Transcriptomic Signatures of Interspecific Brassica Hybrids Reveal the Molecular Basis of Viviparous Seed Development

Vivipary threatens seed quality and viability in Brassica species, particularly in interspecific hybrids where genetic incompatibility and environmental factors disrupt dormancy. We previously reported that using Brassica rapa as the maternal parent in hybridization with Brassica napus induces vivipary. Here, we investigate its molecular basis through transcriptomic and physiological analyses of reciprocal F1 hybrids from B. napus (cv. Youngsan, YS) and B. rapa ssp. pekinensis (cv. Jangkang, JK). The JK × YS hybrid exhibited precocious germination (vivipary-positive, PC), whereas YS × JK maintained dormancy (vivipary-negative, NC). In this study, we found that dormant PC seeds had lower germination rates (10% at 40 DAP) than NC (63%) and accumulated higher endogenous ABA (11.2 ± 1.7 µg g^{− 1} DW.) but lower GA₄ (14.23 ± 0.60 ng g^{− 1} DW.) than NC (8.57 ± 0.64 µg g^{− 1} DW. ABA; 22.97 ± 6.1 ng g^{− 1} DW. GA₄), with a strong negative correlation (r = -0.707). RNA-seq (~ 100 million reads/sample) identified 248, 298, and 158 differentially expressed genes (DEGs) at 10, 15, and 20 DAP, respectively, revealing key differences in dormancy, cell wall organization, embryo development, hormone regulation, and stress responses. PC exhibited upregulation of ABA biosynthesis genes (ZEP, NCED), auxin-related genes (GH3.17), and cell wall remodeling genes (EXPA22), while dormancy- and ethylene-related genes were downregulated. Maternal genome influence was evident, with B. rapa (PC) conferring higher dormancy and ABA biosynthesis, while B. napus (NC) contributed reduced dormancy and higher GA₄ levels. Exogenous ABA inhibited vivipary, while Paclobutrazol suppressed vivipary and improved seed development in PC. These findings highlight maternal genome effects and transcriptomic regulation of dormancy and vivipary, providing insights for breeding strategies to mitigate pre-harvest sprouting in Brassica species.