title: Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice.
abstract: Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line 'SNUSG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Lim
authors.forename: Hyun-Jung
authors.initials: HJ
authors.lastname: Yang
authors.forename: Ki-Hong
authors.initials: KH
authors.lastname: Jung
authors.forename: Soo-Cheul
authors.initials: SC
authors.lastname: Yoo
authors.forename: Nam-Chon
authors.initials: NC
authors.lastname: Paek
mesh_terms: D032461:Chromosomes, Plant; D017343:Genes, Plant; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D018515:Plant Leaves / Q000235:genetics; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000379:methods*