The increase of spikelet number in the panicles of modern super rice has made the architecture compact, as the extra spikelets are accommodated mostly on secondary branches than on primary branches. However, the grain yield did not improve because of poor grain filling, which was more visible in the basal spikelets than apical spikelets. The objective of this study was to examine the effect of the compactness and positional difference of spikelets in the panicle on grain filling by comparing the activity and genetic expression of starch synthesising enzymes in the developing kernels of lax-(Upahar and CR3856-45-11-2-7-2-5 (CR-45)) and compact-(Mahalaxmi and CR3856-29-14-2-1-1-1 (CR-29)) panicle cultivars. Upahar and Mahalaxmi are genetically related, whereas CR-45 and CR-29 are recombinant inbred lines. The grain carbohydrate concentration and activity of sucrose synthase (SUS) enzyme were estimated during the active period of grain filling. Further, expression of isoforms of SUS, ADP glucose pyrophosphorylase (APL and APS for large and small units respectively) and starch synthase (SS and GBSS for soluble and granule bound starch synthases respectively) were also assayed through PCR studies. The genotype approach used revealed grain SUS activity and starch concentration high and sugar concentration low in the lax-compared with compact-panicle cultivars and in the apical spikelets compared with basal ones. The margin of variation between apical and basal spikelets was higher in the compact-than the lax-panicle cultivars. Genetic expression of most of the isoforms of the enzymes was higher in the lax-than the compact-panicle cultivars as seen in RT-PCR studies. A quantitative appraisal of transcript levels of isoforms in the qRT-PCR identified greater expression of SUS3 in the basal spikelets of Upahar than that in Mahalaxmi and in CR-45 over CR-29, most prominently during the active period of grain filling. We conclude that proximal location as well as increased density of spikelets on panicles affected SUS3 expression in the basal spikelets. The metabolic dominance of a spikelet in rice panicle is dependent on the expression of the genes for different isoforms of starch synthesising enzymes, but the expression of SUS3 could be more specific than the others. SUS3 expression is most active during grain filling of the lax-panicle cultivars, but its dominance is reduced significantly in the kernels of the compact-panicle cultivars.

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High grain number is positively correlated with grain yield in rice, but it is compromised because of poor filling of basal spikelets in dense panicle bearing numerous spikelets. The phenomenon that turns the basal spikelets of compact panicle sterile in rice is largely unknown. In order to understand the factor(s) that possibly determines such spikelet sterility in compact panicle cultivars, QTLs and candidate genes were identified for spikelet fertility and associated traits like panicle compactness, and ethylene production that significantly influences the grain filling using recombinant inbred lines developed from a cross between indica rice cultivars, PDK Shriram (compact, high spikelet number) and Heera (lax, low spikelet number). Novel QTLs, qSFP1.1, qSFP3.1, and qSFP6.1 for spikelet fertility percentage; qIGS3.2 and qIGS4.1 for panicle compactness; and qETH1.2, qETH3.1, and qETH4.1 for ethylene production were consistently identified in both kharif seasons of 2017 and 2018. The comparative expression analysis of candidate genes like ERF3, AP2-like ethylene-responsive transcription factor, EREBP, GBSS1, E3 ubiquitin-protein ligase GW2, and LRR receptor-like serine/threonine-protein kinase ERL1 associated with identified QTLs revealed their role in poor grain filling of basal spikelets in a dense panicle. These candidate genes thus could be important for improving grain filling in compact-panicle rice cultivars through biotechnological interventions.

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Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (osa-novmiR1, osa-novmiR2, osa-novmiR3, osa-novmiR4, and osa-novmiR5) and three known (osa-miR166c-3p, osa-miR2102-3p, and osa-miR530-3p) miRNAs were selected for their expression validation through miRNA-specific qRT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress.