Across the globe, rice cultivation is seriously affected by blast disease, caused by Magnaporthe oryzae. This disease has caused heavy yield loss to farmers over the past few years. In this background, the most affordable and eco-friendly strategy is to introgress blast-resistant genes from donors into elite rice cultivars. However, it is not only challenging to evolve such resistance lines using conventional breeding approaches, but also a time-consuming process. Therefore, the marker-assisted introduction of resistance genes has been proposed as a rapid strategy to develop durable and broad-spectrum resistance in rice cultivars. The current study highlights the successful introgression of a blast resistance gene, i.e., Pi9, into CO 51, an elite rice cultivar which already has another resistance gene named Pi54. The presence of two blast resistance genes in the advanced backcross breeding materials (BC₂F_2:3) was confirmed in this study through a foreground selection method using functional markers such as NBS4 and Pi54MAS. The selected positive introgressed lines were further genotyped for background selection with 55 SSR markers that are specific to CO 51. Consequently, both Pi9 as well as Pi54 pyramided lines, with 82.7% to 88.1% of the recurrent parent genome recovery, were identified and the selected lines were evaluated under hotspot. The analysis outcomes found that both the lines possessed a high level of resistance against blast disease during the seedling stage itself. In addition to this, it was also noticed that the advanced breeding rice lines that carry Pi9 + Pi54 were effective in nature and exhibited a higher degree of resistance against blast disease compared to the lines that were introgressed with a single blast resistance gene. Thus, the current study demonstrates a rapid and a successful introgression and pyramiding of two blast resistance genes, with the help of markers, into a susceptible yet high-yielding elite rice cultivar within a short period of time. Those gene pyramided rice lines can be employed as donors to introgress the blast-resistant genes in other popular susceptible cultivars.

Sheath blight disease is accountable for substantial loss in rice production worldwide. Endophytic bacteria are exploited as biocontrol agents due to their effectiveness in antagonizing a wide range of phytopathogens through a multifaceted approach. In the present study, the potentiality of deploying endophytic bacteria for the sustainable management of rice sheath blight was investigated. Over 40 bacterial endophytes were obtained and screened for their antagonistic activity against Rhizoctonia solani by a dual-culture assay. Among them, B. velezensis B13 exhibited higher mycelial inhibition (77.33%) against R. solani. A scanning electron microscopic study of the interaction of R. solani with B13 revealed distorted and deformed mycelia of R. solani. An analysis of secondary metabolites produced by B. velezensis B13 at their zone of interaction with R. solani confirmed the presence of various bioactive compounds of an antifungal and antimicrobial nature. A molecular docking study revealed that the compound 3′,8,8′-Trimethoxy-3-piperidyl-2,2′-binaphthalene-1,1′,4,4′-tetrone exhibited the highest binding affinity for Actin like protein (−7.6 kcal/mol), β-1,3 glucan synthase (−7.7 kcal/mol), Pectinesterase (−4.2 kcal/mol) and Polygalacturonase (−6.5 kcal/mol) protein targets of R. solani compared to the commercial fungicide carbendazim. In vivo experiments also proved the efficacy of B. velezensis B13 in suppressing rice sheath blight disease reduction upto 16.8± 0.2 besides enhancing the growth of the plant. Furthermore, B. velezensis B13 upregulated the expression of rice transcription factors and defense genes, viz., WRKY, PR1, PAL, LOX, FLS2 and CERK1, by several folds related to the inoculated and healthy control, leading to the suppression of R. solani. Our results suggest that B. velezensis (B13) could be a potential candidate for developing a bioconsortia for the sustainable management of rice sheath blight.

Effect of Seed-BorneSarocladium Oryzae, the Incitant of Rice Sheath Rot on Rice Seed Quality: Rice seeds collected fromSarocladium oryzaeinoculated plants produced more discoloured grain, chaffiness and recorded much lower seed germination than seeds collected from healthy plants in all the three cultivars tested. The germination, chaffiness and discolouration in healthy plants were found to be in the range of 70.50 to 93.50 per cent, 5.5 to 17.75 per cent and 4 to 18 per cent respectively. There was a progressive and significant reduction in total sugar, reducing sugar and non reducing sugar content of rice seeds with varying degree of seed infection caused byS. oryzaeThe increase in phenol content due toS. oryzaeinfection ranged from 15.74 to 70.78 per cent and increase being proportional to the per centS. oryzaeseed infection.

Sarocladium oryzae is a widely prevalent seed-borne pathogen of rice. The development of a rapid and on-site detection method for S. oryzae is therefore important to ensure the health of rice seeds. Loop-mediated isothermal amplification (LAMP) is ideal for field-level diagnosis since it offers quick, high-specific amplification of target template sequences at a single temperature. We designed primers based on the β-tubulin region of S. oryzae. The LAMP technique devised was extremely sensitive, detecting the presence of the S. oryzae template at concentrations as low as 10 fg in 30 minutes at 65°C. The assay specificity was confirmed by performing the experiment with genomic DNA isolated from 22 different phytopathogens. Through the addition of hydroxy naphthol blue in the reaction process prior to amplification, a colour shift from violet to deep sky blue was seen in the vicinity of the target pathogen only. Finally, the LAMP assay was validated using live infected tissues, weeds and different varieties of seeds collected from different locations in Tamil Nadu, India. If developed into a detection kit, the LAMP assay developed in this study has potential applications in seed health laboratories, plant quarantine stations, and on-site diagnosis of S. oryzae in seeds and plants.

The increased use of chemicals in rice farming poses significant issues regarding the emergence of pesticide/fungicide resistance and environmental sustainability concerns. This study was aimed at the genetic improvement of blast, bacterial leaf blight (BB) and gall midge resistance in a popular rice variety CO 51 which already harbours a blast resistance gene Pi54. Efforts were made to pyramid an additional blast resistance gene Pi9 along with two BB resistance genes (xa13 and Xa21) and two gall midge resistance genes (Gm1 and Gm4) into an elite rice variety CO 51 to enhance the resistance level to biotic stresses. The superior lines were selected using functional markers conferring resistance to blast (NBS4 and Pi54MAS linked to Pi9 and Pi54 genes, respectively) and BB [(xa13Prom (xa13) and pTA248 (Xa21)] and SSR markers linked to Gm1 (RM1328) and Gm4 (RM22550) for phenotypic screening and agronomic evaluation. The genotyping and phenotyping of F₆ and BC₂F₆ progenies of CO 51 X 562-4, for agronomic traits and resistance to BB and blast, identified ten superior progenies in F₆ and five superior progenies in BC₂F₆. The breeding lines harbouring both xa13+Xa21 exhibited high levels of resistance to BB (score ≤ 1 cm) and Pi9+Pi54 exhibited strong resistance to blast (score ≤ 2). Identified lines can be evaluated further for varietal improvement or utilised as genetic stocks in breeding programs.