Publications of NIPGR Scientists

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Author: search.filters.author.Ranjan, AashishSubject: search.filters.subject.Tomato

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    Brassinosteroids-regulated nitrogen metabolism fine-tunes growth physiology and low nitrogen response in tomato
    (Elsevier B.V., 2023) Yadav, Ritesh Kumar; Analin, Benedict; Panda, Mahesh Kumar; Ranjan, Aashish; Singh, Amar Pal
    Nitrogen (N) is a crucial nutrient for plants and its limited availability in the soils significantly affects plant growth and development. To adapt under low N condition, plants undergo various changes such as root system reprogramming to explore deeper soil horizons and metabolic activity adjustment. These N dependent responses and the genetic factors governing them are poorly known in crop plants. In this study, we investigated the effect of BRs on N metabolism in tomato. BRs application improved N assimilation and metabolic responses. By using the transgenic approach, we demonstrated the essential role of tomato Brassinazole resistant (BES1/BZR1) homolog 4 (BEH4) protein in regulating N metabolic response, growth physiology, and fruit quality. Overexpression of BEH4 promoted deeper root system architecture and improved physiological performance by adjusting N metabolic activity and photosynthetic efficiency in low N-grown plants. The BEH4 transgenic lines exhibited increased expression of genes involved in N uptake and assimilation which are associated with the improved N content and assimilation (root and shoot). Altogether, data suggested an essential role of BRs in plant adaptation to altered N regimes and appears potential target for genetic manipulation to improve nitrogen use efficiency (NUE) and nutritional quality in crops.
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    eQTL regulating transcript levels associated with diverse biological processes in tomato
    (American Society of Plant Biologists, 2016) Ranjan, Aashish; Budke, Jessica; Rowland, Steven D.; Chitwood, Daniel H; Kumar, Ravi; Carriedo, Leonela G.; Ichihashi, Yasunori; Zumstein, Kristina; Maloof, Julin N.; Sinha, Neelima R.
    Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression Quantitative Trait Loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato Solanum lycopersicum to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome, and identified ~7,200 eQTL regulating the steady state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hotspots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity, and hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive expression QTL analysis details the influence of these loci on plant phenotypes, and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.
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    Light-induced indeterminacy alters shade avoiding tomato leaf morphology
    (American Society of Plant Biologists, 2015) Chitwood, Daniel H.; Kumar, Ravi; Ranjan, Aashish; Pelletier, Julie M.; Townsley, Brad T.; Ichihashi, Yasunori; Martinez, Ciera C.; Zumstein, Kristina; Harada, John J.; Maloof, Julin N.; Sinha, Neelima R.
    Plants sense the foliar shade of competitors and alter their developmental programs through the shade-avoidance response. Internode and petiole elongation, and changes in overall leaf area and leaf mass per area, are the stereotypical architectural responses to foliar shade in the shoot. However, changes in leaf shape and complexity in response to shade remain incompletely, and qualitatively, described. Using a meta-analysis of more than 18,000 previously published leaflet outlines, we demonstrate that shade avoidance alters leaf shape in domesticated tomato (Solanum lycopersicum) and wild relatives. The effects of shade avoidance on leaf shape are subtle with respect to individual traits but are combinatorially strong. We then seek to describe the developmental origins of shade-induced changes in leaf shape by swapping plants between light treatments. Leaf size is light responsive late into development, but patterning events, such as stomatal index, are irrevocably specified earlier. Observing that shade induces increases in shoot apical meristem size, we then describe gene expression changes in early leaf primordia and the meristem using laser microdissection. We find that in leaf primordia, shade avoidance is not mediated through canonical pathways described in mature organs but rather through the expression of KNOTTED1-LIKE HOMEOBOX and other indeterminacy genes, altering known developmental pathways responsible for patterning leaf shape. We also demonstrate that shade-induced changes in leaf primordium gene expression largely do not overlap with those found in successively initiated leaf primordia, providing evidence against classic hypotheses that shaded leaf morphology results from the prolonged production of juvenile leaf types.