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

• Published in: Genetica Vol. 139; no. 11-12; pp. 1383 - 1398
• Main Authors: Bryant, R, Proctor, A, Hawkridge, M, Jackson, A, Yeater, K, Counce, P, Yan, W, McClung, A, Fjellstrom, R
• Format: Journal Article
• Language: English
• Published: Dordrecht Kluwer Academic Publishers 01.12.2011; Springer Netherlands; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Association analysis; Biodegradability; Biodegradation; Biomedical and Life Sciences; Chromosome Mapping; Chromosomes; Chromosomes, Plant; Cultivars; DNA; Evolutionary Biology; Gene mapping; Genetic Association Studies; Genetic diversity; Genetic markers; Genetic Variation; genotype-environment interaction; Germplasm; germplasm conservation; Human Genetics; Life Sciences; Linkage Disequilibrium; Microbial Genetics and Genomics; mineral content; Oryza - genetics; Oryza - metabolism; Oryza sativa; Phylogeny; Plant breeding; Plant Genetics and Genomics; Quantitative trait loci; raw materials; rice; Rice hulls; Silica; Silicon Dioxide - metabolism; USDA; Association mapping; Germplasm; Silica; Grain quality
• ISSN: 0016-6707; 1573-6857
• DOI: 10.1007/s10709-012-9637-x

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.