title: Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.
abstract: Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Chong-Yun
authors.initials: CY
authors.lastname: Fu
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Wu-Ge
authors.initials: WG
authors.lastname: Liu
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Di-Lin
authors.initials: DL
authors.lastname: Liu
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Ji-Hua
authors.initials: JH
authors.lastname: Li
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Man-Shan
authors.initials: MS
authors.lastname: Zhu
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Yi-Long
authors.initials: YL
authors.lastname: Liao
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Zhen-Rong
authors.initials: ZR
authors.lastname: Liu
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Xue-Qin
authors.initials: XQ
authors.lastname: Zeng
authors.affiliation: a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.|b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
mesh_terms: D056915:DNA Copy Number Variations; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D006823:Hybrid Vigor; D054643:INDEL Mutation; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant
keywords: CNV; CNVs; InDel; InDels; SNP; SNPs; genome resequencing; re-séquençage du génome; rice; riz