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CRISPR/Cas9-Mediated pds Knockout in Potato Reveals Network-Level Transcriptomic Reorganization Beyond Pigment Loss
Xianjun Lai1, Yuxin Xiang1, Siqi Liu1
1Panxi Crop Improvement Key Laboratory of Sichuan Province, College of Agriculture Science, Xichang University, Liangshan 615000, China.
Plants (Basel, Switzerland)
|January 10, 2026
Summary
Phytoene desaturase (PDS) gene knockout in potato causes albinism and extensive transcriptomic reprogramming beyond pigment loss. This highlights coordinated metabolic adjustments and regulatory network responses to plastid dysfunction, refining PDS marker utility.
Area of Science:
- Plant Molecular Biology
- Genomics
- Biotechnology
Background:
- Phytoene desaturase (PDS) is a key gene for carotenoid biosynthesis, and its knockout via CRISPR/Cas9 causes a visible albino phenotype in plants.
- The albino phenotype is a common visual marker for confirming successful genome editing but potential off-target transcriptomic effects are not fully understood.
Purpose of the Study:
- To investigate the comprehensive transcriptomic changes associated with PDS gene knockout in potato.
- To determine if PDS disruption elicits molecular responses beyond carotenoid biosynthesis.
- To assess the reliability of phenotype-based screening for CRISPR/Cas9 editing outcomes.
Main Methods:
- CRISPR/Cas9 technology was used to target the PDS gene in diploid potato.
- RNA sequencing (RNA-seq) was performed on albino, non-albino edited, and wild-type potato tissues.
- Differential gene expression, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were employed.
Main Results:
- PDS knockout resulted in stable albino phenotypes and significant transcriptomic reprogramming, affecting over 9700 genes.
- Albino tissues showed suppressed photosynthesis and carbon metabolism, with activated secondary metabolism, stress responses, and cell wall remodeling.
- WGCNA identified distinct regulatory modules linked to albinism, including repressed starch/sucrose metabolism and activated secondary metabolism/barrier biogenesis.
Conclusions:
- PDS knockout in potato induces widespread transcriptomic alterations beyond pigment loss, indicating complex regulatory and metabolic adjustments due to plastid dysfunction.
- Albinism is a result of coordinated network-level responses, not solely pigment deficiency.
- These findings refine the interpretation of PDS as a visual marker in genome editing and offer a framework for understanding genotype-phenotype correlations.
