| Project/Area Number |
15K07175
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Evolutionary biology
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| Research Institution | National Agriculture and Food Research Organization (2016-2017)
国立研究開発法人農業生物資源研究所 (2015) |
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Principal Investigator |
Itoh Takeshi 国立研究開発法人農業・食品産業技術総合研究機構, 高度解析センター, チーム長 (80356469)
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| Co-Investigator(Renkei-kenkyūsha) |
SAKAI Hiroaki 国立研究開発法人農業・食品産業技術総合研究機構, 高度解析センター, 主任研究員 (20455322)
KUMAGAI Masahiko 国立研究開発法人農業・食品産業技術総合研究機構, 高度解析センター, 任期付研究員 (80738716)
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| Project Period (FY) |
2015-04-01 – 2018-03-31
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| Project Status |
Completed (Fiscal Year 2017)
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| Budget Amount *help |
¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
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| Keywords | 栽培化 / 分岐時間 / 集団の大きさ / 大規模ゲノム解析 / 塩基置換推定 / 負の二項分布 / ポワソン分布 / ガンマ分布 / 分子進化 / 分岐年代推定 / 作物栽培化 |
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| Outline of Final Research Achievements |
In this study, to elucidate the process of ancient crop cultivation, it was aimed that the divergence time and effective population size would be estimated accurately through large-scale analysis, which was recently enabled by low-cost, high-throughput DNA sequencing. Whole genome sequence data are first obtained from two different closely-related species or populations, and then a genome-wide distribution of nucleotide substitutions is calculated. The distribution does not obey a Poisson distribution, which assumes an equal substitution rate. Although a negative binomial distribution better fitsto the data, a mixed model of speciation and ancestral polymorphisms was found to best fit to the data. In the data analysis of this study, for example, the divergence time between Asian rice and African rice was much smaller than the previous estimate, which means that the past estimation overlooked the inflation of the estimated values that was caused by ancestral polymorphisms.
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