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

Bryant, R., Proctor, A., Hawkridge, M., Jackson, A., Yeater, K., Counce, P., Yan, W., McClung, A., Fjellstrom, R.
Genetica 2011 v.139 no.11-12 pp. 1383
Oryza sativa, USDA, chromosome mapping, chromosomes, genetic markers, genetic variation, genotype-environment interaction, germplasm, germplasm conservation, mineral content, quantitative trait loci, raw materials, rice, rice hulls, silica, United States
An 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 genomewide DNA markers. Among the accessions, the average silica concentration ranged from 120 to 251 mg g-1. Ample variation was seen within each of the five sub-populations 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 (G X E) interaction demonstrating the importance of assessing silica concentration across multiple environments. Twelve markers on ten chromosomes were significantly associated with hull silica concentration. Six markers (RM5644, RM5371, RM1335, RM283, RM263, and RM178) corroborated quantitative trait locus 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 either high or low hull silica concentration. High silica hulls are good raw material for silica based industrial compounds, while low silica hulls are more biodegradable.