Institutional Publications

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Author: search.filters.author.Singh, Anuradha

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    Integration of metabolite and transcriptome profiles of cultivated and wild rice to unveil gene regulatory networks and key genes determining rice source and sink strength
    (Springer Nature Publishing AG, 2025) Singh, Anuradha; Mathan, Jyotirmaya; Dwivedi, Aditi; Rani, Ruchi; Ranjan, Aashish
    Targeting source and sink strength for crop yield increase requires a comprehensive genetic and metabolic understanding of desirable source and sink features. We performed comprehensive metabolite and transcriptomic comparisons of the photosynthetic flag leaves and milky-stage developing grains of two cultivated rice varieties (Oryza sativa L. ssp. Indica cv. IR64 and Oryza sativa L. ssp. Japonica cv. Nipponbare) and two wild rice accessions (Oryza rufipogon and Oryza australiensis). The selected wild rice accessions had stronger source strength as evidenced by a higher photosynthesis rate and more abundance of primary metabolites in the photosynthetic leaves than the cultivated varieties. In contrast, cultivated varieties had efficient sink as grains were bigger and accumulated more sugars, amino acids, and fatty acids than the selected wild rice. Transcriptomic analyses identified 9,309 genes for efficient source in wild rice, enriched for biological pathways related to photosynthesis, carbohydrate metabolism, and sucrose transport. 7,062 genes, enriched for starch biosynthesis and lipid metabolism, were associated with the efficient sink strength in the cultivated varieties. Gene co-expression networks showed 267 hub genes for source strength in wild rice that included important genes for photosynthetic reactions and sucrose metabolism. 196 hub genes for sink strength in cultivated rice included genes involved in sucrose, amino acid, and fatty acid metabolism. Gene co-expression modules further identified the candidate transcription regulators, such as zinc finger proteins and NAC for source strength and MYB55/80 and MADS64 for sink strength. Moreover, our analyses suggested a complex interplay of phytohormones regulating rice source and sink strength.
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    High photosynthesis rate in two wild rice species is driven by leaf anatomy mediating high Rubisco activity and electron transport rate
    (Oxford University Press, 2021) Mathan, Jyotirmaya; Singh, Anuradha; Jathar, Vikram; Ranjan, Aashish
    The importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences, and underlying biochemical, photochemical, and developmental bases. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice accessions. Fitting A/Ci curves and biochemical analyses showed that the leaf photosynthesis in cultivated rice varieties, IR64 and Nipponbare, was limited due to leaf nitrogen content, Rubisco activity, and electron transport rate compared to photosynthetically efficient accessions of wild rice Oryza australiensis and Oryza latifolia. The selected wild rice accessions with high leaf photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells with more chloroplasts, fewer mesophyll cells between two consecutive veins, and higher mesophyll cell and chloroplast surface area exposed to intercellular space. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and leaf anatomical features in the rice system itself that could be targeted for increasing the photosynthetic efficiency of cultivated rice varieties.
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    Sucrose transport and metabolism control carbon partitioning between stem and grain in rice
    (Oxford University Press, 2021) Mathan, Jyotirmaya; Singh, Anuradha; Ranjan, Aashish
    The source-sink relationship is key to overall crop performance. Detailed understanding of the factors that determine source-sink dynamics is imperative for the balance of biomass and grain yield in crop plants. We investigated the differences in the source-sink relationship between a cultivated rice Oryza sativa cv. Nipponbare and a wild rice Oryza australiensis that show striking differences in biomass and grain yield. Oryza australiensis, accumulating higher biomass, not only showed higher photosynthesis per unit leaf area but also exported more sucrose from leaves than Nipponbare. However, grain features and sugar levels suggested limited sucrose mobilization to the grains in the wild rice due to vasculature and sucrose transporter functions. Low cell wall invertase activity and high sucrose synthase cleavage activity followed by higher expression of cellulose synthase genes in Oryza australiensis stem utilized photosynthates preferentially for the synthesis of structural carbohydrates, resulting in high biomass. In contrast, the source-sink relationship favored high grain yield in Nipponbare via accumulation of transitory starch in the stem, due to higher expression of starch biosynthetic genes, which is mobilized to panicles at the grain filling stage. Thus, vascular features, sucrose transport, and functions of sugar metabolic enzymes explained the differences in the source-sink relationship between Nipponbare and Oryza australiensis.
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    Sucrose transport in response to drought and salt stress involves ABA-mediated induction of OsSWEET13 and OsSWEET15 in rice
    (John Wiley & Sons, 2021) Mathan, Jyotirmaya; Singh, Anuradha; Ranjan, Aashish
    Abiotic stresses, including drought and salinity, negatively affect plant development and physiology at molecular and metabolic levels. Sucrose transport, mediating distribution of photosynthates in plant, is a key physiological process impacted by drought and salinity stresses, as sucrose is a prime energy and signaling molecule as well as an osmolyte. Therefore, understanding the effects of abiotic stresses on sucrose transport and transporters, and underlying genetic and molecular mechanisms is imperative to maintain sugar homeostasis in plants under stress. Here, we investigated the effects of drought and salinity stresses on sucrose transport and distribution, and on expression levels of genes encoding SWEET transporters, along with a potential transcription factor regulating SWEET expression in rice. We observed that drought and salinity stresses increased the sucrose content in leaf and root tissues, and in phloem sap of rice indica varieties. Expression analyses of SWEET genes and histochemical analysis of GUS reporter transgenic plants suggested that OsSWEET13 and OsSWEET15 are major SWEET transporters regulating the sucrose transport and levels in response to the abiotic stresses. Transactivation analyses showed that an ABA‐responsive transcription factor OsbZIP72 directly binds to the promoters of OsSWEET13 and OsSWEET15, and activates their expression. Taken together, the results showed that the higher expressions of OsSWEET13 and OsSWEET15 genes, induced by binding of an ABA‐responsive transcription factor OsbZIP72 to the promoters, potentially modulate sucrose transport and distribution in response to the abiotic stresses. The mechanism could possibly be targeted for maintaining sugar homeostasis in rice under drought and salinity stresses.