrease, causing 30 to 50% yield loss. Since bacterial pathogen is difficult to manage by other means effectively, developing host plant resistance is the most effective way to control this disease. So, the study was carried out during rain-fed season (July–November 2019) at Agricultural Research Station (ARS) Gangavati, Karnataka, India to identify the bacterial leaf blight resistance reaction among 22 medium slender genotypes of rice by both phenotyping and genotyping by using molecular markers linked with resistance governing bacterial leaf blight genes. Alongside TN-1 was used as susceptible check and screening was done by artificial clip inoculation method. The disease reactions were recorded one week after inoculation, with Standard Evaluation Scale (SES) for BLB ranging from 0–9, when the susceptible check (TN-1) was completely killed. None of the genotypes showed a resistant reaction, but three genotypes viz. IET-27904, IET-25520 and Rp Bio-226 showed resistant reaction against BLB. The six major BLB resistant genes genetic frequencies varied from 42.85% to 14.28% in the molecular evaluation of promising genotypes for major BLB resistant genes using three Simple Sequence Repeats (SSR) and Sequence Tagged Sites (STS) markers respectively.

Distribution of Xanthomonas oryzae pv. oryzae Pathotypes in Basmati-Rice-Growing Areas of Jammu and Kashmir, India

Rice is an important staple food for more than half of the world’s population. Though the genetic potential of commonly cultivated varieties of rice is diminished due to various biotic and abiotic constraints, bacterial leaf blight (BLB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is considered one of its most destructive diseases in India. Based on morpho-cultural characteristics, bacterial pathogens isolated from the leaves of a rice plant showing typical BLB symptoms were identified as Xanthomonas oryzae pv. oryzae. Morphological studies revealed that the pathogen is Gram-negative, a short rod, with rounded ends, single or in pairs, light yellow, circular, whitish yellow to straw-colored, convex, yellow, slightly raised, motile with a single polar flagellum, capsulate and non-spore-forming. Biochemical tests, viz., the Gram reaction, KOH test and catalyst test, showed a positive reaction for all the isolates. Twenty isolates of Xoo were collected from the basmati-growing areas of the Jammu, Samba and Kathua districts in the Jammu sub-tropics during 2019, and their pathogenicity was confirmed on five susceptible rice cultivars, viz., Basmati-370, Pusa-1121, TN-1, SJR and Jaya, by the leaf-clipping method, and subsequently, Koch’s postulate was established in each case. Seven Xoo pathotypes, viz., Pathotype 1, Pathotype 2, Pathotype 3, Pathotype 4, Pathotype 5, Pathotype 6 and Pathotype 7, were identified from the total sample of 20 isolates. Pathotype 2 was the most dominant (100%), followed by Pathotype 5 (44.44%), Pathotype 4 (40%), Pathotype 6 (40%), Pathotype 7 (33.33%), Pathotype 3 (22.22%) and Pathotype 1 (20%), in the Jammu sub-tropics. In Jammu district, Pathotype 5 was highly distributed (44.44%) followed by Pathotype 7 (33.33%) and Pathotype 3 (22.22%). Pathotype 4 and Pathotype 6 each showed a 40 percent distribution in Kathua district, followed by Pathotype 1 (20%). Only one pathotype, i.e., Pathotype 2, was recorded in Samba district with a 100 percent distribution. Five genes, viz., Xa13, Xa4, Xa13 and Xa5 + Xa13, showed complete resistance, whereas Xa4, Xa5, Xa7, Xa8, Xa21, Xa4 + Xa5 and Xa4 + Xa21 showed susceptible response against the test isolates. It was observed that most of the single BLB-resistant genes were moderately to highly susceptible to almost all the Xoo isolates, whereas combinations of BLB resistance genes possessed high resistance against all the Xoo isolates. The studies revealed that diverse pathogenic variations existed in the Xoo population in the basmati-growing region of Jammu and Kashmir. Based on the response exhibited by Xoo isolates on differential lines, seven pathotypes (Pathotype 1–7) were identified, and their virulence spectrum on rice differentials showed the occurrence of 5, 3, 10, 10, 20, 10 and 15 percent, respectively, in the Jammu sub-tropics. To develop durable and sustainable resistant cultivars, it is essential to identify predominate race(s) in a specific geographical area and continuously monitor the virulence pattern there.

Backcrossing with Marker Assistance to Introduce Broad-Spectrum Bacterial Leaf Blight Resistance in the Malaysian Elite Variety MR297

A significant part of marker-assisted backcross breeding (MABB) is recurrent parent genome recovery (RPGR). The purpose of this study was to introduce MABB-mediated resistance genes against numerous bacterial leaf blight (BLB) pathogens. Here, we examine the introgression of four Xoo resistance genes to the high-yielding Malaysian MR297 lineage Xa21, xa13, xa5, and Xa4 from the IRBB60 lineage. To accomplish both foreground and background selection, we employed polymorphic functional linked markers to target genes and simple sequence repeat (SSR) markers. We used 83 of the 475 authorized polymorphic microsatellite markers to determine the proportion of RPGR in the chosen lines. According to the data, the RPGR at BC1F1, BC2F1, and BC2F2 are 81.94, 92.30, and 95.04%, respectively. Incorporating the four BLB resistance genes into the newly created lines would result in long-lasting and comprehensive protection against BLB. Therefore, a resistant gene may be introduced into a population more quickly with MABB than through conventional breeding. All ten lines tested showed a significant level of resistance to BLB, with three lines displaying very high levels of resistance. Consequently, it was recommended that new lines should be used to produce commercially viable rice varieties.

SCREENING OF RICE LINES OF DIVERSE ORIGIN RESISTANT TO BACTERIAL LEAF BLIGHT UNDER LOCAL CONDITIONS


 
 
 Current study comprised of 20 donor parent lines and four indica elite strains resistant against bacterial leaf blight having diversity in origin viz. Bangladesh, Philippine, Indonesia, Senegal and India. The lines were tested to check resistance against Bacterial Leaf Blight (BLB), having BLB resistance genes Xa-4, xa-5, Xa-7 and xa-13. The experiment was conducted at Agronomic Research Station, Farooqabad, Sheikhupura. Artificial inoculation was done to study disease reaction. DNA marker analysis was also conducted to study the gene status of these lines. Results indicated that seven donor lines were completely resistant to Bacterial Leaf Blight whereas twelve lines exhibited moderate resistance. Among rest of the five susceptible genotypes, three were showing comparatively low susceptibility whereas two completely susceptible to BLB. Most of the lines with three or four gene combinations showing resistant behavior against BLB except AUS-298 that showed moderately susceptible behavior. Combination of genes for Bacterial Leaf Blight resistance can be explored further in targeted research program for disease resistance.
 
 

Genotypic and Phenotypic Selection of Newly Improved Putra Rice and the Correlations among Quantitative Traits

This experiment was conducted to genotypically and phenotypically select new rice lines pyramided with blast and bacterial leaf blight disease resistance genes after a marker-assisted backcross breeding programme. The inter-relationship among agro-morphological characteristics and their effect on yield was also studied. The polymorphic functional and microsatellite markers Xa21FR and pTA248 (Xa21), Xa13prom (xa13), RM21 (xa5), MP (Xa4), RM6836 (Pi2, Pi9 & Piz) and RM8225 (Piz) were first confirmed for the target genes. The selected markers were used for foreground selection of BC2F2 homozygous progenies with the target genes. Plants that had homozygous IRBB60 alleles for these markers were evaluated for their recovery of the recurrent parent genome. IRBB60 was used as the donor parent for bacterial blight resistance genes while Putra-1 served as a recipient/recurrent parent with background blast-resistance genes and high yield. After the foreground selection, 79 polymorphic simple sequence repeat markers identified from the marker polymorphism survey were used for marker-assisted background selection to determine the percentage recovery of the recurrent parent genome. In order to make a selection on a phenotypic basis, 14 agro-morphological traits were measured and recorded. The result obtained from the study showed that 16 lines received the seven resistance genes in sufficiently varied numbers and were selected. The distribution of yield per hectare showed that about 50% of the selected lines had yields as high as 5 t/ha and above. Some of the lines produced as high as 8.4 t/ha. These lines demonstrated the potential of recording uniform 8t/ha upon recombination at BC2F2. The study also indicated that the number of panicles per hill correlated strongly, significantly and positively with the number of tillers (r = 0.962 **), total grain weight per hill (r = 0.928 **) and yield per hectare (r = 0.927 **). It was concluded that the newly improved resistant lines which were selected have the capability to compete with Putra-1 in terms of its productivity and yield. The newly developed lines would be useful in future breeding programmes as donors for bacterial leaf blight and blast resistance genes. These lines are recommended for release to farmers in Malaysia and other rice-growing agro-ecologies for commercial cultivation.

Genotype and Phenotype Interaction between OsWKRYq6 and BLB after Xanthomonas oryzae pv. Oryzae Inoculation in the Field

Bacterial leaf blight (BLB) is an important and devastating rice disease caused by the pathogen Xanthomonas oryzae pv. Oryzae (Xoo). In particular, in recent years, the occurrence of abnormal climate and warming phenomena has produced a good environment for the occurrence of BLB, and the rice yield due to the occurrence of BLB continues to decrease. Currently, molecular breeding is applied by searching for resistant genes to development of BLB resistance cultivar. In addition, there are many methods for screening resistant genes, and among them, phenotype analysis in the field and applied research is rarely conducted. Due to recent rapid climate change, BLB is a major problem that has a more serious negative effect on rice yield. Therefore, we suggest OsWRKYq6 to be effectively used for breeding BLB-resistant cultivars by screening BLB-resistant genes. In this study, the BLB-resistant gene was screened using the lesion length, which most definitely changes to the phenotype when Xoo is infected. OsWRKYq6 was finally selected as a BLB resistance gene by analyzing the phenotype and genotype after inoculating Xoo in 120 Cheongcheong/Nagdong double haploid (CNDH) lines in the field. After Xoo inoculation, lesion length and yield were investigated, and 120 CNDH lines were divided from BLB-resistant and susceptible lines. Moreover, when the transcription level of OsWRKYq6 was analyzed in the resistant and susceptible lines after Xoo inoculation in the field, the expression level was regulated to a high level in the resistant line. In this study, we propose OsWRKYq6 as a transcription factor involved in BLB resistance. Currently, the differentiation of various races is proceeding rapidly due to rapid climate change. In addition, screening of transcription factor genes involved in BLB resistance in the field can be effectively applied to molecular breeding to develop resistant cultivars in preparation for rapid climate change.

Molecular Analyses and Resistance Evaluation to Bacterial Leaf Blight on Swampy Rice Genotypes

<p>Swampland is a prospective marginal land to be developed for rice cultivation. Rice plants that are adaptive to swampland usually have good tolerance to Fe. Previously, we obtained several rice lines tolerant to Fe toxicity in the field. This study aimed to analyze the swampy rice genotypes using STS molecular markers linked to bacterial leaf blight (BLB)-resistant genes and evaluate the resistance level of the genotypes against three BLB races under the greenhouse condition. This research was conducted in the Molecular Biology Laboratory and Greenhouse of the Indonesian Center for Agricultural Biotechnology and<br />Genetic Resources Research and Development from January to May 2021. Eighteen swampy rice varieties/lines and two check varieties for Fe toxicity and BLB, respectively, were used in this research. The eight STS molecular markers linked to BLB resistance genes were used for genotyping analysis. The results showed that all rice plants tested contained xa5 allele gene, 19 genotypes had Xa4 allele gene, 17 genotypes had Xa7 allele gene, 9 genotypes had xa13 allele gene, 5 genotypes had xa13 allele gene, and 6 genotypes had Xa4 and Xa21 allele genes. Line B146E-4 was estimated to have 7 resistance alleles genes, meanwhile lines B14301E-KA-17-a, B14315E-KA-1, and B13-1-a have 6 resistance allele genes. The resistance evaluation of the genotypes against the three BLB races (races III, IV, and VIII) under the greenhouse condition showed that line B14315E-KA-1 was confirmed to be highly resistant to BLB disease. This line can be a promising candidate for swampy rice that is resistant to<br />BLB disease.</p>

Development of New Rice (Oryza. sativa L.) Breeding Lines through Marker-Assisted Introgression and Pyramiding of Brown Planthopper, Blast, Bacterial Leaf Blight Resistance, and Aroma Genes

Brown planthopper, blast, and bacterial blight are the main biotic stressors of rice and can cause a massive loss in rice production. Aroma is an important character of rice quality. It is of far-reaching significance to breed resistant and high-quality varieties using germplasms with objective genes. In this study, the introgression and pyramiding of brown planthopper (BPH), blast, and bacterial leaf blight (BLB) resistance genes and aroma genes into elite rice maintainers and restorers were conducted through conventional cross-breeding coupled with the marker-assisted selection (MAS) breeding method. Single-plant selection was performed from F2 onwards to select desirable recombinants possessing alleles of interest with suitable phenotypes. Respective linked markers were used in each generation from intercrossing to the F7 generation for tracking the presence of targeted genes. A total of 74 improved lines (ILs) have been developed which possess a combination of 1 to 4 genes for BPH, blast, and BLB resistance and aroma. These ILs showed moderate to high resistance to multiple biotic stresses (BPH, blast and BLB) or aromatic fragrance without obvious negative effects on agronomic traits. As multiple resistance and aromatic traits have become significant objectives in rice breeding, these resistance and/or aroma gene introgressed or pyramided lines have important application prospects. Core ideas: (1) marker-assisted breeding was used to pyramid multiple genes for an elite breeding line; (2) improved lines with the introgression of 1–4 genes were developed to achieve high resistance against various biotic stresses and aroma; (3) new lines were used as donor parents to introgress multiple genes in other genetic backgrounds.

Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)

BackgroundRice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB.ResultsHere, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (–log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice.ConclusionsTogether, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.

Improvement of rice cultivar for bacterial blight disease through marker assisted breeding approach

The present investigation was undertaken with the objective to develop high yielding, fine grain rice varieties possessing broad spectrum durable resistance by transferring bacterial leaf blight (BLB) resistant genes viz., xa13 and Xa21 from Improved Pusa Basmati 1. A popular high yielding and fine grain rice variety, HUBR 2-1 (Malviya Dhan 2-1), susceptible to BLB and Improved Pusa Basmati 1 carrying resistant genes for BLB (xa13 & Xa21 genes) were selected as parents for crossing. Improved Pusa Basmati 1 was verified for the presence of target genes by using gene linked primers viz., xa13 promotor and pTA 248. The cross viz., HUBR 2-1 x Improved Pusa Basmati 1 was undertaken during Kharif 2011 and F1 progenies were confirmed during rabi 2011. The F1 plants confirmed as true hybrids for both the genes were advanced to the F2 generation and foreground selection was done using gene linked markers. Genetic analysis in the F2 population confirmed that the genes (xa13 & Xa21) governing BLB resistance followed Mendelian inheritance. The phenotypic data analysis revealed that the plants carrying two resistance gene combinations (xa13xa13 Xa21Xa21, xa13xa13Xa21xa21) showed BLB resistance (0-3 scale), while the gene combinations viz., Xa13Xa13Xa21Xa21, Xa13Xa13Xa21xa21 and Xa13xa13Xa21Xa21, Xa13xa13Xa21xa21 showed BLB resistance (5-30).

Genetic relationship, population structure analysis and pheno-molecular characterization of rice (Oryza sativa L.) cultivars for bacterial leaf blight resistance and submergence tolerance using trait specific STS markers.

The online version contains supplementary material available at 10.1007/s12298-021-00951-1.

Characterization of pathogenic variability of Xanthomonas oryzae pv oryzae isolates causing bacterial leaf blight disease in Malaysian rice granaries

Xanthomonas oryzae pv oryzae, the causative pathogen of bacterial leaf blight (BB) disease is one of the most prevalent rice diseases in Malaysia. Breeding for resistance requires information on the pathogenic variability of X. oryzae for decision-making on the deployment of appropriate resistance genes. In this study, nine Near Isogenic rice Lines (NILs) carrying single BB resistance genes (Xa) used to characterize the virulence of 40 X. oryzae isolates collected from Malaysian rice granaries. The results revealed a highly diverse pathogenic profile, consisting of 21 distinct X. oryzae races named R1 to R21. Race R20, followed by R16 were identified as dominant, showing the highest frequency. Although no Xa genes have been used in Malaysian rice granaries up to now, unexpectedly race R20 was found virulent to most of the NILs carrying the Xa genes. However, the wide distribution of avirulence gene avrxa5 and avrXa7 among the isolates indicated that the population was most effective to NILs carrying the xa5 and Xa7 genes. The information obtained helps to understand the virulence of X. oryzae population and facilitates an adequate gene deployment to increase BB disease resistance in Malaysia.

Rapid genotyping of bacterial leaf blight resistant genes of rice using loop-mediated isothermal amplification assay.

The use of resistant (R) genes is the most effective strategy to manage bacterial leaf blight (BLB) disease of rice. Several attempts were made to incorporate R genes into susceptible rice cultivars using marker-assisted backcross breeding (MABB). However, MABB relies exclusively on PCR for foreground selection of R genes, which requires expensive equipment for thermo-cycling and visualization of results; hence, it is limited to sophisticated research facilities. Isothermal nucleic acid amplification techniques such as loop-mediated isothermal amplification (LAMP) assay do not require thermo-cycling during the assay. Therefore, it will be the best alternative to PCR-based genotyping. In this study, we have developed a LAMP assay for the specific and sensitive genotyping of seven BLB resistance (R) genes viz., Xa1, Xa3, Xa4, Xa7, Xa10, Xa11, and Xa21 in rice. Gene-specific primers were designed for the LAMP assay. The LAMP assay was optimized for time, temperature, and template DNA concentration. For effective detection, incubation at 60°C for 30min was optimum for all seven R genes. A DNA intercalating dye ethidium bromide and a calorimetric dye hydroxynaphthol blue was used for result visualization. Further, sensitivity assay revealed that the LAMP assay could detect R genes at 100fg of template DNA compared to 1ng and 10pg, respectively, in conventional PCR and q-PCR assays. The LAMP assay developed in this study provides a simple, specific, sensitive, robust, and cost-effective method for foreground selection of R genes in the resistance breeding programs of resource-poor laboratory.