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Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms.

Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M - BMC Genomics (2010)

Bottom Line: The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67,051 SNPs.Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties.We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding.

View Article: PubMed Central - HTML - PubMed

Affiliation: QTL Genomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.

ABSTRACT

Background: To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.

Results: The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7 x the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67,051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity

Conclusions: Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.

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Distribution of SNPs between Koshihikari and Nipponbare in the 12 rice chromosomes. The number of SNPs in each chromosome is shown in brackets. The x-axis represents the physical distance along each chromosome, split into 500-kb windows. The orange lines represent regions in which no SNPs were detected. The y-axis indicates the common logarithm of the number of SNPs.
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Figure 2: Distribution of SNPs between Koshihikari and Nipponbare in the 12 rice chromosomes. The number of SNPs in each chromosome is shown in brackets. The x-axis represents the physical distance along each chromosome, split into 500-kb windows. The orange lines represent regions in which no SNPs were detected. The y-axis indicates the common logarithm of the number of SNPs.

Mentions: We detected a total of 67 051 SNPs between Koshihikari and Nipponbare (Table 1; http://koshigenome.dna.affrc.go.jp/). Although the average SNP density was 1 per 5.7 kb, the density varied among the chromosomes (Table 1), from 1/134.0 kb (178 SNPs) on chromosome 9 to 1/2.5 kb (12 216 SNPs) on chromosome 11. Moreover, the distributions of the SNPs were uneven within a chromosome (Figure 2); for example, there were 17 high-density regions with >0.5 SNPs/kb, including 1853 SNPs in 2.5-3 Mb on chromosome 1, and 1745 SNPs in 27-27.5 Mb on chromosome 12. We randomly selected 64 SNPs from all chromosomes for validation. Of these, we confirmed 63 SNPs using the traditional Sanger method using a capillary sequencer, indicating a high level of reliability in SNP detection.


Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms.

Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, Shibaya T, Yano M - BMC Genomics (2010)

Distribution of SNPs between Koshihikari and Nipponbare in the 12 rice chromosomes. The number of SNPs in each chromosome is shown in brackets. The x-axis represents the physical distance along each chromosome, split into 500-kb windows. The orange lines represent regions in which no SNPs were detected. The y-axis indicates the common logarithm of the number of SNPs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2874813&req=5

Figure 2: Distribution of SNPs between Koshihikari and Nipponbare in the 12 rice chromosomes. The number of SNPs in each chromosome is shown in brackets. The x-axis represents the physical distance along each chromosome, split into 500-kb windows. The orange lines represent regions in which no SNPs were detected. The y-axis indicates the common logarithm of the number of SNPs.
Mentions: We detected a total of 67 051 SNPs between Koshihikari and Nipponbare (Table 1; http://koshigenome.dna.affrc.go.jp/). Although the average SNP density was 1 per 5.7 kb, the density varied among the chromosomes (Table 1), from 1/134.0 kb (178 SNPs) on chromosome 9 to 1/2.5 kb (12 216 SNPs) on chromosome 11. Moreover, the distributions of the SNPs were uneven within a chromosome (Figure 2); for example, there were 17 high-density regions with >0.5 SNPs/kb, including 1853 SNPs in 2.5-3 Mb on chromosome 1, and 1745 SNPs in 27-27.5 Mb on chromosome 12. We randomly selected 64 SNPs from all chromosomes for validation. Of these, we confirmed 63 SNPs using the traditional Sanger method using a capillary sequencer, indicating a high level of reliability in SNP detection.

Bottom Line: The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67,051 SNPs.Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties.We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding.

View Article: PubMed Central - HTML - PubMed

Affiliation: QTL Genomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.

ABSTRACT

Background: To create useful gene combinations in crop breeding, it is necessary to clarify the dynamics of the genome composition created by breeding practices. A large quantity of single-nucleotide polymorphism (SNP) data is required to permit discrimination of chromosome segments among modern cultivars, which are genetically related. Here, we used a high-throughput sequencer to conduct whole-genome sequencing of an elite Japanese rice cultivar, Koshihikari, which is closely related to Nipponbare, whose genome sequencing has been completed. Then we designed a high-throughput typing array based on the SNP information by comparison of the two sequences. Finally, we applied this array to analyze historical representative rice cultivars to understand the dynamics of their genome composition.

Results: The total 5.89-Gb sequence for Koshihikari, equivalent to 15.7 x the entire rice genome, was mapped using the Pseudomolecules 4.0 database for Nipponbare. The resultant Koshihikari genome sequence corresponded to 80.1% of the Nipponbare sequence and led to the identification of 67,051 SNPs. A high-throughput typing array consisting of 1917 SNP sites distributed throughout the genome was designed to genotype 151 representative Japanese cultivars that have been grown during the past 150 years. We could identify the ancestral origin of the pedigree haplotypes in 60.9% of the Koshihikari genome and 18 consensus haplotype blocks which are inherited from traditional landraces to current improved varieties. Moreover, it was predicted that modern breeding practices have generally decreased genetic diversity

Conclusions: Detection of genome-wide SNPs by both high-throughput sequencer and typing array made it possible to evaluate genomic composition of genetically related rice varieties. With the aid of their pedigree information, we clarified the dynamics of chromosome recombination during the historical rice breeding process. We also found several genomic regions decreasing genetic diversity which might be caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.

Show MeSH