Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups.
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonic...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3897683?pdf=render |
| _version_ | 1818035172450238464 |
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| author | Yuko Arai-Kichise Yuh Shiwa Kaworu Ebana Mari Shibata-Hatta Hirofumi Yoshikawa Masahiro Yano Kyo Wakasa |
| author_facet | Yuko Arai-Kichise Yuh Shiwa Kaworu Ebana Mari Shibata-Hatta Hirofumi Yoshikawa Masahiro Yano Kyo Wakasa |
| author_sort | Yuko Arai-Kichise |
| collection | DOAJ |
| description | Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html). |
| first_indexed | 2024-12-10T06:50:50Z |
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| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T06:50:50Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS ONE |
| spelling | doaj.art-f8d07b508b3e4b6fa6f2db3b13cdb92e2022-12-22T01:58:34ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0191e8631210.1371/journal.pone.0086312Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups.Yuko Arai-KichiseYuh ShiwaKaworu EbanaMari Shibata-HattaHirofumi YoshikawaMasahiro YanoKyo WakasaElucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html).http://europepmc.org/articles/PMC3897683?pdf=render |
| spellingShingle | Yuko Arai-Kichise Yuh Shiwa Kaworu Ebana Mari Shibata-Hatta Hirofumi Yoshikawa Masahiro Yano Kyo Wakasa Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. PLoS ONE |
| title | Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. |
| title_full | Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. |
| title_fullStr | Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. |
| title_full_unstemmed | Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. |
| title_short | Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. |
| title_sort | genome wide dna polymorphisms in seven rice cultivars of temperate and tropical japonica groups |
| url | http://europepmc.org/articles/PMC3897683?pdf=render |
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