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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Research Project #425079

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

2018 Annual Report

4. Accomplishments
1. Public release of “Scarlett”- the first red bran rice variety high in anti-oxidants. The outer bran layer of the rice grain is the site of most of the nutritional value of the grain as compared to the interior endosperm which is composed primarily of starch. Although most rice that is consumed has brown bran, varieties with purple or red brans exist and generally have greater contents of health beneficial compounds. In an effort to develop new high value markets, ARS researchers at Stuttgart, Arkansas, and at Cornell University have developed Scarlett rice which contains high levels of lipophilic antioxidants and polyphenols in its red bran. The source of the red bran comes from one of the parents which is a weedy wild relative of cultivated rice. Scarlett rice will benefit rice growers because of the high yield potential when grown in the southern U.S. along with its nutritionally dense red bran.

2. Genotypes with low lipase activity for improving shelf life of whole grain rice. Whole grain rice, which has the bran layer intact, contains more nutrients and health beneficial compounds than milled rice (bran moved) and its consumption was associated with reduction of several chronic diseases. However, the bran layer is also where most lipids are deposited along with lipid degrading enzymes, lipase and lipoxygenase, which shorten the shelf life of whole grain rice. ARS researchers at Stuttgart, Arkansas, determined lipase induced hydrolytic rancidity (HR) levels in the bran of a set of diverse cultivars and found more than 15-fold variation in HR. Among them, genotypes of red and brown brans had lower HR than other bran color classes, purple, light brown and white. Total phenolic compounds in the purple brans was negatively associated with HR. Within the light brown bran color class, the typical bran color of U.S. cultivars, genotypes of lower lipase activity than U.S. cultivars were found and could be used as breeding materials to improve storage stability of U.S. cultivars.

3. New yield enhancing genes found for rice. To meet the growing demand for food, it is essential to understand the plant processes that control grain yield. ARS researchers in Stuttgart, Arkansas, in collaboration with scientists at Cornell University and support from the National Science Foundation previously evaluated a collection of over 400 diverse rice cultivars, identified as the Rice Diversity Panel 1 (RDP1), for 25 traits related to yield improvement. Quantitative trait loci (QTL) were identified that are linked to rice grain yield. To genetically dissect yield related traits a mapping population of the tropical japonica cultivars, Estrela and NSFTV199, was evaluated and 41 known genes for yield-related traits were identified and two regions had no known gene. Based on these results, DNA markers associated with panicle architecture and seed size are under development and selected lines are being evaluated in field trials for release as germplasm lines to breeders. Having both the germplasm lines and DNA markers will allow breeders to accelerate their breeding efforts to increase U.S. rice yields by incorporating and selecting for panicle and seed traits.

4. Purple bran rice is high in tricin, a flavonoid compound with numerous health benefits. Tricin, a flavonoid compound, has been reported to have numerous health benefits including anti-cancer properties and has been proposed as a candidate for cancer prevention clinical trials. Tricin has been identified in many plant species including rice. ARS researchers at Stuttgart, Arkansas, in collaboration with Rutgers University, studied the flavonoid compounds in rice of four bran color classes, light brown, brown, red and purple. Purple bran had higher tricin content as well as a broader range of other flavonoid compounds, including the anthocyanins that give the bran purple color. These results provide direction to breeders interested in improving the nutritional content of whole grain rice.

5. Allele mining for grain quality traits in diverse U.S. rice germplasm collections. A broad range of traits determine rice grain quality including grain shape, translucency, milling yield, cooking characteristics, sensory traits, and nutritional aspects. U.S. rice germplasm collections contain a diversity of rice with a tremendous range in grain quality traits. ARS researchers at Stuttgart, Arkansas, evaluated a genetically diverse panel of rice cultivars using high density genotyping data and genome-wide association (GWA) analysis of grain quality. Molecular markers were discovered that are associated with starch, cooking quality, grain dimensions, translucency, and protein content. Molecular markers will be deployed for use in marker assisted selection (MAS) to accelerate breeding for grain quality.

6. Detection of genes controlling grain chalk using NIR spectroscopy. One of the bottlenecks in germplasm evaluation is the labor intensive and time-consuming nature of phenotyping. Having a means to rapidly and accurately evaluate thousands of genotypes is needed to fully utilize the wealth of genomic data currently available. ARS researchers at Stuttgart, Arkansas, in collaboration with ARS researchers at Beltsville, Maryland, have evaluated 200 diverse rice accessions of the USDA Rice Minicore with a genomic data set of 3.3 million SNP markers along with hyperspectral imaging as a high-throughput phenotyping tool to understand the genetic control of grain physicochemical traits. A specific wavelength range detected rice grain chalk and was linked with novel chalk related genes. These results will assist breeders in developing environmentally resilient rice varieties with ideal grain quality.

7. Breeding rice varieties with increased concentration of molybdenum (Mo) in grains and tolerant of Mo-deficient soils. Molybdenum (Mo) is an essential micronutrient for most living organisms, and cereal grains are the major dietary source of Mo for humans and animals. Although cases of Mo deficiency in humans is rare, Mo deficiency in plants is fairly common, especially in the tropics, where rice is predominantly grown. ARS researchers at Stuttgart, Arkansas, in collaboration with University researchers in China, the United Kingdom, and Delaware, U.S. determined that the gene underlying a QTL for grain-Mo concentration in a biparental population was the OsMOT1;1 molybdate transporter gene, which was mainly expressed in roots, and affected uptake of Mo from the soil as well as translocation to shoots. This newly discovered natural allelic variation in OsMOT1;1 can be used by breeders to develop rice varieties more tolerant of Mo-deficient soil, as well as, producing rice varieties with increased grain-Mo concentrations.

8. Whole grain rice bran is a rich source of bioactive components that have potential to promote gastrointestinal health. Among these components, feruloylated arabinoxylan oligosaccharides, a soluble portion of non-digestible fiber after enzymatic hydrolysis (FAXO), and red pigmented rice bran polyphenols (RBPP) were investigated for their prebiotic potential and the impact on human gut microbiota in vitro by ARS researchers at Stuttgart, Arkansas, in collaboration with researchers at University of Arkansas, Fayetteville and at Arkansas State University, Jonesboro. Fresh fecal samples collected from ten healthy adults with no signs or symptoms of bowel diseases or conditions received 5 treatments including FAXO and RBPP, separately and combined. Results showed that treatment with FAXO significantly increased the production of short chain fatty acids, the fermentation products of the colonic bacteria that are beneficial to the gut health. FAXO and RBPP had synergistic effects on increasing the abundance of bacteria that generate butyrate short chain fatty acid, a fatty acid with protective effects of colon cells against cancer. Results from this study suggested that FAXO and RBPP from rice bran can potentially promote colon health through a prebiotic function.

9. Rice cultivars with low glycemic index and preferred sensory properties. Rice has high glycemic index (GI) and diets high in GI are associated with chronic diseases. Decreasing the rate of starch digestion lowers GI, improving nutritional properties of rice. However, the effects of starch digestive fractions, rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS), on cooked rice texture which impact end-use properties need to be understood. ARS researchers at Stuttgart, Arkansas, and at New Orleans, Louisiana, evaluated seven U.S. rice cultivars for contents of starch digestive fractions and for texture attributes by a descriptive sensory panel. In addition, apparent amylose (AAC), lipid contents, and paste viscosities were determined. Multiple linear regression models showed that RS and AAC were the major predictors and lipids and SDS played minor roles in texture attributes. Among high amylose cultivars, preferred digestive properties and palatable texture can be selected to meet diverse consumer markets.

10. Improvement of whole grain nutritional quality can be accomplished by increasing the proportion of bran in whole grain rice. Rice bran, the outer most layer of the whole grain, is the primary site of deposition of most nutrients, minerals and bioactive compounds, however, rice bran accounts for a very small portion of the whole grain by weight. Increasing the weight proportion of the bran to whole grain will enhance whole grain rice nutritional value. ARS researchers at Stuttgart, Arkansas, determined the total bran weight and bran weight per surface area (BWS) of the whole grain for 134 diverse rice genotypes and found more than 2.3- and 2.5-fold variation, respectively. Mean comparison of BWS among bran color classes showed that purple bran genotypes had the highest BWS, followed by red, white, light brown and brown. This report showed high bran weight genotypes can be selected for in a breeding program to improve whole grain nutritional quality.

Review Publications
Poulev, A., Chen, M., Cherravuru, S., Raskin, I., Belanger, F.C. 2017. Variation in levels of the flavone tricin in bran from rice genotypes varying in pericarp color. Journal of Cereal Science. 79:226-232.
Pham, T., Savary, B., Chen, M., Lee, S., Mcclung, A.M. 2017. In vitro fermentation patterns of rice bran components by human gut microbiota. Nutrients. 9(11):1237.
Zhao, D., Hamilton, J.P., Vailancourt, B., Zhang, W., Eizenga, G.C., Cui, Y., Jiang, J., Buell, C., Jiang, N. 2018. Evolutionary trajectory of Pack-MULEs is determined by their epigenetic status. Nucleic Acids Research.
Heuschele, D.J., Pinson, S.R., Smith, A.P. 2017. Metabolic responses to arsenic in rice seedlings that differed in grain arsenite concentration. Crop Science.
Chen, M., Mcclung, A.M., Bergman, C.J. 2017. Phenolic content, anthocyanins and antiradical capacity of diverse purple bran rice genotypes as compared to other bran colors. Journal of Cereal Science. 77:110-119.
Pinson, S.R., Jia, Y., Jia, M.H., Gibbons, J.W. 2018. Novel QTLs affecting rice kernel fissure resistance discovered in the cultivar ‘Saber’ augment those from ‘Cybonnet’. Crop Science.
Eizenga, G.C., Sanchez, P., Jackson, A.K., Edwards, J., Hurwitz, B.L., Wing, R.A., Kudrna, D. 2017. Genetic variation for domestication related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population. Molecular Breeding.