Fine Mapping Of A QTL For Silicon Content In The Hull Of Rice By Using RHL Population

High accumulation of silicon is a character distinguishing rice from other grass crops, and hull is the rice organ containing the highest content. Up to date, most studies work on the physiological effects of silicon fertilizers, while the genetic mechanism responsible for the high uptake of Si has attracted little attention. In present study, a RHL population was constructed according to results of previous QTL mapping and used for fine mapping a QTL for the silicon content in the hull.In a previous study, a QTL (qHUS-6), which explained 17.4% of the phenotypic variance, was located on the short arm of chromosome 6 by using the Zhenshan 97B/Milyang 46 RIL population. In present study, 612 RILs of the same cross were assayed by using SSR (simple sequence repeat) markers. A single plant, which is heterozygous in the genomic region flanked by RM587 and RM276 on the short arm of chromosome 6 and homozygous in other regions of the genome, was selected. An F2:3 population consisting of 221 lines was derived and used to fine map qHUS-6. The mapping results are summarized as the followings.1. A genetic map containing 16 SSR markers from RM587 to RM276 was constructed by using the 221 F2 plants. With the phenotypic data collected from the F3 lines, a QTL controlling silicon content in the hull was detected with a LOD score of 20.4. This QTL was located in the interval RM510-RM204 with peak LOD position 0.1 cM away from RM510. It had an additive effect of 1.88% and a dominant effect of 1.41%, showing the genetic mode of partial dominance with the degree of dominance of 0.75 and the variant ratio is 34.9%. This QTL was located in the same region for qHUS-6, and the allele for increasing silicon content in the hull remained from the paternal parent Milyang46.2. QTL analysis was also performed based on phenotypic data of 105 lines that showing recombination in the target region. With the genetic map of the unseleted population, qHUS-6 was located in the orginal position in interval RM587-RM510. The LOD score of 17.1, additive effect of 1.97%, dominant effect of 1.15% and degree of dominance of 0.58 were similar to the values estimated from the unselected population, but the phenotypic variance explained was increased to 51.0%.3. Based on the marker genotypes of the 221 lines, 10 lines that had heterozygous genotypes at marker loci RM587 and RM510 and homozygous genotypes at the remaining 14 marker loci were selected. Ten individual progenies from each of the lines were assayed with RM587 and RM510. Seventy-one plants having identical genotypes across the two marker loci were selected and classified as three genotype groups, i.e., maternal homozygous, paternal homozygous and heterozygous. They were meaured for silicon content in the hull and analyzed with ANOVA. Highly significant differences among the three genotype groups were shown, indicating a QTL for silicon content in the hull was linked to RM587 and RM510. An additive effect of 0.69% and a dominant effect of–0.81% were estimated from the average values in each genotype group. The allele for increasing the silicon content was still from the paternal parent Milyang 46, but the genetic mode was changed to complete dominance with negative effect. The result validated that qHUS-6 is tightly linked to RM587and RM510, and it also indicated that the QTL effect of qHUS might be sensible to environmental factors.This study verified the genomic location and QTL effect of qHUS-6 on the short arm of chromosome 6. In addition, this QTL displayed a major effect in the isogenic genetic background. The fine mapping of this QTL and searching for the candidate gene are underway.