Location: Responsive Agricultural Food Systems Research Unit
Project Number: 3093-10700-001-008-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 1, 2026
End Date: Jun 30, 2029
Objective:
This project will conduct research to quantify nutrient profiles using diverse germplasm collections in rice and sorghum grain to benefit farmers and producers, with the goal of increasing the nutritional and healthfulness of these two crops.
Objective 1: Quantify nutritional and bioactive metabolite diversity across diverse rice germplasm to identify the underlying genetic variation controlling these traits.
Rice is primarily a source of carbohydrates, especially starch, which provides energy, and it also contains small amounts of protein with a relatively good amino acid profile compared to other cereals. Rice also contains bioactive metabolites, including phenolic compounds, flavonoids, and ¿-oryzanol, which have antioxidant and anti-inflammatory properties. In pigmented varieties like red and black rice, anthocyanins are present and are associated with additional antioxidant and potential cardioprotective health benefits.
Objective 2. Identify key genes controlling micronutrient accumulation in sorghum grain using a mutant population.
Compared with rice, sorghum generally contains more protein, fiber, and micronutrients, especially when both are consumed as whole grains. Sorghum is typically richer in iron, zinc, magnesium, and B vitamins, and it often has a higher overall antioxidant capacity due to its higher levels of phenolic compounds. While brown rice provides beneficial metabolites such as y-oryzanol and ferulic acid, sorghum is particularly notable for its diverse polyphenols, including tannins and unique 3-deoxyanthocyanidins, which have strong antioxidant and anti-inflammatory properties.
Approach:
Objective 1: Generate untargeted metabolome and ionome data from a diverse USDA collection of 315 Oryza sativa lines. The samples will be analyzed using LC-Q-TOF and ICP-MS. The cooperator will conduct feature and peak annotation and conduct calculations of metabolite diversity and metabolic gene cluster analyses, followed by genome wide association studies (GWAS) using metabolites and micronutrients (mGWAS). The mGWAS will be used to identify candidate loci associated with high production of nutrients and other agronomic traits in rice. Using comparative genomics and other statistical tools, comparisons between rice from the current study and sorghum from the cooperator’s previous research will be done to identify both conserved and species specific genetic mechanisms associated with metabolite accumulation in grains of both species.
Objective 2: Study EMS mutagenized-high micronutrient Sorghum bicolor (sorghum). Quantification of micronutrients in a collection of 350 ethylmethanesulfonate (EMS) lines of sorghum that were grown at the USDA-ARS Plant Stress and Germplasm Research (PSGR) unit in Lubbock, TX, will be measured using ICP-MS. Micronutrients such as iron (Fe) and zinc (Zn) that can combat nutrient deficiencies in at-risk individuals and populations. Preliminary data has shown that mutations in micronutrient transporter genes such as SbOTP3, SbBTS, SbNRAMP6 and others show a significant increase in Fe and Zn accumulation relative to wild-type Btx623 genotype. Following the measurement of the EMS mutant collection, we will conduct statistical analysis to determine the quantitative variation in micronutrient accumulation in the EMS mutant collection. Illumina sequencing has been conducted on several of the lines in this collection, and additional lines will be sequenced and genotyped using GATK and SNPeff. Together, the rice and sorghum metabolite and micronutrient data will accompany SNP marker data that can be used to breed high nutrient accumulating. A major challenge in agriculture is producing high yielding biofortified crops due to trade-offs that can affect yield when selecting for non-carbohydrate based traits such as phytochemicals or phytonutrients. Therefore, breeding for biofortified crops must focus simultaneously on increasing plant nutrients and yield.