Increased Catalase Activity and Maintenance of Photosystem II Distinguishes High-Yield Mutants From Low-Yield Mutants of Rice var. Nagina22 Under Low-Phosphorus Stress

An upland rice variety, Nagina22 (N22) and its 137 ethyl methanesulfonate (EMS)-induced mutants, along with a sensitive variety, Jaya, was screened both in low phosphorus (P) field (Olsen P 1.8) and in normal field (Olsen P 24) during dry season. Based on the grain yield (YLD) of plants in normal field and plants in low P field, 27 gain of function (high-YLD represented as hy) and 9 loss of function (low-YLD represented as ly) mutants were selected and compared with N22 for physiological and genotyping studies. In low P field, hy mutants showed higher P concentration in roots, leaves, grains, and in the whole plant than in ly mutants at harvest. In low P conditions, Fv/Fm and qN were 24% higher in hy mutants than in ly mutants. In comparison with ly mutants, the superoxide dismutase (SOD) activity in the roots and leaves of hy mutants in low P fields was 9% and 41% higher at the vegetative stage, respectively, but 51% and 14% lower in the roots and leaves at the reproductive stage, respectively. However, in comparison with ly mutants, the catalase (CAT) activity in the roots and leaves of hy mutants in low P fields was 35% higher at the vegetative stage and 15% and 17% higher at the reproductive stage, respectively. Similarly, hy mutants in low P field showed 20% and 80% higher peroxidase (POD) activity in the roots and leaves at the vegetative stage, respectively, but showed 14% and 16% lower POD activity at the reproductive stage in the roots and leaves, respectively. Marker trait association analysis using 48 simple sequence repeat (SSR) markers and 10 Pup1 gene markers showed that RM3648 and RM451 in chromosome 4 were significantly associated with grain YLD, tiller number (TN), SOD, and POD activities in both the roots and leaves in low P conditions only. Similarly, RM3334 and RM6300 in chromosome 5 were associated with CAT activity in leaves in low P conditions. Notably, grain YLD was positively and significantly correlated with CAT activity in the roots and shoots, Fv/Fm and qN in low P conditions, and the shoots’ P concentration and qN in normal conditions. Furthermore, CAT activity in shoots was positively and significantly correlated with TN in both low P and normal conditions. Thus, chromosomal regions and physiological traits that have a role in imparting tolerance to low P in the field were identified

Fine mapping and sequence analysis reveal a promising candidate gene encoding a novel NB-ARC domain derived from wild rice (Oryza officinalis) that confers bacterial blight resistance

Bacterial blight disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious constraints in rice production. The most sustainable strategy to combat the disease is the deployment of host plant resistance. Earlier, we identified an introgression line, IR 75084-15-3-B-B, derived from Oryza officinalis possessing broad-spectrum resistance against Xoo. In order to understand the inheritance of resistance in the O. officinalis accession and identify genomic region(s) associated with resistance, a recombinant inbred line (RIL) mapping population was developed from the cross Samba Mahsuri (susceptible to bacterial blight) × IR 75084-15-3-B-B (resistant to bacterial blight). The F2 population derived from the cross segregated in a phenotypic ratio of 3: 1 (resistant susceptible) implying that resistance in IR 75084-15-3-B-B is controlled by a single dominant gene/quantitative trait locus (QTL). In the F7 generation, a set of 47 homozygous resistant lines and 47 homozygous susceptible lines was used to study the association between phenotypic data obtained through screening with Xoo and genotypic data obtained through analysis of 7K rice single-nucleotide polymorphism (SNP) chip. Through composite interval mapping, a major locus was detected in the midst of two flanking SNP markers, viz., Chr11.27817978 and Chr11.27994133, on chromosome 11L with a logarithm of the odds (LOD) score of 10.21 and 35.93% of phenotypic variation, and the locus has been named Xa48t. In silico search in the genomic region between the two markers flanking Xa48t identified 10 putatively expressed genes located in the region of interest. The quantitative expression and DNA sequence analysis of these genes from contrasting parents identified the Os11g0687900 encoding an NB-ARC domain-containing protein as the most promising gene associated with resistance. Interestingly, a 16-bp insertion was noticed in the untranslated region (UTR) of the gene in the resistant parent, IR 75084-15-3-B-B, which was absent in Samba Mahsuri. The association of Os11g0687900 with resistance phenotype was further established by sequence-based DNA marker analysis in the RIL population. A co-segregating PCR-based INDEL marker, Marker_Xa48, has been developed for use in the marker-assisted breeding of Xa48t

Key Enzymes and Proteins of Crop Insects as Candidate for RNAi Based Gene Silencing

RNA interference (RNAi) is a mechanism of homology dependent gene silencing present in plants and animals. It operates through 21-24 nucleotides small RNAs which are processed through a set of core enzymatic machinery that involves Dicer and Argonaute proteins. In recent past, the technology has been well appreciated towards the control of plant pathogens and insects through suppression of key genes/proteins of infecting organisms. The genes encoding key enzymes/proteins with the great potential for developing an effective insect control by RNAi approach are actylcholinesterase, cytochrome P450 enzymes, amino peptidase N, allatostatin, allatotropin, tryptophan oxygenase, arginine kinase, vacuolar ATPase, chitin synthase, glutathione-S-transferase, catalase, trehalose phosphate synthase, vitellogenin, hydroxy-3-methylglutaryl coenzyme A reductase, and hormone receptor genes. Through various studies, it is demonstrated that RNAi is a reliable molecular tool which offers great promises in meeting the challenges imposed by crop insects with careful selection of key enzymes/proteins. Utilization of RNAi tool to target some of these key proteins of crop insects through various approaches is described here. The major challenges of RNAi based insect control such as identifying potential targets, delivery methods of silencing trigger, off target effects, and complexity of insect biology are very well illustrated. Further, required efforts to address these challenges are also discussed

Silencing of CYP6 and APN genes affects the growth and development of rice yellow stem borer, Scirpophaga incertulas

RNAi is a powerful tool to target the insect genes involved in host-pest interactions. Key insect genes are the choice for silencing to achieve pest derived resistance where resistance genes are not available in gene pool of host plant. In this study, an attempt was made to determine the effect of dsRNA designed from two genes Cytochrome P450 derivative (CYP6) and Aminopeptidase N (APN) of rice yellow stem borer (YSB) on growth and development of insect. The bioassays involved injection of chemically synthesized 5ꞌ FAM labeled 21-nt dsRNA into rice cut stems and allowing the larvae to feed on these stems which resulted in increased mortality and observed growth and development changes in larval length and weight compared with its untreated control at 12-15 days after treatment. These results were further supported by observing the reduction in transcripts expression of these genes in treated larvae. Fluorescence detection in treated larvae also proved that dsRNA was readily taken by larvae when fed on dsRNA treated stems. These results from the present study clearly show that YSB larvae fed on dsRNA designed from Cytochrome P450 and Aminopeptidase N has detrimental effect on larval growth and development. These genes can be deployed to develop YSB resistance in rice using RNAi approach

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Not AvailableNitrogen is one of the most critical nutrients in rice production and increased rice productivity is attributed mostly to the nitrogen fertilizer responsive rice varieties. With its relevance to environment, breeding for nitrogen use efficiency is now a research priority in rice. Based on the physiological, biochemical and genetic studies, several genes have been identified for nitrogen uptake, transport, remobilization and assimilation. Many of the genes and gene families associated with tissues like root, shoot, leaf and panicle have been characterized under differential nitrogen conditions. Functional validation of the identified genes in nitrogen use efficiency, yield and other agro-morphological traits demonstrated their potential for deployment in rice breeding programs. In the present review, the information on possible genes associated with nitrogen use efficiency has been presented. The epigenetic regulation of genes including the non-coding RNA and new breeding technologies like genome editing have also been discussed for identification and validation of genes for NUE. We propose a combinatorial approach of deploying the information available for genes reported to be associated with NUE of rice by haplotyping, allele mining, spatial and temporal expression analyses, gene networking and validation through genome editing towards development of high yielding rice varieties under optimum nitrogen.Not Availabl

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Not AvailableBeyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.DST-SER

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Not AvailableRice (Orzya sativa L.) is one of the important staple food crops for more than half of the world and is being grown in most of the countries in the world. Varietal improvement and identification of novel sources for low nitrogen and phosphorus (N and P) tolerance helps in reducing the application of these fertilizers, import burdens, and environmental contaminations due to fertilizer run–offs and for getting sustainable yields, thus enhancing the income of farmers. Various novel biotechnology tools such as quantitative trait loci (QTL) mapping, Marker–assisted selection, Genome–Wide Association mapping (GWAS) and Genome editing techniques are discussed in this paper. At the ICAR–Indian Institute of Rice Research, in addition to screening genotypes for higher nutrient–use efficiency, lot of studies were carried out on genetic improvement of rice for development efficient genotypes in rice to minimize the application of fertilizers, which is not only necessary for increasing farmers’ income by saving on the cost of fertilizers but also to sustain the rice production.Not Availabl