title: Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare.
abstract: Chromosome segment substitution lines (CSSLs) are useful for the precise mapping of quantitative trait loci (QTLs) and dissection of the genetic basis of complex traits. In this study, two whole-genome sequenced rice cultivars, the japonica Nipponbare and indica 9311 were used as recipient and donor, respectively. A population with 57 CSSLs was developed after crossing and back-crossing assisted by molecular markers, and genotypes were identified using a high-throughput resequencing strategy. Detailed graphical genotypes of 38 lines were constructed based on resequencing data. These CSSLs had a total of 95 substituted segments derived from indica 9311, with an average of about 2.5 segments per CSSL and eight segments per chromosome, and covered about 87.4% of the rice whole genome. A multiple linear regression QTL analysis mapped four QTLs for 1000-grain weight. The largest-effect QTL was located in a region on chromosome 5 that contained a cloned major QTL GW5/qSW5 for grain size in rice. These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice, and offer ideal materials and foundations for japonica breeding.
authors.affiliation: Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou 225009, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Zhang
authors.forename: Qiang
authors.initials: Q
authors.lastname: Zhao
authors.forename: Zhi-Zhong
authors.initials: ZZ
authors.lastname: Sun
authors.forename: Chang-Quan
authors.initials: CQ
authors.lastname: Zhang
authors.forename: Qi
authors.initials: Q
authors.lastname: Feng
authors.forename: Shu-Zhu
authors.initials: SZ
authors.lastname: Tang
authors.forename: Guo-Hua
authors.initials: GH
authors.lastname: Liang
authors.forename: Ming-Hong
authors.initials: MH
authors.lastname: Gu
authors.forename: Bin
authors.initials: B
authors.lastname: Han
authors.forename: Qiao-Quan
authors.initials: QQ
authors.lastname: Liu
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D003433:Crosses, Genetic; D005819:Genetic Markers; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D012275:Oryza / Q000235:genetics*; D030821:Plants, Genetically Modified; D040641:Quantitative Trait Loci
chemical_list: D005819:Genetic Markers