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Rice production is adversely affected by biotic and abiotic stresses. Among the biotic stresses, brown planthopper (BPH) majorly affects the rice yield. Comprehending the genome and candidate players is essential for the resistance to BPH. This holistic study aimed to dissect the complex BPH resistance mechanism of the host against pathogen. Transcriptome analysis of six samples comprising of two-resistant (PTB33, BM71) and one-sensitive (TN1) genotypes under control and stress conditions was carried-out. A total of 148 million filtered reads were generated after quality check. Among these, 127 million filtered reads were aligned to the rice genome. These aligned reads were taken for further analysis. A total of 14,358 DEGs across the genotypes under stress were identified. Of which, 4820 DEGs were functionally annotated from 9266 uniquely mapped DEGs. Fifty-five potential BPH stress players were selected from the in-silico analysis of DEGs. qRT-PCR results revealed key players were differentially regulated in both resistant and sensitive genotypes. Spatio-temporal and hormone level expression signature of 55 BPH associated players were analyzed and noted their differential expression in tissues and hormones, respectively. This study inferred the significant differences in gene expression signatures may contribute to the process of BPH resistance mechanism in rice.

The development and utilization of molecular-markers play an important role in genomics-assisted breeding during pyramiding of valuable genes. The aim of present study was to develop and validate a novel core-set of KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving rice grain yield and adaptability under direct-seeded cultivation conditions. The 110 phenotypically validated KASP assays out of 171 designed KASP, include assays for biotic-resistance genes, anaerobic germination, root-traits, grain yield, lodging resistance and early-uniform emergence. The KASP assays were validated for their robustness and reliability at five different levels using diverse germplasm, segregating and advanced population, comparison with SSR markers and on F

Simple Summary Endophytic bacteria are plant-associated bacteria that live in the internal tissues of the plant without harming the host plant. They have an important role in plant growth promotion, as they directly or indirectly promote plant growth. They do it by inhibiting the growth of plant pathogens, and/or by producing various secondary metabolites. They are used in the agricultural sector as an eco-friendly alternative tool that helps to improve crop yield. Detection of plant defense response and identification of compounds synthesized by root endophytes are an effective means for their utilization in the agriculture sector as biofertilizers. Therefore, it is important to study the diversity of root endophytic microbial community, endophyte-host plant interactions and their colonization, and their activity for successful application in agricultural lands. Here, in this review, the potential of the root endophytic microbial community, colonization, and role in the improvement of plant growth has been explained. This could mark the potential use of endophytes for the benefit of plant growth and enhanced yield. Abstract The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in ‘omic’ technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.

Rice blast is one of the most widespread diseases threatening rice production and crop damage accounts for a major loss to rice farmers worldwide. To identify genetic regions associated with leaf blast resistance, a genome-wide association study was performed with 391 MAGIC indica plus rice accessions developed at IRRI, Philippines. Evaluation of leaf blast severity was performed in the uniform blast nursery (UBN) during 2016 and 2017 at ICAR-IIRR, Hyderabad, India. Genome-Wide Association Study was performed using six different statistical models with GBS data on 27041 single nucleotide polymorphisms (SNPs) distributed on all 12 rice chromosomes. A total of 130 associated SNP were detected and only seven common SNPs were identified with all the models on chromosome 3, 8, and 12. Farm CPU and Blink gave similar results and detected 31 associated SNPs on chromosome 3, 8, and 12. The highest number of annotated genes were identified on chromosome 12 followed by 8 and 3. Chromosome 12 harboring a major cluster of blast resistant genes and at least 20 blast resistant genes were mapped on this chromosome. Candidate genes identified in associated SNP regions on chromosome 12 in our study are encoding disease resistance genes; stripe rust resistance protein, MLA12, NBS-LRR disease resistance protein, NB-ARC domain-containing protein, CC-NBS-LRR resistance protein MLA13, indicating the possibility of developing casual SNPs/QTNs for leaf blast resistance in rice from these regions.

Maintenance of seed purity is an important skill-demanding aspect in seed production and multiplication. DNA fingerprinting allows identification of plant genotypes with high precision and stability as it is not influenced by environment, epistatic interactions and pleiotropic effects. DNA barcodes, the unique pattern of SSR polymorphism from the allelic variation data were developed for 14 visually similar varieties of medium grained rice and eight varieties of long slender grain types, having high market demand. Single-tube multiplex assays and DNA barcodes were generated using the available data on 32 markers for medium slender and 35 markers for long slender varieties to make variety identification easy and precise, which can supplement traditional standard practices in determining purity and certification.