Bulked Segregant RNA-Seq analysis reveals a distinct expression profile associated with seed physical dormancy in Chinese bottle gourd hybrid variety 'Zhepu No. 9'.

Higher plants commonly exhibit the adaptive characteristic of seed physical dormancy (PY). The resolution of breaking seed PY is thus of considerable significance for bottle gourd breeding and seed quality improvement. However, the molecular mechanism of PY remains indistinct. Here, by bulked segregant RNA-Seq (BSR-Seq), we used an F2 population derived from a cross between two bottle gourd inbred lines, PY-D (dormant) and PY-ND (non-dormant), to explore the molecular mechanism of PY. A QTL for seed dormancy designated Qsd2.1 was identified on chromosome 2. A total of 3250 differentially expressed genes (DEGs) between the two bulks were analyzed, and 15 DEGs were involved in the biosynthesis and degradation of pectin. Through the measurement of pectin contents and reverse transcriptase-PCR (RT-PCR) analyses, we finally identified HG_GLEAN_10014054 as a strong candidate gene for seed PY, which shows the sequence polymorphisms between the parents and encodes the exocyst complex component SEC3A. Furthermore, a core collection of 193 bottle gourd accessions was screened using a kompetitive allele specific PCR (KASP) marker developed from HG_GLEAN_10014054. Based on the examination of core samples, natural variation in the HG_GLEAN_10014054 allele was also noted. Our findings open up new genetic insights for breaking PY in the further application of bottle gourd breeding and help clarify the genetic underpinnings of seed PY in bottle gourd. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-025-01667-2.