title: qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.).
abstract: Low-temperature germination (LTG) is an important agronomic trait for direct seeding of rice in temperate regions of East Asia. To dissect the genetic control of LTG, we constructed a recombinant inbred line (RIL) population derived from a cross of japonica variety USSR5 and indica variety N22. Three putative QTL involved in LTG were detected and named qLTG-7, qLTG-9 and qLTG-12. They explained 9.5, 12.12 and 7.08 % of the phenotypic variation, respectively, and the alleles from USSR5 enhanced LTG. A set of advanced backcross lines selected for the presence of qLTG-9 (with the biggest contribution of the three QTL), by both linked markers and phenotype, was used to validate qLTG-9 in different generations, years and locations. A near-isogenic line in USSR5 background with a qLTG-9 insertion from N22 had retarded germination under low-temperature conditions. Finally, qLTG-9 was fine mapped between markers L9-25D and ID-1, to a 72.3-kb region in chromosome 9, which in the Nipponbare genome contains five predicted genes. This result provides a springboard for map-based cloning of qLTG-9 and is helpful in understanding the mechanism of seed germination under low-temperature conditions.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Agriculture Ministry Key Laboratory of Biology, Genetics and Breeding of Japonica Rice in Mid-lower Yangtse River, Nanjing Agricultural University, Nanjing, China.
authors.forename: Linfang
authors.initials: L
authors.lastname: Li
authors.forename: Xi
authors.initials: X
authors.lastname: Liu
authors.forename: Kun
authors.initials: K
authors.lastname: Xie
authors.forename: Yihua
authors.initials: Y
authors.lastname: Wang
authors.forename: Feng
authors.initials: F
authors.lastname: Liu
authors.forename: Qiuyun
authors.initials: Q
authors.lastname: Lin
authors.forename: Wenyan
authors.initials: W
authors.lastname: Wang
authors.forename: Chunyan
authors.initials: C
authors.lastname: Yang
authors.forename: Bingyue
authors.initials: B
authors.lastname: Lu
authors.forename: Shijia
authors.initials: S
authors.lastname: Liu
authors.forename: Liangming
authors.initials: L
authors.lastname: Chen
authors.forename: Ling
authors.initials: L
authors.lastname: Jiang
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wan
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D003080:Cold Temperature; D003433:Crosses, Genetic; D018744:DNA, Plant / Q000235:genetics; D008040:Genetic Linkage; D014644:Genetic Variation; D018525:Germination / Q000235:genetics*; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D040641:Quantitative Trait Loci
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins