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Fukuie Y, Shimoyama H, Morishita T, Tsugama D, Fujino K. A putative AGAMOUS ortholog is a candidate for the gene determining ease of dehulling in Tartary buckwheat (Fagopyrum tataricum). PLANTA 2020; 251:85. [PMID: 32198546 DOI: 10.1007/s00425-020-03374-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/10/2020] [Indexed: 05/08/2023]
Abstract
Tartary buckwheat rice-type cultivars, which allow easy dehulling, lacked periclinal cell divisions that proceed underneath the epidermis in the proximity of ovary midribs in non-rice-type cultivars. The easy dehulling in these cultivars was associated with a G→A substitution in an AGAMOUS ortholog. Ease of dehulling in Tartary buckwheat (Fagopyrum tataricum) can affect the quality of its products. Tartary buckwheat cultivars that allow easy dehulling are called rice-type cultivars. The rice and non-rice hull types are determined by a single gene, but this gene is unclear. Here, we show that cells underneath the epidermis in the proximity of ovary midribs undergo periclinal cell divisions in non-rice-type cultivars but do not in a rice-type cultivar. The cells that arose from the periclinal cell divisions later underwent lignification, which should increase mechanical strength of hulls. In RNA sequencing, a partial mRNA of an AGAMOUS ortholog in Tartary buckwheat (FtAG) was found to be absent in the rice-type cultivar. Cloning of this gene revealed that this is a 42-bp deletion due to a G→A substitution at a splice acceptor site in the FtAG genomic region. In F2 progeny derived from a cross between non-rice-type and rice-type cultivars, all the rice-type plants exhibited the homozygous A/A allele at this site, whereas all the Tartary-type plants exhibited either the homozygous G/G allele or the heterozygous A/G allele. These results suggest that FtAG is a candidate for the gene that determines ease of dehulling in Tartary buckwheat. The DNA marker that we developed to distinguish the FtAG alleles can be useful in breeding Tartary buckwheat cultivars.
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Affiliation(s)
- Yuka Fukuie
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
| | - Hana Shimoyama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
- Division of African Area Studies, Graduate School of Asian and African Area Studies, Kyoto University, 46 Yoshida-shimo-adachi-cho, Sakyo-ku, Kyoto-shi, Kyoto, 606-8304, Japan
| | - Toshikazu Morishita
- National Agriculture and Food Research Organization (NARO) Hokkaido Agricultural Research Center, Memuro Upland Farming Research Station, Shinsei, Memuro, Kasai, Hokkaido, 082-0081, Japan
- Radiation Breeding Division, Institute of Crop Science, NARO, 2425 Kamimurata, Hitachiomiya, Ibaraki, 319-2293, Japan
| | - Daisuke Tsugama
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan
- Asian Natural Environmental Science Center, The University of Tokyo, 1-1-1 Midori-cho, Nishi-tokyo-shi, Tokyo, 188-0002, Japan
| | - Kaien Fujino
- Laboratory of Crop Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9 Kita-ku, Sapporo-shi, Hokkaido, 060-8589, Japan.
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Tsugama D, Fujino K. Data of whole genome sequencing of five garden asparagus ( Asparagus officinalis) individuals with the MinION nanopore sequencer. Data Brief 2019; 28:104838. [PMID: 31832531 PMCID: PMC6889792 DOI: 10.1016/j.dib.2019.104838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 11/18/2022] Open
Abstract
Garden asparagus (Asparagus officinalis) is a perennial, dioecious crop. Genomic DNA samples were prepared from five A. officinalis individuals that differ in sex and phenotypes, and sequenced with the MinION nanopore sequencer. The obtained data were 1.5–5 Gb/sample, and the average read length was larger than 1.4 kb for all the samples. The resulting reads were mapped to the existing A. officinalis genome sequence. The existing A. officinalis transcript sequences were mapped to the MinION-derived reads. On the basis of these mapping results, flanking sequences of five partial gene fragments that previously had not been mapped to any region of the existing genome were determined by genomic PCR followed by Sanger sequencing. These sequences enabled to estimate the genomic positions of those five partial gene fragments. The MinION-derived data and the flanking sequences of the five gene fragments were deposited in the NCBI (National Center for Biotechnology Information) SRA (Sequence Read Archive) database and the NCBI Nucleotide database, respectively.
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Affiliation(s)
- Daisuke Tsugama
- Asian Natural Environmental Science Center, The University of Tokyo, Japan.,Research Faculty of Agriculture, Hokkaido University, Japan
| | - Kaien Fujino
- Research Faculty of Agriculture, Hokkaido University, Japan
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