Scientists Unlock Largest Map of Any Crop to Fast-Track Rice Breeding

By Paul M. Icamina

The genetic variations of cultivated Asian rice have been mapped.

The map of 3,010 accessions, or the unique identifier given to a DNA, is the largest for a crop’s genome, the complete set of DNA—including all of its genes that contains all of the information needed to build and maintain a particular rice variety. The map is important in rice research because genomic variation is responsible for all the differences that make each rice variety different from another.

The genetic map will enable scientists to discover new gene variants and characterize known genes for important traits, such as the natural ability of a particular variety to resist diseases and withstand floods, drought,and salty water.

Molecular breeders could use the genetic markers to select rice plants that are more likely to carry a desired trait before they are planted in the field, the International Rice Research Institute (IRRI) said in a press statement.

About 780,000 rice accessions are available in gene banks worldwide. To enable the more efficient use of these accessions in future rice improvement, the Chinese Academy of Agricultural Sciences (CAAS), Beijing Genomics Institute (BGI-Shenzhen) and IRRI sequenced the 3,000-plus rice genomes.

“This information leads to faster and more accurate development of varieties suited to various agricultural environments, especially for unfavorable rice-growing areas where the poorest and
most vulnerable farmers reside,” said Dr. Jacqueline Hughes, IRRI Deputy Director General for Research.

“Plant breeders can make more intelligent choices in selecting traits for improved varieties that farmers can cultivate, which leads to food and nutrition security. This is how advancements in rice science can impact the lives of millions of farmers and consumers.”

Rice is the staple food of half the world. By 2035, an additional 112 million metric tons of rice needs to be produced on a smaller area of land, using less water and under more fluctuating climatic conditions, which will require that future rice cultivated varieties be higher yielding and resilient to multiple stresses.

“What could previously take up to 40 years from trait discovery to varietal development can now only take just a few years,” said Dr. Ruaraidh Sackville Hamilton, IRRI principal scientist and head of the IRRI International Rice Genebank. “We are also able to make the breeding process more efficient and precise, being more responsive in delivering varieties with traits that can adapt to the increasingly complex production environment.”

The new research revealed that among the 3,000 rice genomes, there are significant variations in gene content and immense sequence variation. Researchers identified more than 10,000 new rice genes and over 29 million simple variations throughout the genome.

Within the two major rice variety groups, the analysis revealed the existence of previously unreported populations that are unique to specific geographic origins. Other evidence revealed that Asian rice was domesticated multiple times thousands of years ago.

It is the largest set of genomic variants discovered for a crop species, said Dr. Kenneth McNally, IRRI senior scientist. The information is freely and publicly available for plant breeders and scientists worldwide, he said, adding it already serves as material for training a new generation of plant biologists.

Dr. Zhikang Li, a collaborating scientist from the CAAS Institute of Crop Sciences, reported that the research results have ushered in a “new era of genome- and information-based breeding.” He added that it has been a vital and extensive resource for CAAS scientists as they work on large-scale trait discovery and allelic mining, or looking for one of two or more alternative forms of a gene found at the same place on a chromosome. It is a good way to find new genes.

The mapping also identifies rice variety parents for breeding programs and establishing a comprehensive genome-based trait database for future rice improvement.

There is still considerable work to be done to discover and understand other rice genomic variations in the collection of the International Rice Genebank at IRRI and other collections around the world, said Dr. Hei Leung, IRRI principal scientist and geneticist. “Next, we will explore the largely untapped diversity in wild rice species,” he said. “This will greatly aid in defining genotype-phenotype relationships as well as improving our understanding of plant biology. To achieve this goal, we must continue the spirit of providing access to new information to the global community.”

The genome mapping was a collaborative research among IRRI, CAAS, BGI-Shenzhen and 13 other partner institutions.

The Philippine Genome Center Core Facilities for Bioinformatics of the Advanced Science and Technology Institute, Department of Science and Technology, contributed in computing and bioinformatics support.

The study, published online April 25 in the Nature journal, opens the possibility to accelerate rice breeding to achieve food security for some of the world’s most vulnerable rice farmers.

This appeared in Agriculture Monthly’s June 2018 issue. 

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