Identification of a Novel Grain Size QTL and Candidate Gene in Sorghum Through Integrated BSA-Seq and RNA-Seq Analysis

  • SorghumBase Team
  • 3 February 2026

Scientists identified a novel grain size QTL (qGS1) in sorghum and proposed Sobic.001G230700 as a candidate gene using integrated BSA-Seq and RNA-Seq analyses, advancing the genetic understanding of yield-related traits.

Keywords: BSA-Seq, RNA-Seq, candidate genes, grain size, sorghum

Grain size in sorghum, a critical determinant of yield and market value, is shaped by a complex interplay of genetic and environmental factors. While multiple hormonal, transcriptional, sugar metabolic, and epigenetic pathways contribute to grain development, the specific genes and regulatory mechanisms governing grain size in sorghum remain insufficiently characterized. Hormones such as auxin, cytokinin, gibberellin, and abscisic acid play distinct roles at different developmental stages, from endosperm cellularization to grain dormancy. Transcription factors including MADS-box and AP2/ERF families, as well as sugar transport and signaling pathways, modulate nutrient allocation during grain filling. Epigenetic regulators further refine these processes by influencing gene expression during seed development. Although over 180 QTLs associated with grain size have been mapped in sorghum, fine-mapping efforts have been limited, leaving many functional genes unidentified.

Researchers from Anhui Science and Technology University, International Joint Research Center of Forage Bio-Breeding in Anhui Province and University of Louisiana at Lafayette aimed to refine the genetic basis of sorghum grain size using selective genotyping and integrated BSA-Seq and RNA-Seq analyses. From an F₂ population derived from contrasting grain size lines, researchers narrowed the qGS1 locus to a 1 Mb region on chromosome 1 (22.00–23.03 Mb), distinct from previously reported QTLs, suggesting it is a novel grain size locus. The zinc-finger gene Sobic.001G230700 emerged as a strong candidate based on expression patterns and functional analogs in other cereals. The combined genomic and transcriptomic approach identified two candidate genes associated with grain size, underscoring the value of integrative methods in elucidating yield-related traits. These findings provide a foundation for marker-assisted selection and future functional studies in sorghum breeding.

SorghumBase examples: 

We selected the Sobic.001G230700, a novel gene that was identified by authors for a novel grain size QTL in sorghum to explore SorghumBase. 

Figure 1: The location tab of the SorghumBase search interface of Sobic.001G230700 (similar to CHY zinc finger family protein) shows that this gene is located on chromosome 1:22271637-22276450. 
Figure 2: The phylogenetic tree in the homology tab of the sorghumbase search interface displays the relationship of Sobic.001G230700 (similar to CHY zinc finger family protein) across species. The alignment is color coded based on InterPro domain classification. There are a total 51 orthologs and 7 paralogs of this gene. DCA1 is the closest annotated homolog in rice by 79% identity. 
Figure 3: The “All Studies” tab of expression view of Sobic.001G230700 (similar to CHY zinc finger family protein) from the SorghumBase search interface displays the transcription profiling of this gene across 11 experiments in different tissue types. This tab provides detailed insights into the gene’s expression notably in the reproductive tissues and seeds. Clicking on inflorescence on anatomogram highlights the expression level in early, emerging and mature inflorescence. The datasets are curated and processed by EMBL-EBI expression atlas in collaboration with the SorghumBase team. 
 

Figure 4: The eFP browser tab of Expression tab allows the visualization of Sobic.001G230700 (similar to CHY zinc finger family protein) to compare gene expression patterns across different tissues and conditions across 10 studies. The eFP browser paints data from large scale data sets onto pictographic representations of the experimental samples. The plant tissue is colored based on the expression level of the gene in a particular tissue under a particular treatment. This figure shows that the Sobic.001G230700 gene is expressed (yellow) in flag leaf and inflorescence and stronger expressed (red) in seed.
Figure 5: The germplasm tab of the SorghumBase search interface shows that many accessions harbor variants that are predicted to impact the function of Sobic.001G230700 (similar to CHY zinc finger family protein). This tab lists accessions with predicted consequence (splice donor variants), zygosity (homozygous or heterozygous) and the associated genotyping study in which the variant was identified. 
Reference:
Shen Q, Wang K, Hu L, Li L, Wang L, Wang Y, Wang YH, Li J. Combined Analysis of BSA-Seq and RNA-Seq Reveals Candidate Genes for qGS1 Related to Sorghum Grain Size. Plants (Basel). 2025 Jun 11;14(12):1791. PMID: 40573777. doi: 10.3390/plants14121791. Read more