Rice, Marker-Assisted Breeding, and Disease Resistance

Mehta, Sahil; Singh, B. M.; Dhakate, Priyanka; Rahman, M H; Islam, Aminul

doi:10.1007/978-3-030-20728-1_5

Cited by 32 publications

(11 citation statements)

References 118 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Conventional backcross breeding is the primary method used to develop highly BB-resistant rice cultivars, but it cannot accurately transfer multiple genes into the cultivar by phenotypic screening and the process requires a significant amount of time [21,22]. Modified backcross pyramid breeding, combined with molecular marker-assisted selection, has already been demonstrated to increase the precision and efficiency of breeding [23][24][25].…”

Section: Discussionmentioning

confidence: 99%

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

Hsu

Chiu²,

Yap

et al. 2020

IJMS

View full text Add to dashboard Cite

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

show abstract

Section: Discussionmentioning

confidence: 99%

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

Hsu

Chiu²,

Yap

et al. 2020

IJMS

View full text Add to dashboard Cite

show abstract

“…Since the traditional times, both cereal and cereal products act as pre-eminent and substantial carbohydrate food resources for much of the human population, especially in Asian countries 1 , 2 . Among the pre-harvest production constraints, the global cultivation of many cereals including rice and pearl millet is mostly affected by a blast disease-causing filamentous ascomycete fungus, Magnaporthe (Hebert) Barr (anamorph: Pyricularia ) 3 . This devastating hemibiotrophic pathogen belongs to the family Magnaporthaceae and is of principal concern due to the wide distribution, rapid aerial transmissions, seed-borne latent infection, and associated yield losses 2 , 4 , 5 .…”

Section: Introductionmentioning

confidence: 99%

“…Out of all reported species belonging to the genus Magnaporthe , both Magnaporthe oryzae (Anamorph: Pyricularia oryzae ) and Magnaporthe grisea (Anamorph: Pyricularia grisea ) have emerged as forage and grain production affecting pathogen that annually contributes to the substantial losses of grains 3 , 4 , 8 . In order to control the spread and minimize the associated losses with the blast, farmers depend largely on resistant host cultivars, and application of fungicides especially tricyclazole 9 .…”

Section: Introductionmentioning

confidence: 99%

Hybrid de novo genome-reassembly reveals new insights on pathways and pathogenicity determinants in rice blast pathogen Magnaporthe oryzae RMg_Dl

Reddy

Kumar

Mehta

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Blast disease incited by Magnaporthe oryzae is a major threat to sustain rice production in all rice growing nations. The pathogen is widely distributed in all rice paddies and displays rapid aerial transmissions, and seed-borne latent infection. In order to understand the genetic variability, host specificity, and molecular basis of the pathogenicity-associated traits, the whole genome of rice infecting Magnaporthe oryzae (Strain RMg_Dl) was sequenced using the Illumina and PacBio (RSII compatible) platforms. The high-throughput hybrid assembly of short and long reads resulted in a total of 375 scaffolds with a genome size of 42.43 Mb. Furthermore, comparative genome analysis revealed 99% average nucleotide identity (ANI) with other oryzae genomes and 83% against M. grisea, and 73% against M. poe genomes. The gene calling identified 10,553 genes with 10,539 protein-coding sequences. Among the detected transposable elements, the LTR/Gypsy and Type LINE showed high occurrence. The InterProScan of predicted protein sequences revealed that 97% protein family (PFAM), 98% superfamily, and 95% CDD were shared among RMg_Dl and reference 70-15 genome, respectively. Additionally, 550 CAZymes with high GH family content/distribution and cell wall degrading enzymes (CWDE) such endoglucanase, beta-glucosidase, and pectate lyase were also deciphered in RMg_Dl. The prevalence of virulence factors determination revealed that 51 different VFs were found in the genome. The biochemical pathway such as starch and sucrose metabolism, mTOR signaling, cAMP signaling, MAPK signaling pathways related genes were identified in the genome. The 49,065 SNPs, 3267 insertions and 3611 deletions were detected, and majority of these varinats were located on downstream and upstream region. Taken together, the generated information will be useful to develop a specific marker for diagnosis, pathogen surveillance and tracking, molecular taxonomy, and species delineation which ultimately leads to device improved management strategies for blast disease.

show abstract

“…The rice phyllosphere is also a habitat for foliar pathogens likeMagnaporthe and Xanthomonas that cause leaf-diseases.Blast disease caused by Magnaporthe oryzae (anamorph Pyricularia oryzae Sacc.) remains a global production constraint and a threat to food security in developing nations [24][25][26][27]. Blast disease of rice accounts for nearly 30 % production loss, which is enough to feed 60 million world's population if managed preemptively [28].…”

Section: Introductionmentioning

confidence: 99%

Deciphering Core-Phyllomicrobiome of Rice Genotypes Grown In Contrastingmountain And Island Agroclimatic Zones: Implications For Phyllomicrobiome Engineering Against Blast Disease

Sahu

Kumar

Krishnan

et al. 2021

Preprint

View full text Add to dashboard Cite

Background The fundamental role and contributions of phyllosphere habitat in shaping plant functional ecology are poorly investigated, and often underestimated. Phyllosphere -the harsh and dynamic foliar-photosynthetic-habitat is continuously exposed to vagaries of changing weather events during the entire plant life. With its adapted microbiota, the phyllosphere-niche brings microbial diversity to the plant-holobiont pool and potentially modulates a multitude of plant and agronomic traits. The phyllomicrobiome structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic-factors (Environment) which is further compounded by agronomic-transactions on domesticated agricultural crops. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most under-studied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria on phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet adequately explored.Currently, the metagenomic-Next-Generation-Sequencing (mNGS) technique scanning the conserved V3-V4 region of ribosomal RNA gene is a widely adopted strategy for microbiome-investigations. However, the structural and functional validation of mNGS annotations by microbiological methods is not integrated into the microbiome exploration-programs. In the present study, we combined the high throughput mNGS approach with conventional microbiological methods to decipher the core-functional-phyllomicrobiome of contrasting rice genotypes varying in their response to blast disease grown in contrasting agroclimatic zones in India. We, further, scanned the rice phyllosphere by electron microscopy to show the microbial communities on leaf. Magnaporthe oryzae-the phyllosphere pathogen inciting necrotic lesion on cereal crops is managed by the deployment of ‘non-durable’blast resistance genes and ‘toxic’ fungicidal molecules. Nowadays, there is a growing consensus for devising an alternative strategy for mitigating blast owing to a recent ban on the use of most commonly used fungicidal molecule, tricyclazole. In the present work, we further identified phyllosphere- core-functional microbial groups leading tothe proposal of phyllomicrobiome assisted rice blast management strategy.Multi-pronged activities of phyllomicrobiome against Magnaporthe oryzae (antifungal activity), rice innate immunity (defense elicitation), and rice blast disease (disease suppression) have beenelaborated for effective management of blast by phyllomicrobiome re-engineering. ResultsRice phyllomicrobiome of tropical “Island-Zone” displayed marginally more bacterial community diversity than that of temperate ‘Mountain-Zone’. Principal coordinate analysis based on Bray Curtis and ANoSIM method indicated nearly converging-phyllomicrobiome profiles on two contrasting rice genotypes grown in the same agroclimatic zone. However, the rice genotype grown in the contrasting Mountain-zone and Island-zone displayed diverse-phyllomicrobiome profiles indicating a strong influence of environmental factors rather than the genotype on phyllomicrobiome structure and assembly. The predominance of Phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed on the rice phyllosphere irrespective of the genotypes and environmental conditions. The core-microbiome analysis showed multi-microbiota-core consisting of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyceson phyllosphere of rice genotypes grown in contrasting agroclimaticzones. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed ten and two distinct bacterial genera in blast-resistant and -susceptible genotypes, respectively. The analysis further indicated 15 and 16 climate-zone specific bacterial genera for Mountain and Island zone, respectively. SparCC based network analysis of phyllomicrobiome showed hundreds of complex intra-microbial cooperative or competitive interactions on the rice genotypes and agroclimatic zones. Our microbiological validation of mNGS data further confirmed the presence of resident Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, andSphingomonason the rice phyllosphere.Strikingly,the two contrastingagroclimatic zones displayed genetically identical bacterial isolates on the phyllosphere that could be attributed to the spatio-temporal transmission of core-phyllomicrobiome, perhaps, aided by rice seeds. A total of 59 distinct bacterial isolates were obtained, identified, and evaluated for their functional attributes on Magnaporthe oryzae and rice plant. The phyllomicrobiome associated core-bacterial communities showed secreted-metabolite and volatile-compound mediated antifungal activity on M. oryzae.Uponphyllobacterization (a term coined for spraying of bacterial cells on the phyllosphere), the core bacterial species such as Acinetobacter baumannii, Aureimonas sp., Pantoea ananatis, P. eucrina,andPseudomonas putidaelicited plant defense and contributed significantly to blast disease suppression. Transcriptional analysis by qPCR indicated induction of rice innate immunity associated genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, andOsCERK1in phyllobacterized rice seedlings. ConclusionsThe rice genotypes growing in a particular agroclimatic zone showed a convergent phyllomicrobiome assemblage and composition. Conversely, diverging phyllomicrobiome assembly was observed on rice genotype cultivated in the contrasting agroclimatic zones.Agroclimatic zones and the associated climatic-factors rather than plant-genotypesper se appeared to drive phyllomicrobiome structure and composition on the rice genotypes. Our integrated mNGS method and microbiological validation divulged Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, andSphingomonasas core phyllomicrobiome of rice. Genetically identical bacterial communities belonging to Pantoea intercepted on the phyllosphere of rice grown in the two contrasting agroclimatic zones are suggestive of spatio-temporal transmission of phyllomicrobiome aided by seed. The core-microbiome mediated phyllobacterization showed potential for blast disease suppression by direct-antibiosis and defense elicitation. The identification of phyllosphere adapted functional core-bacterial communities in our study and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.

show abstract

Rice, Marker-Assisted Breeding, and Disease Resistance

Cited by 32 publications

References 118 publications

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

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

Hybrid de novo genome-reassembly reveals new insights on pathways and pathogenicity determinants in rice blast pathogen Magnaporthe oryzae RMg_Dl

Deciphering Core-Phyllomicrobiome of Rice Genotypes Grown In Contrastingmountain And Island Agroclimatic Zones: Implications For Phyllomicrobiome Engineering Against Blast Disease

Contact Info

Product

Resources

About