Plasticity of Tiller Dynamics in Wild Rice Oryza rufipogon Griff.: A Strategy for Resilience in Suboptimal Environments

Rice cultivation in tropical Asia is susceptible to drought and flood and the need is high for stress resistant genes. Wild rice Oryza rufipogon Griff., grows in close sympatric association with cultivated rice in various habitats across the globe and possesses traits for survival under challenging environments. The species adapts according to the level of soil moisture available and modifies phenology, biomass production and grain yield. Variation in tiller dynamics of the species between contrasting environments gives an estimate of the adaptation. The species possesses AA genome, which permits genetic compatibility for cross breeding with cultivated rice. Utility of the species as possible repository of stress resistant genes is evaluated in this review by examining variation in assimilate partitioning between different classes of tillers of ecotypes growing across a gradation of habitats against background knowledge available for cultivated rice. Models have been constructed to explain mechanisms of tillering and tiller dynamics, and reveal the genotypic permissibility for resilience in sub-optimal environments. It is concluded that environmentally cued alteration in assimilate production and partitioning mask genetic potential for tiller production and survival. Tiller number in excess of resource capacity is corrected by senescence of late-tillers possibly through an ethylene-mediated signal

Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics (vol 46, pg 507, 2019)

Corrigendum to: Controlling the trade-off between spikelet number and grain filling: the hierarchy of starch synthesis in spikelets of rice panicle in relation to hormone dynamics, Functional Plant Biology 46 (6), 2019, 595 - 595, WOS:000469437400002International audienc

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RT-qPCR of total RNA isolated from superior and inferior spikelets of <i>O</i>. <i>sativa</i> cultivars on various days after anthesis (DAA) for genes identified in the Apical-forward SSH cDNA library.

<p>Each bar represents the relative expression (in fold change) of a gene in superior compared with inferior spikelets in Mahalaxmi (A), Upahar (B), OR-1918 (D) and Lalat (E), in inferior spikelets of Upahar compared with inferior spikelets of Mahalaxmi (C) and in inferior spikelets of Lalat compared with inferior spikelets of OR-1918 (F). cDNA was prepared as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145749#pone.0145749.g001" target="_blank">Fig 1</a> and used as the template for RT-qPCR, which was conducted using QuantiFast SYBR Green PCR Kit (Qiagen) and a Roche LightCycler 480 thermocycler. Each gene, as well as actin as the reference control, was amplified using gene-specific primers (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145749#pone.0145749.s009" target="_blank">S2 Table</a>) designed with Primer Blast. The fold change in expression was calculated by the ΔΔCt method with actin as the reference. Each bar represents the mean ± SD from three independent estimations. The asterisks (*) against each bar represent statistically significant changes in expression (either higher or lower in terms of fold change), at p ≤ 0.05, as determined by the ‘t’ test. The genes examined included 2-oxoglutarate dehydrogenase E1 component (<i>OGDE1</i>, LOC_OS04G32020.1), glycogen synthase kinase 3 (<i>GSK3</i>) <i>MsK3</i> homolog (LOC_OS04G31240.1), hypothetical protein (LOC_OS03G12670.1), sucrose synthase2 (<i>SUS2</i>, LOC_OS06G09450.2), AAA+ type ATPase (LOC_OS01G04814.1), and C3HC4 RING finger protein (LOC_OS07G31850.1).</p

RT-PCR of total RNA isolated from superior (A) and inferior (B) spikelets of O. sativa cv. Mahalaxmi panicles on 0, 3 and 6 days after anthesis (DAA or simply D) for analysis of genes overexpressed in the superior compared with inferior spikelets (I) and genes overexpressed in the inferior compared with superior spikelets (II).

<p>Total RNA was isolated using TRIzol (Life Technologies) and reverse-transcribed using QuantiTect Reverse Transcription Kit (Qiagen). Each gene was amplified using gene-specific primers designed using Primer Blast. Actin and 18S rRNA were amplified for 30 and 25 cycles, respectively, as positive and loading controls. The other reactions were performed for 30 cycles, and the amplified products were separated on an agarose gel containing ETBR and visualized and photographed using a Gel Doc (Bio-Rad). The primer sequences are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145749#pone.0145749.s009" target="_blank">S2 Table</a>.</p

Identification and Characterization of Differentially Expressed Genes in Inferior and Superior Spikelets of Rice Cultivars with Contrasting Panicle-Compactness and Grain-Filling Properties

<div><p>Breeding programs for increasing spikelet number in rice have resulted in compactness of the panicle, accompanied by poor grain filling in inferior spikelets. Although the inefficient utilization of assimilate has been indicated as responsible for this poor grain filling, the underlying cause remains elusive. The current study utilized the suppression subtractive hybridization technique to identify 57 and 79 genes that overexpressed in the superior and inferior spikelets (with respect to each other), respectively, of the compact-panicle rice cultivar Mahalaxmi. Functional categorization of these differentially expressed genes revealed a marked metabolic difference between the spikelets according to their spatial location on the panicle. The expression of genes encoding seed storage proteins was dominant in inferior spikelets, whereas genes encoding regulatory proteins, such as serine-threonine kinase, zinc finger protein and E3 ligase, were highly expressed in superior spikelets. The expression patterns of these genes in the inferior and superior spikelets of Mahalaxmi were similar to those observed in another compact-panicle cultivar, OR-1918, but differed from those obtained in two lax-panicle cultivars, Upahar and Lalat. The results first suggest that the regulatory proteins abundantly expressed in the superior spikelets of compact-panicle cultivars and in both the superior and inferior spikelets of lax-panicle cultivars but poorly expressed in the inferior spikelets of compact-panicle cultivars promote grain filling. Second, the high expression of seed-storage proteins observed in the inferior spikelets of compact-panicle cultivars appears to inhibit the grain filling process. Third, the low expression of enzymes of the Krebs cycle in inferior spikelets compared with superior spikelets of compact-panicle cultivars is bound to lead to poor ATP generation in the former and consequently limit starch biosynthesis, an ATP-consuming process, resulting in poor grain filling.</p></div

RT-qPCR of total RNA isolated from superior and inferior spikelets of <i>O</i>. <i>sativa</i> cultivars on various days after anthesis (DAA) for five mitochondrial genes.

<p>Each bar represents the relative expression (in fold change) in superior (A) or inferior (B) spikelets of Upahar compared with those of Mahalaxmi and in superior (C) inferior (D) spikelets of Lalat compared with those of OR-1918. 19S rRNA was used as the reference gene. The genes examined included 2-oxoglutarate dehydrogenase E1 component (<i>OGDE1</i>, LOC_OS04G32020.1), succinyl CoA synthase (LOC_Os07g38970.1), succinate dehydrogenase (LOC_OS07G04240.1), isocitrate dehydrogenase (LOC_Os01g46610.1), and malate dehydrogenase (LOC_Os01g46070.1). Additional details of the analysis are described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145749#pone.0145749.g002" target="_blank">Fig 2</a>.</p