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Rhizosphere essentially harbours native bioagents that are beneficial to plants growth and development, stress tolerance and competitive advantage over its rivals. The bioagents often exhibits multiple mechanisms including secretion of secondary metabolites, phytohormones and defense enzymes to offer such advantages to the host plants. Stem rot and false smut caused by Sclerotium hydrophilumand Ustilaginoidea virensrespectively, are two major constraints in India and other countries where rice is cultivated. There are reports on the critical role of microbial phytohormones viz., ABA and SA, IAA, GA, zeatin on growth and stress of plants. They play a role in the regulation of plant immune responses by eliciting induced systemic resistance (ISR) in host plants against invading pathogens. Accordingly, we studied the activity of native bioagents viz., Trichoderma asperellum strain TAIK 1, Bacillus cabrialesii strain BIK3, Pseudomonas putida strain PIK1 and Pseudomonas otitidis strain POPS1 on enhancement of plant growth, increase in defence enzymes and reduction in severity of stem rot and false smut diseases of rice. We followed the Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC-ESI-MS/MS) method for the analysis of the phytohormones viz., IAA, GA, Zeatin, SA and ABA released by the bioagents. Bioagents treated plants showed 100% germination, enhanced plant growth parameters and reduction in percent disease index like 20.98% (stem rot), 23.14% (false smut) over the control plants (70.01% for stem rot and 75.24% for false smut). Our study indicated a direct relationship between the number and intensity of phytohormones released by the bioagents and the plant growth and disease suppression in rice.

Background: Rice, being the principal food crop and major nutritional source for more than half of the global population, is also an important source of livelihood in many South and South-East Asian countries. Amidst diminishing natural resources and many biotic-abiotic stresses, increasing the yield of rice varieties remains a challenging task. Identification of novel and yield augmenting alleles from stable rice hybrids is crucial to facilitate their marker-assisted transfer into various genetic backgrounds. Results: Quantitative trait loci (QTL) mapping using a population of 125 doubled haploid (DH) lines developed from the cross IR58025A/KMR3R and 126 polymorphic SSR; EST-derived SSR markers led to the identification of 12 each of major-minor effect QTLs for yield related traits. Major effect QTLs were detected for traits namely days to fifty percent flowering, test (1,000) grain weight, plant height, panicle weight, panicle length, flag leaf width, flag leaf length, biomass and total grain yield/plant explaining the phenotypic variability in the range of 29.95%-56.75%. QTL hotspots were detected on chromosome 3 for the traits, panicle length and total grain yield/plant and on chromosome 6 for the traits, panicle length, flag leaf length and total grain yield/plant. Though many of these QTLs were noted to co-localize with the QTL regions reported in earlier studies, five novel and major effect QTLs for panicle length, biomass, flag leaf width, panicle weight, plant height and three novel minor effect QTLs for panicle weight and fertile grains per panicle, were identified in this study. Conclusions: Through this study, both major-minor effect novel QTLs for crucial yield related traits, viz., fertile grains per panicle, panicle length, panicle weight were identified. Further, the QTL hotspots identified on two different chromosomes for flag leaf length, panicle length and total grain yield/plant shall not only help in understanding the underlying genetic mechanisms of yield regulation but also would provide an insight into the genetic synchrony among the various yield related traits in contributing for yield heterosis. The identified QTL hotspots after their validation can be deployed in breeding programs targeted towards improvement of yield heterosis.

To combat the dreaded diseases in rice like bacterial blight and blast, host plant resistance has been advocated as a sustainable method. Through the present study, we have successfully incorporated three major bacterial blight (BB) resistance genes viz., 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 PCR based, gene-specific markers viz., 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 and possessing all the three bacterial blight resistance genes was forwarded to BC2F2 generation. A solitary BC2F2 plant viz., NLR-87-10-106 possessing all the three resistance genes and > 90% genome recovery was identified and advanced through selfing till BC2F4 generation by adopting pedigree method. Three best lines at BC2F4 lines, possessing high level of resistance against bacterial blight and blast and equivalent or superior to NLR 34449 in terms of yield, grain quality and agro-morphological traits have been identified and advanced for multi-location trials.