Genetic dissection of transpiration efficiency and shoot traits in sorghum reveals genetic loci relevant to drought tolerance

Sorghum serves as a critical crop for drought-prone regions. Enhancing its water use efficiency and biomass production is a key priority for sustainable agriculture, yet the genetic mechanisms underlying these traits remain poorly understood. Hence, we evaluated 284 sorghum lines under greenhouse conditions and performed SNP genotyping to identify genetic loci associated with key drought adaptive traits, including shoot transpiration efficiency (STE), shoot biomass, chlorophyll content and leaf characters. All traits showed significant variation and high heritability, indicating strong genetic control. Population structure analysis revealed five ancestral subpopulations with genetic admixture among the lines. A genome-wide association study (GWAS) using six multi-locus models identified 29 reliable markers, of which 19 were novel. Four markers were associated with shoot transpiration efficiency (STE), and genotypes ETSC17129–6–1 and ETSC17300–4–1 exhibited high STE while carrying favorable alleles at all four loci. From several pleiotropic markers identified, marker S9_57480917, linked to a GATA transcription factor implicated in stomatal regulation, showed pleiotropic effects on both transpiration efficiency and shoot dry weight, underscoring its potential role in coordinating drought-responsive traits. Additionally, shoot biomass-related markers co-localized with genes involved in energy metabolism (Phosphofructokinase) and stress signaling (SnRK2 kinase). Similarly, markers associated with chlorophyll content and leaf traits were linked to genes implicated in stress signaling and developmental pathways, including PDCD4, LEA proteins, and Cytochrome P450. These findings advance our understanding of the genetic architecture underlying drought-adaptive traits in sorghum and provide both molecular markers and promising genotypes to support genomics-assisted breeding for improved water-use efficiency and biomass productivity. ML-GWAS identified 29 reliable markers linked to six drought-adaptive traits in sorghum. Genetic structure revealed five subpopulations with admixture among 284 sorghum lines. Novel loci (19) and many pleiotropic markers for TE and shoot traits were identified. Study provides candidate markers for drought-resilient sorghum breeding.