title: Microarray-assisted fine-mapping of quantitative trait loci for cold tolerance in rice.
abstract: Many important agronomic traits, including cold stress resistance, are complex and controlled by quantitative trait loci (QTLs). Isolation of these QTLs will greatly benefit the agricultural industry but it is a challenging task. This study explored an integrated strategy by combining microarray with QTL-mapping in order to identify cold-tolerant QTLs from a cold-tolerant variety IL112 at early-seedling stage. All the early seedlings of IL112 survived normally for 9 d at 4-5°C, while Guichao2 (GC2), an indica cultivar, died after 4 d under the same conditions. Using the F2:3 population derived from the progeny of GC2 and IL112, we identified seven QTLs for cold tolerance. Furthermore, we performed Affymetrix rice whole-genome array hybridization and obtained the expression profiles of IL112 and GC2 under both low-temperature and normal conditions. Four genes were selected as cold QTL-related candidates, based on microarray data mining and QTL-mapping. One candidate gene, LOC_Os07g22494, was shown to be highly associated with cold tolerance in a number of rice varieties and in the F2:3 population, and its overexpression transgenic rice plants displayed strong tolerance to low temperature at early-seedling stage. The results indicated that overexpression of this gene (LOC_Os07g22494) could increase cold tolerance in rice seedlings. Therefore, this study provides a promising strategy for identifying candidate genes in defined QTL regions.
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants Rice, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Fengxia
authors.initials: F
authors.lastname: Liu
authors.forename: Wenying
authors.initials: W
authors.lastname: Xu
authors.forename: Qian
authors.initials: Q
authors.lastname: Song
authors.forename: Lubin
authors.initials: L
authors.lastname: Tan
authors.forename: Jiayong
authors.initials: J
authors.lastname: Liu
authors.forename: Zuofeng
authors.initials: Z
authors.lastname: Zhu
authors.forename: Yongcai
authors.initials: Y
authors.lastname: Fu
authors.forename: Zhen
authors.initials: Z
authors.lastname: Su
authors.forename: Chuanqing
authors.initials: C
authors.lastname: Sun
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D003080:Cold Temperature; D003433:Crosses, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D056726:Genetic Association Studies; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000502:physiology*; D020161:Physical Chromosome Mapping; D030821:Plants, Genetically Modified; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D013312:Stress, Physiological / Q000235:genetics