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

Altered 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 Na2WO4 treatments in selected tetraploid recombinant inbred lines further supported an association between ABA homeostasis and salinity tolerance. Our results suggest post-WGD regulatory diversification contributes to adaptive phenotypic variation in polyploids.