title: Re-sequencing and genetic variation identification of a rice line with ideal plant architecture.
abstract: BACKGROUND
  The ideal plant architecture (IPA) includes several important characteristics such as low tiller numbers, few or no unproductive tillers, more grains per panicle, and thick and sturdy stems. We have developed an indica restorer line 7302R that displays the IPA phenotype in terms of tiller number, grain number, and stem strength. However, its mechanism had to be clarified.
  
  
  RESULTS
  We performed re-sequencing and genome-wide variation analysis of 7302R using the Solexa sequencing technology. With the genomic sequence of the indica cultivar 9311 as reference, 307 627 SNPs, 57 372 InDels, and 3 096 SVs were identified in the 7302R genome. The 7302R-specific variations were investigated via the synteny analysis of all the SNPs of 7302R with those of the previous sequenced none-IPA-type lines IR24, MH63, and SH527. Moreover, we found 178 168 7302R-specific SNPs across the whole genome and 30 239 SNPs in the predicted mRNA regions, among which 8 517 were Non-syn CDS. In addition, 263 large-effect SNPs that were expected to affect the integrity of encoded proteins were identified from the 7302R-specific SNPs. SNPs of several important previously cloned rice genes were also identified by aligning the 7302R sequence with other sequence lines.
  
  
  CONCLUSIONS
  Our results provided several candidates account for the IPA phenotype of 7302R. These results therefore lay the groundwork for long-term efforts to uncover important genes and alleles for rice plant architecture construction, also offer useful data resources for future genetic and genomic studies in rice.
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.|Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.|Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014, Ya'an, Sichuan, China.
authors.forename: Shuangcheng
authors.initials: S
authors.lastname: Li
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Kailong
authors.initials: K
authors.lastname: Xie
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Li
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Zou
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Ren
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.|Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.|Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014, Ya'an, Sichuan, China.
authors.forename: Shiquan
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.|Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.|Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014, Ya'an, Sichuan, China.
authors.forename: Qiming
authors.initials: Q
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.|Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.|Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Huainian
authors.initials: H
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China.
authors.forename: Lingxia
authors.initials: L
authors.lastname: Wang
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Ai
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Fengyan
authors.initials: F
authors.lastname: Gao
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Huang
authors.affiliation: Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Cao
authors.affiliation: State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu, 611130, China. liping6575@163.com.|Rice Research Institute, Sichuan Agricultural University, 211 Huimin Road, 611130, Wenjiang, Sichuan, China. liping6575@163.com.|Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, 625014, Ya'an, Sichuan, China. liping6575@163.com.
authors.forename: Ping
authors.initials: P
authors.lastname: Li
keywords: IPA; InDel; Re-sequencing; Rice; SNP; SV