Biology subjects

Neelima R Sinha

Publications and source records attributed to Neelima R Sinha.

3 recordsLinked to original sources

bioRxiv2016

Left-right leaf asymmetry in decussate and distichous phyllotactic systems

Leaves in plants with spiral phyllotaxy exhibit directional asymmetries, such that all the leaves originating from a meristem of a particular chirality are similarly asymmetric relative to each other. Models of auxin flux capable of recapitulating spiral phyllotaxis predict handed auxin asymmetries in initiating leaf primordia with empirically verifiable effects on superficially bilaterally symmetric leaves. Here, we extend a similar analysis of leaf asymmetry to decussate and distichous phyllotaxy. We found that our simulation models of these two patterns predicted mirrored asymmetries in auxin distribution in leaf primordia pairs. To empirically verify the morphological consequences of asymmetric auxin distribution, we analyzed the morphology of a tomato sister-of-pinformed1a (sopin1a) mutant, entire-2, in which spiral phyllotaxy consistently transitions to a decussate state. Shifts in the displacement of leaflets on the left and right sides of entire-2 leaf pairs mirror each other, corroborating predicted model results. We then analyze the shape of >800 commonivy (Hedera helix) and >3,000 grapevine (Vitis and Ampelopsis spp.) leaf pairs and find statistical enrichment of predicted mirrored asymmetries. Our results demonstrate that left-right auxin asymmetries in models of decussate and distichous phyllotaxy successfully predict mirrored asymmetric leaf morphologies in superficially symmetric leaves.

Plant Biology↗

bioRxiv2016

eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

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.

Genomics↗

bioRxiv2015

Auxin signaling is a common factor underlying natural variation in tomato shade avoidance

Light is an essential resource for photosynthesis. Limitation of light by shade from plant neighbors can induce a light competition program known as the shade avoidance response (SAR), thereby altering plant growth and development for the sake of survival. Natural genetic variation in SAR is found in plants adapted to distinct environments, including domesticated tomato Solanum lycopersicum and its wild relative Solanum pennellii. QTL mapping was used to examine variation of the SAR between these two species. We found organ specific responses in the elongation of the stem and petiole, including developmental acceleration of growth. Through RNAseq analysis we identified a number of ILs with reduced expression of auxin-related genes in shade treatment. These same ILs display a shade tolerant phenotype in stem growth and overall height. We also identified ILs with altered SAR expression of cell wall expansion genes, although these genotypes had no accompanying alteration in phenotype. Examination of weighted gene co-expression Connectivity networks in sun- and shade-treated plants revealed Connectivity changes in auxin and light signaling genes; this result was supported by the Identification of motifs within the promoters of a subset of shade-responsive genes that were enriched in light signaling, developmental pathways, and auxin responsive transcriptional domains. The Identification ofboth systemic and organ-specific shade tolerance in the ILs, as well as associated changes in the transcriptome, has the potential to inform future studies for breeding plants able to be grown closely (while neighbor-shaded), yet still maintaining high yield.\n\nSummaryGrowth plasticity in response to shade involves expression of specific auxin signaling and cell wall expansion genes, and shade avoidance QTL affect both stem elongation and developmental rate.

Plant Biology↗