Rice gene map to enable breeding of improved varieties

BEIJING -- Chinese scientists have devised a detailed map of wild and cultivated rice genes, providing resources for the development of superior and more productive crop varieties to tackle global food shortages and environmental challenges.

Published in Nature this week, the study compiled 145 representative rice samples, most of which were wild species. Using advanced gene sequencing technology and computational methods, researchers at the Chinese Academy of Sciences' Center for Excellence in Molecular Plant Sciences completed a comprehensive analysis of rice genes. They established a "pangenome" collection -- a map that covers nearly all of the rice plant's genetic diversity, including tens of thousands of genes specific to wild rice.

Lead researcher Han Bin believes that the development of such a large data set is worthwhile, as previous studies of rice genes relied solely on a single reference genome that could establish just a small part of the plant's genetic diversity. In contrast, the pangenome allows scientists to explore the rich diversity of wild rice, which has been shaped by thousands of years of natural selection and has crucial traits that have ensured its survival over centuries of cultivation.

Michelle Trenkmann, senior editor at Nature, said that the study shows that "wild rice has a large repertoire of resistance genes. These could be helpful in crop-improvement efforts, which are vital for future food security."

More than 69,000 genes are included in the map, nearly 20 percent of which exist only in wild rice and are linked to disease resistance and environmental adaptability.

The study found that wild rice has a higher abundance and diversity of disease-resistant genes than cultivated rice. Han's team located 1,184 gene sites with higher disease-fighting potential than cultivated rice, including two genes that have proved resistant to rice blast, a major rice disease.

"This confirms that wild rice species can offer a valuable and direct genetic source for the development of rice varieties that are resilient to diseases and challenging conditions," Han said.

Other discoveries highlighted in the study include the confirmation of the single-domestication origin hypothesis for all Asian cultivated rice species -- resolving a long-standing academic debate -- and the identification of a new cultivated group in South Asia, establishing a complete picture of rice evolution.

About 60 percent of the world's population eats rice as a staple food. China is the largest producer of rice and a leading contributor to numerous sci-tech advancements in rice cultivation.

With this pangenome reference -- the latest breakthrough in the field -- scientists can now accurately identify advantageous genes in wild rice, trace the origins of important genes, and understand how rice adapts to different environments and changes its traits.

Furthermore, the study enables the extension of lab discoveries to field application, providing key genetic resources to develop rice varieties with high disease resistance, and enabling the precise breeding of new varieties that can withstand environmental stresses, as well as improved resource-use efficiency and higher yield potential, Han noted.