Combined Analysis of Transcriptome and Metabolome Explains the Differences in Pulp Color in Jackfruit

Jianjun Liang; Xiangwei Ma; Chenxin Yi; Hailan Zhou; Zhuangmin Wei; Xiuguan Tang; Weiyan Ye; Hailing Tang; Pengjin Zhu

doi:10.1002/pld3.70127

Combined Analysis of Transcriptome and Metabolome Explains the Differences in Pulp Color in Jackfruit

Plant Direct. 2026 Feb 11;10(2):e70127. doi: 10.1002/pld3.70127. eCollection 2026 Feb.

Authors

Jianjun Liang^{1

2

3}, Xiangwei Ma^{1

2

3}, Chenxin Yi^{1

2

3}, Hailan Zhou^{1

2

3}, Zhuangmin Wei^{1

2

3}, Xiuguan Tang^{1

2

3}, Weiyan Ye^{1

2

3}, Hailing Tang⁴, Pengjin Zhu^{1

2

3}

Affiliations

¹ Guangxi Subtropical Crops Research Institute Guangxi Academy of Agricultural Sciences Nanning China.
² Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits Nanning China.
³ Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable Ministry of Agriculture and Rural Affairs Nanning China.
⁴ School of Tropical Agriculture and Forestry Hainan University Haikou China.

Abstract

The pulp color of jackfruit reflects variations in its nutritional composition and influences market preference. We investigated the mechanism underlying pulp coloration through an integrated transcriptomic and metabolomic analysis of three jackfruit cultivars-light yellow "THA", yellow "GTM", and orange "YNH". Twenty-five differentially accumulated flavonoids and 32 differentially accumulated carotenoids were identified. Naringenin chalcone, eriodictyol, taxifolin, zeaxanthin, and lutein were identified as the key flavonoids and carotenoids associated with the light-yellow tone of THA pulp. Phlorizin and lutein were associated with the yellow tone of GTM pulp, whereas apigenin, luteolin, zeaxanthin, and violaxanthin dipalmitate were the key pigments regulating the orange tone of YNH pulp. Differentially expressed genes involved in flavonoid and carotenoid biosynthesis included PAL, C4H, 4CL, F3H, FLS, ANS, ANR, PSY, PDS, ZDS, LCYE, LUT5, ZEP, and VDE. This study provides a foundation for elucidating the molecular mechanisms underlying jackfruit pulp coloration at transcriptional and metabolic levels.

Keywords: carotenoid biosynthesis; flavonoid biosynthesis; fruit pigmentation; jackfruit; metabolome; pulp color; transcriptome.