Genes Xa21 Research Articles

Genome Resource of a Hypervirulent Strain LN4 of Xanthomonas oryzae pv. oryzae Causing Bacterial Blight of Rice.

Xanthomonas oryzae pv. oryzae is the causative agent of bacterial blight of rice and causes severe harvest loss and challenges to a stable food supply globally. In this study, a hypervirulent strain, LN4, compatible in rice varieties carrying Xa3, Xa4, xa13, and xa25 resistance genes, was used to generate DNA for nanopore sequencing. After assembly, the genome comprises a single chromosome of 5,012,583 bp, consisting of a total of 6,700 predicted coding sequences. Seventeen transcription activator-like effectors (TALEs) were encoded in the genome, of which two (Tal7 and Tal6c) were major TALEs. The approach and genome data provide information for the discovery of new virulence effectors and understanding of the virulence mechanism of TALEs in rice.

Cloning of the Rice Xo1 Resistance Gene and Interaction of the Xo1 Protein with the Defense-Suppressing Xanthomonas Effector Tal2h.

The Xo1 locus in the heirloom rice variety Carolina Gold Select confers resistance to bacterial leaf streak and bacterial blight, caused by Xanthomonas oryzae pv. oryzicola and X. oryzae pv. oryzae, respectively. Resistance is triggered by pathogen-delivered transcription activator-like effectors (TALEs) independent of their ability to activate transcription and is suppressed by truncated variants called truncTALEs, common among Asian strains. By transformation of the susceptible variety Nipponbare, we show that one of 14 nucleotide-binding, leucine-rich repeat (NLR) protein genes at the locus, with a zinc finger BED domain, is the Xo1 gene. Analyses of published transcriptomes revealed that the Xo1-mediated response is more similar to those mediated by two other NLR resistance genes than it is to the response associated with TALE-specific transcriptional activation of the executor resistance gene Xa23 and that a truncTALE dampens or abolishes activation of defense-associated genes by Xo1. In Nicotiana benthamiana leaves, fluorescently tagged Xo1 protein, like TALEs and truncTALEs, localized to the nucleus. And endogenous Xo1 specifically coimmunoprecipitated from rice leaves with a pathogen-delivered, epitope-tagged truncTALE. These observations suggest that suppression of Xo1-function by truncTALEs occurs through direct or indirect physical interaction. They further suggest that effector coimmunoprecipitation may be effective for identifying or characterizing other resistance genes.

Distribution of Bacterial Blight Resistance Genes in the Main Cultivars and Application of Xa23 in Rice Breeding.

Bacterial blight (BB) is an important constraint on achieving a high and stable rice grain yield. An increasing number of BB resistance (R) genes have been identified and cloned to increase the available options for rice disease resistance breeding. However, it is necessary to understand the distribution of R genes in rice varieties for rational distribution and breeding. Here, we genotyped five R genes, i.e. Xa4, Xa7, Xa21, Xa23, and Xa27, in seventy main cultivars from Guangdong Province, South China using the corresponding specific markers. Our results showed that 61 varieties carried Xa4, only three varieties carried Xa27, and Xa7, Xa21, or Xa23 was not detected in all tested varieties. Notably, only 33 varieties exhibited resistance to pathotype IV Xoo strains. These results indicate that Xa4 is no longer suitable for widespread use in rice breeding, although Xa4 is widely present in tested varieties. Remarkably, the strongly virulent BB strains of pathotype IX evolved quickly in southern China, and Xa23 was found to effectively confer resistance against the pathotype IX strains. Subsequently, we successfully bred two novel inbred rice varieties as also being restorer lines and two photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines using the broad-spectrum resistance gene Xa23 through marker-assisted selection (MAS) combined with phenotypic selection. All of the developed lines and derived hybrids exhibited enhanced resistance to BB with excellent yield performance. Our research may potentially facilitate both of the inbred and hybrid rice disease resistance breeding.

Assessment of Bacterial Leaf Blight Disease of Indonesian Rice Germplasms Using SSR Markers

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious disease in rice plants worldwide. Yield losses caused by Xoo can be as high as 50% in some parts of Asia. Xa7 gene can potentially confer a broad resistance to BLB. Evaluation of disease resistance characteristics in early breeding generations of rice is important to develop varieties with better resistance. This study reports the evaluation of 167 Indonesian rice germplasms against three BLB isolates/pathotypes in a green house setting and the genotyping of 56 Indonesian rice germplasm using 12 SSR markers linked to Xa7 BLB resistance gene. The majority of the indigenous rice germplasms was found to be susceptible to three BLB isolates/pathotypes tested. Sate Liko from Bantul, Yogyakarta, Horeg from Cirebon, West Java and Sijem from Malang, East Java revealed consistent resistance to three isolates/pathotypes tested based on BLB evaluation in a greenhouse, UPGMA analysis, and genotyping. Pathotype XII displayed more virulence to Indonesian rice varieties tested compared to pathotypes VI and V. The association analysis using the General linear model identified six markers associated with BLB resistance and two markers were highly associated (RM20589 and RM20590). This information will be useful for future studies of BLB resistance in rice plants.

Marker-assisted selection for transfer of submergence tolerance, bacterial blight resistance and yield enhancement in the rice backcross derivatives

Achieving the demand and supply of rice for the increasing global population will be a challenging task beyond 2040. Therefore, the yield potential of popular rice varieties needs to be increased. The production from lowland rice can be enhanced by managing the major biotic and abiotic stresses faced in the ecology. In this work, we have developed the pipelines for gene stacking of submergence tolerance, bacterial blight resistance and yield component QTLs in the popular rice variety ‘Swarna’ by marker-assisted backcross breeding approach. Genotyping results of 796 BC1F1 backcross derived lines showed the presence of GW2, OsSPL14, SCM2 yield component QTLs, Sub1A for submergence tolerance and bacterial blight resistance genes xa5 and Xa21 in the progenies. The four stacked QTLs and two resistance genes were observed in six backcrosses derived progenies only. These progenies will be used in the next generation for further selection and evaluation for enhancing submergence tolerance, yield potential and bacterial blight resistance in Swarna rice variety background.

Xa1 Allelic R Genes Activate Rice Blight Resistance Suppressed by Interfering TAL Effectors

Xanthomonas oryzae pathovar oryzae (Xoo) uses transcription activator-like effectors (TALEs) to cause bacterial blight (BB) in rice. In turn, rice has evolved several mechanisms to resist BB by targeting TALEs. One mechanism involves the nucleotide-binding leucine-rich repeat (NLR) resistance gene Xa1 and TALEs. Reciprocally, Xoo has evolved TALE variants, C-terminally truncated versions (interfering TALEs or iTALEs), to overcome Xa1 resistance. However, it remains unknown to what extent the two co-adaptive mechanisms mediate Xoo–rice interactions. In this study, we cloned and characterized five additional Xa1 allelic R genes, Xa2, Xa31(t), Xa14, CGS-Xo111, and Xa45(t) from a collection of rice accessions. Sequence analysis revealed that Xa2 and Xa31(t) from different rice cultivars are identical. These genes and their predicted proteins were found to be highly conserved, forming a group of Xa1 alleles. The XA1 alleles could be distinguished by the number of C-terminal tandem repeats consisting of 93 amino acid residues and ranged from four in XA14 to seven in XA45(t). Xa1 allelic genes were identified in the 3000 rice genomes surveyed. On the other hand, iTALEs could suppress the resistance mediated by Xa1 allelic R genes, and iTALE genes were prevalent (∼95%) in Asian, but not in African Xoo strains. Our findings demonstrate the prominence of a defense mechanism in which rice depends on Xa1 alleles and a counteracting mechanism in which Xoo relies on iTALEs for BB.

A novel intragenic marker targeting the ectodomain of bacterial blight-resistance gene Xa21 for marker-assisted selection in rice

ABSTRACT The rice (Oryza sativa L.) Xa21 gene is known to confer resistance against Xanthomonas oryzae pv. oryzae, the causal organism of bacterial blight (BB) through its involvement in pathogen recognition and immunity responses. The closely linked sequence-tagged site marker pTA248 is frequently used for marker-assisted selection (MAS) of Xa21. However, lower precision and linkage drag of linked-markers hinders its reliability and effectiveness in MAS compared to flanking/intergenic markers. In the current study, a diagnostic intragenic marker was developed for MAS of Xa21 in rice. The new marker ABUOP0001 targets a 19-bp insertion/deletion on the ectodomain of Xa21 and amplifies a 200-bp amplicon from rice line IRBB 62 (known to carry the “resistance allele”), and a 181-bp amplicon from IRBB 7 (known to carry the “susceptible allele”). The ABUOP0001 marker assay identified the resistance allele in 15 rice lines/accessions. In a field study, 14 of these lines/accessions had highly resistant BB responses, and one had an intermediate response. Further, Xa21 resistance allele was identified in 1,675 rice accessions through an in-silico genomic sequence analysis. The marker ABUOP0001 performs better than the previously used linked-marker pTA248 (anchored to a gene 225 kbp upstream of Xa21) as ABUOP0001 is an intragenic marker targeting the functionally important ectodomain of Xa21. Further, ABUOP0001 is compatible for high-throughput screening with high-resolution melting and can be multiplexed effectively with an intragenic marker of BB resistance gene Xa4. Therefore, ABUOP0001 can be recommended as a high-throughput diagnostic intragenic marker for MAS of Xa21 in rice.

OsNPR3.3-dependent salicylic acid signaling is involved in recessive gene xa5-mediated immunity to rice bacterial blight

Salicylic acid (SA) is a key natural component that mediates local and systemic resistance to pathogens in many dicotyledonous species. However, its function is controversial in disease resistance in rice plants. Here, we show that the SA signaling is involved in both pathogen-associated-molecular-patterns triggered immunity (PTI) and effector triggered immunity (ETI) to Xanthomonas oryzae pv. Oryzae (Xoo) mediated by the recessive gene xa5, in which OsNPR3.3 plays an important role through interacting with TGAL11. Rice plants containing homozygous xa5 gene respond positively to exogenous SA, and their endogenous SA levels are also especially induced upon infection by the Xoo strain, PXO86. Depletion of endogenous SA can significantly attenuate plant resistance to PXO86, even to 86∆HrpXG (mutant PXO86 with a damaged type III secretion system). These results indicated that SA plays an important role in disease resistance in rice plants, which can be clouded by high levels of endogenous SA and the use of particular rice varieties.

Gene expression studies in bacterial leaf blight resistant and susceptible rice (Oryza sativa) lines

Bacterial leaf blight of rice is a major constraint in tumbling productivity of the crop which shows the precarious nature of the disease. Host resistance is an effective strategy for the management of bacterial leaf blight disease over the cultural, chemical and biological management methods. Glass house and field studies were performed during 2017–19 at Paddy Breeding Station, TNAU, Coimbatore and also the molecular laboratory facility at Department of Plant Pathology was utilized. The objective of the study was to perform gene expression studies resistance genes (Xa21, xa5, xa13 genes) and defense genes (LOX and PAL) in bacterial leaf blight resistance (IRBB 60) and susceptible rice line (TN1) after application of Xanthomonas oryzae. pv. oryzae and/or riboflavin. Genotyping of IRBB 60 which showed lowest lesion length validated the presence of Xa21, xa5 and xa13 resistance genes using corresponding gene specific primers. Application of riboflavin (0.5mM) along with the Xanthomonas oryzae. pv. oryzae suspension resulted in the highest expression level of these R genes and defense genes except xa13 gene which showed its highest expression level with the inoculation of Xoo alone. Expression of Xa13 gene was meagre with the treatment of riboflavin where rest of the gene expression was noticeably enhanced when compared to the control. In brief, study performed showed that application of abiotic agent (Riboflavin) enhanced the gene expression of both the resistance and defense gene in rice line when compared to the susceptible variety.

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.

TALEN-based editing of TFIIAy5 changes rice response to Xanthomonas oryzae pv. Oryzae

The xa5 gene encodes a basal transcription factor (TFIIAγ) protein with wide spectrum resistance to bacterial blight caused by Xanthomonas oryzae pv. Oryzae (Xoo) in rice. It was only found in a few rice ecotypes, and the recessive characteristics limited its application in breeding. Here, we employed a TALEN-based technique to edit its dominant allelic TFIIAγ5 and obtained many mutant TFIIAγ5 genes. Most of them reduced rice susceptibility to varying degrees when the plants were challenged with the Xoo. In particular, the knocked-out TFIIAγ5 can reduce the rice susceptibility significantly, although it cannot reach the xa5-mediated resistance level, indicating TFIIAγ5 is a major component involved in disease susceptibility. In addition, the mutant encoding the protein with deletion of the 32nd amino acid or amino acid insertion between 32nd and 33rd site confers rice with the similar resistance to that of the knocked-out TFIIAγ5. Thus, the amino acids around 32nd site are also the important action sites of TFIIAγ5 besides the 39th amino acid previously reported. Moreover, the integration of xa5 into TFIIAγ5-knockout plants conferred them with a similar resistance as IRBB5, the rice variety containing the homozygous xa5 gene. Thus, TFIIAγ5 was not simply regarded as a resistant or a susceptible locus, as the substitution of amino acids might shift its functions.

Pyramiding insect and disease resistance in an elite indica rice cultivar asd16

Pyramiding transgenes of interest is one of the strategies to engineer multiple stress resistance in crop plants. Transgenic plants which stably express different genes can be hybridized to bring these genes together in one plant. Transgenic rice (Oryza sativa L. cv. ASD 16) plants harbouring genes Xa21 (conferring bacterial blight resistance), tlp (conferring resistance to sheath blight), or gna (conferring resistance to brown planthopper) were used in hybridization experiments. Sexual hybridization was carried out in two different gene combinations: Xa21 × gna and tlp × gna. Molecular analyses were carried out to confirm the presence of transgenes. In F1 generation, lines harbouring either gene in each of the cross-combination were selected and forwarded to F2 generation. The presence of genes in F2 generation was confirmed by PCR, Southern blot hybridization, and Western blotting. The F2 progeneis harbouring Xa21 and gna exhibited resistance against bacterial blight and moderate resistance against brown planthopper. Similarly, the F2 lines of tlp and gna combination provided resistance against sheath blight and moderate resistance against brown planthopper. The level of resistance observed in pyramided lines for insect or pathogens was comparable to the resistance observed in their parental lines. Our study shows that pyramiding genes by hybridization between transgenic plants could be one of the strategies to develop cultivars with multiple biotic stress resistances.

Introgression of bacterial blight resistance gene Xa7 into popular Indonesian rice varieties through backcross and molecular breeding

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of major diseases in rice production. The BB resistance gene Xa7 is one of effective genes against Xoo strains in Indonesia. This study aimed to introgress BB resistance gene Xa7 into submergence tolerant rice variety Inpara 5 (IR64 Sub1) and brown plant hopper (BPH) resistant rice variety Inpari 13. Stable BB resistant rice lines have been successfully developed after three backcrossing and four generations of fixation (BC3F4). Screening for BB resistance were conducted in generative stage using Xoo strains IV and VIII. The reaction pattern of the backcross lines against these two Xoo strains were similar to the BB resistant parent Conde. The introgression of the Xa7 gene in Inpara 5 and Inpari 13 genome have been confirmed by using SSR markers RM20589 and RM20590; and Xa7 gene specific marker Xa7-LD34. Agronomic characters and grain quality properties of the backcross lines were comparable to the recurrent parents. Other desirable traits from recurrent parents including submergence tolerance and BPH resistance retained in the selected backcross lines. The BB resistance rice lines with popular rice varieties genetic background developed through this study have potential to be released for farmers adoption.

Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight

Rice bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) implies substantial yield loss to rice. In times of climate change, increasing temperatures are observed and further acceleration is expected worldwide. Increasing temperature often turns into inhibition of host plant defense to pathogens. Recently, a reduced resistance in rice IRBB4 carrying Xa4, but an increase in resistance in IRBB7 carrying Xa7 resistance by increasing temperature has been reported. Influence of high temperature on both R genes (Xa4+Xa7) combined in IRBB67 was analyzed under growth chamber conditions and transcriptomic analysis performed. The pyramided line IRBB67 showed no differences in lesion length between both temperature regimes, demonstrating that non-effectiveness of Xa4 at high temperature did not affect IRBB67 resistance. Moreover, Xa4 complements Xa7 resistance with no Xoo spread in planta beyond the symptomatic area under both temperature regimes in IRBB67. Time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartments and point at a role of the cell wall involved in Xoo resistance and heat stress tolerance in both susceptible (IR24) and the resistant (IRBB67) NILs. Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature which may have enhanced its resistance. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plants cope with combined biotic and abiotic stresses.

Uji Daya Hasil Lanjutan Dua Puluh Tujuh Galur Padi Code-qTSN4 dan Code-qDTH8

ABSTRACT The locus that regulates total spikelet number (qTSN4) and days to heading (qDTH8) is expected to increase rice yields. Both of these loci are used to increase the yield of Code varieties through the marker-assisted backcrossing method. This study aimed to evaluate the yield of Code-qTSN4 and Code-qDTH8 lines at two location and to analyze existence of target gene locus associated with qTSN4, qDTH8, and Xa7. This research was conducted in March to July 2017. The study was divided into two parts: (i) field analyses at the Kuningan field station (uplandirrigated) and Sukamandi field station (lowland-irrigated), and (ii) molecular tests at the Molecular Biology Laboratory, ICABIOGRAD, Bogor. The material used were 27 crossing lines of Code-qTSN4 and Code-qDTH8 (BC1, BC2, BC3), 5 comparative varieties, and molecular markers that were linked to the loci of genes of qTSN4, qDTH8, and Xa7. The results showed different altitude positions affected the agronomic performance of the lines. At Kuningan location, Code-qTSN4 and Code-qDTH8 lines showed number of grain total (empty and filled) per panicle was 110.84−165.98 grains, while Code 153.51 grains. While at Sukamandi, the number of grains per panicle obtained by the lines was higher, that is 157.27-227.9 grains and 186.56 grains for Code. The highest number of total grains was achieved by line B6-2 (Code-qTSN4) (8.12%) for Kuningan, while at Sukamandi the highest was in line B22-1 (Code-qTSN4) (22.16%). The effect of the qTSN4 gene locus has been shown to increase the number of grains per panicle. The heading date of Code-qDTH8 lines at two locations was 4−6 days faster than Code. The yield potencial of lines at Kuningan and Sukamandi were 4.43−6.88 t/ha and 3.71−5.89 t / ha, while for Code 6.24 t/ha and 4.83 t/ha, respectively. The highest potential yield of Code-qTSN4 lines was B6-2 with an increase of 20.5%, while Code-qDTH8 lines was obtained on E13-1 with an increase 10.26%. Based on molecular analysis, all test lines already have the qTSN4 or qDTH8 gene locus, and all test lines also have the Xa7 gene locus. Keywords: Rice, Code, qTSN4, qDTH8, Xa7, yield trial

Uji Daya Hasil Lanjutan Dua Puluh Tujuh Galur Padi Code-qTSN4 dan Code-qDTH8

The locus thatregulates totalspikelet number (qTSN4) and days to heading (qDTH8) is expected to increase rice yields.Both of these loci are used to increase the yield of Code varieties through the marker-assisted backcrossing method. This study aimed to evaluate the yield of Code-qTSN4 and Code-qDTH8 lines at two location and to analyze existence of target gene locus associated with qTSN4, qDTH8, and Xa7. This research was conducted in March to July 2017. The study was divided into two parts: (i) field analyses at the Kuningan field station (uplandirrigated) and Sukamandi field station (lowland-irrigated), and (ii) molecular tests at the Molecular Biology Laboratory, ICABIOGRAD, Bogor. The material used were 27 crossing lines of Code-qTSN4 and Code-qDTH8 (BC1, BC2, BC3), 5 comparative varieties, and molecular markers that were linked to the loci of genes of qTSN4, qDTH8, and Xa7. The results showed different altitude positions affected the agronomic performance of the lines. At Kuningan location, Code-qTSN4 and Code-qDTH8 lines showed number of grain total (empty and filled) per panicle was 110.84−165.98 grains, while Code 153.51 grains. While at Sukamandi, the number of grains per panicle obtained by the lines was higher, that is 157.27-227.9 grains and 186.56 grains for Code. The highest number of total grains was achieved by line B6-2 (Code-qTSN4) (8.12%) for Kuningan, while at Sukamandi the highest was in line B22-1 (Code-qTSN4) (22.16%). The effect of the qTSN4 gene locus has been shown to increase the number of grains per panicle. The heading date of Code-qDTH8 lines at two locations was 4−6 days faster than Code. The yield potencial of lines at Kuningan and Sukamandi were 4.43−6.88 t/ha and 3.71−5.89 t / ha, while for Code 6.24 t/ha and 4.83 t/ha, respectively. The highest potential yield of Code-qTSN4 lines was B6-2 with an increase of 20.5%, while Code-qDTH8 lines was obtained on E13-1 with an increase 10.26%. Based on molecular analysis, all test lines already have the qTSN4 or qDTH8 gene locus, and all test lines also have the Xa7 gene locus.

Transcriptomic data-driven discovery of global regulatory features of rice seeds developing under heat stress

Plants respond to abiotic stressors through a suite of strategies including differential regulation of stress-responsive genes. Hence, characterizing the influences of the relevant global regulators or on stress-related transcription factors is critical to understand plant stress response. Rice seed development is highly sensitive to elevated temperatures. To elucidate the extent and directional hierarchy of gene regulation in rice seeds under heat stress, we developed and implemented a robust multi-level optimization-based algorithm called Minimal Regulatory Network identifier (MiReN). MiReN could predict the minimal regulatory relationship between a gene and its potential regulators from our temporal transcriptomic dataset. MiReN predictions for global regulators including stress-responsive gene Slender Rice 1 (SLR1) and disease resistance gene XA21 were validated with published literature. It also predicted novel regulatory influences of other major regulators such as Kinesin-like proteins KIN12C and STD1, and WD repeat-containing protein WD40. Out of the 228 stress-responsive transcription factors identified, we predicted de novo regulatory influences on three major groups (MADS-box M-type, MYB, and bZIP) and investigated their physiological impacts during stress. Overall, MiReN results can facilitate new experimental studies to enhance our understanding of global regulatory mechanisms triggered during heat stress, which can potentially accelerate the development of stress-tolerant cultivars.

Marker-Assisted Introgression of Multiple Resistance Genes Confers Broad Spectrum Resistance against Bacterial Leaf Blight and Blast Diseases in PUTRA-1 Rice Variety

Bacterial leaf blight caused by Xanthomonas oryzae pv oryzae (Xoo) and blast caused by Magnaporthe oryzae are major diseases responsible for significant yield loss in rice production across all rice growing regions. Host plant resistance has been advocated as a sustainable means of guarding against the diseases. This experiment was conducted with the aim to introgress multiple resistance genes against bacterial leaf blight and blast diseases through marker-assisted backcross breeding. Two dominant (Xa4 and Xa21) and two recessive (xa5 and xa13) Xoo resistance genes were introgressed into a high yielding Malaysian rice variety Putra-1 with genetic background of three blast resistance (Piz, Pi2 and Pi9) genes. Eight polymorphic tightly linked functional and SSR markers were used for foreground selection of target genes. Seventy nine polymorphic SSR markers were used in background selection. The plants were challenged at initial stage of breeding and challenged again at BC2F2 with the most virulent Malaysian pathotypes of Xoo (P7.7) and Magnaporthe oryzae (P7.2) to test their resistance. Results obtained from foreground marker segregation analysis at BC1F1 and BC2F1 showed that the marker polymorphism both fitted into the Mendel’s single gene segregation ratio of 1:1 for both Xoo and blast resistance. At BC2F2, results indicated that foreground marker polymorphism fitted into the expected Mendelian ratio of 1:2:1 for blast resistance only. Marker-assisted background selection revealed high percentage of recurrent parent genome recovery (95.9%). It was concluded that the inheritance of blast resistance in the introgressed lines was mainly due to single gene action while the inheritance of Xoo resistance was substantially due to single nuclear gene action. The incorporation of four bacterial leaf blight and three blast resistance genes (Xa4 + xa5 + xa13 + Xa21; Pi9 + Pi2 + Piz) in the newly developed lines would provide for broad spectrum and durable resistance against the two major diseases studied.

Characterization of New Races of Xanthomonas oryzae pv. oryzae in Mali Informs Resistance Gene Deployment.

Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae represents a severe threat to rice cultivation in Mali. Characterizing the pathotypic diversity of bacterial populations is key to the management of pathogen-resistant varieties. Forty-one X. oryzae pv. oryzae isolates were collected between 2010 and 2013 in the major rice growing regions in Mali. All isolates were virulent on the susceptible rice variety Azucena; evaluation of the isolates on 12 near isogenic rice lines, each carrying a single resistance gene, identified six new races (A4 to A9) and confirmed race A3 that was previously reported in Mali. Races A5 and A6, isolated in Office du Niger and Sélingué, were the most prevalent races in Mali. Race A9 was the most virulent, circumventing all of the resistance genes tested. Xa3 controlled six of seven races (i.e., 89% of the isolates tested). The expansion of race A9 represents a major risk to rice cultivation and highlights the urgent need to identify a local source of resistance. We selected 14 isolates of X. oryzae pv. oryzae representative of the most prevalent races to evaluate 29 rice varieties grown by farmers in Mali. Six isolates showed a high level of resistance to X. oryzae pv. oryzae and were then screened with a larger collection of isolates. Based on the interactions among the six varieties and the X. oryzae pv. oryzae isolates, we characterized eight different pathotypes (P1 to P8). Two rice varieties, SK20-28 and Gigante, effectively controlled all of the isolates tested. The low association observed among races and pathotypes of X. oryzae pv. oryzae suggests that the resistance observed in the local rice varieties does not simply rely on single known Xa genes. X. oryzae pv. oryzae is pathogenically and geographically diverse. Both the races of X. oryzae pv. oryzae characterized in this study and the identification of sources of resistance in local rice varieties provide useful information to inform the design of effective breeding programs for resistance to bacterial leaf blight in Mali.

Evaluation of resistance of rice genotypes (derived from the cross between HKR-127 and IRBB-60) against bacterial blight caused by Xanthomonas oryzae pv. oryzae

Rice crop is susceptible to various bacterial diseases and one such commonly known disease is Bacterial Blight (BB) caused by the pathogenic bacteria Xanthomonas oryzae pv. oryzae (Xoo). Rice variety HKR-127 is widely accepted by rice farmers, users and buyers in Haryana (India) owing to its high agricultural produce, medium lanky grains, and outstanding cooking characteristics, however, HKR-127 exhibits less endurance to BB. The aim of the study conducted at CCS Haryana Agricultural University was to investigate the genetic potential of BC3F2 and BC3F3 pyramided rice genotypes (cross HKR-127 x IRBB -60) having resistance genes (Xa21, xa13, and xa5). These genotypes were tested for virulence against BB under artificial conditions using Clip method of artificial inoculation. On average, five leaves per plant were inoculated and visually scored after 14 days. Disease reaction rating was done on a 0-9 scale of the standard evaluation system (SES) for rice. Rice genotypes with all the three genes exhibited relatively low mean lesion length compared to single or double combinations thus establishing higher resistance of threegene genotypes to BB. The lines obtained in our study can be used as genetic resources for BB resistance in breeding programs that will be paving the way for an environmentally-friendly means to achieve a better disease management. Moreover, the success will facilitate future efforts to transfer combinations of BB resistance genes into other preferred rice cultivars.