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Pigmented rice is known to be more nutritious than white rice, making it an important resource for improving human health and combating malnutrition. However, these varieties, which include black, brown and red, require improved yield and agronomic properties if they are to be widely accepted by farmers.
An international team led by KAUST’s Magdi Mahfouz and Khalid Sediq has demonstrated that desirable agronomic traits such as short stem length and early maturity can be introduced into black rice(1).
Sedeeq, a postdoc in Mahfouz’s lab, says the first step to making these improvements is collecting comprehensive genomic information.
“Although several japonica and indica rice genomes have been assembled, complete genome sequences are available for only a few pigmented varieties,” he says.
The researchers selected three black and two red rice cultivars for whole-genome sequencing. To detect more genetic variation, they sequenced an additional 46 species.
“The next step was to analyze the composition of these species and identify those with better nutrition as candidates for improvement,” says Sedek. To do this, researchers examined 63 varieties of black, red, and brown rice, and black rice showed the best nutritional content in various compounds, including carbohydrates, amino acids, secondary metabolites, lipids, peptides, and vitamins.
Pigmented rice (especially black rice) is rich in essential nutrients including iron, zinc, copper, manganese and selenium. In particular, the black Indonesian rice Cempo Ireng (the rice richest in iron and the black rice genotype richest in zinc) can provide the daily requirements of these essential elements.
The researchers used these nutrient and metal-ion profiles to identify several nutrient-rich varieties with high levels of antioxidants and other beneficial compounds and elements that could be potential varieties for improvement.
Sempo Ireng is one of them. However, despite its pest and disease resistance, farmers are reluctant to cultivate Chempo Ireng due to its long stem and five-month life cycle. Sedek established a regeneration and transformation system in Sempo Ireng, then used CRISPR/Cas 9 to knock out three flowering time repressors, resulting in fewer early-maturing varieties.
Improved agronomic traits in pigmented rice cultivars can make them more suitable for cultivation and inclusion in the food chain. However, Mahfouz notes that more work is needed to determine whether these engineered traits can co-exist with other important traits, such as yield, in pigmented rice.
“However, this research provides important resources for crop bioengineers and breeders to continue to improve pigmented rice and exploit its potential benefits for human health.”
Mahfouz and his team now plan to improve a local red rice known as Hassawi rice. This particular rice crop from Saudi Arabia is of great cultural and economic importance in the region. By leveraging CRISPR technology, the group aims to increase the productivity and other key characteristics of Hasawi rice to meet the unique needs of the local Saudi market.
Reference: Sedeek K, Zuccolo A, Fornasiero A, et al. Multi-omics resources for targeted agronomic improvement of pigmented rice. Nat food. 2023;4(5):366-371. doi:10.1038/s43016-023-00742-9
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