ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Crop and Product Physiology
When Genes Turn Traitor: De Novo Transcriptomics Uncovers Pearl Millet's Rancidity Machinery
Provisionally accepted
Ranjeet Ranjan Kumar1*
Suneha Goswami1
Nitin Kumar Singhal2
Ulaganathan Mabalirajan3
Gyan P Mishra4
GIRISH JHA5
Gyanendra Kumar Rai6
Shelly Praveen4
Tara Satyavathi Chellapilla7- 1Indian Agricultural Research Institute (ICAR), New Delhi, India
- 2National Agri-Biotechnology Institute, Mohali, India
- 3CSIR - Indian Institute of Chemical Biology, Kolkata, India
- 4ICAR - Indian Agricultural Research Institute, New Delhi, India
- 5ICAR - Indian Agricultural Statistics Research Institute, New Delhi, India
- 6Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
- 7ICAR - Indian Institute of Millets Research, Hyderabad, India
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Pearl millet flour is highly nutritious but prone to rancidity, leading to off-odour development and reduced shelf-life. To understand the molecular basis of this phenomenon, we performed de novo transcriptome sequencing on diverse pearl millet genotypes (landraces, hybrids, and composites) and identified 219,965 genes and 386,184 transcripts with functional annotation revealing key pathways linked to lipid and starch degradation. Differential gene expression (DGE) analysis identified significant upregulation of rancidity-linked genes (lipases, lipoxygenases, peroxidases, and polyphenol oxidases) in high-rancid genotypes. Data mining for characterizing rancid pathway showed the presence of 2038 lipase (LIP), 209 lipoxygenase (Lox), 26 hydroperoxide lyase (HPL), 1023 peroxidase (POX) and 17 polyphenol oxidase (PPO) genes. Tissue specific expression analysis of variants of Lip, Lox, Pox and PPO during different sub-stages of endosperm development showed abundance of transcripts of Lip-2, LOX-3, and POX-4 during seed hardening stage. Enzymatic assays confirmed increased lipase (up to 200.5 µmol h⁻¹ g⁻¹), LOX (184 nM HPOD min⁻¹ mg⁻¹), peroxidase, and PPO activities in stored flour, correlating with rancidity progression. Notably, landraces exhibited lower expression of rancidity-linked genes compared to hybrids and composites, suggesting genetic variability in flour shelf-life stability. Our study provides the first comprehensive transcriptomic resource for pearl millet rancidity, identifying candidate genes and enzymatic markers for future breeding programs aimed at improving flour storage quality.
Keywords: Rancidity, DEGs, Differentially expressed transcripts, Lipase, Landrace, Lipids
Received: 08 Aug 2025; Accepted: 27 Oct 2025.
Copyright: © 2025 Kumar, Goswami, Singhal, Mabalirajan, Mishra, JHA, Rai, Praveen and Chellapilla. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ranjeet Ranjan Kumar, ranjeetranjaniari@gmail.com
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