20 years on from the rice Genome project: What have we learnt?

  (photo credit: SHUTTERSTOCK)
(photo credit: SHUTTERSTOCK)

For many, rice is a staple feature at the dining table, with more than three billion people worldwide relying on the grain as a cornerstone of their diet. This is not just a modern phenomenon – far from it. Rice has sustained humanity for generations, with the grain found in archaeological sites dating back 12,000 years

Rice may be one of the world’s most important and popular foodstuffs. But until 20 years ago, we knew virtually nothing about it. In a move that would radically change this, BGI Group made history in 2002 by mapping the genetic code of rice in its entirety, the world’s first whole genome sequencing of a crop, unveiling the DNA sequence of the rice plant to reveal clues as how to improve crop quality, resistance and yield.

“This is a breakthrough of inestimable significance,” said Joachim Messing of Rutgers University. “Not only for science and agriculture, but also for all those people who depend on rice as their primary dietary staple — more than half the world’s population.”

Using the so-called whole-genome shotgun technique, BGI Group mapped the most common rice strain in the Asia-Pacific known as indica by blasting the genome into around 100,000 smaller, more manageable pieces, which were then reassembled with the aid of high-powered computers. Through this process, BGI Group discovered that indica rice contains between 45,000 and 56,000 genes – a far greater number than the average 30,000 to 40,000 genes in the human genome.

For most of human history, unlocking the entire genetic code of an organism was an unimaginable scientific feat. However, in decoding the genome of the very first crop plant, BGI Group has ushered in a new era in agriculture and food production. 

Unveiling the genetic code of the rice plant has paved the way for breeders to develop better varieties of rice with improved nutrient and growing qualities, such as pest-resistance or higher yield. Likewise, scientists have also discovered ways to make rice survive drought, withstand extreme temperatures and even cope with saline soils. For instance, scientists developed rice strains that can grow in the salty, alkaline conditions of the Jinghai district in northern China, with test fields in Tianjin – the municipality that encompasses Jinghai – recording a yield of 4.6 metric tons per acre last year, higher than the national average for production of standard rice varieties and making this a commercially viable way to grow rice.

These developments have real world consequences. 

As the global population skyrockets, food sources are coming under increasing pressure. At the same time, the food supply continues to be threatened by the effects of climate change and rising sea levels, with urbanisation, pollution and the overuse of fertilisers leading to a dramatic reduction in arable land by 6 per cent from 2009 to 2019. 

By tackling the issue head on and developing varieties of rice that can withstand these environmental stresses, we can raise the quality and quantity of food for those who need it most. As Ronald Cole-Turner of Pittsburgh Theological Seminary explains, “The benefits of this breakthrough are likely to touch the world’s neediest people, those whose very existence is threatened daily by drought or poor growing conditions.”

The implications of the research do not end there. In fact, sequencing the rice genome has led to the development of “perennial rice”, with BGI Group scientists pioneering the development of crops that can be continuously harvested for three to five years without tilling the fields or transplanting rice seedlings after harvesting. 

As Wang Ren, director of Shenzhen National Gene Bank explains, "Perennial rice is a revolutionary innovation in agricultural production mode. It has changed traditional agricultural production methods and brought very good economic and ecological benefits to agricultural production."

Likewise, mapping the rice genome has also proved critical in understanding the characteristics of related crops, unlocking a treasure trove of genetic information in the world’s seed banks.

Much has changed in the years since BGI Group first sequenced the rice genome in 2002, with genetic sequencing capacity continuing to develop and expand. In the years that have passed, we have seen the advent of the Earth BioGenome Project, which aims to sequence, catalogue and characterise the genomes of all of Earth’s eukaryotic biodiversity. Likewise, more recently, the U.S.’s National Institutes of Health’s All of Us Research Programme published the first genomic dataset of nearly 100,000 whole genome sequences, with public and private research bodies across the globe recognising the importance of genomics.

It is clear cracking the genetic code of the rice plant 20 years ago proved a major step forward for agriculture, with the effects still felt today. Armed with rice’s full genetic sequence, scientists can now identify beneficial genes much more quickly and accurately to develop strains that can meet the challenges of the growing food security crisis. 

It appears genomics will sow the seeds of future prosperity. 

The Article was written in cooperation with Thomas Herd