Nagano, Atsushi

写真a

Affiliation

Graduate School of Media and Governance (Shonan Fujisawa)

Position

Project Professor (Non-tenured)
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Papers 【 Display / hide 】

  • Combination of genetic analysis and ancient literature survey reveals the divergence of traditional Brassica rapa varieties from Kyoto, Japan

    Kawakatsu Y., Sakamoto T., Nakayama H., Kaminoyama K., Igarashi K., Yasugi M., Kudoh H., Nagano A.J., Yano K., Kubo N., Notaguchi M., Kimura S.

    Horticulture Research (Horticulture Research)  8 ( 1 )  2021.12

    ISSN  20527276

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    Since ancient times, humans have bred several plants that we rely on today. However, little is known about the divergence of most of these plants. In the present study, we investigated the divergence of Mibuna (Brassica rapa L. subsp. nipposinica L. H. Bailey), a traditional leafy vegetable in Kyoto (Japan), by combining genetic analysis and a survey of ancient literature. Mibuna is considered to have been bred 200 years ago from Mizuna, another traditional leafy vegetable in Kyoto. Mibuna has simple spatulate leaves, whereas Mizuna has characteristic serrated leaves. The quantitative trait loci (QTL) and gene expression analyses suggested that the downregulation of BrTCP15 expression contributed to the change in the leaf shape from serrated to simple spatulate. Interestingly, the SNP analysis indicated that the genomic region containing the BrTCP15 locus was transferred to Mibuna by introgression. Furthermore, we conducted a survey of ancient literature to reveal the divergence of Mibuna and found that hybridization between Mizuna and a simple-leaved turnip might have occurred in the past. Indeed, the genomic analysis of multiple turnip cultivars showed that one of the cultivars, Murasakihime, has almost the same sequence in the BrTCP15 region as Mibuna. These results suggest that the hybridization between Mizuna and turnip has resulted in the establishment of Mibuna.

  • Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq

    Premarathne M.D.G.P., Fukutome N., Yamasaki K., Hayakawa F., Nagano A.J., Mizuno H., Ibaragi N., Nagano Y.

    Scientific Reports (Scientific Reports)  11 ( 1 )  2021.12

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    Japanese pepper, Zanthoxylum piperitum, is native to Japan and has four well-known lineages (Asakura, Takahara, Budou, and Arima), which are named after their production area or morphology. Restriction-site associated DNA sequencing (RAD-Seq) was used to analyse 93 accessions from various areas, including these four lineages. Single nucleotide variant analysis was used to classify the plants into eight groups: the Asakura and Arima lineages each had two groups, the Takahara and Budou lineages each had one group, and two additional groups were present. In one Asakura group and two Arima groups, the plants were present in agricultural fields and mountains, thus representing the early stage of domestication of the Japanese pepper. The second Asakura lineage group was closely related to plants present in various areas, and this represents the second stage of domestication of this plant because, after early domestication, genetically related lineages with desirable traits spread to the periphery. These results demonstrate that domestication of Japanese pepper is ongoing. In addition, this study shows that spineless plants are polyphyletic, despite the spineless lineage being considered a subspecies of Japanese pepper.

  • Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere

    Yamazaki S., Mardani-korrani H., Kaida R., Ochiai K., Kobayashi M., Nagano A.J., Fujii Y., Sugiyama A., Aoki Y.

    Scientific Reports (Scientific Reports)  11 ( 1 )  2021.12

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    The plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere are different from the outer soil region (bulk soil). They establish characteristic conditions including microbiota, metabolites, and minerals, and they can directly affect plant growth and development. However, comprehensive insights into those characteristic environments, especially the rhizosphere, and molecular mechanisms of their formation are not well understood. In the present study, we investigated the spatiotemporal dynamics of the root-associated environment in actual field conditions by multi-omics analyses (mineral, microbiome, and transcriptome) of soybean plants. Mineral and microbiome analyses demonstrated a characteristic rhizosphere environment in which most of the minerals were highly accumulated and bacterial communities were distinct from those in the bulk soil. Mantel’s test and co-abundance network analysis revealed that characteristic community structures and dominant bacterial taxa in the rhizosphere significantly interact with mineral contents in the rhizosphere, but not in the bulk soil. Our field multi-omics analysis suggests a rhizosphere-specific close association between the microbiota and mineral environment.

  • Relationship between gene regulation network structure and prediction accuracy in high dimensional regression

    Okinaga Y., Kyogoku D., Kondo S., Nagano A.J., Hirose K.

    Scientific Reports (Scientific Reports)  11 ( 1 )  2021.12

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    The least absolute shrinkage and selection operator (lasso) and principal component regression (PCR) are popular methods of estimating traits from high-dimensional omics data, such as transcriptomes. The prediction accuracy of these estimation methods is highly dependent on the covariance structure, which is characterized by gene regulation networks. However, the manner in which the structure of a gene regulation network together with the sample size affects prediction accuracy has not yet been sufficiently investigated. In this study, Monte Carlo simulations are conducted to investigate the prediction accuracy for several network structures under various sample sizes. When the gene regulation network is a random graph, a sufficiently large number of observations are required to ensure good prediction accuracy with the lasso. The PCR provided poor prediction accuracy regardless of the sample size. However, a real gene regulation network is likely to exhibit a scale-free structure. In such cases, the simulation indicates that a relatively small number of observations, such as N= 300 , is sufficient to allow the accurate prediction of traits from a transcriptome with the lasso.

  • Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan

    Imai R., Tsuda Y., Ebihara A., Matsumoto S., Tezuka A., Nagano A.J., Ootsuki R., Watano Y.

    Scientific Reports (Scientific Reports)  11 ( 1 )  2021.12

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    Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.

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