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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

Title: Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection

Authors
item Bryant, Rolfe
item Proctor, Andrew -
item Hawkridge, Michael -
item Jackson, Aaron
item Yan, Wengui
item Counce, Paul -
item McClung, Anna
item McClung, Anna
item Fjellstrom, Robert

Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 15, 2012
Publication Date: May 15, 2012
Repository URL: http://handle.nal.usda.gov/10113/58017
Citation: 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.

Interpretive Summary: Rice can accumulate silicon (Si) from the soil and although it is not an essential nutrient, it plays an important role in the growth and health of rice plants. Silica is concentrated in the hulls, which are a by product of the milling process, and in straw resulting in large amounts of biomass that is a major disposal problem for the US rice industry. Some rice hulls are burned to produce steam or electricity. However, the rice hull ash is usually disposed of in landfills where it remains for years due to its chemical stability. Due to the high silicon concentration, rice hulls and ash can also used as raw materials in the production of Si-based industrial materials with high economic value. This study was conducted to determine the genetic variability present in the USDA world collection of rice that could be used in the development of new cultivars that have dual purpose for use as a food crop and as an agricultural feedstock for high value Si-based industrial products. One hundred and seventy-four diverse rice accessions were evaluated for hull silica concentration in trials conducted at two locations and with 164 genome-wide DNA markers. The average silica concentration ranged two-fold with a mean of 200 mg g-1. Most of the accessions from Central America had a higher silica concentration while those from the Mideast and Eastern European had lower silica concentrations compared to accessions from other parts of the world. Accessions from the tropical japonica subpopulation had some of the highest Si concentrations. This is the same genepool that most of the U.S. long grain rice is developed from, suggesting it is a rich resource for modifying Si in rice cultivars. Location effects were important, indicating the necessity of having multiple test sites for silica evaluation. Four significant marker-trait associations were found at each of the two locations and seven marker-trait associations were found when the data were combined over locations. Five of the markers were close to markers associated with silica concentration that had been identified in previous genetic mapping studies. This research demonstrates the potential of using genomics to develop the rice crop for use as an industrial feedstock, without competing with its use as a globally important staple food.

Technical Abstract: Association analysis on the genetic variability for silica concentration in rice hulls was performed using a “Mini-Core” set of 174 accessions representative of the germplasm diversity found in the USDA world collection of rice. Hull silica concentration was determined in replicated trials conducted in two southern states in the USA and was analyzed for its association with 164 genome-wide DNA markers. Among the accessions, the average silica concentration ranged from 120 mg g-1 to 251 mg g-1. Ample variation was seen within each of the five subpopulations of rice, as well as the 14 geographic regions that the accessions originated from. There was also an effect due to location and accession x location (GxE) interaction demonstrating the importance of assessing silica concentration across different environments. Association mapping identified 12 significant markers that correlated with hull silica concentration. Six markers (RM5644, RM5371, RM1335, RM283, RM263, and RM178) corroborated QTLs for silica concentration identified in other mapping studies. Our results provide germplasm and genetic markers that will assist breeding efforts to develop cultivars that have high hull silica concentration which could be used as agricultural feedstocks for silica based industrial compounds or cultivars with low hull silica that are more biodegradable.

Last Modified: 4/17/2014