Genome-Wide Association Study and Haplotype Analyses Reveal Genetic Architecture of Agronomic Traits and Brix Content in Sweet Sorghum, April 29, 2025

AUTHORS: Abdullah Bin Umar1, Ajay Prasanth Ramalingam2, Bushra Sadia1*, Guihua Bai2, Faisal Saeed Awan1, Farooq Ahmad Khan1, Mariam Nasir1, Paul St. Amand3, Amy Bernardo3, Vara Prasad P.V.2, Ramasamy Perumal4*1 Center of Agricultural. Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan2 Kansas State University, Department of Agronomy, Manhattan, Kansas, USA3 USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, USA4 Kansas State University, Agricultural Research Center, Hays, Kansas, USA*CORRESPONDENCE:Bushra Sadia bushra.sadia@uaf.edu.pk andRamasamy Perumal perumal@ksu.edu ORCID: (https://orcid.org/0000-0002-0649-8853)KEYWORDS: sweet sorghum, brix, agronomic traits, GWAS, haplotype analysis.ABSTRACT: Sweet sorghum is a C4 tropical grass species gaining importance quickly as a major bioenergy crop. This genome-wide association study (GWAS) utilized a sweet sorghum panel (SSP) of 183 diverse sweet sorghum accessions genotyped by 14,819 high-quality single nucleotide polymorphism (SNP) markers to identify novel genetic loci associated with major agronomic traits and brix content. Population stratification revealed clear separation of the accessions based on geographical origins. The initial 50% linkage disequilibrium (LD) decay was approximately 5 Kb, and the background level was around 80 Kb, similar to previously reported the sorghum association panel (SAP), indicating the panel's effectiveness and reliability for GWAS. This study identified 21 significant quantitative trait nucleotides (QTNs) for the studied traits using the three (compressed) variance component multi-locus random-SNP-effect mixed linear model (3VmrMLM) model, which were co-localized with previously reported quantitative trait loci (QTL). The phenotypic variance (R2) explained by these QTNs ranged from 5.11 to 13.86%. Additionally, haplotype analysis revealed significant phenotypic differences between haplotypes for four candidate genes, including Sobic.006G128200 (a threonine-specific protein kinase gene) for days to flowering, Sobic.001G387600 (an ethylene-insensitive gene) for brix content, Sobic.003G069950 (a protein kinase domain gene), and Sobic.003G214400 (an amino acid transporter gene) for fresh biomass.