WHIRLY Gene Family in Oryza: Genome-Wide Identification, Conserved Organellar Roles and Paralog-Specific Abiotic Stress Responses in Rice

Abstract

The WHIRLY (WHY) protein family plays an indispensable role in regulation of mitochondrial and plastid genomes and stress adaptation across plant species. However, a comprehensive genome-wide characterization of WHY gene family among the members of Oryza has not yet been studied. Here, 14 WHY genes were identified throughout seven Oryza species, comprising a pair of members per species present on chromosomes 6 (WHY1-type) and 2 (WHY2-type). Phylogenetic evaluation clustered all WHY members into two principal clades associated with chloroplastic and mitochondrial targeting patterns. Gene architecture characterization identified a predominantly six-exon structural organization in WHY1 genes, while WHY2 members exhibited more intricate structure at intronic regions. Motif analysis revealed conserved pattern of six core motifs. Motif 7 was exclusively present in all WHY2 type, while Motif 5 and 10 were found within WHY1 type. All WHY genes evolved through segmental or whole genome duplication under purifying selection. Promoter analysis found 33 types of cis-acting regulatory elements; the DRE core element was conserved across all 14 WHY gene promoters, while ABA-responsive elements occurred in only a subset. Protein–protein interaction analysis suggested that OsWHY1 and OsWHY2 are involved in the maintenance of organelle genomes, DNA repair, and RNA regulation. In silico expression analysis in O. sativa revealed that OsWHY1 is downregulated under drought and heat, while OsWHY2 is particularly downregulated under ABA treatment, highlighting differential stress response between two genes. These findings present the first genus-wide genomic characterization of the WHY gene family across seven Oryza species, complemented by in silico expression analysis in O. sativa. This study provides a foundation for future experimental validation of WHY gene functions in rice stress adaptation and crop improvement.

Plant Tissue Cult. & Biotech. 36(1): 237-257, 2026 (June)