Scientists unlock wild rice genes for “climate ready” varieties amid global crop yield pressures

Researchers in Saudi Arabia and the Netherlands have investigated rice genetics to understand how years of artificial selection for valuable traits like nutritional profile have unintentionally reduced the crop’s resilience to climate change. Their findings could help boost rice yields and introduce it into regions where rice production is “currently untenable.”

According to the Sustainable Rice Platform, nearly 3.5 billion people consume rice as a staple food, and almost 60% of those experiencing hunger rely on rice for food and income.

“Domesticated rice is part of the genus Oryza with 27 species, of which nine are polyploids. 

However, we know very little about how these rice polyploid relatives have evolved, and often one or both of the parental ancestors are now extinct,” M. Eric Schranz, author and professor of the Biosystematics Group at Wageningen University & Research (WUR), tells Food Ingredients First.

“Thus, we were doing a sort of genome archeology to unravel the genomic history of the whole genus. Many of these polyploids have interesting traits, such as being able to grow in very salty conditions.”

He believes that understanding how different rice species can be combined and lead to new traits or adaptations to abiotic factors might allow the team to improve or expand rice production.

“It’s not quite Jurassic Park, but the genome of at least five now extinct diploid rice species are now known thanks to this work.”

The research was led by Abdullah University of Science and Technology (KAUST) in Saudi Arabia and WUR in the Netherlands.

The genome analysis of this work explains how rice and its complex wild relatives have evolved, says Schranz.

Tapping polyploidy for crop innovation

The findings, published in Nature Genetics, state that the rice genus Oryza possesses a “virtually untapped reservoir of genes” that can be used for crop improvement.

Polyploid plants can receive multiple sets of chromosomes from their parents. These extra sets result in a larger genome that can facilitate adaptation to new or stressful environments, evolution of novel traits and even new species.

Schranz explains that polyploidy, and particularly the merging of two different species by hybridization, contributes to evolutionary change and innovation.

“We see the importance and contributions of very old polyploidy events occurring millions and millions of years ago, such that the progenitors of the most important crop families all had genome duplications such as the grass (rice, wheat, corn), legume (beans, peas, alfalfa), crucifer (broccoli, cabbage, and watercress), and Solanaceae (potato, tomato, and peppers).”

“We also see many recent polyploid species that give wild and crop plants a potential boost, such as hexaploid wheat or cotton.”

In December, a Saudi Arabia-based ag-tech firm also tapped polyploidy by developing a hybridization grafting process that makes farming easier at high temperatures and can boost tomato yields by 20-25% over top commercial varieties.

“Neo domestication” for climate resilience

Author Alice Fornasiero, a postdoctoral research associate at KAUST, tells us that the team’s work with gene analysis represents the first step in addressing the long-standing problems of food security and sustainable agriculture.

Naturally submergence-tolerant species like O. grandiglumis can withstand climate stressors (Image credit: Maria Navarrete, KAUST).“A new promising approach to generate climate-resilient crops is neodomestication. Neodomestication allows generating new crop varieties from wild relatives or landraces that possess natural resistance to abiotic and biotic stress and are adapted to local climates.”

“Thanks to the use of genome editing techniques, such as CRISPR/Cas9, researchers can introduce precise modifications in the sequences of key genes for domestication, such as the genes controlling seed shattering (i.e., the dispersal of the seeds to the ground), grain size, flowering time, and plant height.”

These novel “climate-ready” crops retain resilience and adaptation to local climates and show key domesticated traits like non-shattering seeds, higher yields, longer flowering, and shorter, sturdier plants.

Expanding rice into harsh landscapes

Fornasiero says the wild rice relatives’ adaptation to harsh climates offers promising solutions for climate-resilient agriculture, especially given predicted environmental conditions due to climate change.

“For instance, neodomesticated and naturally submergence-tolerant species like O. glumipatula and O. grandiglumis could be cultivated in their native flooded habitats along the Amazon basin.”

Similarly, neodomesticated and “naturally salt-tolerant” species such as O. coarctata could be grown in coastal regions increasingly affected by sea-level rise and saltwater intrusion — conditions now threatening rice production in areas like the Satkhira River in Bangladesh.

Neo domestication offers a new promising approach to generate climate-resilient crops, says Fornasiero.

Beyond rice fields

Schranz believes the study’s genomic framework will be extended to other staple crops as shifting weather and warmer temperatures batter crop production worldwide.

“We definitely already see it happening and it will continue to do so as sequencing costs drop and analysis methods improve. Just a few years ago, a single reference genome of one species was a milestone. Increasingly sequencing 10s or even 100s of genomes is par for the course.”

While the current study focused on more recent polyploid evolution in a single plant genus, the team is also looking at the ancient polyploidy event and its consequences in the Asteraceae plant family, including lettuce, sunflower, chrysanthemum, and daisies, he concludes.