Pan-genomic characterization of the NCED genes and their response to abiotic stresses in wheat species

Plant stress adaptation and development are regulated by abscisic acid (ABA), whose biosynthesis is catalyzed by the 9-cis-epoxycarotenoid dioxygenase (NCED) enzymes. In wheat ( Triticum aestivum L.), a comprehensive pan-phylogenomic and functional characterization of the NCED gene family remains underexplored despite its role in ABA synthesis and its likely resilience to abiotic stresses. This study conducts pan-genomic identification, genomic diversity, and functional analyses of the NCED gene family across 14 wild and modern wheat species. A total of 443 non-redundant NCED genes were identified and classified into distinct NCED and carotenoid cleavage dioxygenase (CCD) clades. Gene structure and motifs demonstrated high conservation of the functional RPE65 domain, with promoter-region cis-acting elements enriched for motifs responsive to abiotic stresses and hormone signaling. Expression analysis and RT-qPCR validation identified core stress-responsive genes, including TaCSNCED18 , TaCSNCED26 , and TaCSNCED27 , significantly upregulated under drought and heat stress. TaCSNCED33 is enriched in transfer tissues (aleurone layer and seed coat) and in other storage tissues, as revealed by a spatial transcriptome analysis. Moreover, a haplotype analysis reveals its significant association with thousand-kernel weight (TKW), an agronomic trait related to yield. This work presents a comprehensive genomic atlas of the wheat NCED gene family, detailing its evolutionary history, regulatory architecture, and functional diversification. These findings provide a valuable genetic resource for breeding climate-resilient wheat varieties by optimizing the ABA pathway. • Pan-genome-wide identification of NCED genes, expanding with ploidy • Key genes validated as core responders to abiotic stress • TaCSNCED33 localizes to grain tissues mapped via spatial transcriptomics • TaCSNCED33 haplotype associates with thousand‑kernel weight in wheat