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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.

Identification of novel QTLs for grain fertility and associated traits to decipher poor grain filling of basal spikelets in dense panicle rice