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

Sudhanshu Sekhar,Lambodar Behera,Soumya Mohanty,Jitendra Kumar,Niharika Mohanty,Rudraksh Shovan Panda,Birendra Prasad Shaw,Swagatika Das

doi:10.1038/s41598-021-93134-7

Sudhanshu Sekhar, Lambodar Behera + Show 6 more

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https://doi.org/10.1038/s41598-021-93134-7

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Abstract

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.

Highlights

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 research conducted so far has revealed that the poor filling of grain in the basal spikelets compared with apical ones could be the low activity of the starch synthesizing enzymes, like sucrose synthase (SUS), starch synthase (SS), granule bound starch synthase (GBSS), UDPase, adenosine diphosphate glucose pyrophosphorylase (AGPase), starch debranching enzymes (DBE) and starch branching enzyme (SBE)[14,15,16,17], the evidences are only circumstantial
In the present study, an attempt was made to identify novel QTLs and candidate genes associated with spikelet fertility, panicle compactness, and phytohormone ethylene production using RIL mapping population developed from the cross between two indica rice cultivars, PDK Shriram and Heera and further to investigate the possible cause of poor grain filling or sterility in basal spikelets of the dense panicle

Summary

Introduction

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 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. In the present study, an attempt was made to identify novel QTLs and candidate genes associated with spikelet fertility, panicle compactness (inter-grain space), and phytohormone ethylene production using RIL mapping population developed from the cross between two indica rice cultivars, PDK Shriram (compact panicle, high spikelet number per panicle) and Heera (lax panicle, low spikelet number per panicle) and further to investigate the possible cause of poor grain filling or sterility in basal spikelets of the dense panicle

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