Genome-wide association studies for transpiration efficiency and physiological traits in Ethiopian Sorghum genotypes

Sorghum (Sorghum bicolor L. Moench) is a drought-tolerant crop, with its resilience essentially attributed to high transpiration efficiency (TE), and simply defined as the biomass produced per unit of water transpired. Understanding the genetic architecture of TE is crucial for breeding water-efficient varieties. This study undertook a genome-wide association study (GWAS) using SNP marker on 112 sorghum genotypes to identify genomic regions controlling TE and related physiological traits at the flag leaf stage using 17,637 imputed SNP markers. Phenotypic evaluation revealed significant variation for key traits like root dry wight (RDW), shoot dry weight (SDW), plant dry weight (PDW), water used efficiency (WUE), Root plant ratio (RTR), chlorophyll a concentration (Chla), Transpiration rate (TR) and TE, with moderate to high heritability. Using a multi-locus GWAS approach, we identified 23 robust quantitative trait nucleotides (QTNs) associated with eight traits except WUE. Notably, we discovered pleiotropic genomic hotspots on chromosomes 2, 3, 6, and 9 that simultaneously influence biomass (PDW, SDW) and TE. A meta-analysis showed that 86.9% of these QTNs co-located with previously reported QTLs, validating these regions, while three QTNs were novel. Candidate gene analysis within the QTN regions pinpointed 218 genes with different functions such as hormone signaling (auxin, cytokinin), stomatal regulation (S-type anion channel), root development (glutamate synthase), and photosynthesis (chlorophyll biosynthesis). Six QTNs also found intergenic, between start/end regions of the genes. Our findings provide valuable molecular tools for marker-assisted selection and highlight key candidate genes for enhancing transpiration efficiency and drought adaptation in sorghum.