Genetic discovery may benefit rice breeding

Researchers learn diversity was inherited through just two maternal genomes that were identified in all the rice varieties

Researchers at Australia’s University of Queensland have been investigating the heritage of more than 3,000 rice genotypes as part of a long-term project to improve rice varieties by using wild rice to expand the gene pool.

What they discovered was that rice diversity was inherited through just two maternal genomes that were identified in all the rice varieties.

“The idea (behind the research) is that rice was diverse across the natural range in Asia, but it was domesticated in two distinct places in the last 5,000 to 10,000 years,” said Robert Henry, professor of innovation in agriculture and director of the Queensland Alliance for Agriculture and Food Innovation.

“The two wild rices used were from lineages that probably diverged in the wild around one million years ago.”

He said that interbreeding continues at some level with wild populations exposed to gene flow from large, domesticated populations.

“The key point is that we do not know the genetic effect of these two different lineages yet but would like to bring many more into the domesticated rice gene pool,” he said.

The discovery of the two maternal genomes could help address the issue of global food security by being able to breed more rice varieties for local adaptation and changing regional climate. The goal would be to make all rice crops more resistant to future environmental challenges in order to maintain both plant health and yield.

Rice is the staple food of more than half the world’s population and is grown in more than 100 countries, with a total harvested area of approximately 390 million acres. Production is more than 700 million tons annually (470 million tons of milled rice). Nearly 640 million tons of rice are grown in Asia, representing 90 percent of global production.

“(The finding) gives us clues as to how we might try to capture more of the diversity in the wild and bring it into the domesticated gene pool to improve rice crops,” said Henry.

In the report published in BMC Plant Biology, the scientists recognized that, with the critical global importance of rice, enhancement of genetic diversity is key to improving crop resilience to climate change and managing food security.

In the past, rice breeding has not focused on selection of maternal genomes. The study suggested that the analysis of the different chloroplast genomes (the two types in domesticated rice and others from wild populations) with a common nuclear genome may likely be necessary to clarify the potential for genome selection to improve on the performance and yield of rice in various locations. The maternal genomes that were discovered could have an effect on traits that influence environmental adaptation, which will then determine crop performance.

“The maternal lineage is preserved via the seed and we’ve identified that because rice farmers have collected and still continue to collect the seed from the field,” said Henry.

“The local varieties become very much like the local wild rices.”

He emphasized that discovering the two maternal genomes has implications that could take breeding to the next level in terms of producing rice with higher performance, yield and other qualities.

“It points to the need to understand the significance of the maternal genotype in terms of performance of rice because we did not previously understand that there are two very distinct maternal functional types.”

The research will now involve measures to bring much more diversity from the wild into the domesticated gene pool and the process will start with crossing wild and domestic rice.

“(The finding) points to the need to understand the significance of the maternal genotype in terms of performance of rice because we did not previously understand that there are two very distinct maternal functional types,” he said.

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