ORIGINAL RESEARCH article
Front. Genet.
Sec. Genomics of Plants and the Phytoecosystem
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1611863
This article is part of the Research TopicPrecision Trait Mapping and Molecular Breeding in High-Impact Crop PlantsView all 5 articles
Genome-wide association study and haplotype analyses reveal genetic architecture of agronomic traits and sugars in sweet sorghum
Provisionally accepted
Abdullah Bin Umar1
Ajay Prasanth Ramalingam2
Bushra Sadia1*
Faisal Saeed Awan1Farooq Ahmad Khan1Mariam Nasir1
Amy Bernardo3
Paul St. Amand3
Guihua Bai3
P. V. Vara Prasad2
Ramasamy Perumal2*- 1University of Agriculture, Faisalabad, Faisalabad, Punjab, Pakistan
- 2Kansas State University, Manhattan, United States
- 3Hard Winter Wheat Genetics Research Unit, Center for Grain and Animal Health, Agricultural Research Service (USDA), Manhattan, Kansas, United States
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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 sugars (brix units, %). 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 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 (QTL). The phenotypic variance (R 2 ) 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, Sobic.003G069950 (a protein kinase domain gene), and Sobic.003G214400 (an amino acid transporter gene) for fresh biomass.
Keywords: sweet sorghum1, brix2, agronomic traits3, GWAS4, haplotype analysis5
Received: 14 Apr 2025; Accepted: 10 Jun 2025.
Copyright: © 2025 Bin Umar, Ramalingam, Sadia, Awan, Khan, Nasir, Bernardo, St. Amand, Bai, Prasad and Perumal. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Bushra Sadia, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
Ramasamy Perumal, Kansas State University, Manhattan, United States
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