Soybean genome study pinpoints leaflet shape genes across leaf positions

Researchers have mapped new genetic loci that control the shape of soybean leaflets, combining two complementary mapping approaches across large, multi-location soybean panels. The study, published in BMC Plant Biology, identified six quantitative trait loci (QTLs) associated with leaflet width, leaflet length-to-width ratio and leaflet area, and put forward six putative candidate genes, four from genome-wide association analysis and two from transcriptome-wide association analysis. Leaf shape is a key determinant of how much light a soybean canopy intercepts, which in turn influences yield.

Because leaflet traits vary naturally across genetic backgrounds and environments, the authors argued that identifying QTLs that depend on leaflet position is essential for understanding leaf development and for breeding varieties with an ideal plant architecture. The team built separate association panels for each method and environment. For genome-wide association studies (GWAS), they used 1,062 accessions grown at Jingzhou in 2019 and 1,161 accessions grown at Beijing in 2020.

For transcriptome-wide association studies (TWAS), which link gene expression variation to trait variation, they used 285 accessions from Jingzhou in 2019 and 231 accessions from Beijing in 2020. Three of the detected loci stood out. On chromosome 3, an interval spanning roughly 40.53 to 40.83 million base pairs carried an independent, newly identified association signal affecting lateral leaflet width and the leaflet length-to-width ratio at the fourth upper node.

On chromosome 19, a hotspot between about 44.52 and 45.10 million base pairs was associated with lateral leaflet width, length-to-width ratio and leaflet area at both the fourth and fifth upper nodes. The third notable interval, on chromosome 20 between approximately 35.78 and 36.56 million base pairs, contains Ln, a gene that had been previously characterized. In this study, the Ln-containing region was associated with the leaflet length-to-width ratio across lateral leaflets at the fourth and fifth upper nodes as well as terminal leaflets at those same nodes, underscoring how a single locus can influence leaflet shape at multiple positions on the plant.

To move from statistical associations to plausible genes, the researchers integrated gene expression profiling with haplotype analysis of the GWAS signals. This combination flagged four genes, Glyma.03G196600 and Glyma.03G196700 on chromosome 3, and Glyma.19G193700 and Glyma.19G194600 on chromosome 19, as putative candidate genes modulating leaflet shape. The TWAS arm of the study added two further candidates.

Glyma.05G019900 on chromosome 5 and Glyma.20G119400 on chromosome 20 showed suggestive associations with the leaflet length-to-width ratio, and both were supported by transcriptome variation and haplotype analysis. The authors positioned the work as a step forward in understanding the genetic basis of soybean leaflet shape, describing the identified loci and candidate genes as valuable gene resources and theoretical insights for molecular breeding aimed at ideal plant architecture.

The findings are specific to the panels, environments and leaflet positions studied, and the candidate genes are described as putative rather than functionally confirmed. By analyzing leaflets at different upper nodes separately, the study also highlights the position-dependent nature of leaflet shape genetics in soybean, an aspect the authors say is essential for unraveling leaf development.

The study’s multi-location design, spanning panels grown at Jingzhou in 2019 and Beijing in 2020, allowed the researchers to test associations across different genetic backgrounds and environments. The combination of GWAS, which scans DNA sequence variation for links to measurable traits, and TWAS, which instead tests whether variation in gene expression tracks trait variation, produced overlapping but distinct sets of candidate genes anchored to the same trait measurements.

For soybean breeders, the practical value of the work lies in the mapped intervals themselves. The chromosome 19 hotspot, associated with three leaflet traits at two upper nodes, and the newly identified chromosome 3 signal offer markers that could be tracked in selection programs, while the Ln-containing interval on chromosome 20 connects the new results to a gene already known to affect soybean leaf morphology. The authors emphasize that these resources support molecular breeding targeting ideal plant architecture, though confirming the biological function of each candidate gene remains future work beyond this association study.

Subject of Research: Genetic loci and candidate genes associated with soybean leaflet shape traits identified through combined GWAS and TWAS

Article Title: GWAS combined with TWAS reveals the QTLs and putative candidate genes associated with leaflet shape-associated traits in soybean (Glycine max (L.) Merr.)

Article References: Zhang, Z., Chen, Y., Su, X., Zhou, Y., Zhang, F., Wang, J., Li, Y.-H., & Qiu, L.-J. (2026). GWAS combined with TWAS reveals the QTLs and putative candidate genes associated with leaflet shape-associated traits in soybean (Glycine max (L.) Merr.). BMC Plant Biology. https://doi.org/10.1186/s12870-026-09865-0

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09865-0

Keywords: soybean, GWAS, TWAS, QTL, leaflet shape, candidate genes, plant architecture, Ln gene, haplotype analysis, molecular breeding, BMC Plant Biology, combined