Transcriptome analysis of two photo-thermo-sensitive genic male-sterile lines reveal GA-mediated regulatory mechanism for rice panicle exsertion

Hybrid rice is pivotal for ensuring food security in China, yet challenges persist in its seed production. Sterile lines commonly face issues such as necking, gibberellins (GAs) are key regulators of panicle exsertion in rice, necessitating increased application of GAs during seed production, leading to elevated costs and environmental pollution. The novel photoperiod-thermosensitive genic male sterile line Shuang 1S addresses these limitations through its unique non-necked morphology and has super high yield of seed production.

To elucidate the regulatory pathways governing panicle exsertion and identify novel potential genes, this study assessed endogenous GA levels and performed RNA-seq analysis on two sterile lines, Shuang 1S and Han 2S, which displayed notable differences in panicle exsertion. Among 20 sterile lines examined, Shuang 1S demonstrated the highest panicle grains exsertion rate (91.03%) and the longest inverted first internode (28.24 cm). The findings revealed a 1.5-fold increase in GA content in Shuang 1S compared to Han 2S. Additionally, 2,147 up-regulated and 2,709 down-regulated genes were identified between SP (Shuang 1S) and HP (Han 2S), including 15 genes (10 up-regulated and 5 down-regulated) involved in GA biosynthesis and metabolism. KEGG enrichment analysis of the differentially expressed genes (DEGs) revealed significant enrichment in pathways including diterpenoid biosynthesis and plant hormone signal transduction, which are associated with gibberellic acid (GA) synthesis and catabolism.

We found that panicle exsertion was directly related to GAs content, and mainly enriched in diterpenoid biosynthesis, plant hormone signal transduction. These findings present new potential candidate genes for future investigations into the molecular mechanisms underlying the regulation of panicle exsertion in rice.