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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS

Location: Dale Bumpers National Rice Research Center

2012 Annual Report


1a.Objectives (from AD-416):
Objective 1: Phenotypically and genotypically characterize the rice National Small Grains Germplasm Collection (NSGC) and conserve genetic stocks, mutants, and mapping populations in the Genetic Stocks Oryza (GSOR) to promote greater use by the research community. Sub-objective 1.A. Characterize accessions in the NSGC rice collection for 27 descriptors and rejuvenate seed of low inventory genetic seedstocks. Sub-objective 1.B. Perform structure analysis following genotypic and phenotypic evaluation of the NSGC Core collection. Sub-objective 1.C. Expand the GSOR collection to 15,000 accessions and establish a web-based ordering and distribution system. Objective 2: Evaluate rice germplasm to identify genetic resources having enhanced nutritional properties and added-value for the food industry. Sub-objective 2.A. Identify genetic variability for antioxidant capacity and the content of main classes of polyphenols and carotenoids in rice germplasm. Sub-objective 2.B. Structurally identify and quantify major flavonoid and proanthocyanidin compounds in rice genotypes with different bran color. Sub-objective 2.C. Determine the effect of processing on rice bran phytochemicals. Sub-objective 2.D. Identify quantitative trait loci (QTL) associated with rice grain elemental content. Sub-objective 2.E. Measure genotype and environment interactions on starch structure and grain quality. Sub-objective 2.F. Determine the impact of non-conventional cultural management practices on rice grain quality. Objective 3: Map new resistance genes for blast disease and straighthead disease identified in germplasm accessions. Sub-objective 3.A. Mine novel blast resistance genes from indica rice germplasm for use in U.S. breeding programs. Sub-objective 3.B. Decipher genetic mechanism for resistance to straighthead, a physiological disease. Objective 4: Map genes associated with grain quality traits, including rice paste viscosity and grain chalk. Sub-objective 4.A. Genetically map starch paste viscosity variation as a predictor of rice processing quality. Sub-objective 4.B. Genetically map grain chalk formation which influences milling quality.


1b.Approach (from AD-416):
Additional germplasm and data will be added to the NSGC rice collection for distribution to the public via GRIN. The Core collection will be characterized for sheath blight disease resistance, grain mineral accumulation, straighthead tolerance, protein content, and cold tolerance, and genetic markers will be identified that are associated with these traits. The Genetics Stocks Oryza (GSOR) collection will be expanded to 15,000 accessions that are curated and distributed to the research community through a searchable on-line database. Selected accessions from the NSGC collection will be evaluated for health beneficial compounds like polyphenols, flavonoids, and carotenoids and the influence of the environment and processing methods on levels of these compounds will be evaluated. Germplasm will be evaluated under flooded and aerobic conditions to understand the genetic mechanisms controlling nutrient uptake. Mapping populations will be developed, and rice gene microarray chips will be used to identify chromosomal regions associated with nutrient uptake. The genotype x environment interaction on key enzymes in the starch pathway will be studied to determine how they impact starch structure and processing quality. In an effort to understand how rice quality will be impacted by crop rotation systems, 5 to 10 rice cultivars will be grown using conventional tillage/no-till, permanent flood/intermittent-flushing, different fertilization rates, and different crop rotations, and agronomic and cooking quality traits will be evaluated to provide insight as to how changing cropping systems will impact rice milling and cooking quality. Novel genes for blast and straighthead disease resistance will be identified using mapping populations. Markers and germplasm will be released to breeders for developing improved cultivars. Sequence variation around a SNP in exon 10 of the rice Waxy gene will be evaluated to determine what impact it has on RVA paste viscosity characteristics. Genetic markers will be developed that can be used in breeding for elevated pasting profiles, which is desired for rice used in canning, instantizing, and other food preparation processes. We will fine map several QTL previously identified to be associated with grain chalk. Progeny from the selected recombinant lines will be grown in two environments and chalk amounts quantified with a Winseedle Image analysis system. Segregation of tightly linked SSR and SNP markers will be analyzed to pinpoint recombination points and candidate genes in the finely mapped region. Genetic markers developed from this research will be used by breeders to develop new cultivars that have greater translucency, higher milling yield, and consistent cooking quality.


3.Progress Report:
Due to vacancies and closure of the Beaumont, TX, Rice Research Unit, a few milestones were modified for the remaining two years of this project. Only the most critical NSGC rice accessions were rejuvenated and harvested at the end of 2011. During the 2012 field season, only 300 new accessions that represent the majority of the Brazil germplasm collection were brought through quarantine and are being increased in the field. The GSOR collection now contains over 34,000 accessions, and pictures of many of the mutants have been catalogued. However a number of these need to be grown under greenhouse conditions because of their disease susceptibility, which will be done during the 2012 winter. Over 5400 seed samples were distributed from GSOR, with 121 shipments to domestic customers and 24 international shipments. We host a website for US breeders that was updated with the 2011 Uniform Regional Rice Nursery (URRN) data, a listing of all recent US cultivars and their public/IP status, and a molecular fingerprint chart of all US cultivars. During FY 12, we added two DNA markers for glaborousness and the Pi-km blast resistance gene to the set of markers that are evaluated in the URRN. A total of 143 rice accessions harvested in 2009 were analyzed for antioxidants and polyphenols, and analysis of the 2010 study is more than 80% completed. The first year of a study to look at the influence of fertilizer nitrogen on grain processing quality has been completed, and analysis of several starch pathway enzymes is 60% completed. These and the second year study samples will be completed in FY13. The identification of DNA markers associated with seven rice grain antioxidants is near completion. Similar progress has been made in identifying genetic markers associated with rice cooking and processing quality traits. Three genes affecting the ability of rice grains to resist fissuring (cracking) under stressed field and post-harvest conditions have been identified, two on chromosome 1 and another on chromosome 8. A gene affecting accumulation of copper in rice grain that was previously mapped to a 14-cM region of chromosome 2 was fine-mapped to a 1-cM region. Candidate genes in this region include two heavy metal ATPases and a protein known to affect the transfer of zinc and iron across plant membranes. We collaborated on a study to use genetic markers to identify global regions that may have influenced rice introduction and adoption in Africa. We evaluated 167 accessions from Africa and from potential points of introduction in Asia, the Americas, and southern Europe with 50 genome-wide markers. We tentatively concluded that rice was introduced to different regions of Africa as a result of four independent processes. Temperate rice is found along the Mediteranean, two subgroups of tropical japonicas found on the east and west African coasts, and indica rice in the Senegambia region.


4.Accomplishments
1. Pigmented rice bran suppresses the growth of in vitro human cancer cells. Pigmented rice bran has higher concentrations of phenolics than light brown rice bran. The bioactivity of the phenolics in pigmented bran extracts on cancer cell growth have not been explored. ARS scientists in Stuttgart, Arkansas, and Albany, California, in collaboration with scientists in South Korea, evaluated extracts from red and purple bran on the growth inhibition of various human cancer cell lines in vitro. Both pigmented bran extracts suppressed the growth of cervical and leukemia cancer cells, and additionally, red bran extract inhibited the growth of stomach cancer cells. Through statistical analysis, analytical methods, and cell assays of red bran extracts, the phenolic compounds of proanthocyanidins were identified to be the primary bioactive compounds in vitro.

2. Bioactive compounds in rice bran slows in vitro colorectal cancer growth. Rice bran contains both lipophilic and phenolic phytochemicals. ARS scientists in Stuttgart, Arkansas, in collaboration with university scientists, evaluated the contribution of lipophilic phytochemicals and total phenolics in bran extracts of five rice varieties in preventing colon cancer cell growth in a cell culture assay. Using correlation analysis between antioxidant contents and percent cell growth inhibition demonstrated that the content of total phenolics and gamma-tocotrienol in the rice bran extracts were contributing to the inhibitory activity on the growth of colon cancer cells.

3. Identifying genetic loci affecting the nutritional value of rice grain. Enhancing the nutritional value of rice is important because rice is a primary dietary component for more than half of the world's population, and is particularly important in underdeveloped countries that have higher rates of malnutrition. As part of a study funded by the National Science Foundation, ARS researchers at Beaumont, Texas, in collaboration with university scientists in Texas, New Hampshire, and Scotland, identified genes affecting the nutritional value of rice. Because soil moisture and chemistry are known to influence nutrient uptake by the plant, two genetic populations were grown under flooded and unflooded field environments. Genomic analysis revealed 127 chromosomal regions (QTLs) that were associated with grain concentration of individual elements. These QTLs tended to cluster into 40 genomic regions, often with multiple elements associated with a specific region. This suggests that the changes in one element can affect the uptake and accumulation of other elements. Identifying these genes is an important first step toward breeding new rice varieties enhanced for the concentration of key nutritional elements such as calcium, magnesium, or iron with reduced concentration of undesirable elements, such as arsenic.

4. Multiple genes for resistance to sheath blight disease found in global rice accessions. Sheath blight is one of the most devastating diseases in rice production worldwide. No genetic sources of immunity have been found; thus, identification of resistance genes that can be used in breeding is essential for cultivar improvement. ARS scientists at Stuttgart, Arkansas, the University of Arkansas, and Zhejiang University in China evaluated the USDA Mini-Core collection of rice accessions from around the world for sheath blight resistance and genotypic diversity using 155 genome-wide molecular markers. This work led to the identification of 10 marker loci significantly associated with sheath blight resistance. Genetic accessions that had greater numbers of resistant genes displayed enhanced disease resistance. The markers linked to these resistance genes can be used by breeders to efficiently move these genes into new rice cultivars.

5. Improving grain production efficiency in rice using genetic markers. Harvest index is a measure of the proportion of carbohydrates produced during photosynthesis by the vegetative plant that are deposited in the grain. Improving harvest index in rice increases production efficiency by allowing more photosynthetic carbohydrate to be harvested rather than left behind in plant tissue at harvest. ARS scientists at Stuttgart, Arkansas, and researchers at the University of Arkansas and Zhejiang University in China evaluated the USDA rice Mini-Core collection for 14 agronomic traits in both Arkansas and Texas, and with 155 genome-wide molecular markers. This work led to the identification of six traits significantly contributing to harvest index and 36 markers directly associated with the traits. These markers and the characterized genetic accessions can be used by breeders to improve the production efficiency in new rice cultivars.

6. Genes for silica content in rice may impact disposal and utilization of rice hulls. Rice hulls are a waste product of the rice milling process. Because they are high in silica content, they are resistant to biodegradation. However, the non-crystaline form of silica found in rice hulls is desired for some high-valued industrial materials, like silicon carbide, pure silicon, and zeolites. ARS researchers in Stuttgart, Arkansas, and at the University of Arkansas evaluated 174 rice cultivars from around the world for hull silica content and using 164 genome-wide markers. A two-fold variation in silica content was found among the cultivars, and 12 markers on 10 chromosomes were linked with this trait. The research confirmed six of the markers that had been previously reported in the literature. These results demonstrate genetic resources are available that can be used to change silica content in rice plants through breeding. Cultivars high in silica content may bring added value to rice hulls for use in producing industrial compounds. Low silica varieties would likely allow rice hulls to degrade more rapidly reducing land fill waste.

7. Genetic markers linked with rice grain protein content. Research has shown that consuming whole grains like brown, unmilled rice is considered an important component of a healthy diet. Most of the protein in rice is concentrated in the bran layer of brown rice. However, little is known about the genetic diversity for protein content in brown rice. ARS researchers at Stuttgart, Arkansas, evaluated 202 global rice accessions for protein content that had been grown at two US locations. Genome-wide genetic markers were used to identify 10 markers across eight chromosomes that were linked with protein content. Five of these had not been previously reported. The cultivars and genetic markers identified in this study will assist breeders in developing cultivars to meet applications requiring specific protein concentrations in the rice grain, and contribute to the potential discovery of novel rice storage protein pathways in the endosperm.

8. Genetic markers developed for resistance to straighthead in rice. Straighthead is a physiological disease of rice that is observed under certain soil chemistry conditions and results in a reduced amount of grain being developed in the rice seed head. Currently, farmers drain and reflood rice paddies early in the season to prevent this condition from occurring, which results in inefficient use of water resources. Two genetic populations were evaluated for straighthead susceptibility along with over 136 genome-wide markers. A region on chromosome 8 was found to explain over 46% of the variation in susceptibility. This region was reduced to a much smaller chromosomal area through fine mapping. Two genetic markers in this region linked with straighthead resistance were validated in a small set of global rice germplasm. These markers and genetic resources will aid breeders in developing new rice cultivars that are resistant to this physiological stress.

9. Sensory attributes of whole grain rice with having different bran colors. The key sensory attributes of cooked pigmented whole grain rice and the chemical and physical traits associated with these sensory traits were determined. The health benefits associated with the consumption of whole grain were documented, and the major bioactive compounds in the pigmented whole grain rice were reported. However, the key to successful commercialization in the market is consumer acceptance of the cooking quality and sensory characteristics of new rice varieties. ARS scientists in Stuttgart, Arkansas, and in New Orleans, Louisiana, evaluated the interrelationship of sensory attributes, chemical and physical traits, and the cooking properties of whole grain rice of various bran colors. Key flavors and texture descriptors associated with the pigmented bran rice were determined, and the contribution of physical and chemical traits to these flavor descriptors was revealed.

10. Developing rice germplasm having improved plant architecture. Plant architecture is the three-dimensional arrangement of the above-ground parts of a plant, including tillering pattern, plant height, leaf shape, size and angle in a plant. The architecture is of major agronomic importance as it contributes to the adaptability of the plant to cultivation as well as grain yield potential. ARS scientists at Stuttgart, Arkansas, and researchers in University of Arkansas and four institutions in China developed a mutant with an improved architecture from the variety 'Khao Dwak Mali 105' which is considered a premium aromatic rice in the world market. This germplasm can be used by breeders to improve cultivars for greater agronomic value and by researchers to map the genes and elucidate genetic mechanism for improved plant architecture in rice.


Review Publications
Nelson, J.C., Jodari, F., Roughton, A.I., McKenzie, K.S., McClung, A.M., Fjellstrom, R.G., Scheffler, B.E. 2012. QTL mapping for milling quality in elite western U.S. rice germplasm. Crop Science. 52:242-252.

Li, X., Yan, W., Agrama, H., Jia, L., Jackson, A.K., Moldenhauer, K., Yeater, K.M., McClung, A.M., Wu, D. 2012. Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.). PLoS One. 7(1):Article e29350.

Yan, W. 2012. Genetic characterization of global rice germplasm for sustainable agriculture. In: Aladjadjiyan, A. editor. Food Production - Approaches, Challenges and Tasks. Rijeka, Croatia: InTech. p. 243-270. Available: http://www.intechopen.com/articles/show/title/genetic-characterization-of-global-rice-germplasm-for-sustainable-agriculture.

Jia, L., Yan, W., Zhu, C., Agrama, H.A., Jackson, A.K., Yeater, K.M., Li, X., Huang, B., Hu, B., McClung, A.M., Wu, D. 2012. Allelic analysis of sheath blight resistance with association mapping in rice. PloS One 7(3):Article e32703.

Rang, R., Sun, C., Bai, J., Luo, Z., Shi, B., Zhang, J., Yan, W., Piao, Z. 2012. A putative gene sbe3-rs for resistant starch mutated from SBE3 for starch branching enzyme in rice (Oryza sativa L.). PLoS One. 7(8):Article e43026.

Bryant, R.J., Proctor, A., Hawkridge, M., Jackson, A.K., Yan, W., Counce, P., McClung, A.M., Fjellstrom, R.G. 2012. Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection. Genetica.139(11):1383-1398.

Agrama, H.A., Yan, W., Jia, M.H., Fjellstrom, R.G., McClung, A.M. 2010 Genetic structure associated with diversity and geographic distribution in the USDA rice world collection. Natural Science. 2(4):247-291.

Agrama, H.A., McClung, A.M., Yan, W. 2011. Using minimum DNA marker loci for accurate population classification in rice (Oryza sativa L.). Molecular Breeding. 29:413-425.

Pillai, T.R., Yan, W., Agarma, H.A., James, W.D., Ibrahim, A.M., Gentry, T.J., McClung, A.M., Loeppert, R.H. 2010. Total grain-arsenic and arsenic-species concentrations in diverse rice cultivars under flooded conditions. Crop Science. 50(1):2065-2075.

Yan, W., Agrama, H., Jia, M.H., Fjellstrom, R.G., McClung, A.M. 2010. Geographic description of genetic diversity and genetic relationships in the USDA Rice World Collection. Crop Science. 50:2406-2417.

Bryant, R.J., McClung, A.M., Grimm, C.C. 2012. Development of a single kernel analysis method for detection of 2-acetyl-1-pyrroline in aromatic rice germplasm. Sensing and Instrumentation for Food Quality and Safety. 5::147-154.

Last Modified: 7/11/2014
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