High-resolution genetic mapping of a novel bacterial blight resistance gene xa-45(t) identified from Oryza glaberrima and transferred to Oryza sativa

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

BACKGROUND

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of rice leading to huge yield losses in Southeast Asia. The recessive resistance gene xa-45(t) from Oryza glaberrima IRGC102600B, mapped on rice chromosome 8, spans 80 Kb with 9 candidate genes on Nipponbare reference genome IRGSP-1.0. The xa-45(t) gene provides durable resistance against all the ten Xanthomonas pathotypes of Northern India, thus aiding in the expansion of recessive bacterial blight resistance gene pool. Punjab Rice PR127, carrying xa-45(t), was released for wider use in breeding programs. This study aims to precisely locate the target gene among the 9 candidates conferring resistance to bacterial blight disease.

METHODS AND RESULTS

Sanger sequencing of all nine candidate genes revealed seven SNPs and an Indel between the susceptible parent Pusa 44 and the resistant introgression line IL274. The genotyping with polymorphic markers identified three recombinant breakpoints for LOC_Os08g42370, and LOC_Os08g42400, 15 recombinants for LOC_Os08g423420 and 26 for LOC_Os08g42440 out of 190 individuals. Relative expression analysis across six time intervals (0, 8, 24, 48, 72, and 96 h) after bacterial blight infection showed over expression of LOC_Os08g42410-specific transcripts in IL274 compared to Pusa 44, with a significant 4.46-fold increase observed at 72 h post-inoculation.

CONCLUSIONS

The Indel marker at the locus LOC_Os08g42410 was found co-segregating with the phenotype, suggesting its candidacy towards xa-45(t). The transcript abundance assay provides strong evidence for the involvement of LOC_Os08g42410 in the resistance conferred by the bacterial blight gene xa-45(t).

Action mechanism of the potential biocontrol agent Brevibacillus laterosporus SN19-1 against Xanthomonas oryzae pv. oryzae causing rice bacterial leaf blight

The causal agent of rice bacterial leaf blight (BLB) is Xanthomonas oryzae pv. oryzae (Xoo), which causes serious damage to rice, leading to yield reduction or even crop failure. Brevibacillus laterosporus SN19-1 is a biocontrol strain obtained by long-term screening in our laboratory, which has a good antagonistic effect on a variety of plant pathogenic bacteria. In this study, we investigated the efficacy and bacterial inhibition of B. laterosporus SN19-1 against BLB to lay the theoretical foundation and research technology for the development of SN19-1 as a biopesticide of BLB. It was found that SN19-1 has the ability to fix nitrogen, detoxify organic phosphorus, and produce cellulase, protease, and siderophores, as well as IAA. In a greenhouse pot experiment, the control efficiency of SN19-1 against BLB was as high as 90.92%. Further investigation of the inhibitory mechanism of SN19-1 on Xoo found that the biofilm formation ability of Xoo was inhibited and the pathogenicity was weakened after the action of SN19-1 sterile supernatant on Xoo. The activities of enzymes related to respiration and the energy metabolism of Xoo were significantly inhibited, while the level of intracellular reactive oxygen species was greatly increased. Scanning electron microscopy observations showed folds on the surface of Xoo. A significant increase in cell membrane permeability and outer membrane permeability and a decrease in cell membrane fluidity resulted in the extravasation of intracellular substances and cell death. The results of this study highlight the role of B. laterosporus SN19-1 against the pathogen of BLB and help elucidate the underlying molecular mechanisms.

Improvement of bacterial blight resistance of the high yielding, fine-grain, rice variety, Gangavati sona through marker-assisted backcross breeding

Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB.

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

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

D, Sk H, Solanki M, Gokulan CG, Das A, Miriyala A, Gonuguntala R, Elumalai P, M. B. V. N K, S. K. M, Kumboju C, Arra Y, G. S. L, Chirravuri NN, Patel HK, Ghazi IA, Kim SR, Jena KK, Hanumanth SR, Oliva R, Mangrauthia SK, Sundaram RM. Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance

Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t.

Complete genome resource unravels the close relation of an Indian Xanthomonas oryzae pv. oryzae strain IXOBB0003 with Philippines strain causing bacterial blight of rice

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogen of concern for rice growers as it limits the production potential of rice varieties worldwide. Due to their high genomic plasticity, the pathogen continues to evolve, nullifying the deployed resistance mechanisms. It is pertinent to monitor the evolving Xoo population for the virulent novel stains, and the affordable sequencing technologies made the task feasible with an in-depth understanding of their pathogenesis arsenals. We present the complete genome of a highly virulent Indian Xoo strain IXOBB0003, predominantly found in northwestern parts of India, by employing next-generation sequencing and single-molecule sequencing in real-time technologies. The final genome assembly comprises 4,962,427 bp and has 63.96% GC content. The pan genome analysis reveals that strain IXOBB0003 houses total of 3655 core genes, 1276 accessory genes and 595 unique genes. Comparative analysis of the predicted gene clusters of coding sequences and protein count of strain IXOBB0003 depicts 3687 of almost 90% gene clusters shared by other Asian strains, 17 unique to IXOBB0003 and 139 CDSs of IXOBB0003 are shared with PXO99A. AnnoTALE-based studies revealed 16 TALEs conferred from the whole genome sequence. Prominent TALEs of our strain are found orthologous to TALEs of the Philippines strain PXO99A. The genomic features of Indian Xoo strain IXOBB0003 and in comparison with other Asian strains would certainly contribute significantly while formulating novel strategies for BB management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03596-x.

Chromosomal Location of xa19, a Broad-Spectrum Rice Bacterial Blight Resistant Gene from XM5, a Mutant Line from IR24

Bacterial blight is an important rice disease caused by bacteria named Xanthomonas oryzae pv. oryzae (Xoo). XM5 is an Xoo resistant mutant line with the genetic background of IR24, an Indica Xoo susceptible cultivar, induced by a chemical mutagen N-methyl-N-nitrosourea (MNU). XM5 carries a recessive Xoo resistant gene, xa19. Trisomic analysis was conducted using the cross between XM5 and the trisomic series under the genetic background of IR24, showing that xa19 was located on chromosome 7. The approximate chromosomal location was found using 37 surely resistant plants in the F₂ population from XM5 × Kinmaze, which was susceptible to most Japanese Xoo races. The IAS44 line carries a Japonica cultivar Asominori chromosomal segment covering the xa19 locus under the IR24 genetic background. Linkage analysis using the F₂ population from the cross between XM5 and IAS44 revealed that xa19 was located within the 0.8 cM region between RM8262 and RM6728. xa19 is not allelic to the known Xoo resistant genes. However, its location suggests that it might be allelic to a lesion-mimic mutant gene spl5, some alleles of which are resistant to several Xoo races. Together with xa20 and xa42, three Xoo resistant genes were induced from IR24 by MNU. The significance of chemical mutagen as a source of Xoo resistance was discussed.

Pyramiding of Four Broad Spectrum Bacterial Blight Resistance Genes in Cross Breeds of Basmati Rice

Pyramiding of major resistance (R) genes through marker-assisted selection (MAS) is a useful way to attain durable and broad-spectrum resistance against Xanthomonas oryzae pv. oryzae pathogen, the causal agent of bacterial blight (BB) disease in rice (Oryza sativa L.). The present study was designed to pyramid four broad spectrum BB-R genes (Xa4, xa5, xa13 and Xa21) in the background of Basmati-385, an indica rice cultivar with much sought-after qualitative and quantitative grain traits. The cultivar, however, is susceptible to BB and was therefore, crossed with IRBB59 which possesses R genes xa5, xa13 and Xa21, to attain broad and durable resistance. A total of 19 F1 plants were obtained, some of which were backcrossed with Basmati-385 and large number of BC1F1 plants were obtained. In BC1F2 generation, 31 phenotypically superior genotypes having morphological features of Basmati-385, were selected and advanced up to BC1F6 population. Sequence-tagged site (STS)-based MAS was carried out and phenotypic selection was made in each successive generation. In BC1F6 population, potentially homozygous recombinant inbred lines (RILs) from each line were selected and evaluated on the bases of STS evaluation and resistance to local Xanthomonas oryzae pv. oryzae (Xoo) isolates. Line 23 was found pyramided with all four BB-R genes i.e., Xa4, xa5, xa13 and Xa21. Five genotypes including line 8, line 16, line 21, line 27 and line 28 were identified as pyramided with three R genes, Xa4, xa5 and xa13. Pathological study showed that rice lines pyramided with quadruplet or triplet R genes showed the highest level of resistance compared to doublet or singlet R genes. Thus, line 23 with quadruplet, and lines 8, 16, 21, 27, and 28 with triplet R genes, are recommended for replicated yield and resistance trials before release as new rice varieties. Further, traditional breeding coupled with MAS, is a solid way to attain highly effective BB-resistant rice lines with no yield cost.

A new NLR disease resistance gene Xa47 confers durable and broad-spectrum resistance to bacterial blight in rice

Bacterial blight (BB) induced by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating bacterial disease in rice. The use of disease resistance (R) genes is the most efficient method to control BB. Members of the nucleotide-binding domain and leucine-rich repeat containing protein (NLR) family have significant roles in plant defense. In this study, Xa47, a new bacterial blight R gene encoding a typical NLR, was isolated from G252 rice material, and XA47 was localized in the nucleus and cytoplasm. Among 180 rice materials tested, Xa47 was discovered in certain BB-resistant materials. Compared with the wild-type G252, the knockout mutants of Xa47 was more susceptible to Xoo. By contrast, overexpression of Xa47 in the susceptible rice material JG30 increased BB resistance. The findings indicate that Xa47 positively regulates the Xoo stress response. Consequently, Xa47 may have application potential in the genetic improvement of plant disease resistance. The molecular mechanism of Xa47 regulation merits additional examination.

Identification and fine-mapping of Xo2, a novel rice bacterial leaf streak resistance gene

A novel rice resistance gene, Xo2, influencing pathogenesis of the bacterial leaf streak disease, has been identified, and candidate genes for Xo2 in the fine mapping region have been shown to be involved in bacterial leaf streak resistance. Rice (Oryza sativa) bacterial leaf streak, caused by Xanthomonas oryzae pv. oryzicola (Xoc), is one of the most serious rice bacterial diseases. The deployment of host resistance genes is an effective approach for controlling this disease. The cultivar BHADOIA 303 (X455) from Bangladesh is resistant to most of Chinese Xoc races. To identify and map the resistance gene(s) involved in Xoc resistance, we examined the association between phenotypic and genotypic variations in two F₂ populations derived from crosses between X455/Jingang 30 and X455/Wushansimiao. The segregation ratios of the F₂ progeny were consistent with the action of a single dominant resistance gene, which was designated as Xo2. Based on rice SNP chip (GSR40K) assays of X455, Jingang 30, and resistant and susceptible pools thereof, we mapped Xo2 to the region from 10 Mb to 12.5 Mb on chromosome 2. The target gene was further finely mapped between the markers RM12941 and D6-1 within an approximately 110-kb region. The de novo sequencing and gene annotation of X455 and Jingang 30 revealed nineteen predicted genes within the target region. RNA-seq and expression analysis showed that four candidate genes, including Osa002T0115800, encoding an NLR resistance protein, were distinctly upregulated. Differential sequence and synteny analysis between X455 and Jingang 30 suggested that Osa002T0115800 is likely the functional Xo2 gene. This study lays a foundation for marker-assisted selection resistance breeding against rice bacterial leaf streak and the further cloning of Xo2.

DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials

BACKGROUND

Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6-11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29).

RESULTS

Foreground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC₃F₂ generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC₃F₄ generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K⁺ Concentration 1).

CONCLUSION

DRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.

Genetic characterization and fine mapping of qHMS4 responsible for pollen sterility in hybrids between Oryza sativa L. and Oryza glaberrima Steud

African cultivated rice (Oryza glaberrima Steud) contains many favorable genes for tolerance to biotic and abiotic stresses and F1 hybrids between Asian cultivated rice (Oryza sativa L.) show strong heterosis. However, the hybrids of two species often exhibit hybrid sterility. Here, we identified a male sterility locus qHMS4 on chromosome 4 (Chr.4), which induces pollen semi-sterility in F1 hybrids of japonica rice variety Dianjingyou1 (DJY1) and a near-isogenic line (NIL) carrying a Chr.4 segment from Oryza glaberrima accession IRGC101854. Cytological observations indicated that non-functional pollen grains produced by the hybrids and lacking starch accumulation abort at the late bicellular stage. Molecular genetic analysis revealed distorted segregation in male gametogenesis carrying qHMS4 allele from DJY1. Fine-mapping of qHMS4 using an F2 population of 22,500 plants delimited qHMS4 to a region of 110-kb on the short arm of Chr.4. Sequence analysis showed that the corresponding sequence region in DJY1 and Oryza glaberrima were 114-kb and 323-kb, respectively, and that the sequence homology was very poor. Gene prediction analysis identified 16 and 46 open reading frames (ORFs) based on the sequences of DJY1 and O. glaberrima, respectively, among which 3 ORFs were shared by both. Future map-based cloning of qHMS4 will help to understand the underlying molecular mechanism of hybrid sterility between the two cultivated rice species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01306-8.

Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L

As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.

BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima

Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC₁F₁ population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.

A review of approaches to control bacterial leaf blight in rice

The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.

Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives

Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into cultivated rice to improve critical traits. Here, we summarize the beneficial traits in Australian wild rice, the available genomic information and the potential of gene editing to discover and understand the functions of novel alleles. Moreover, we discuss the potential domestication of these wild rice species for health and economic benefits to rice production globally.

Marker-assisted forward breeding to develop a drought-, bacterial-leaf-blight-, and blast-resistant rice cultivar

Among the different challenges related to rice (Oryza sativa L.) cultivation, drought, bacterial leaf blight (BLB), and blast are the key stresses that significantly affect grain yield (GY) in rice. To ameliorate this issue, marker-assisted forward breeding (MAFB) coupled with a simultaneous crossing approach was used to combine three drought tolerant quantitative trait loci (QTL)-qDTY_1.1 , qDTY_3.1 , and qDTY_12.1 -four BLB genes-Xa4, xa5, xa13, and Xa21-and one blast-resistance gene, Pi9, in the elite rice cultivar Lalat. The introgression lines (ILs) developed in the current study were phenotypically screened for drought, BLB, and blast resistance at the F₇ -F₈ generation. Under the reproductive stage (RS) drought stress, the yield advantage of ILs, with major-effect QTL (qDTY) over elite parent Lalat, ranges from 9 to 124% in DS2019 and from 7 to 175% in WS2019. The selected ILs were highly resistant to BLB, with lesion lengths ranging from 1.3 to 3.0 cm and blast scores ranging from 1 to 3. ILs that were tolerant to RS drought, resistant to BLB, and blast disease and had similar or higher yields than Lalat were analyzed for grain quality. Six ILs were found to have similar grain quality characteristics to Lalat including hulling, milling, head rice recovery (HRR), chalkiness, alkali spreading value (ASV), and amylose content (AC). This study showed that MAFB, together with simultaneous crossing, would be an effective strategy to rapidly combine multiple stresses in rice. The ILs developed in this study could help to ensure yield sustainability in rainfed environments or be used as genetic material in future breeding programs.

Multiparent-Derived, Marker-Assisted Introgression Lines of the Elite Indian Rice Cultivar, ‘Krishna Hamsa’ Show Resistance against Bacterial Blight and Blast and Tolerance to Drought

Major biotic stresses viz., bacterial blight (BB) and blast and brown plant hopper (BPH) coupled with abiotic stresses like drought stress, significantly affect rice yields. To address this, marker-assisted intercross (IC) breeding involving multiple donors was used to combine three BB resistance genes—xa5, xa13 and Xa21, two blast resistance genes—Pi9 and Pi54, two BPH resistance genes—Bph20 and Bph21, and four drought tolerant quantitative trait loci (QTL)—qDTY1.1, qDTY2.1, qDTY3.1 and qDTY12.1—in the genetic background of the elite Indian rice cultivar ‘Krishna Hamsa’. Three cycles of selective intercrossing followed by selfing coupled with foreground selection and phenotyping for the target traits resulted in the development of 196 introgression lines (ILs) with a myriad of gene/QTL combinations. Based on the phenotypic reaction, the ILs were classified into seven phenotypic classes of resistance/tolerance to the following: (1) BB, blast and drought—5 ILs; (2) BB and blast—10 ILs; (3) BB and drought—9 ILs; (4) blast and drought—42 ILs; (5) BB—3 ILs; (6) blast—84 ILs; and (7) drought—43 ILs; none of the ILs were resistant to BPH. Positive phenotypic response (resistance) was observed to both BB and blast in 2 ILs, BB in 9 ILs and blast in 64 ILs despite the absence of corresponding R genes. Inheritance of resistance to BB and/or blast in such ILs could be due to the unknown genes from other parents used in the breeding scheme. Negative phenotypic response (susceptibility) was observed in 67 ILs possessing BB-R genes, 9 ILs with blast-R genes and 9 ILs harboring QTLs for drought tolerance. Complex genic interactions and recombination events due to the involvement of multiple donors explain susceptibility in some of the marker positive ILs. The present investigation successfully demonstrates the possibility of rapid development of multiple stress-tolerant/resistant ILs in the elite cultivar background involving multiple donors through selective intercrossing and stringent phenotyping. The 196 ILs in seven phenotypic classes with myriad of gene/QTL combinations will serve as a useful genetic resource in combining multiple biotic and abiotic stress resistance in future breeding programs.

Exploring of bacterial blight resistance in landraces and mining of resistant gene(s) using molecular markers and pathogenicity approach

Bacterial blight, one of the oldest and most severe diseases of rice poses a major threat to global rice production and food security. Thereafter, sustainable management of this disease has given paramount importance globally. In the current study, we explored 792 landraces to evaluate their disease reaction status against three highly virulent strains (BXo69, BXo87 and BXo93) of Xanthomonas oryzae pv. oryzae (Xoo). Subsequently, we intended to identify the possible candidate resistant (R) genes responsible for the resistant reaction using six STS (Sequence Tagged Site) markers correspond to Xa4, xa5, Xa7, xa13, Xa21 and Xa23 genes and finally, we evaluated morphological variability of the potential bacterial blight resistant germplasm using quantitative traits. Based on pathogenicity test, a single germplasm was found as highly resistant while, 33 germplasm were resistant and 40 were moderately resistant. Further molecular study on these 74 germplasm divulged that 41 germplasm carried Xa4 gene, 15 carried xa5 gene, 62 carried Xa7 gene, 33 carried xa13 gene, and 19 carried Xa23 gene. Only a single germplasm found to carry Xa21 gene. Interestingly, we found a wide range of gene combinations ranged from 2 to 4 genes among the germplasm, where 10 germplasm carried 4 genes, 15 germplasm carried 3 genes and 38 germplasm carried 2 genes of various combinations. Notably, G3 genotype (Acc. No. 4216; highly resistant) having Xa4, Xa7, xa13, Xa21 and G43 genotype (Acc.No. 1523; resistant) having Xa4, xa5, xa13 and Xa23 gene combination being the most effective against all the Xoo strains. Nonetheless, UPGMA dendrogram and heatmap analysis based on quantitative traits identified two clusters viz. cluster-III and cluster-VIII with multiple desired traits. The outcome of this study would enrich and diversify the rice gene pool and would be useful for the development of durable bacterial blight resistant varieties.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01139-x.

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 seven different 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.

Introgression of Bacterial Blight Resistance Genes in the Rice Cultivar Ciherang: Response against Xanthomonas oryzae pv. oryzae in the F6 Generation

Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported; however, introgression of a single gene into rice has not been able to sufficiently protect rice against BB infection. Pyramiding of effective BB resistance genes (i.e., Xa genes) into background varieties is a potential approach to controlling BB infection. In this study, combinations of four BB resistance genes, Xa4, xa5, xa13, and Xa21, were pyramided into populations. The populations were derived from crossing Ciherang (a widespread Indonesian rice variety) with IRBB60 (resistance to BB). Promising recombinants from the F₆ generation were identified by scoring the phenotype against three virulent bacterial strains, C5, P6, and V, which cause widespread BB infection in most rice-growing countries. Pyramiding of genes for BB resistance in 265 recombinant introgressed lines (RILs) were confirmed through marker-assisted selection (MAS) of the F₅ and F₆ generations using gene-specific primers. Of these 265 RILs, 11, 34 and 45 lines had four, three, or two BB resistance genes, respectively. The RILs had pyramiding of two or three resistance genes, with the Xa4 resistance gene showing broad spectrum resistance against Xoo races with higher agronomic performance compared to their donor and recipients parents. The developed BB-resistant RILs have high yield potential to be further developed for cultivation or as sources of BB resistance donor material for varietal improvement in other rice lines.

Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.

Genetics and breeding for climate change in Orphan crops

Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.

Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice

Using genome-wide SNP association mapping, a total of 77 and 7 loci were identified for rice bacterial blight and bacterial leaf streak resistance, respectively, which may facilitate rice resistance improvement. Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R²) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.

TALE-triggered and iTALE-suppressed Xa1-mediated resistance to bacterial blight is independent of rice transcription factor subunits OsTFIIAγ1 or OsTFIIAγ5

Xa1-mediated resistance to rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is triggered by transcription activator-like effectors (TALEs) and suppressed by interfering TALEs (iTALEs). TALEs interact with the rice transcription factor OsTFIIAγ1 or OsTFIIAγ5 (Xa5) to activate expression of target resistance and/or susceptibility genes. However, it is not clear whether OsTFIIAγ is involved in TALE-triggered and iTALE-suppressed Xa1-mediated resistance. In this study, genome-edited mutations in OsTFIIAγ5 or OsTFIIAγ1 of Xa1-containing rice 'IRBB1' and Xa1-transgenic plants of xa5-containing rice 'IRBB5' did not impair the activation or suppression of Xa1-mediated resistance. Correspondingly, the expression pattern of Xa1 in mutated OsTFIIAγ5 and OsTFIIAγ1 rice lines and 'IRBB1' rice was similar. In contrast, the expression of OsSWEET11 was repressed in rice lines mutated in OsTFIIAγ5 and OsTFIIAγ1. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation assays showed that both TALE PthXo1 and iTALE Tal3a interacted with OsTFIIAγ1 and OsTFIIAγ5 in plant nuclei. These results indicated that TALE-triggered and iTALE-suppressed Xa1-mediated resistance to bacterial blight is independent of OsTFIIAγ1 or OsTFIIAγ5 in rice, and suggest that an unknown factor is potentially involved in the interaction of Xa1, TALEs and iTALEs.

Genome-Wide Association Study Dissects Resistance Loci against Bacterial Blight in a Diverse Rice Panel from the 3000 Rice Genomes Project

BACKGROUND

Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating bacterial diseases of rice in temperate and tropical regions. Breeding and deployment of resistant cultivars carrying major resistance (R) genes has been the most effective approach for BB management. However, because of specific interaction of each R gene with the product of the corresponding pathogen avirulence or effector gene, new pathogen strains that can overcome the deployed resistance often emerge rapidly. To deal with ever-evolving Xoo, it is necessary to identify novel R genes and resistance quantitative trait loci (QTL).

RESULTS

BB resistance of a diverse panel of 340 accessions from the 3000 Rice Genomes Project (3 K RGP) was evaluated by artificial inoculation with four representative Xoo strains, namely Z173 (C4), GD1358 (C5), V from China and PXO339 (P9a) from Philippines. Using the 3 K RG 4.8mio filtered SNP Dataset, a total of 11 QTL associated with BB resistance on chromosomes 4, 5, 11 and 12 were identified through a genome-wide association study (GWAS). Among them, eight resistance loci, which were narrowed down to relatively small genomic intervals, coincided with previously reported QTL or R genes, e.g. xa5, xa25, xa44(t). The other three QTL were putative novel loci associated with BB resistance. Linear regression analysis showed a dependence of BB lesion length on the number of favorable alleles, suggesting that pyramiding QTL using marker-assisted selection would be an effective approach for improving resistance. In addition, the Hap2 allele of LOC_Os11g46250 underlying qC5-11.1 was validated as positively regulating resistance against strain C5.

CONCLUSIONS

Our findings provide valuable information for the genetic improvement of BB resistance and application of germplasm resources in rice breeding programs.

Mapping QTL hotspots associated with weed competitive traits in backcross population derived from Oryza sativa L. and O. glaberrima Steud

To improve grain yield under direct seeded and aerobic conditions, weed competitive ability of a rice genotype is a key desirable trait. Hence, understanding and dissecting weed competitive associated traits at both morphological and molecular level is important in developing weed competitive varieties. In the present investigation, the QTLs associated with weed competitive traits were identified in BC1F2:3 population derived from weed competitive accession of O. glaberrima (IRGC105187) and O. sativa cultivar IR64. The mapping population consisting of 144 segregating lines were phenotyped for 33 weed competitive associated traits under direct seeded condition. Genetic analysis of weed competitive traits carried out in BC1F2:3 population showed significant variation for the weed competitive traits and predominance of additive gene action. The population was genotyped with 81 genome wide SSR markers and a linkage map covering 1423 cM was constructed. Composite interval mapping analysis identified 72 QTLs linked to 33 weed competitive traits which were spread on the 11 chromosomes. Among 72 QTLs, 59 were found to be major QTLs (> 10% PVE). Of the 59 major QTLs, 38 had favourable allele contributed from the O. glaberrima parent. We also observed nine QTL hotspots for weed competitive traits (qWCA2a, qWCA2b, qWCA2c, qWCA3, qWCA5, qWCA7, qWCA8, qWCA9, and qWCA10) wherein several QTLs co-localised. Our study demonstrates O. glaberrima species as potential source for improvement for weed competitive traits in rice and identified QTLs hotspots associated with weed competitive traits.

An xa5 Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae Is Nearly Identical to a Thai Strain

The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) constrains production in major rice growing countries of Asia. Xoo injects transcription activator-like effectors (TALEs) that bind to and activate host “susceptibility” (S) genes that are important for disease. The bacterial blight resistance gene xa5, which reduces TALE activity generally, has been widely deployed. However, strains defeating xa5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major S gene SWEET11 strongly enough to be effective even when diminished by xa5. The findings suggest international migration of the xa5-compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.

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.

Identification of the novel bacterial blight resistance gene Xa46(t) by mapping and expression analysis of the rice mutant H120

Rice bacterial leaf blight is caused by Xanthomonas oryzae pv. oryzae (Xoo) and produces substantial losses in rice yields. Resistance breeding is an effective method for controlling bacterial leaf blight disease. The mutant line H120 derived from the japonica line Lijiangxintuanheigu is resistant to all Chinese Xoo races. To identify and map the Xoo resistance gene(s) of H120, we examined the association between phenotypic and genotypic variations in two F₂ populations derived from crosses between H120/CO39 and H120/IR24. The segregation ratios of F₂ progeny consisted with the action of a single dominant resistance gene, which we named Xa46(t). Xa46(t) was mapped between the markers RM26981 and RM26984 within an approximately 65.34-kb region on chromosome 11. The 12 genes predicted within the target region included two candidate genes encoding the serine/threonine-protein kinase Doa (Loc_Os11g37540) and Calmodulin-2/3/5 (Loc_Os11g37550). Differential expression of H120 was analyzed by RNA-seq. Four genes in the Xa46(t) target region were differentially expressed after inoculation with Xoo. Mapping and expression data suggest that Loc_Os11g37540 allele is most likely to be Xa46(t). The sequence comparison of Xa23 allele between H120 and CBB23 indicated that the Xa46(t) gene is not identical to Xa23.

The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology

The pathogenic bacterial genus Xanthomonas infects a wide variety of host plants and causes devastating diseases in many crops. Transcription activator-like effectors (TALEs) are important virulence factors secreted by Xanthomonas with the ability to directly bind to the promoters of target genes in plant hosts and activate their expression, which often facilitates the proliferation of pathogens. Understanding how plants cope with TALEs will provide mechanistic insights into crop breeding for Xanthomonas defense. Over the past 30 years, numerous studies have revealed the modes of action of TALEs in plant cells and plant defense strategies to overcome TALE attack. Based on these findings, new technologies were adopted for disease management to optimize crop production. In this article, we will review the most recent advances in the evolutionary arms race between plant resistance and TALEs from Xanthomonas, with a specific focus on TALE applications in the development of novel breeding strategies for durable and broad-spectrum resistance.

Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice-Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice

Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.