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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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Plant phenotypes of the three core restorer lines and their cross genealogies.a, Plant phenotypes of the three core restorer lines; shown from left to right are IR24, MH63, and SH527. b, Cross genealogies of the three core restorer lines showing that MH63 and SH527 were indirectly generated from IR24. A new rice line (at the head of an arrow) was bred by crossing of two or more parents (at the tail of an arrow) and by several turns of subsequent selfing and selection. A straight line in the figure indicates a backcross.
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pone-0030952-g001: Plant phenotypes of the three core restorer lines and their cross genealogies.a, Plant phenotypes of the three core restorer lines; shown from left to right are IR24, MH63, and SH527. b, Cross genealogies of the three core restorer lines showing that MH63 and SH527 were indirectly generated from IR24. A new rice line (at the head of an arrow) was bred by crossing of two or more parents (at the tail of an arrow) and by several turns of subsequent selfing and selection. A straight line in the figure indicates a backcross.

Mentions: IR24, MH63, and SH527 (Fig. 1A) are considered hybrid rice core restorer lines because of the large number of elite commercial hybrid rice cultivars and useful restorer lines bred and generated from them. Based on their cross genealogies, MH63 and SH527 were both indirectly generated from IR24 (Fig. 1B), indicating that these three lines originate from the same restoring genes. We examined the field performances of these lines by selfing (Table 1). Performances of the hybrid rice made by crossing these three lines with six other widely used CMS lines, namely, G3A, Zhongjiu A, II-32A, G46A, 92A, and Chuangu A, were also examined (Table 1). No obvious differences were found in the yield components of MH63 and IR24 except for plant height, while the hybrid rice of MH63 was significantly different from that of IR24 in growth period, plant height, panicles per plant and seed setting rate. Between SH527 and IR24, significant differences were detected in plant height, panicles per plant and 1000-grains weight. Significant differences between their hybrid rice were also detected in growth period, plant height, seed setting rate and 1000-grains weight. In general, from the breeding stage of IR24, MH63 to SH527, combinations of these changes lead to an apparent yield increase for hybrid rice, although no obvious yield differences were found in the restorer lines themselves. Since the yield increase was evaluated on the average performance of hybrid rice generated from these three restorer lines with several common CMS lines, the yield increase of hybrid rice reflect an obvious genetic improvement of the restorer lines, possibly by improving the combining ability of the restorer lines.


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)

Plant phenotypes of the three core restorer lines and their cross genealogies.a, Plant phenotypes of the three core restorer lines; shown from left to right are IR24, MH63, and SH527. b, Cross genealogies of the three core restorer lines showing that MH63 and SH527 were indirectly generated from IR24. A new rice line (at the head of an arrow) was bred by crossing of two or more parents (at the tail of an arrow) and by several turns of subsequent selfing and selection. A straight line in the figure indicates a backcross.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0030952-g001: Plant phenotypes of the three core restorer lines and their cross genealogies.a, Plant phenotypes of the three core restorer lines; shown from left to right are IR24, MH63, and SH527. b, Cross genealogies of the three core restorer lines showing that MH63 and SH527 were indirectly generated from IR24. A new rice line (at the head of an arrow) was bred by crossing of two or more parents (at the tail of an arrow) and by several turns of subsequent selfing and selection. A straight line in the figure indicates a backcross.
Mentions: IR24, MH63, and SH527 (Fig. 1A) are considered hybrid rice core restorer lines because of the large number of elite commercial hybrid rice cultivars and useful restorer lines bred and generated from them. Based on their cross genealogies, MH63 and SH527 were both indirectly generated from IR24 (Fig. 1B), indicating that these three lines originate from the same restoring genes. We examined the field performances of these lines by selfing (Table 1). Performances of the hybrid rice made by crossing these three lines with six other widely used CMS lines, namely, G3A, Zhongjiu A, II-32A, G46A, 92A, and Chuangu A, were also examined (Table 1). No obvious differences were found in the yield components of MH63 and IR24 except for plant height, while the hybrid rice of MH63 was significantly different from that of IR24 in growth period, plant height, panicles per plant and seed setting rate. Between SH527 and IR24, significant differences were detected in plant height, panicles per plant and 1000-grains weight. Significant differences between their hybrid rice were also detected in growth period, plant height, seed setting rate and 1000-grains weight. In general, from the breeding stage of IR24, MH63 to SH527, combinations of these changes lead to an apparent yield increase for hybrid rice, although no obvious yield differences were found in the restorer lines themselves. Since the yield increase was evaluated on the average performance of hybrid rice generated from these three restorer lines with several common CMS lines, the yield increase of hybrid rice reflect an obvious genetic improvement of the restorer lines, possibly by improving the combining ability of the restorer lines.

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
Related in: MedlinePlus