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. 2025 Jul 3:16:1611863.
doi: 10.3389/fgene.2025.1611863. eCollection 2025.

Genome-wide association study and haplotype analyses reveal the genetic architecture of agronomic traits and sugars in sweet sorghum

Abdullah Bin Umar  1 , Ajay Prasanth Ramalingam  2 , Bushra Sadia  1 , Faisal Saeed Awan  1 , Farooq Ahmad Khan  1 , Mariam Nasir  1 , Amy Bernardo  3 , Paul St Amand  3 , Guihua Bai  3 , P V Vara Prasad  2 , Ramasamy Perumal #  4
Affiliations

Genome-wide association study and haplotype analyses reveal the genetic architecture of agronomic traits and sugars in sweet sorghum

Abdullah Bin Umar et al. Front Genet. .

Abstract

Introduction: Sweet sorghum is a C4 tropical grass species that has gained importance quickly as a major bioenergy crop.

Methods: 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 that are associated with major agronomic traits and sugars (Brix units, %).

Results: Population stratification revealed a 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 approximately 80 kb, similar to that of the previously reported 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), which were colocalized with previously reported quantitative trait loci (QTLs). The phenotypic variance (R2) explained by these QTNs ranged from 5.11% to 13.86%.

Discussion: Additionally, haplotype analysis revealed significant phenotypic differences between haplotypes for four candidate genes, namely, Sobic.006G128200 (a threonine-specific protein kinase gene) for days to flowering, Sobic.001G387600 (an ethylene-insensitive gene) for Brix, Sobic.003G069950 (a protein kinase domain gene), and Sobic.003G214400 (an amino acid transporter gene) for fresh biomass.

Keywords: Brix; GWAS; agronomic traits; haplotype analysis; sweet sorghum.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Principal component analysis (PCA), population stratification, and LD decay of the SSP (n = 183). (a) Principal component analysis of the SSP (n = 183) plotted on the PCA axis individually and PCA axes built with SAP (n = 401) showing wide diversity and distinct grouping based on the geographical origins. (b) LD decay of the SSP and SAP, indicating decay to the background level (r2 < 0.1) within ∼ 80 kb. (c) Population stratification using the model-based maximum likelihood approach at K = 8 showed a distinct separation between geographical origins. Green (K1), Europe; orange (K2), Middle East; blue (K3), North Africa; pink (K4), South Africa; light green (K5), South Asia; yellow (K6), United States; brown (K7), East and North Africa; gray (K8), East and South Africa. (d) Cross-validation (CV) error for population stratification indicated that the optimal number of subpopulations (K) for grouping the 183 sweet sorghum panel was K = 8.
FIGURE 2
FIGURE 2
Significant quantitative trait nucleotides (QTNs) mapped by genome-wide association studies (GWAS) for all the traits evaluated on the sweet sorghum panel (SSP) using the 3VmrMLM model. Yellow bars are QTN positions in the chromosomes (1–10). The putative candidate genes are listed at the top, and the dashed lines show the relative positions of QTNs with the candidate genes.
FIGURE 3
FIGURE 3
Haplotype analysis revealed four candidate genes with significant phenotypic differences among their respective haplotypes.
See this image and copyright information in PMC

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