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Identification of genome-wide variations among three elite restorer lines for hybrid-rice.

Li S, Wang S, Deng Q, Zheng A, Zhu J, Liu H, Wang L, Gao F, Zou T, Huang B, Cao X, Xu L, Yu C, Ai P, Li P - PLoS ONE (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.

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.

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Comparative distributions of variation frequency on 12 chromosomes.s1, IR24; S2, MH63; S3,SH527.
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pone-0030952-g003: Comparative distributions of variation frequency on 12 chromosomes.s1, IR24; S2, MH63; S3,SH527.

Mentions: The frequencies of SNPs, InDels, and SVs for each sample were plotted at a 100 kb sliding window with a step size of 50 kb along each chromosome. SNP/InDel/SV frequency was defined as the corresponding number of SNPs/InDels/SVs divided by the number of nucleotides within the 100 kb interval, excluding the uncovered nucleotides. Each sample was compared with the corresponding intervals to identify regions that showed non-random variation frequencies. In total, 227/936 SNP high/low regions, 298/889 InDel high/low regions, and 188/1899 SV high/low regions were identified between IR24 and MH63; 339/914 SNP high/low regions, 440/1,030 InDel high/low regions, and 267/2,052 SV high/low regions were identified between IR24 and SH527; and 507/825 SNP high/low regions, 523/1,266 InDel high/low regions, and 235/2,684 SV high/low regions were identified between MH63 and SH527. Out of these, 135/450 SNP high/low regions, 229/297 InDel high/low regions, and 87/1,058 SV high/low regions were found to be identical among the three restorer lines (Figs. 3 and 4).


Identification of genome-wide variations among three elite restorer lines for hybrid-rice.

Li S, Wang S, Deng Q, Zheng A, Zhu J, Liu H, Wang L, Gao F, Zou T, Huang B, Cao X, Xu L, Yu C, Ai P, Li P - PLoS ONE (2012)

Comparative distributions of variation frequency on 12 chromosomes.s1, IR24; S2, MH63; S3,SH527.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3285608&req=5

pone-0030952-g003: Comparative distributions of variation frequency on 12 chromosomes.s1, IR24; S2, MH63; S3,SH527.
Mentions: The frequencies of SNPs, InDels, and SVs for each sample were plotted at a 100 kb sliding window with a step size of 50 kb along each chromosome. SNP/InDel/SV frequency was defined as the corresponding number of SNPs/InDels/SVs divided by the number of nucleotides within the 100 kb interval, excluding the uncovered nucleotides. Each sample was compared with the corresponding intervals to identify regions that showed non-random variation frequencies. In total, 227/936 SNP high/low regions, 298/889 InDel high/low regions, and 188/1899 SV high/low regions were identified between IR24 and MH63; 339/914 SNP high/low regions, 440/1,030 InDel high/low regions, and 267/2,052 SV high/low regions were identified between IR24 and SH527; and 507/825 SNP high/low regions, 523/1,266 InDel high/low regions, and 235/2,684 SV high/low regions were identified between MH63 and SH527. Out of these, 135/450 SNP high/low regions, 229/297 InDel high/low regions, and 87/1,058 SV high/low regions were found to be identical among the three restorer lines (Figs. 3 and 4).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Rice Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China.

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.

Show MeSH