BB 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.

Evaluation of hybrid rice parental lines against bacterial blight disease and detection of resistant gene (s) by gene‐specific, linked markers

AbstractBacterial blight (BB) disease, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the major bottlenecks of rice (Oryza sativa) production. The present study was undertaken to identify BB‐resistant parental lines of hybrid rice based on pathogenicity tests and molecular screening. Three virulent races of Xoo, i.e. BXo93, BXo822 and BXo887 were used to evaluate the 66 maintainers and 200 elite restorer lines against BB. Based on the pathogenicity test, none of the maintainer lines was found resistant, whereas 16 restorers were resistant against the three races and 15 restorers were resistant to a single race (Bxo93). These 31 restorer lines were selected to detect the presence of major bacterial blight resistance genes, i.e. Xa4, xa5, Xa7, xa13, Xa21 and Xa23 using molecular markers. Thirteen restorer lines carried the Xa4 gene but were not resistant to all three races of BB. Fourteen restorers and one restorer had two (Xa4 + xa5; Xa4 + Xa7; Xa4 + Xa21 and Xa7 + Xa21) and three (Xa4 + xa5 + Xa7) BB resistance genes, respectively. Genotypes having Xa21, Xa7 + Xa21 or Xa4 + Xa21 had reduced lesion lengths that ranged from 1.4 cm (against BXo93)–3.0 cm (against BXo887), 1.6 cm (against BXo93)–2.0 cm (against BXo822 and BXo887) and 2.5 cm (against BXo887)–3 cm (against BXo822), respectively, and were found to be the most effective resistance genes against bacterial blight. The restorer lines having the Xa21, Xa7 + Xa21 or Xa4 + Xa21 could be used as parental lines for the development of bacterial blight‐resistant hybrid varieties.

Understanding the variability of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae in Andhra Pradesh, India.

Bacterial blight (BB) of rice is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). The evolution of new pathogenic races of bacterial blight pathogen is always a potential threat for rice production. The deployment of pathotype-specific resistant genes in the host plants is a feasible strategy to develop BB-resistant varieties. Therefore, continuous disease monitoring, identification of Xoo pathotypes, and their distribution are crucial to managing BB. In this study, 71 Xoo isolates were collected from the Godavari delta in Andhra Pradesh (India) and their virulence profiles on rice BB differentials were characterized. Data revealed that different International Rice Bacterial Blight (IRBB) lines with single BB resistance genes were susceptible to 73.2%-97.2% of the isolates, except IRBB13 (possessing BB resistance gene, xa13) which showed a moderately susceptible or susceptible reaction to 47.9% of the isolates. Three gene combination rice differentials like IRBB56 (Xa4 + xa5 + xa13), IRBB57 (Xa4 + xa5 + Xa21), IRBB58 (Xa4 + xa13 + Xa21), and IRBB59 (xa5 + xa13 + Xa21) showed very broad-spectrum resistance to majority of the Xoo isolates from the region. None of the tested Xoo isolates were virulent on IRBB58 (Xa4 + xa13 + Xa21), IRBB60 (Xa4 + xa5 + xa13 + Xa21), and IRBB66 (Xa4 + xa5 + Xa7 + xa13 + Xa21). Based on the virulence reaction, 71 Xoo isolates were grouped into 10 major pathotypes. Highly virulent pathotypes viz., IXoPt # 14, 17, 19, and 22 can break the resistance of major BB-resistant genes and were commonly distributed throughout the surveyed regions. Genotypic data of 71 Xoo isolates using J3 primer divided them into three major clusters. Cluster I consisted of 24 Xoo isolates that belonged to pathotype IXoPt-19. Cluster II consisted of 41 Xoo isolates belonging to sevendifferent pathotypes, and Cluster III was composed of six isolates from three different pathotypes. The findings of this study will be helpful to develop rice varieties with pathotype-specific broad-spectrum resistance against BB.

Gene Pyramiding for Achieving Enhanced Resistance to Bacterial Blight, Blast, and Sheath Blight Diseases in Rice.

Bacterial blight, blast, and sheath blight are the commonest diseases causing substantial yield loss in rice around the world. Stacking of broad-spectrum resistance genes/QTLs into popular cultivars is becoming a major objective of any disease resistance breeding program. The varieties ASD 16 and ADT 43 are the two popular, high yielding, and widely grown rice cultivars of South India, which are susceptible to bacterial blight (BB), blast, and sheath blight diseases. The present study was carried out to improve the cultivars (ASD 16 and ADT 43) through introgression of bacterial blight (xa5, xa13, and Xa21), blast (Pi54), and sheath blight (qSBR7-1, qSBR11-1, and qSBR11-2) resistance genes/QTLs by MABB (marker-assisted backcross breeding). IRBB60 (xa5, xa13, and Xa21) and Tetep (Pi54; qSBR7-1, qSBR11-1, and qSBR11-2) were used as donors to introgress BB, blast, and sheath blight resistance into the recurrent parents (ASD 16 and ADT 43). Homozygous (BC3F3 generation), three-gene bacterial blight pyramided (xa5 + xa13 + Xa21) lines were developed, and these lines were crossed with Tetep to combine blast (Pi54) and sheath blight (qSBR7-1, qSBR11-1, and qSBR11-2) resistance. In BC3F3 generation, the improved pyramided lines carrying a total of seven genes/QTLs (xa5 + xa13 + Xa21 + Pi54 + qSBR7-1 + qSBR11-1 + qSBR11-2) were selected through molecular and phenotypic assay, and these were evaluated for resistance against bacterial blight, blast, and sheath blight pathogens under greenhouse conditions. We have selected nine lines in ASD 16 background and 15 lines in ADT 43 background, exhibiting a high degree of resistance to BB, blast, and sheath blight diseases and also possessing phenotypes of recurrent parents. The improved pyramided lines are expected to be used as improved varieties or used as a potential donor in breeding programs. The present study successfully introgressed Pi54, and qSBR QTLs (qSBR7-1, qSBR11-1, and qSBR11-2) from Tetep and major effective BB-resistant genes (xa5, xa13, and Xa21) from IRBB60 into the commercial varieties for durable resistance to multiple diseases.

Bacterial blight resistance in cotton: genetic basis and molecular mapping

Bacterial blight (BB, caused by Xanthomonas citri pv. malvacearum, Xcm) is a worldwide disease of cotton (Gossypium spp.). The disease has been effectively controlled through the use of BB resistant cultivars and planting of acid-delinted seed. However, a resurgence of BB has been noted in the US in recent years due to the spread of Xcm race 18 and growing of susceptible transgenic cultivars, which calls for a renewed effort to develop new BB resistant cultivars. However, there has been a paucity of information in genetics and breeding for BB resistance since the 1990s due to the lack of research efforts. This review was prepared to fill this void with an objective to provide detailed results from past qualitative and quantitative genetic studies on BB resistance, including genetic designs and specific germplasm used for conducting research. More than 20 major resistance B genes (B1 to B8, B9K, B9L, B10K, B10L, B11, B12, BIn, Bn, Bs, and more than 4 unnamed genes), with at least two polygene complexes (BSm and BDm), have been identified. One B gene may be resistant to a single or multiple Xcm races, and pyramiding of several B genes can enhance resistance to a single or multiple Xcm races. Allelic relationships among some of the genes are currently unknown. Quantitative genetics has been employed to estimate heritability, gene effects, additive and dominance variances, and effective number of genes for BB resistance. The studies suggest that the additive effect and additive variance play a predominant role in BB resistance, while the dominant effect and variance play a reduced role in resistance. Heritability estimates are moderate to high depending on environmental errors, and 1–2 effective numbers of genes have been estimated, consistent with Mendelian genetic studies. Studies in molecular mapping of several BB resistance genes (B2, B3, b6, and B12) have been conducted with the focus on B12 as it is resistant to races 1 through 19. Portable DNA markers have been developed and used in marker-assisted selection for BB resistance. Finally, areas where there is a lack of information and controversies are identified and assessed. This review provides an updated comprehensive account of the genetic basis for BB resistance in cotton.

Pyramiding Bacterial Blight Resistance Genes in Tainung82 for Broad-Spectrum Resistance Using Marker-Assisted Selection.

Tainung82 (TNG82) is one of the most popular japonica varieties in Taiwan due to its relatively high yield and grain quality, however, TNG82 is susceptible to bacterial blight (BB) disease. The most economical and eco-friendly way to control BB disease in japonica is through the utilization of varieties that are resistant to the disease. In order to improve TNG82’s resistance to BB disease, five bacterial blight resistance genes (Xa4, xa5, Xa7, xa13 and Xa21) were derived from a donor parent, IRBB66 and transferred into TNG82 via marker-assisted backcrossing breeding. Five BB-resistant gene-linked markers were integrated into the backcross breeding program in order to identify individuals possessing the five identified BB-resistant genes (Xa4, xa5, Xa7, xa13 and Xa21). The polymorphic markers between the donor and recurrent parent were used for background selection. Plants having maximum contribution from the recurrent parent genome were selected in each generation and crossed with the recipient parent. Selected BC3F1 plants were selfed in order to generate homozygous BC3F2 plants. Nine pyramided plants, possessing all five BB-resistant genes, were obtained. These individuals displayed a high level of resistance against the BB strain, XF89-b. Different BB gene pyramiding lines were also inoculated against the BB pathogen, resulting in more than three gene pyramided lines that exhibited high levels of resistance. The five identified BB gene pyramided lines exhibited yield levels and other desirable agronomic traits, including grain quality and palatability, consistent with TNG82. Bacterial blight-resistant lines possessing the five identified BB genes exhibited not only higher levels of resistance to the disease, but also greater yield levels and grain quality. Pyramiding multiple genes with potential characteristics into a single genotype through marker-assisted selection can improve the efficiency of generating new crop varieties exhibiting disease resistance, as well as other desirable traits.

Differential expression of Xoo-induced kinase 1 (XIK1), a Xanthomonas oryzae pv. oryzae responsive gene, in bacterial blight-susceptible and Xa21-mediated resistant indica rice cultivars

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is a costly disease in rice that threatens global rice production. The Xa21 gene is a broad spectrum BB-resistance gene that is extensively used for improving BB resistance in rice. The Xoo responsive gene,Xoo-induced kinase 1 (XIK1), recently characterized in japonica rice, was also found to be involved in Xa21-mediated resistance. The current study investigated the differential expression of XIK1 in the BB-susceptible indica rice cultivar RD47 and its improved BB-resistant progenies BC3F3 (Xa21/Xa21) in various growth stages and during Xoo inoculation. The results showed that the expression of XIK1 was development-dependent and induced earlier in BB-resistant progenies BC3F3 than in the susceptible cultivar RD47 after Xoo inoculation. However, the expression levels of XIK1 substantially dropped after a peak of expression. Interestingly, the XIK1 expression tended to increase again in the succeeding hours post-inoculation in BC3F3 but not in RD47. Similar development and induction patterns were also observed when the expression of XIK1 and Xa21 was analyzed in the same runs in the BB-resistant BC3F3 under different growth stages and during Xoo inoculation. The findings suggested that XIK1 may also be involved in the Xa21-mediated resistance pathway of indica rice.

Identification of Rice Genotypes Resistant To Bacterial Leaf Blight Disease Using Ssr Markers

Bacterial blight disease of rice is a growing and challenging concern in Nepal. Since bacterial pathogen (Xanthomonas oryzae pv. oryzae) is difficult to manage by other means effectively, development of host plant resistance is the most effective mean to control this disease. This study was carried out to identify the bacterial leaf blight resistant genotypes of rice by using of molecular markers linked with bacterial blight resistant genes. Sixty genotypes of rice were screened at glass house for BB resistance and they were tested for the presence of Xa4, Xa5, Xa7 and Xa21 genes using markers MP, RM122, M5 and pTA248 respectively. IRBB 60 and Jumli Marshi were used as resistant and susceptible check respectively. Twenty five genotypes of rice were detected with presence of Xa4 gene, 24 genotypes with Xa5 gene and fourteen genotypes with Xa7 gene. Twenty four genotypes did not showed presence of any gene. Twenty four genotypes showed the presence of more than one gene with the specific molecular markers. Almost all genotypes that did not show presence of any gene were found highly susceptible in greenhouse conditions with both inoculums. Genotypes having more than one BB resistance gene were found resistant in greenhouse conditions with both inoculums suggesting combination of BB resistance gene through gene pyramiding will provide BB resistant varieties in rice breeding.

Incorporation of the novel bacterial blight resistance gene Xa38 into the genetic background of elite rice variety Improved Samba Mahsuri.

Bacterial blight (BB) in rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major global production constraint, particularly in irrigated and rain-fed lowland areas. Improved Samba Mahsuri (ISM) is an elite, high-yielding, fine-grain type, BB-resistant rice variety possessing three BB-resistant genes (Xa21, xa13 and xa5) and is highly popular in the southern parts of India. As the BB pathogen is highly dynamic and the evolution of pathogen virulence against the deployed resistance genes is common, we added a novel BB-resistant gene, Xa38, into ISM through marker-assisted backcross breeding (MABB) to increase the spectrum and durability of BB resistance. The breeding line PR 114 (Xa38) was used as the donor for Xa38, whereas ISM was used as the recurrent parent. Foreground selection was conducted using PCR-based gene-specific markers for the target genes, whereas background selection was conducted using a set of polymorphic SSR markers between the parents and backcrossing that continued until the third generation. Eighteen homozygous BC3F2 plants possessing all four BB-resistant genes in the homozygous state and with a recurrent parent genome (RPG) recovery of more than 92% were identified and advanced to the BC3F6 generation. These 18 backcross-derived lines (BDLs) exhibited very high level of resistance against multiple Xoo strains and displayed agro-morphological traits, grain qualities and yield levels similar to or better than those of the recurrent parent ISM.

Improved Tapaswini having four BB resistance genes pyramided with six genes/QTLs, resistance/tolerance to biotic and abiotic stresses in rice

Rice, a major food crop, is grown in a wide range of ecological conditions and suffers significant yield losses as it is constantly exposed to a wide range of environmental and biotic stresses. The prevalence of different biotypes/strains has necessitated assembling of numerous resistance genes/QTLs into elite genotypes to confer a broader scale of resistance. The current study reports successful pyramiding of genes/QTLs that confer tolerance/resistance to submergence (Sub1), salinity (Saltol), blast (Pi2, Pi9) and gall midge (Gm1, Gm4) to supplement the four bacterial blight resistance genes (Xa 4, xa5, xa13, Xa21) present in Improved Tapaswini, an elite cultivar. The precise transfer of genes/QTLs was accomplished through effective foreground selection and suitable gene pyramids were identified. Background selection was practiced using morphological and grain quality traits to enhance the recovery of the recurrent parental genome. In the bioassays, the pyramids exhibited higher levels of resistance/ tolerance against the target stresses. The novel feature of the study was successful pyramidization and demonstration of the function of ten genes/QTLs in a new genotype. This success can stimulate several such studies to realize the full potential of molecular plant breeding as the foundation for rice improvement.

Multiplex PCR genotyping for five bacterial blight resistance genes applied to marker‐assisted selection in rice (Oryza sativa)

AbstractBacterial blight (BB) is the most economically damaging disease of rice in Asia and other parts of the world. In this study, a multiplex PCR genotyping method was developed to simultaneously identify genotypes of five BB resistance genes, Xa4, xa5, Xa7, xa13 and Xa21. The resistance R alleles were amplified using five functional markers (FMs) to generate amplicons of 217, 103, 179, 381 and 595 bp in IRBB66. Amplicons of 198, 107, 87, 391 and 467 bp corresponded to susceptible alleles in Taiwanese japonica rice cultivars. In backcross breeding programmes, the multiplex PCR assay was integrated into selection from a population using BB resistance donor IRBB66 crossed to rice cultivar ‘Tainung82’. Two plants with homozygosity for Xa4, xa5, Xa7, xa13 and Xa21 were selected from 1100 BC2F2 plants. In addition, the five BB resistance genes were also accurately identified in F2 populations. This multiplex PCR method provides a rapid and efficient method for detecting various BB resistance genes, which will assist in pyramiding genes to improve durability of BB resistance in Taiwanese elite rice cultivars.

Identification of resistance sources in wild species of rice against two recently evolved pathotypes ofXanthomonas oryzaepvoryzae

AbstractBacterial blight (BB) of rice caused byXanthomonas oryzaepv.oryzae(Xoo) is a major biotic constraint of rice production in all the major irrigated/lowland rice growing regions of Asia, including Punjab and its adjoining states in India. None of the individual BB resistantXa/xagenes is effective against Punjab pathotypes. In the present study, we have screened 1176 accessions, comprising 1007 accessions of A genome speciesOryza glaberrima, O. barthii, O. nivara, O. rufipogon, O. longistaminata, O. meridionalis, O. glumaepatulaand 169 accessions from ten other wild species having CC, FF, EE, BBCC and CCDD genomes against two most recently evolvedXoopathotypes viz. PbXo-10 and PbXo-8 in Punjab state of India, for two constitutive years 2014 and 2015. Based on 2 years of data, four accessions ofO. glaberrima(IRGC102206, IRGC1022445, IRGC102512 and IRGC102520) and two of theO. longistaminataaccessions (IRGC92624 and IRGC101754) were identified with immune reaction against PbXo-8. For PbXo-10,O. longistaminatashowed large number of accessions with complete to partial resistance followed byO. rufipogon(8),O. nivara(2),O. punctata(2) andO. officinalis(1). Two of theO. longistaminataaccessions IRGC92624 and IRGC92644 from Mali were found to have resistance against both theXoopathotypes indicating presence of BB resistance gene other thanXa21. These can be transferred to elite cultivars ofO. sativafor better management of BB.

A Brief Comparative Effectiveness Research (CER) about Conventional and Homeopathic Treatment of Type 2 Diabetic Patients

A Brief Comparative Effectiveness Research (CER) about Conventional and Homeopathic Treatment of Type 2 Diabetic Patients Bacterial leaf blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is one of the most severe diseases effecting Basmati rice production in India. CSR-30 is widely grown in Haryana and is extremely popular amongst rice farmers and consumers because of its salt tolerance, aroma, high yield, medium slender grains and excellent cooking and eating qualities. CSR-30 lacks tolerance to BB. The present investigation was therefore planned to introgress BB resistance genes (xa5, xa13 & Xa21) from IRBB-60 to CSR-30. The pyramided BC3 F1 genotypes were evaluated for BB incidence under artificial field inoculation. Scoring of inoculated plant was done 14 days after inoculation. The triple and double resistance genes pyramided genotypes provided enhanced resistance as expressed by smaller mean lesion length in comparison to genotypes with individual genes...

Improvement of bacterial blight and brown planthopper resistance in an elite restorer line Huazhan of Oryza

Development of resistant varieties is one of the most economical and effective strategies to prevent rice from bacterial blight disease (BB) and brown planthopper (BPH), the two main pests jeopardizing rice production. The hybrid rice Tianyouhuazhan (TianfengA/Huazhan) has been widely used in rice production in China, but this hybrid is susceptible to BB and BPH. In this study, one BB resistance gene (Xa23) and two BPH resistance genes (Bph14 and Bph15) were simultaneously introgressed into the restorer line Huazhan to improve the BB and BPH resistance of Tianyouhuazhan using marker-assisted backcrossing (MABC) strategy coupled with phenotypic selection. The results of identification of BB and BPH resistance revealed that almost all of the improved restorer lines and their derived hybrids showed high resistance (HR) or resistance (R) to BB and BPH. Almost all of the agronomic traits of improved restorer lines and their hybrids were similar to those of their respective original versions in field trial, except the 1000-grain weight of improved hybrids showed an extremely significant increase than that of Tianyouhuazhan. Plot yields test in 2013 and 2014 suggested that two improved hybrid combinations named as TianfengA/R43-06 and TianfengA/R43-07 had higher grain yields per plot than Tianyouhuazhan and other improved hybrids. These results clearly indicate that pyramiding of Xa23, Bph14 and Bph15 genes is a useful approach for improving BB and BPH resistance, two hybrid combinations TianfengA/R43-06 and TianfengA/R43-07 could replace Tianyouhuazhan for extension in BB and/or BPH epidemic area in China.

Introgression of bacterial blight (BB) resistance genes Xa7 and Xa21 into popular restorer line and their hybrids by molecular marker-assisted backcross (MABC) selection scheme

Yihui1577 is an elite restorer line widely used in hybrid rice production in China, however, both the restorer and their derived hybrids are susceptible to bacterial blight (BB) caused by Xathomonas oryzae pv. oryzae ( Xoo ). In order to overcome this problem, we had introgressed two resistant genes Xa7 and Xa21 into Yihui1577 by marker-assisted backcross (MABC) with foreground selection scheme to speed up the process. Six breeding lines with different BB resistance genes: HH1202 ( Xa7 ), HH1203 ( Xa7 ), HH1204 ( Xa21 ), HH1205 ( Xa21 ), HH1206 ( Xa7+Xa21 ) and HH1207 ( Xa7+Xa21 ) were selected and crossed with four CMS and one TGMS lines. Seven most virulent and prevalent Xoo strains (PXO61, PXO99, ZHE173, GD1358, FuJ, YN24 and HeN11) from the Philippines and different provinces of China were inoculated for evaluating the BB-resistance of the selected lines and their derived hybrids. The results reveal that the two lines and their derived hybrids with single resistance gene Xa7 were resistant against six of the seven Xoo strains, except for PXO99. The lines with single resistance gene Xa21 were only susceptible to the Xoo strain FuJ, but some of their derived hybrids were susceptible to the Xoo strains FuJ and GD1358. Interestingly, the pyramiding lines carrying the two resistance genes Xa7 and Xa21 and also their derived hybrids were resistant against all the seven Xoo strains. The data of agronomic and grain quality characteristics demonstrated that the selected lines were similar to that of the recurrent parent Yihui1577. Corrective measures taken by way of introgression of BB-resistance genes: Xa7 and Xa21 into the popular restorer line, Yihui1577 through MABC approach for enhancing the BB-resistance level was effective and timely. Keywords: Bacterial blight, resistance gene, Xa7 and Xa21 , MABC, inoculation and reaction, agronomic traits, grain quality

Genotypic and Pathotypic Diversity of Xanthomonas oryzae pv. oryzae, the Cause of Bacterial Blight of Rice in Punjab State of India

AbstractBacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major biotic constraint in the intensive irrigated rice belt comprising Punjab and adjoining north‐western states of India. Development and deployment of host resistance is the only effective means of BB management. The pathogen is highly variable, and the current Xoo population from the state could be classified into seven distinct pathotypes (PbXo‐1 to PbXo‐7) by inducing differential reactions on a set of near‐isoganic lines in the background of IR24 and some international, national and regional cultivars. Known BB resistance genes (Xa1, Xa3, Xa10, Xa11, Xa14, Xa18) were ineffective, whereas xa13, Xa4 + xa13, xa5 + xa13, xa13 + Xa21, Xa4 + xa5 + xa13, Xa4 + xa5 + Xa21, Xa4 + xa13 + Xa21, xa5 + xa13 + Xa21 and Xa4 + xa5 + xa13 + Xa21 and rice line IET8585/Ajaya were effective against all the seven pathotypes analysed. Xa21 was effective against all the pathotypes except PbXo‐3 and PbXo‐4. PbXo‐7, the most dominant pathotype, was found to be virulent and induced susceptible/moderately susceptible reaction on 22 of the 40 test genotypes followed by PbXo‐1, PbXo‐5 and PbXo‐6; PbXo‐2 was the least virulent pathotype. Molecular profiling of these pathotypes using random amplified polymorphic DNA (RAPD) and IS1112‐based polymerase chain reaction (PCR) generated specific and reproducible fingerprint patterns. Primers S1117, S112, S109, S1106 and JEL are more informative in distinguishing pathotypes. At a similarity of 0.50, pathotypes PbXo‐1 and PbXo‐2 were grouped together, whereas other five pathotypes showed separate lineage. The data using RAPD‐PCR and IS1112‐based PCR approaches revealed their potential in generating unique DNA fragments specific for different pathotypes that may lead to the rapid assessment of genetic variation in the pathogen population. Pyramiding of two/more partially effective known Xa genes and/or search for new disease resistance genes effective against the wider Xoo population appears to be the most appropriate approach for BB management in the near future.

Detection of bacterial blight resistant gene xa5 using linked marker approaches

Rice is the primary source of food for 57% of the world’s population. Genetic resistance is important to control many kinds of pathogenic diseases. Bacterial blight caused by Xanthomonas oryzae pv oryzae (Xoo) decreases rice production by 20 – 30% and up to about 90% loss of grain weight. xa5 is an important recessive bacterial blight resistant gene, which is effective and important in Asian rice breeding program. It was also used in combination by incorporation with various recessive and dominant BB resistant genes. The purpose of our study was to identify the bacterial blight resistant genes xa5 in Pakistani rice germplasm including Basmati varieties. The seeds were collected from different research institute and then sowed in the National Institute for Biotechnology and Genetic Engineering (NIBGE) in pots. DNAs were extracted and surveyed for polymorphism by using DNA marker linked to xa5 gene. During this polymorphic survey, out of 88 germplasm lines, 45 lines showed the presence of xa5 gene like MB 2, MB 33 MB 57 and MB 66. All these lines showed the amplification of 240 bp corresponding to resistant source IRBB-5 line, while 43 germplasm lines showed no such fragment and elucidated same bands as susceptible source IR-24 having fragment of about 230 base pair. The 10 Pakistani Basmati varieties were also surveyed for xa5 gene. It was observed that none of our cultivated basmati varieties exhibited the presence of xa5 gene. The purpose of screening of xa5 gene in Pakistani rice germplasm is to utilize the local source of xa5 gene for elite molecular breeding program being carried out at NIBGE in future including pyramiding of different disease resistant gene in Basmati varieties.

Identification and Molecular Mapping of Xa32(t), a Novel Resistance Gene for Bacterial Blight ( Xanthomonas oryzae pv. oryzae) in Rice

The rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae ( Xoo), is the most devastating bacterial disease of rice worldwide. Because of the rapid changes in the pathogenicity of the pathogen ( Xoo), novel BB-resistance genes are always needed for rice (Oryza sativa L.) breeding. In this article, a novel BB-resistance gene was identified from a wild rice ( Oryzae ustraliensis) introgression line, C4064, and its chromosomal location was reported. On the basis of the resistance spectrum analysis, C4064 presented resistance to Xoo strains P1 (PXO61), P4 (PXO71), P5 (PXO112), P6 (PXO99), P7 (PXO145), P8 (PXO280), P9 (PXO339), and KX085, but susceptible to P2 (PXO86) and P3 (PXO79). Therefore, the resistance gene harbored in C4064 was a novel BB-resistance gene and tentatively designated as Xa32(t). Furthermore, the chromosomal position of this gene was located using bulked segregant analysis with the help of simple sequence repeat and expressed sequence tag markers. Of the 299 markers tested, 6 markers, i.e., RM27256, RM27274, RM2064, ZCK24, RM6293, and RM5926 on the long arm of chromosome 11, were linked with Xa32(t) with genetic distances of 2.1, 1.0, 1.0, 0.5, 1.5, and 2.6 cM between the resistance gene and the markers, respectively. The resistance gene was located between markers RM6293 and RM5926 at the end side of long arm and the other 4 markers at the centromere side. Finally, Xa32(t) was mapped within a length of 2.0 cM on the long arm of rice chromosome 11.

A novel bacterial blight resistance gene fromOryza nivaramapped to 38 kb region on chromosome 4L and transferred toOryza sativaL.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv oryzae (Xoo) is one of the major constraints to productivity in South-East Asia. The strategy of using major genes, singly or in combination, continues to be the most effective approach for BB management. Currently, more than two dozen genes have been designated but not all the known genes are effective against all the prevalent pathotypes. The challenge, therefore, is to continue to expand the gene pool of effective and potentially durable resistance genes. Wild species constitute an important reservoir of the resistance genes including BB. An accession of Oryza nivara (IRGC 81825) was found to be resistant to all the seven Xoo pathotypes prevalent in northern states of India. Inheritance and mapping of resistance in O. nivara was studied by using F2, BC2F2, BC3F1 and BC3F2 progenies of the cross involving Oryza sativa cv PR114 and the O. nivara acc. 81825 using the most virulent Xoo pathotype. Genetic analysis of the segregating progenies revealed that the BB resistance in O. nivara was conditioned by a single dominant gene. Bulked segregant analysis (BSA) of F2 population using 191 polymorphic SSR markers identified a approximately 35 centiMorgans (cM) chromosomal region on 4L, bracketed by RM317 and RM562, to be associated with BB resistance. Screening of BC3F1 and BC2F2 progenies and their genotyping with more than 30 polymorphic SSR markers in the region, covering Bacterial artificial chromosome (BAC) clone OSJNBb0085C12, led to mapping of the resistance gene between the STS markers based on annotated genes LOC_Os04g53060 and LOC_Os04g53120, which is approximately 38.4 kb. Since none of the known Xa genes, which are mapped on chromosome 4L, are effective against the Xoo pathotypes tested, the BB resistance gene identified and transferred from O. nivara is novel and is tentatively designated as Xa30(t). Homozygous resistant BC3F3 progenies with smallest introgression region have been identified.

Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation.

The Xa1 gene in rice confers resistance to Japanese race 1 of Xanthomonas oryzae pv. oryzae, the causal pathogen of bacterial blight (BB). We isolated the Xa1 gene by a map-based cloning strategy. The deduced amino acid sequence of the Xa1 gene product contains nucleotide binding sites (NBS) and a new type of leucine-rich repeats (LRR); thus, Xa1 is a member of the NBS-LRR class of plant disease-resistance genes, but quite different from Xa21, another BB-resistance gene isolated from rice. Interestingly, Xa1 gene expression was induced on inoculation with a bacterial pathogen and wound, unlike other isolated resistance genes in plants, which show constitutive expression. The induced expression may be involved in enhancement of resistance against the pathogen.