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Researchers at the National Institute of Plant Genome Research (NIPGR) in New Delhi have identified a 'master’gene in rice that breeders can target for better yields1.

Rice yield is mainly measured by the number of grains per plant and grain weight. Breeders try to enhance these parameters to increase rice productivity. The grain size of rice is determined by multiple genes or genomic loci known as Quantitative Trait Loci or QTL. Till now, scientists have identified more than 40 major QTLs or genes in the rice genome associated with grain size and weight. However, how these genes coordinate to regulate the grain size and shape was not known.

Jitendra Thakur and his team at NIPGR have identified a ‘cofactor’ OsMed15a as the master gene of grain size and weight trait. "OsMed15a governs the seed size by regulating the expression of three associated genes GW2, GW5 and D11,” Thakur, the lead author of the study, told Nature India . Within this master gene, the researchers also characterized the nucleotide variations (known as Single Nucleotide Polymorphism or SNPs) associated with longer or smaller size grains.

The researchers validated that the master gene was responsible in determining the size and weight of rice grain in transgenic plants that they grew in a lab. When they suppressed the expression of OsMed15a using RNA interference technology, the seeds in transgenic rice plants became smaller, while over-expression of OsMed15a made the rice seeds bigger.

“In addition to nucleotide composition of OsMed15a, its expression level also has a profound effect on rice grain size and weight," the authors say. They found that OsMed15a governs seed size by regulating the expression of associated genes GW2, GW5 and D11.

The area under rice cultivation in India is one of the highest in the world but productivity (at around 2300 kg/hectare) remains far lesser than other rice producing countries such as Japan or China.

The scientists say introgression (or transfer of genetic information from one species to another by crossing and backcrossing) of the long grain allele of OsMed15a into the genome of short grain varieties will help enhance the grain size and weight trait. OsMed15a, they propose, could be "the smart choice" for modulating the size of rice grain. Thakur’s laboratory is collaborating with some expert breeders for field trials.

This approach to study seed size and the elucidation using tools of molecular biology are significant, says geneticist Parthasarathy Chenna Kesavan, a Distinguished Fellow at the M. S. Swaminathan Research Foundation in Chennai.

OsMed15a seems to be the main 'regulator of regulators' of seed development and seed morphology in rice, says Neel Sarovar Bhavesh from the International Centre for Genetic Engineering and Biotechnology in New Delhi. The study has used an integrative approach to conclusively establish Med15a protein in rice as a converging point of different transcriptional signals. Further study may be needed, he feels, to ensure that other traits in rice are not affected.

Bhavesh says India’s policy around modified plant varieties needs an urgent look in order to enable such experiments to reach farmers so that country can meet it target of doubling farmers' income by 2022.


1. Dwivedi, N. et al. The Mediator subunit OsMED15a is a transcriptional co-regulator of seed size/weight–modulating genes in rice. BBA – Gene Regul. Mech. (2019) doi: 10.1016/j.bbagrm.2019.194432