Rice researchers in India have identified1 an important region in the rice genome that harbours a gene determining the size and weight of the grain.
Though India has the world's largest area under rice cultivation, it is not the biggest producer of rice due to low productivity. Grain size being one of the key factors determining yield, rice breeders aim to develop varieties producing heavy grains.
For their genome sequencing study, the researchers selected four Indian varieties – two possessing long grains and high seed weight (Pusa Basmati 1121 and IC 301206 , commonly known as Long Grain Rice), and two having short grains with lower seed weight (Sonasal and Bindli).
Analysing the DNA from these and 3000 global rice accessions, the authors identified a six megabases (6 Mb) long stretch of DNA on chromosome 5. "This site, named Low Diversity Region (LDR), was found to harbour one major Quantitative Trait Loci (QTL), containing the gene (OsTOR) that determines the size of the rice grain", says corresponding author Jitendra Thakur of the National Institute of Plant Genome Research (NIPGR) in New Delhi. Plant biologists from the University of Delhi and institutes under the Indian Council of Agricultural Research also collaborated in the study.
The LDR also harbours QTLs for domestication-related traits. “This LDR could be utilised for improving rice production by targeting various traits including the seed size gene identified here," the authors say.
The study further showed varying degrees of this LDR stabilisation across different rice groups. For instance, the LDR footprint was found high in 97% of japonica and 83% of indica varieties, but was not so prevalent in "aus" (Oryza sativa L.), another rice population abundantly grown in eastern India and Bangladesh.
1. Kumar, A. et al. Genome‐wide analysis of polymorphisms identified domestication‐associated long low diversity region carrying important rice grain size/weight QTL. Plant J. (2020) doi: 10.1111/tpj.14845