Linkage map construction based on LD and its application to polyploid species
| Project/Area Number |
15H04441
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Science in genetics and breeding
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| Research Institution | Kazusa DNA Research Institute |
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Principal Investigator |
Sachiko Isobe 公益財団法人かずさDNA研究所, 先端研究部, 室長 (20343973)
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| Co-Investigator(Kenkyū-buntansha) |
中谷 明弘 大阪大学, 医学系研究科, 特任教授(常勤) (60301149)
田中 勝 国立研究開発法人農業・食品産業技術総合研究機構, 九州沖縄農業研究センター, グループ長 (60391455)
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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 |
¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Fiscal Year 2017: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2016: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2015: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
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| Keywords | 連鎖地図 / 高次倍数性 / 連鎖不平衡 / ゲノム配列 / 育種学 / 遺伝学 |
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| Outline of Final Research Achievements |
Linkage analysis was performed with a S1 population of strawberry derived from a Japanese variety, ‘Reiko’, a S1 population of sweetpotato derived from a Chinese variety, ‘Xushu 18’, and a F1 population cross between ‘Xhushu 18’ and an Ipomoea trifida accession, ‘K123-11’.
Although linkage maps were successfully constructed in the S1 populations of strawberry and sweetpotato, it was difficult to generate linkage groups in the sweetpotato F1 population with typical approach in linkage map construction. A sofrtware was developed for generation on linkage groups based on linkage disequilibrium (LD) between the two loci. The software calculates indexes representing LDs between the all combinations of two loci and constructing hierarchic structure based on the LD indexes.
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Report
(4 results)
Research Products
(18 results)
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[Journal Article] 3.A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas).2017
Author(s)
Shirasawa K, Tanaka M, Takahata Y, Ma D, Cao Q, Liu Q, Zhai H, Kwak SS, Jeong JC, Yoon UH, Lee HU, Hirakawa H, Isobe S
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Journal Title
Nature Scientific Report
Volume: 7
Issue: 1
Pages: 44207-44207
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
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[Presentation] A high-density SNP linkage map toward whole genome sequencing in autohexaploid sweetpotato2017
Author(s)
Shirasawa K, Tanaka M, Takahata Y, Ma D, Cao Q, Liu Q, Zhai H, Kwak S, Jeong J, Yoon U, Lee H, Hirakawa H, Isobe S
Organizer
PAG Asia
Related Report
Int'l Joint Research / Invited
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[Presentation] Genetic map with SNPs from ddRAD-Seq analysis in sweetpotato2016
Author(s)
Shirasawa K, Tanaka M, Takahata Y, Ma D, Cao Q, Liu Q, Zhai H, Kwak SS, Jeong JC, Yoon UH, Hirakawa H, Isobe S
Organizer
7th Internatinal Sweetpotato Workshop
Place of Presentation
済南、中国
Year and Date
2016-10-10
Related Report
Int'l Joint Research
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