Genome-Wide Association Uncovered SbERF60 Positively Regulates Mesocotyl Length in Sorghum

Mesocotyl length is a key factor affecting deep-seedling emergence and consequently influences grain yield in sorghum. However, at present, limited genes regulating mesocotyl elongation have been identified and the underlying molecular mechanisms remain unclear in sorghum. Here, we combined a genome-wide association study (GWAS) on 232 diverse sorghum accessions with transcriptomic analysis to identify key genes controlling mesocotyl length. We identified SbERF60, an AP2/ERF transcription factor, as a strong candidate based on its functional annotation and differential expression patterns in sorghum varieties with contrasting mesocotyl lengths and its increased transcript levels during mesocotyl development. It was discovered that natural variation in its promoter enhances SbERF60 expression by increasing promoter activity, thereby leading to longer mesocotyl length. Functional validation confirmed that SbERF60 promotes mesocotyl elongation and significantly improves deep-seeding emergence in rice. These findings provide valuable genetic insights and identify a key target for molecular breeding strategies to improve sorghum deep-seedling emergence.