Isolation and characterization of the barley gene controlling hulled or naked caryopsis

• Project/Area Number: 15580007
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Breeding science
• Research Institution: Kagawa University
• Principal Investigator: TAKETA Shin Kagawa University, Faculty of Agriculture, Professor, 農学部, 教授 (40216891)
• Project Period (FY): 2003 – 2005
• Project Status: Completed (Fiscal Year 2005)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,900,000); Fiscal Year 2005: ¥1,100,000 (Direct Cost: ¥1,100,000); Fiscal Year 2004: ¥900,000 (Direct Cost: ¥900,000); Fiscal Year 2003: ¥1,900,000 (Direct Cost: ¥1,900,000)
• Keywords: barley / seed / mapping / gene isolation / genome / physical map / 遺伝子 / 皮麦 / 裸麦 / ポジショナルクローニング / 分子マーカー / 裸性

Research Abstract

In barley, the hulled or naked caryopsis trait is one of essential agronomic characters because it is closely associated with the utility of harvested barley grains either as malting/feeding purpose or human food.. We attempted isolation and characterization of the barley gene controlling hulled or naked caryopsis using a positional cloning approach. First, we developed linked molecular markers by using AFLP and bulked segregant analysis. Putative linked AFLP bands were sequenced to develop PCR based markers. Then, large segregating populations were analyzed for a fine mapping of the gene. This mapping resulted in the state where the gene was flanked by two co-dominant markers with genetic distance of 0.6 cM in proximal side and 0.06 cM in distal side, respectively. Next, bioinformatics were applied to identify microsynteny between the naked caryopsis gene in the barley genome and the rice genome. We successfully identified microcollinearity with the long arm of rice chromosome 6. Rice genome sequence information was effectively used to further narrow down the naked caryopsis gene in the barley genome. We then started the physical map construction of the entire locus. We have successfully constructed the barley BAC contig of about 500 kb, which spans the hulled or naked caryopsis gene. On the bases of available information, we have identified a candidate gene for the hulled or naked caryopsis character in barley. Expression analysis seems to support the identity of this gene. We also analyzed induced naked caryopsis mutants and found non-synonymous mutations, which solidified our conclusion. We conclude that naked barley in the world has a single origin, which appears to have occurred in the Middle East. On the basis of allelic variation of a molecular marker that was tightly linked to the naked caryopsis gene, we elucidated two independent migratory routes of naked barley into East Asia.

Research Products

• [Journal Article] High-resolution mapping of the nud locus controlling the naked caryonsis in harley (2006)
  • Author(s): Taketa, S., T.Awayama, S.Aamano, Y.Sakurai, M.Ichii
  • Journal Title: Plant Breeding (印刷中)
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] High-re solution mapping of the nud locus controlling the naked caryopsis in barley (2006)
  • Author(s): Taketa, S., T.Awayama, S.Amano, Y.Sakurai, M.Ichii
  • Journal Title: Plant Breeding 125(印刷中)
• [Journal Article] Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA (2005)
  • Author(s): Taketa, S., Ando, H., Takeda, K., Ichii, M., yon Bothmer.
  • Journal Title: Annals of Botany 96 Pages: 23-33
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Molecular cytogenetic identification of nullisomy-5B induced homoeologous recombination between wheat chromosome 5D and harley chromosome 5H (2005)
  • Author(s): Taketa, S., Awayama, T., Ichii, M., Sunakawa, M., Kawahara, T., Murai, K.
  • Journal Title: Genome 48 Pages: 115-124
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Molecular cytogenetic identification of nullisomy-5B induced homoeologous recombination between wheat chromosome 5D and barley chromosome 5H. (2005)
  • Author(s): Taketa, S., Awayama, T., Ichii, M., Sunakawa, M., Kawahara, T., Murai, K.
  • Journal Title: Genome 48 Pages: 115-124
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA. (2005)
  • Author(s): Taketa, S., Ando, H., Takeda, K., Ichii, M., von Bothmer, R.
  • Journal Title: Annals of Botany 96 Pages: 23-33
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Molecular cytogenetic identification of nullisomy-5B induced homoeologous recombination between wheat chromosome 5D and barley chromosome 5H. (2005)
  • Author(s): Taketa, S., Awayama, T., Ichii, M., Sunakawa, M., Kawahara, T., Murai
  • Journal Title: Genome 48 Pages: 115-124
• [Journal Article] Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud) (2004)
  • Author(s): Taketa, S., Kikuchi, S., Awayama, T., Yamamoto, S., Ichii, M., Kawasaki, S.
  • Journal Title: Theoretical and Applied Genetics 108 Pages: 1236-1242
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud). (2004)
  • Author(s): Taketa, S., Kikuchi, S., Awayama, T., Yamamoto, S., Ichii, M., Kawasaki, S.
  • Journal Title: Theoretical and Applied Genetics 108 Pages: 1236-1242
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] High-resolution mapping of the naked-caryopsis gene (nud) and the origin of naked barley. (2004)
  • Author(s): Taketa, S., Kikuchi, S., Awayama, T., Yamamoto, S., Ichii, M., Kawasaki, S.
  • Journal Title: Proceedings of the 9^<th> International Barley Genetics Symposium (Spunar, I.J., Janokova, J. eds.) Pages: 589-594
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud). (2004)
  • Author(s): Taketa, S., Kikuchi, S., Awayama, T., Yamamoto.S., Ichii M., Kawasaki, S.
  • Journal Title: Theoretical and Applied Genetics 108 Pages: 1236-1242
• [Journal Article] Efficient fine mapping of the naked caryopsis gene (nud) by HEGS (High efficiency genome scanning )/AELP in harley (2003)
  • Author(s): Kikuchi, S., Taketa, S., Ichii, M., Kawasaki, S.
  • Journal Title: Theoretical and Applied Genetics 108 Pages: 73-78
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Efficient fine mapping of the naked caryopsis gene (nud) by HEGS (High efficiency genome scanning)/AFLP in barley. (2003)
  • Author(s): Kikuchi, S., Taketa, S., Ichii, M., Kawasaki, S.
  • Journal Title: Theoretical and Applied Genetics 108 Pages: 73-78
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] High-resolution mapping of the nud locus controlling the naked caryopsis in barley.
  • Author(s): Taketa, S., T.Awayama, S.Amano, Y.Sakurai, M.Ichii
  • Journal Title: Plant Breeding (in press)
  • Description: 「研究成果報告書概要(欧文)」より
• [Publications] S.Kikuchi, S.Taketa, M.Ichii, S.Kawasaki: "Efficient fine mapping of the naked caryopsis gene (nud) by HEGS (high Efficiency Genome Scanning)/AFLP in barley"Theoretical and Applied Genetics. 108. 73-78 (2003)