title: Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection.
abstract: 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 genome-wide 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 × location (G × 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.
authors.affiliation: Dale Bumpers National Rice Research Center, U.S. Department of Agriculture/ARS, Highway 130 E., Stuttgart, AR 72160, USA. rolfe.bryant@ars.usda.gov
authors.forename: R
authors.initials: R
authors.lastname: Bryant
authors.forename: A
authors.initials: A
authors.lastname: Proctor
authors.forename: M
authors.initials: M
authors.lastname: Hawkridge
authors.forename: A
authors.initials: A
authors.lastname: Jackson
authors.forename: K
authors.initials: K
authors.lastname: Yeater
authors.forename: P
authors.initials: P
authors.lastname: Counce
authors.forename: W
authors.initials: W
authors.lastname: Yan
authors.forename: A
authors.initials: A
authors.lastname: McClung
authors.forename: R
authors.initials: R
authors.lastname: Fjellstrom
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D056726:Genetic Association Studies; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D012822:Silicon Dioxide / Q000378:metabolism*
chemical_list: D012822:Silicon Dioxide