Open Access

ARTICLE

RNA-Seq Analysis of Quinoa Varieties with Different β-Carotene Contents Reveals Genes Related to Carotenoid Biosynthesis

Yingbo Li^1,2,#, Yingjie Zong^1,2,#, Yulu Tao^1,2, Wenqi Zhang^1,2, Xiang Wang^1,2, Runhong Gao^1,2, Longhua Zhou^1,2, Hongwei Xu^1,2,*, Chenghong Liu^1,2,*

1 Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
2 China (Shanghai) International Quinoa Innovation Center, Shanghai, China

* Corresponding Authors: Hongwei Xu. Email: ; Chenghong Liu. Email:
# These authors contributed equally to this work

Phyton-International Journal of Experimental Botany 2026, 95(9), 13 https://doi.org/10.32604/phyton.2026.087573

Received 23 June 2026; Accepted 26 August 2026; Issue published 24 September 2026

Abstract

Quinoa is a nutrient-enriched pseudocereal with excellent edible value, and its leaves contain abundant β-carotene, which serves as an important criterion for assessing leaf nutritional quality. However, the molecular regulatory pathway of β-carotene biosynthesis in quinoa remains largely unclear. To explore the molecular mechanism of β-carotene accumulation in quinoa leaves, we screened 196 quinoa resources and selected two high β-carotene germplasms (Cq39, Cq138) and two low β-carotene germplasms (Cq35, Cq92) for comparative transcriptome sequencing. Transcriptome profiling revealed divergent transcript profiles among the four quinoa germplasms. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that carotenoid biosynthesis pathway was significantly enriched among the downregulated differentially expressed genes (DEGs) in both Cq39 vs. Cq35 and Cq138 vs. Cq35 comparisons. Expression analysis revealed that core genes involved in carotenoid biosynthesis were relatively stable between contrasting germplasms. In contrast, one gene for carotenoid degradation (CCD4) and two genes associated with ABA metabolic shunt (NCEDs) were downregulated in high-β-carotene germplasms. Quantitative real-time PCR (qRT-PCR) further verified the expression trends of these candidate genes. Collectively, the identified DEGs provide preliminary insights into the potential regulatory mechanism of β-carotene accumulation in quinoa leaves. This study describes the transcriptional characteristics of carotenoid metabolism-related genes and offers valuable candidate gene resources for future nutritional quality improvement of quinoa.

---

Keywords

---

Supplementary Material

Supplementary Material File

---