title: Development and characterization of chromosome segment substitution lines derived from Oryza rufipogon in the genetic background of O. sativa spp. indica cultivar 9311.
abstract: Wild rice (Oryza rufipogon) constitutes a primary gene source for rice breed improvement. Chromosome segment substitution line (CSSL) for O. rufipogon is a powerful tool for fine mapping of quantitative traits, new gene discovery, and marker-assisted breeding. Thus, they provide a basis for a wide range of genomic and genetic studies.
  
  
  
  In this study, a set of 198 CSSLs were developed from a cross between recurrent parent indica var. 9311 and an O. rufipogon donor parent; these were then genotyped using 313 polymorphic SSR markers evenly distributed across the 12 rice chromosomes. On average, each CSSL carried 2.16 introgressed segments, and the genetic distance of each segment was about 6 cM. The segments collectively covered 84.9 % of the wild rice genome. Based on these CSSLs, 25 QTLs involved in 10 agronomic traits were identified. Seven CSSLs were subjected to a whole-genome single nucleotide polymorphism chip assay and two QTLs, qSH4-1 and qDTH10-1, detected. In addition, a new QTL associated with the heading date was detected in a 78-Kb region on chromosome 10, thus proving the ability of these CSSLs to identify new QTLs and genes.
  
  
  
  The newly developed CSSL population proved a useful tool for both gene identification and whole-genome research of wild rice. These CSSL materials will provide a foundation for rice variety improvement.
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.
authors: Weihua
authors: W
authors: Qiao
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.|Institute of Cereal Crop Science, Hainan Academy of Agricultural Sciences, 14 Xingdan Road, Haikou, Hainan, 571100, China.
authors: Lan
authors: L
authors: Qi
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.
authors: Zhijun
authors: Z
authors: Cheng
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.
authors: Long
authors: L
authors: Su
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.
authors: Jing
authors: J
authors: Li
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.
authors: Yan
authors: Y
authors: Sun
authors: Institute of Tropical Horticulture, Hainan Academy of Agricultural Sciences, 14 Xingdan Road, Haikou, Hainan, 571100, China.
authors: Junfang
authors: J
authors: Ren
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China.
authors: Xiaoming
authors: X
authors: Zheng
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, Haidian, 100081, China. yangqingwen@caas.cn.
authors: Qingwen
authors: Q
authors: Yang
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D000068617:Genetic Background; D018745:Genome, Plant; D005838:Genotype; D018895:Microsatellite Repeats; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable
keywords: Chromosome segment substitution lines; Oryza rufipogon; Quantitative trait locus