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Probowati W, Koga S, Harada K, Nagano Y, Nagano AJ, Ishimaru K, Ohshima K, Fukuda S. RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized. Sci Rep 2023; 13:16354. [PMID: 37773322 PMCID: PMC10541398 DOI: 10.1038/s41598-023-43537-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
Allium macrostemon Bunge, commonly referred to as "no-biru" in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, it remains an underutilized crop in Japan. Determining the origins of its domestic populations and understanding their genetic composition is crucial to highlighting the plant's historical significance in Japan. This study aims to bridge this knowledge gap by examining the genetic diversity of 47 A. macrostemon samples from various regions in Japan using RAD-Seq. Our analyses distinguished unique population structures, dividing the samples into three distinct groups: A, B, and C. Notably, groups A and B showed clear evidence of bulb propagation, while group C did not. Group C formed four subgroups: C1, C2, C3, and C4. Hybridization between subgroup C1 and either group A, B, or both, resulted in the emergence of subgroups C2, C3, and C4. Thus, groups A, B, and C1 are posited as the ancestral populations. Additionally, our morphological observations indicated distinct differences among these three groups. Our findings also suggest that human migration may have influenced the plant's distribution, hinting at active usage in the past that later waned, causing its current underutilized status.
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Affiliation(s)
- Wiwit Probowati
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Center for Education and Research in Agricultural Innovation, Saga University, Saga, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | - Shogo Koga
- Center for Education and Research in Agricultural Innovation, Saga University, Saga, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | - Kentaro Harada
- Center for Education and Research in Agricultural Innovation, Saga University, Saga, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | - Yukio Nagano
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kanji Ishimaru
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | - Kazusato Ohshima
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
- Faculty of Agriculture, Saga University, Saga, Japan
| | - Shinji Fukuda
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.
- Center for Education and Research in Agricultural Innovation, Saga University, Saga, Japan.
- Faculty of Agriculture, Saga University, Saga, Japan.
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Narcissus Plants: A Melting Pot of Potyviruses. Viruses 2022; 14:v14030582. [PMID: 35336988 PMCID: PMC8949890 DOI: 10.3390/v14030582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 02/01/2023] Open
Abstract
Our paper presents detailed evolutionary analyses of narcissus viruses from wild and domesticated Narcissus plants in Japan. Narcissus late season yellows virus (NLSYV) and narcissus degeneration virus (NDV) are major viruses of Narcissus plants, causing serious disease outbreaks in Japan. In this study, we collected Narcissus plants showing mosaic or striped leaves along with asymptomatic plants in Japan for evolutionary analyses. Our findings show that (1) NLSYV is widely distributed, whereas the distribution of NDV is limited to the southwest parts of Japan; (2) the genomes of NLSYV isolates share nucleotide identities of around 82%, whereas those of NDV isolates are around 94%; (3) three novel recombination type patterns were found in NLSYV; (4) NLSYV comprises at least five distinct phylogenetic groups whereas NDV has two; and (5) infection with narcissus viruses often occur as co-infection with different viruses, different isolates of the same virus, and in the presence of quasispecies (mutant clouds) of the same virus in nature. Therefore, the wild and domesticated Narcissus plants in Japan are somewhat like a melting pot of potyviruses and other viruses.
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