title: Identification of genome-wide variations among three elite restorer lines for hybrid-rice.
abstract: Rice restorer lines play an important role in three-line hybrid rice production. Previous research based on molecular tagging has suggested that the restorer lines used widely today have narrow genetic backgrounds. However, patterns of genetic variation at a genome-wide scale in these restorer lines remain largely unknown. The present study performed re-sequencing and genome-wide variation analysis of three important representative restorer lines, namely, IR24, MH63, and SH527, using the Solexa sequencing technology. With the genomic sequence of the Indica cultivar 9311 as the reference, the following genetic features were identified: 267,383 single-nucleotide polymorphisms (SNPs), 52,847 insertion/deletion polymorphisms (InDels), and 3,286 structural variations (SVs) in the genome of IR24; 288,764 SNPs, 59,658 InDels, and 3,226 SVs in MH63; and 259,862 SNPs, 55,500 InDels, and 3,127 SVs in SH527. Variations between samples were also determined by comparative analysis of authentic collections of SNPs, InDels, and SVs, and were functionally annotated. Furthermore, variations in several important genes were also surveyed by alignment analysis in these lines. Our results suggest that genetic variations among these lines, although far lower than those reported in the landrace population, are greater than expected, indicating a complicated genetic basis for the phenotypic diversity of the restorer lines. Identification of genome-wide variation and pattern analysis among the restorer lines will facilitate future genetic studies and the molecular improvement of hybrid rice.
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Shuangcheng
authors.initials: S
authors.lastname: Li
authors.forename: Shiquan
authors.initials: S
authors.lastname: Wang
authors.forename: Qiming
authors.initials: Q
authors.lastname: Deng
authors.forename: Aiping
authors.initials: A
authors.lastname: Zheng
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Huainian
authors.initials: H
authors.lastname: Liu
authors.forename: Lingxia
authors.initials: L
authors.lastname: Wang
authors.forename: Fengyan
authors.initials: F
authors.lastname: Gao
authors.forename: Ting
authors.initials: T
authors.lastname: Zou
authors.forename: Bin
authors.initials: B
authors.lastname: Huang
authors.forename: Xuemei
authors.initials: X
authors.lastname: Cao
authors.forename: Lizhi
authors.initials: L
authors.lastname: Xu
authors.forename: Chuang
authors.initials: C
authors.lastname: Yu
authors.forename: Peng
authors.initials: P
authors.lastname: Ai
authors.forename: Ping
authors.initials: P
authors.lastname: Li
mesh_terms: D001947:Breeding / Q000379:methods; D002678:Chimera / Q000235:genetics; D002874:Chromosome Mapping; D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D018744:DNA, Plant