Homoeologous exchange-associated ABA catabolism rewiring contributes to salinity tolerance in a synthetic tetraploid rice.

key messageAltered ABA-related regulation is associated with transgressive salinity tolerance in a synthetic tetraploid rice carrying extensive post-polyploidy homoeologous exchanges. Plant polyploids often show higher environment resilience than their congeneric diploid progenitors. However, it remains unclear whether these traits arise directly from whole-genome duplication (WGD) or evolve through post-WGD changes. Here, we show that transgressive salt tolerance occurs in ca. 1.71% of an early-generation synthetic rice tetraploid from japonica-indica subspecies hybridization. Genome resequencing unravels extensive homoeologous exchanges (HEs) but without genomic features distinguishing the tolerant vs. sensitive plants. In contrast, RNA-seq-based transcriptome-profiling enables distinct separation of the tolerant and sensitive plants. A KEGG pathway analysis indicates that the downregulated genes in tolerant plants are enriched in the abscisic acid (ABA)-degradation pathway. Expression and coding-sequence analyses identified the ABA catabolic gene OsABA8ox3 as a candidate associated with the salt-tolerant phenotype. Endogenous ABA measurements and exogenous ABA and Na