Functional analysis of genes in quinoa using a virus vector system 

Related Research Project
Resilient crops


Quinoa (Chenopodium quinoa Willd.) is an annual protein-rich pseudocereal native to the Andean region of South America. Quinoa has been recognized as a potentially important crop in terms of global food and nutrition security since it can thrive in harsh environments and has an excellent nutritional profile. JIRCAS and collaborative researchers have been analyzing the complex and heterogeneous allotetraploid genome of quinoa, and have recently overcome the challenges, with the whole genome-sequencing of quinoa and the creation of genotyped inbred lines (Research Highlights 2016, B03: Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid pseudocereal crop with high nutritional properties and tolerance to abiotic stresses; Research Highlights 2020, B08: Genetic and phenotypic variation of agronomic traits and salt tolerance among quinoa inbred lines). However, the lack of technology to analyze gene function in planta is a major limiting factor in quinoa research. 

In this study, we demonstrate that the virus-mediated transient gene expression or repression techniques can be used in quinoa plants (Fig. 1). We show that apple latent spherical virus (ALSV) vector can induce gene silencing of a quinoa carotenoid biosynthesis gene, phytoene desaturase (CqPDS1) (Fig. 2). Virus-mediated silencing of CqPDS1 induces decreased accumulation of carotenoids and causes photobleaching symptoms in quinoa plants (Fig. 3). We also show that ALSV-mediated gene silencing can also be used in a broad range of quinoa inbred lines derived from the northern and southern highland and lowland sub-populations. Our data also indicate that repression of a quinoa 3,4-dihydroxyphenylalanine 4,5-dioxygenase gene (CqDODA1) or a cytochrome P450 enzyme gene (CqCYP76AD1) reduces accumulation of red-violet betalain pigments in quinoa plants (Fig. 4). 

Our data demonstrate that the virus vector system is a useful tool for evaluating gene function in quinoa, where molecular breeding techniques such as genetic transformation have not been developed yet. Functional validation of quinoa genes, utilizing the published genomic information, could provide gene resources for molecular breeding of quinoa.  


Figure, table

  1. Fig1

    Fig. 1. Schematic of the virus vector system in quinoa plants 


  2. Fig2

    Fig. 2. ALSV induces silencing of carotenoid biosynthesis genes CqPDS1 in quinoa 
    RT-qPCR quantification of CqPDS1 transcripts in the uninoculated upper leaves of plants inoculated with the indicated inocula. Data are normalized and are shown as means ± SD (n = 3). Different letters indicate significant differences (p < 0.05). 


  3. Fig3

    Fig. 3. Silencing of CqPDS1 induces photobleaching phenotypes in quinoa plants 
    A representative image of quinoa plants (inbred Iw line) at 14 days after virus inoculation with ALSV-wild (control) and ALSV-CqPDS1 is shown.


  4. Fig4

    Fig. 4. Functional analysis of genes for betalain pigments biosynthesis in quinoa using the virus vector system 
    Virus-mediated silencing of CqDODA1 and CqCYP76AD1 inhibits betalain production in quinoa. Representative images of quinoa plants (inbred J056 lines) and aqueous extracts from the uninoculated upper leaves are shown. Quinoa plants inoculated with ALSV-wild were used as a control. 

    Figures reprinted/modified with permission from Ogata et al. (2021).




Research project
Program name


Stable Agricultural Production

Term of research

FY 2016–2025

Responsible researcher

Ogata Takuya ( Biological Resources and Post-harvest Division )

Toyoshima Masami ( Biological Resources and Post-harvest Division )

Yamamizo-Oda Chihiro ( Biological Resources and Post-harvest Division )

Kobayashi Yasufumi ( Biological Resources and Post-harvest Division )

Fujii Kenichiro ( Biological Resources and Post-harvest Division )

Nagatoshi Yukari ( Biological Resources and Post-harvest Division )

MIERUKA ID: 001763

Fujita Yasunari ( Biological Resources and Post-harvest Division )

KAKEN Researcher No.: 00446395
MIERUKA ID: 001776

Kojiro Tanaka ( Actree Corporation )

Tanaka Tsutomu ( Actree Corporation )

Hiroharu Mizukoshi ( Actree Corporation )

Yasui Yasuo ( Kyoto University )

KAKEN Researcher No.: 70293917

Yoshikawa Nobuyuki ( Faculty of Agriculture, Iwate University )

KAKEN Researcher No.: 40191556

Publication, etc.

Ogata et al. (2021) Frontiers in Plant Science 12: 643499

Japanese PDF

2021_B03_ja.pdf359.53 KB

English PDF

2021_B03_en.pdf382.46 KB

Poster PDF

2021_B03_poster.pdf273.91 KB

* Affiliation at the time of implementation of the study.

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