Bacterial Blight Resistance Genes Research Articles

Research Progress on Cloning and Function of Xa Genes Against Rice Bacterial Blight.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious bacterial diseases that hinder the normal growth and production of rice, which greatly reduces the quality and yield of rice. The effect of traditional methods such as chemical control is often not ideal. A series of production practices have shown that among the numerous methods for BB controlling, breeding and using resistant varieties are the most economical, effective, and environmentally friendly, and the important basis for BB resistance breeding is the exploration of resistance genes and their functional research. So far, 44 rice BB resistance genes have been identified and confirmed by international registration or reported in journals, of which 15 have been successfully cloned and characterized. In this paper, research progress in recent years is reviewed mainly on the identification, map-based cloning, molecular resistance mechanism, and application in rice breeding of these BB resistance genes, and the future influence and direction of the remained research for rice BB resistance breeding are also prospected.

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.

Stacking of Pup1 QTL for low soil phosphorus tolerance and bacterial blight resistance genes in the background of APMS6B, the maintainer line of rice hybrid DRRH-3

Phosphorus (P) is one of the macronutrients essential for plant growth and development. Rice (Oryza sativa L.) is sensitive to P starvation and its deficiency influences many key plant functions, resulting in crop yield penalties. Although the hybrid rice segment is well-known for its yield heterosis, P deficiency and bacterial leaf blight diseases are evident limitations. APMS6B, the female parent of DRRH-3 is susceptible to low P and bacterial blight disease. In the present study, the improvement of APMS6B to P starvation and resistance to bacterial leaf blight (BB) was carried out using the marker-assisted backcross breeding approach. Kasalath (+Pup1 QTL) was used as a donor, and a promising IL (ATR 594-1) at BC1F4 generation was identified with 81.15% of recurrent parent genome recovery. Concurrently, this IL was intercrossed with GU-2 (+Xa21 and Xa38). Intercross F1s (ICF1) hybridity was confirmed through foreground selection having maximum RPGR (88.29%) and was selfed to produce ICF2. The resultant progenies were phenotyped for BB using Xoo inoculum (IX-020), simultaneously genotyped with gene-specific functional SSR markers forXa21 and Xa38. The identified BB-resistant plants were subjected to foreground selection for Pup1. Four promising ICF3 plants (BP-10-1, BP-10-3, BP-10-5, and BP-10-15 with Xa21, Xa38, and Pup1) along with parents and checks were screened both in low P plot (< 2 kg P2O5 ha−1) as well as in normal plot (> 25 kg P2O5 ha−1) during dry and wet seasons 2018. The field evaluation identified four promising intercrossed lines with better root growth in the primary root length of extracted zone and root volume. In addition, fewer reductions in grain yield (39.10%) under P starvation and less susceptibility indices values (< 1) for BB were observed. These lines may be exploited in the CMS conversion and development of climate-resilient, biotic and abiotic stress-tolerant rice hybrids.

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.

Marker assisted pedigree breeding based improvement of the Indian mega variety of rice MTU1010 for resistance against bacterial blight and blast and tolerance to low soil phosphorus.

Rice production is affected by many biotic and abiotic stresses; among them, bacterial blight (BB) and blast diseases and low soil phosphorous stress cause significant yield losses. The present study was carried out with the objective of combining the BB resistance gene, Xa21, the blast resistance gene, Pi54, and the low soil phosphorous tolerance QTL/gene, Pup1, into the genetic background of the Indian mega-rice variety, MTU1010 (Cottondora Sannalu), through marker-assisted pedigree breeding. RP5973-20-9-8-24-12-7 [a near isogenic line (NIL) of MTU1010 possessing Pup1] and RP6132 [a NIL of Akshayadhan possessing Xa21 + Pi54] were crossed and ‘true’ F1s were identified, using the target gene-specific markers and selfed. F2 plants, which are homozygous for all the three target genes/QTLs, were identified using PCR based markers and were advanced further through the pedigree method of breeding, with selection based on phenotypic traits specific for MTU1010. At the F5 generation, a set of 15 promising triple positive homozygous lines were identified and screened for their resistance against BB and blast diseases and tolerance to low soil P. Among them, two lines (LPK 30-18-16 and LPK 49-15-22) showed higher yields as compared to MTU1010, along with the desirable long slender grain type in both low soil P and normal soil P plots, and also exhibited high levels of resistance against BB and blast diseases, with lesser grain shattering as compared to MTU1010. These lines are being advanced for multi-location trials for validating their performance.

Improvement of bacterial blight resistance of the popular variety, Nellore Mahsuri (NLR34449) through marker-assisted breeding

To combat the dreaded diseases in rice like bacterial blight (BB) and blast, host plant resistance has been advocated as the most suitable and sustainable method. Through the present study, we have successfully incorporated three major BB resistance genes, namely Xa21, xa13 and xa5 into NLR3449, a high yielding, blast resistant, fine-grain type, popular rice variety through marker-assisted backcross breeding. Foreground selection was carried out using polymerase chain reaction based, gene-specific markers, namely pTA248 (Xa21), xa13prom (xa13) and xa5FM (xa5) at each generation of backcrossing, while 127 polymorphic SSR markers spanning on 12 chromosomes were used for background selection and backcrossing was limited to two rounds. At BC2F1 generation, a single plant (NLR-87-10) with 89.9% recovery, possessing all the three BB resistance genes was forwarded to BC2F2 generation. A solitary BC2F2 plant, namely NLR-87- 10-106 possessing all the three resistance genes and 96% genome recovery was identified and advanced through selfing until BC2F4 generation by adopting pedigree-method of selection. Three best BC2F4 lines, possessing high level of resistance against BB and blast, and equivalent or superior to NLR 34449 in terms of yield, grain quality and agro-morphological traits were identified and advanced for multilocation trials.

Identification of bacterial blight resistance genes in rice landraces from Yunnan Province, China

Bacterial blight (BB), a serious bacterial disease caused by pathogen Xanthomonas oryzae pv. oryzae (Xoo) affects rice growth and yield. Yunnan Province is regarded as a center of rice diversity in China and indeed the world, and has abundant rice landrace resources, which may offer prospective candidate donors in rice improvement and breeding. In this study, a set of 200 rice landraces were evaluated to determine their resistance to 10 pathogenic Xoo strains resistance by the leaf-clipping method. The results indicated that the tested rice landraces had different resistance levels against different Xoo strains. Multiple comparisons showed that the Xoo strain PXO99 was virulent to the tested rice landraces. Sixty-six rice landraces conferred resistance against at least one Xoo strain. These resistant rice landraces screened were then performed the presence of 14 cloned BB resistance genes by closely linked molecular markers and designed specific primers. The results showed that none of these resistant accessions contained xa13, Xa21, Xa27, and Xa45(t) homologous fragments, while 9, 24, 4, 7, 9, 15, 1, 5, 4 and 27 accessions contained Xa1, Xa2/Xa31(t), Xa14, Xa3/Xa26, Xa4, xa5, Xa7, Xa10, Xa23 and xa25 homologous fragments, respectively. Sequence analysis further revealed that nucleotide variations around functional nucleotide polymorphisms region were observed within these accessions containing the Xa1, Xa2/Xa31(t), Xa14, Xa3/Xa26, Xa4, xa5, Xa10, Xa23 and xa25 homologous fragments. These results along with phenotypic resistance spectrum supported that these accessions carried nine resistance homologous genes. Only one accession (Qishanggu_Wenshan) carried the Xa7 resistance gene. We also found that some resistant rice landraces, especially Xilandigu_Baoshan, and Laoyaling_Lincang without the above resistance genes, which mediated broad spectrum resistance to multiple Xoo strains, were identified as potential sources for breeding rice lines resistance to BB.

Variation and Functional Markers of Xa23 Promoter of Rice Bacterial Blight Resistance Gene

Xa23 &nbsp;is a dominant gene with broad spectrum and strong resistance to bacterial blight of rice. The functional difference between&nbsp; Xa23 &nbsp;and the allele susceptible gene&nbsp; xa23 &nbsp;lies in the 28 bp core sequence on the promoter that is recognized and activated by the avirulent effector avrXa23 of&nbsp; Xanthomonas oryzae pv. Oryzae&nbsp; (EBEavrXa23) and development of&nbsp; Xa23 &nbsp;functional markers can speed up the process of rice breeding. In this study, the&nbsp; Xa23 &nbsp;promoters of 43 wild rice and 7 representative conventional rice were tested, and the 200 bp sequence upstream of the promoter was analyzed using Vector NTI .&nbsp; The results showed that only 9 common wild rice and 2 conventional rice could amplify about 200 bp sequence upstream of promoter, and the detection rate was only 22.0%, indicating that&nbsp; Xa23&nbsp; was not widespread in rice. Further sequence analysis showed that there were abundant variations in the sequence of EBE avrXa23 , with at least seven haplotypes in its allele sequence, but EBE avrXa23&nbsp; only exists in rice CBB23. Finally, the&nbsp; Xa23 &nbsp;dominant functional marker was developed based on the sequence of EBE avrXa23 . It was verified that the marker could clearly distinguish whether there was&nbsp; Xa23 &nbsp;gene in rice. This study will be helpful to further study the evolution mechanism of&nbsp; Xa23 &nbsp;and molecular mark assisted breeding.&nbsp

Improving the resistance of the rice PTGMS line Feng39S by pyramiding blast, bacterial blight, and brown planthopper resistance genes

Knowledge of rice (Oryza sativa L.) genes and various DNA markers can be used in genomic breeding programs aimed at developing improved elite rice cultivars. We used an efficient genomic breeding approach to pyramid four resistance genes (Pi2, Xa23, Bph14, and Bph15) in the popular photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice line Feng39S. We performed foreground selection for the target genes, followed by recombinant selection and background selection. This process reduced the sizes of the genomic segments harboring the target genes (566.8 kb for Pi2, 1143.9 kb for Xa23, 774.7 kb for Bph14, and 1574.9 kb for Bph15) and accelerated the recovery of the recurrent parent genome to proportions ranging from 98.77% to 99.16%, thus resulting in four near-isogenic lines. To assemble the four resistance genes in Feng39S, we performed a double-way cross combined with foreground and background selection to generate two improved lines of Feng39S (Pi2 + Xa23 + Bph14 + Bph15) with a recurrent parent genome recovery of 98.98%. The two lines showed agronomic performance, grain quality, and fertility–sterility transition characteristics similar to those of the original Feng39S line. The newly developed PTGMS lines and corresponding hybrid combinations were resistant to various field blast isolates and seven representative isolates of bacterial blight. At the seedling stage, the lines also showed resistance against brown planthopper. This study provides an efficient and accurate genomic breeding approach for introducing desirable traits into PTGMS lines.

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.

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

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

Identification and Fine-Mapping of a New Bacterial Blight Resistance Gene, Xa47(t), in G252, an Introgression Line of Yuanjiang Common Wild Rice (Oryza rufipogon).

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a common, widespread, and highly devastating disease that affects rice yield. Breeding resistant cultivars is considered the most effective measure for controlling this disease. The introgression line G252 derived from Yuanjiang common wild rice (Oryza rufipogon) was highly resistant to all tested strains, including C5, C9, PXO99, PB, T7147Y8, Hzhj19, YM1, YM187, YJdp-2, and YJws-2. To identify the BB resistance gene(s) of G252, we developed an F2 population from the cross between G252 and 02428. A linkage analysis was performed for the phenotype and genotype of the population. A segregation ratio of 3:1 was observed between the resistant and susceptible individuals in the F2 progeny, indicating a dominant resistance gene, Xa47(t), in G252. The resistance gene was mapped within an approximately 26.24-kb physical region on chromosome 11 between two InDel markers, R13I14 and 13rbq-71. Moreover, one InDel marker, Hxjy-1, co-segregated with Xa47(t). Three genes were predicted within the target region, including a promising candidate gene encoding a nucleotide-binding domain and leucine-rich repeat (NLR) protein (LOC_Os11g46200) by combining the structure and expression analysis. Physical mapping data suggested that Xa47(t) is a new broad-spectrum BB resistance gene without identified allelic genes.

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.

Assessment of potentiality of known bacterial blight resistant genes against Xanthomonas oryzae pv. oryzae pathotypes exist in Bangladesh

Bacterial blight (BB) caused by X. oryzae pv. oryzae is a destructive disease of rice and causes 30-50% losses to rice depending on the outbreak. Development BB resistant rice varieties have long been considered as one of the most effective approach to control the disease. However, the durability of host resistance is breaking down due to the change of pathotypes of X. oryzae pv. oryzae globally. Pathotypic analyses of 239 X. oryzae pv. oryzae Bangladeshi isolates on Near Isogenic Lines (NILs) containing resistance (R) gene (s) revealed the existence of eight pathotypes of X. oryzae pv. oryzae. Among eight pathotypes, pathotypes IV and V were considered as major comprising maximum number of isolates, (30.13% and 23.01%, respectively), whereas pathotype VIII considered as minor consisting only 2.51% of total isolates. Pathotype, I showed highest virulence or aggressiveness compatible with all NILs, whereas pathotype VIII exhibited lowest virulence to these NILs. Bacterial blight resistant genes viz. Xa1 (75.00%), Xa11 (62.50%) and Xa21 (50.00%) showed resistance to most of the pathotypes while Xa4 performed worst as compared to all others R-genes. In pyramid lines, IRBBB63 (Xa5+Xa7+Xa13) and IRBB57 (Xa5+Xa7 +Xa21) showed resistance reaction and IRBB61 (Xa4+Xa5+Xa7), IRBB60 (Xa4+Xa5+Xa13+Xa21), IRBB54 (Xa5+Xa21), and IRBB53 (Xa4+Xa21) showed susceptible reaction to X. oryzae pv. oryzae pathotypes. These results collectively indicated the deployment of Xa1, Xa11, Xa4, Xa5, Xa7, Xa13 and Xa21 either alone or in combination against BB would be a best choice for the development of BB resistant rice varieties in Bangladesh.

Development of Submergence-Tolerant, Bacterial Blight-Resistant, and High-Yielding Near Isogenic Lines of Popular Variety, 'Swarna' Through Marker-Assisted Breeding Approach.

The rice variety ‘Swarna’ is highly popular in the eastern region of India. The farmers of eastern India cultivate mainly rainfed rice and face the adverse effects of climate change very frequently. Rice production in this region is not stable. Swarna variety is highly susceptible to bacterial blight (BB) disease and flash floods, which cause a heavy reduction in the yield. Transfer of five target genes/QTLs was targeted into the variety, Swarna by adopting marker-assisted backcross breeding approach. Direct markers for Sub1A, OsSPL14, and SCM2 QTLs and closely linked markers for xa5 and Xa21 BB resistance genes were screened in the backcross progenies. Swarna-Sub1, CR Dhan 800, and Swarna–Habataki near-isogenic lines (NILs) were used as donor parents in the breeding program. True multiple F1 plants were identified for backcrossing, and 796 BC1F1 seeds were generated. Foreground selection detected all the five target genes in six progenies in BC1F1 generation. The progeny containing all the target genes and more similar with the recipient parent was backcrossed, and a total of 446 BC2F1 seeds were produced. Foreground screening detected four BC2F1 plants carrying the five target genes. A total of 2,145 BC2F2 seeds were obtained from the best BC2F1 progeny. Screening of the progenies resulted in one plant with all five desirable genes, three plants with four, and another three progenies carrying three genes in homozygous conditions. The pyramided lines showed higher BB resistance and submergence tolerance than the recipient parent, Swarna. Culm strength of the pyramided lines showed higher breaking force than the recipient parent, Swarna. The pyramided line, SSBY-16-68-69 yielded the highest grain yield of 7.52 t/ha followed by the lines SSBY-16-68-511 (7.34 t/ha) and SSBY-16-68-1633 (7.02 t/ha). The best-pyramided line showed a yield advantage of 18% over the recipient parent and 6.8% over the yield component donor parent. Seven pyramided lines showed higher yield than the recipient parent, while five lines were better yielders than the yield component donor parent. The pyramided line SSBY-16-68-69 produced 365 grains/panicle, while the recipient had 152. The main morphologic and grain quality features of the recipient parent were retained in the pyramided lines.

Identification of quantitative trait loci associated with resistance to Xanthomonas oryzae pv. oryzae pathotypes prevalent in South China

Bacterial blight (BB), which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is an important rice disease responsible for significant yield losses. In the rice-growing regions of South China where BB outbreaks are common, the resistance of cultivars with BB resistance genes Xa4 and Xa21 has been lost because of rapid changes in the Xoo population structure and virulence. In this study, 421 diverse rice accessions were evaluated regarding their resistance to two Xoo strains, namely GD1358 (C5) and IV, which are prevalent pathotypes in South China and overcame the resistance of Xa4 and Xa21, respectively. Using the 4.8mio filtered SNP dataset, we conducted a genome-wide association study, which identified 13 loci associated with BB resistance, including eight new quantitative trait loci (QTL) and five QTL harboring known BB resistance genes: Xa3/Xa26, xa5, Xa35(t), Xa36(t), Xa40, Xa43(t), and xa44(t). Intriguingly, a steep peak was detected on chromosomes 5 and 11. Six QTL including three new ones, were distributed on chromosome 11, whereas a new QTL qBB5.1 and a known QTL were detected on chromosome 5. Haplotype analyses indicated that the LOC_Os05g01610 (OsPRAF2) gene within the qBB5.1 region, which encodes a PRAF protein, is associated with BB resistance. Furthermore, OsPRAF2 knockout lines generated using the CRISPR-Cpf1 system were significantly more resistant to Xoo strains than the wild-type plants. Our results provide researchers and breeders with useful information regarding QTL and gene resources, which may be relevant for developing new BB-resistant rice cultivars.

DRR Dhan 53 (RP-6113-Patho-BB9; IET 27294) – a high yielding, bacterial blight resistant, fine grain type rice variety

DRR Dhan 53 was released for commercial cultivation in Samba Mahsuri/Improved Samba Mahsuri growing regions of Telangana, Andhra Pradesh, Tamilnadu, Karnataka, Chhattisgarh, Orissa, Jharkhand, Bihar, Gujarat and Maharashtra by Central Sub-committee on Crop Standards, Notification and Release of Varieties in 2020. It is a cross between Improved Samba Mahsuri*3/PAU 3554. DRR Dhan 53 (IET 27294) is a marker assisted selection (MAS) derived product in the genetic background of Improved Samba Mahsuri. DRR Dhan 53 is a durable bacterial blight resistant, high-yielding, fine-grain type rice variety having the major bacterial blight resistance genes, Xa21+xa13+xa5+Xa38 with seed to seed maturity of 130-135 days and average yield of 5.5- 6 t/ ha.

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

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

Pathotype profiling, distribution and virulence analysis of Xanthomonas oryzae pv. oryzae causing bacterial blight disease of rice in Bangladesh

AbstractBacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a serious threat to rice production in the world. Identification of Xoo races pattern, distribution and deployment of race‐specific resistant genes is a sustainable strategy to develop bacterial blight resistant varieties. In this study, a total of 118 isolates of Xoo were collected from 8 rice‐growing regions of Bangladesh to identify the existing pathotypes of Xoo. All tested isolates were virulent on the susceptible rice varieties viz. IR24, Purbachi and BR11. The tested isolates were evaluated on 13 near‐isogenic lines of rice and each line consisted of a single bacterial blight resistant gene viz Xa1, Xa2, Xa3, Xa4, xa5, Xa7, xa8, Xa10, Xa11, xa13, Xa14, Xa21 and Xa23. Based on reaction patterns of 118 isolates of Xoo on near‐isogenic lines, 12 pathotypes/races were first time identified in Bangladesh. Race 1, Race 2 and Race 3 were predominantly distributed in the most of the areas of Bangladesh and considered as major races containing the maximum number of isolates (48%, 14% and 11% respectively). Among these, Race 1 was the most prevalent and widely distributed while Race 5 was the most virulent circumventing all of the resistance genes tested. Race 1 was recorded from six rice‐growing regions of Bangladesh. Host plant R‐genes xa5, xa8, xa13, Xa21 and Xa23 have been found as effective against bacterial blight based upon resistance frequencies and the reactions of near‐isogenic lines and pyramid lines. The bacterial blight resistant gene Xa21 showed a resistant reaction against 11 of 12 races (i.e. 94.91% of the isolates tested). Effective genes and information of races generated from this study could be deployed for the development of race‐specific bacterial blight resistant varieties in Bangladesh.

Analysis of immune response-related LRR-RLKs differential genes in the rice blast resistance near-isogenic lines of &amp;lt;italic&amp;gt;Japonica&amp;lt;/italic&amp;gt; Variety Yunyin

Rice ( Oryza sativa L.) is a staple food in the world as well as an important monocotyledonous model plant for molecular biology, which has a long history of cultivation and domestication. However, many diseases will break out during rice production. For example, the rice blast is the most destructive disease, which can cause the heavy loss or even total crop failure. Therefore, there are constant demands to cultivate durably blast-resistant varieties and identify more broad-spectrum blast resistance genes. Besides, it’s also very significant for agricultural production to elucidate the process and mechanism of immune response during the rice blast infection. The whole-genome sequencing of the resistant and susceptible near-isogenic lines derived from the broad-spectrum blast resistance Japonica Variety Yunyin and the universally blast-susceptible variety Lijiangxintuanheigu (LTH) was completed. Eight differential genes were screened from the Go terms that were associated with the immune response based on the whole-genome sequence data. We analyzed their gene structure, evolution and sequence variability between the resistant and susceptible near-isogenic lines. The results indicated that the homology of these protein sequences was between 55% and 80%, and the conserved protein domain analysis showed that most of them contained different numbers and types of leucine-rich repeat domains, a transmembrane domain and a C-terminal kinase domain, which were typical leucine-rich repeat receptor-like protein kinases. Moreover, they are all located within a cluster of chromosome 11 and were homologous to the bacterial blight resistance gene Xa21 . The leucine-rich repeat receptor-like protein kinases (LRR-RLKs) genes are a large conserved superfamily during the plant evolution. In Arabidopsis , there are 14 subfamilies and more than 200 members of LRR-RLKs were identified, whereas the rice genome contained more than 900 LRR-RLKs genes. The perception and recognition of pathogen infection are mainly mediated by the plant cells surface pattern-recognition receptors (PRRs) and intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors. PRRs contain many receptor kinases including the leucine-rich repeat receptor-like protein kinases, which play an important role in the signal transduction during the plant development, immune response and sense of the environmental changes. In order to further explore the potential function of these genes during the rice blast disease response, the rice seedlings were inoculated with Magnaporthe oryzae by spray and punch methods and then the expression pattern of these genes during the fungal infection were analyzed by qRT-PCR. The results showed that some genes response to the blast disease. Thus, we speculated that some of them might be involved in the rice blast disease response. This study laid a foundation for further studying genes related to the rice blast disease response.