This is the first report revealing role of non-coding RNA regulators in domestication

The domestication of rice can be tracked to the loss of a small RNA molecule (miR397), according to a study carried out at the National Centre of Biological Sciences (NCBS), Bengaluru. This finding can be used to improve crops for the future

Thousands of years ago humans domesticated wild plant varieties that yielded flowers, fruit, grains and medicines. In this process, the domesticated species were selected for many useful traits, such as higher yield. While domestication increased the fitness of the species under manmade conditions, it reduced their fitness in the wild. The domesticated species eventually became dependent on human nurturing..

Indica rice, a subspecies of Oryza sativa, was domesticated from two wild species Oryza nivara and Oryza rufipogon. Both the wild species have weak stems and lie prostrate near edges of water bodies. The process of domestication selected useful traits from these: stronger stems, absence of seed shattering, more grains per plant, aroma, colour etc.

For differences seen to manifest in the organism (phenotype), there should be corresponding changes in the genome. However, extensive studies found that the genomes did not show variation proportional to the changes in the phenotype. Researchers failed to identify genes responsible for the changes observed in domesticated Indica rice as compared to its wild relatives. The answer lay in regulatory molecules known as the small RNAs.

“Rice breeders found large regions in genomes that are responsible for a trait/appearance - the Quantitative Trait Loci (QTL). There are 200 such QTLs identified... for rice yield. However, only 20 of them have been identified at the molecular level when we initiated this study,” explains Padubidri V. Shivaprasad of NCBS, in whose lab the study was carried out.

Increasing lignin

Laccases are enzymes involved in polymerisation of monomers of lignin, which contribute to stem woodiness. If the plant produces more laccases then more lignin gets accumulated in the plant.

Small RNA dictate whether a gene may express itself and make a protein; they control the way genes express themselves in the phenotype.

After studying the two wild species, the domesticated high-yielding varieties and several rice lines in between (land races) — they screened 12 and sequenced 7 — the team identified a small RNA controlling laccases; this is named miR397.

While miR397 is expressed in high levels in the wild species, it gradually reduces in intermediate forms.

They observed that miR397 regulated many aspects of rice growth including a change in the amount of lignin present in the plant.

“Increased lignin gives additional strength to the plant to bear more grains and that resulted in improved yield,” says Swetha Chenna, researcher from NCBS who is registered for PhD from SASTRA University and is the first author of the paper published in Plant Cell.

“In our study we show that at least 26 laccases including the miR397 fall into QTLs that are related to yield. These QTLs were identified by many labs worldwide, over many decades,” says Dr Shivaprasad. “This is the first report that reveals role of non-coding RNA regulators in domestication of any species,” he adds.