Abstract
The genetic dissection of agronomically important traits in closely related Japanese rice cultivars is still in its infancy mainly because of the narrow genetic diversity within japonica rice cultivars. In an attempt to unveil potential polymorphism between closely related Japanese rice cultivars, we used a next-generation-sequencing-based genotyping method: genotyping by random amplicon sequencing-direct (GRAS-Di) to develop genetic linkage maps. In this study, four recombinant inbred line (RIL) populations and their parents were used. A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing. Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated. Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively. Markers generated by GRAS-Di were organized into linkage maps and compared with those generated by GoldenGate SNP assay of the same RIL populations; the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps. Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17. Therefore, GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm.
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Claims 12
Claim · model-written summary
GRAS-Di generated 438.7 Mbp of called bases for RIL71.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
GRAS-Di generated 440 Mbp of called bases for RIL98.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
GRAS-Di generated 403.1 Mbp of called bases for RIL16.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
GRAS-Di generated 392 Mbp of called bases for RIL91.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
Genotyping identified 1050 markers in RIL71.
- Taxon
- rice
Oryza sativat0 - Material
- RIL71e1
- Outcome
- markerse0
- Value
- 1050e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
Genotyping identified 1285 markers in RIL98.
- Taxon
- riceOryza sativat0
- Material
- RIL98e1
- Outcome
- markerse0
- Value
- 1285e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
Genotyping identified 1708 markers in RIL16.
- Taxon
- riceOryza sativat0
- Material
- RIL16e1
- Outcome
- markerse0
- Value
- 1708e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
Genotyping identified 1704 markers in RIL91.
- Taxon
- riceOryza sativat0
- Material
- RIL91e1
- Outcome
- markerse0
- Value
- 1704e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
e1“A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing.”
Claim · model-written summary
Integrating GRAS-Di and GoldenGate markers decreased average intermarker genetic distance in four RIL populations.
- Taxon
- riceOryza sativat0
- Outcome
- average genetic distance between markerse0
- Direction
- decreasee0
- Comparator
- both linkage mapse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
Claim · model-written summary
The markers localized five heading-date QTLs on chromosomes 3, 6 and 7 corresponding to Hd1, Hd2, Hd6, Hd16 and Hd17.
- Taxon
- riceOryza sativat0
- Gene
- Hd1, Hd2, Hd6, Hd16, and Hd17e0
- Outcome
- QTLs associated with heading datee0
- Value
- five QTLse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17.”
t0“Japanese Rice japonica Recombinant Inbred Lines”
Claim · model-written summary
GRAS-Di provided low-cost efficient genotyping for closely related Japanese rice cultivars.
- Taxon
- Japanese rice cultivars
_by_Augustus_Binu.jpg?width=60)
Oryza sativa Japonica Groupe0 - Outcome
- low cost and efficient genotypinge0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_by_Augustus_Binu.jpg?width=500)
Verbatim
e0“GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm.”
Claim · model-written summary
GRAS-Di enabled generation of a high-density linkage map.
- Taxon
- Japanese rice cultivarsOryza sativa Japonica Groupe0
- Outcome
- high density linkage mape0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm.”