Lodging occurs when stems lack sufficient mechanical strength to withstand externally imposed bending forces. This phenomenon is a major constraint on global crop yield stability, causing substantial economic losses annually. For flax ( Linum usitatissimum L.), an ancient crop valued for both fiber and oil, stem diameter directly affects lodging resistance and is closely correlated with fiber yield and seed yield. However, the genetic basis underlying stem diameter regulation has long remained poorly understood.
To that end, a research team led by Professor Liqiong Xie at Xinjiang University dissected the genetic architecture of stem diameter in flax using genome-wide association study (GWAS) and identified LuMED25 / PFT1 as a key regulatory gene, offering a novel strategy to resolve the long-standing trade‑off between high yield and lodging resistance in flax breeding. The team published their study in The Crop Journal .
Unlike the strategy of improving lodging resistance through dwarfing breeding in rice and wheat, fiber flax relies on stem fibers as the primary harvestable product; reducing plant height, although lowering the center of gravity, constrains fiber yield.
“Optimizing stem diameter to enhance stem mechanical strength, while balancing high yield and lodging resistance, represents the core strategy for breaking the ‘lodging–yield’ dilemma,” explains Xie.
The research team used a panel of 200 flax accessions from around the world, encompassing three major types (oil flax, fiber flax, and oil–fiber dual-purpose flax), and systematically evaluated agronomic traits, including stem diameter, under three different environments. “Phenotypic analyses revealed extensive natural variation in stem diameter, which was significantly positively correlated with plant height, stem weight per plant, and stem yield, indicating that stem diameter is a key determinant of stem yield,” shares Xie.
To dissect the genetic basis of stem diameter, the team integrated single-locus and multi-locus GWAS models and identified 1134 significant quantitative trait nucleotides (QTNs), which were further consolidated into 368 QTL. Based on stringent triple-filtering criteria encompassing multi‑environment reproducibility, haplotype differentiation, and the proportion of phenotypic variance explained ( R ² > 20%), a total of 12 stable large‑effect QTL were ultimately identified.
The team focused on the major QTL on chromosome 4, which exhibited pleiotropic associations with stem‑related traits including plant height and technical length. “The association signal at this QTL displayed two adjacent sub‑peaks; however, the causal gene LuMED25 / PFT1 , confirmed by transgenic functional validation, was located beneath the weaker sub‑peak,” Xie says.
The researchers found that the LuMED25 / PFT1 locus harbors complex allelic heterogeneity, causing its own LD block to show only a relatively weak association peak, whereas the adjacent LD block exhibited a stronger association signal owing to “indirect association” or “synthetic association”, thereby providing a typical example of such phenomena in GWAS.
To validate the function of LuMED25 / PFT1 , the team cloned its CDS into a plant expression vector and transformed it into Arabidopsis thaliana Col‑0 ecotype. Concurrently, the Arabidopsis med25 / pft1 mutant was used as a loss‑of‑function control. Phenotypic analysis showed that LuMED25 / PFT1 overexpression increased Arabidopsis plant height by 13.09% and stem diameter by 8.46% on average, whereas the loss‑of‑function mutant exhibited reductions of 27.61% and 19.04% in plant height and stem diameter, respectively. These results unequivocally confirmed that LuMED25 / PFT1 positively regulates stem development.
Population genetic analyses indicated that the LuMED25 / PFT1 locus has experienced selection pressure during flax improvement, particularly in the divergence between oil–fiber dual-purpose flax and fiber flax. This finding suggests that this gene is an important selection target in fiber flax improvement.
“Thick‑stem alleles remain relatively rare in current germplasm resources, indicating substantial untapped genetic gain potential for stem diameter in flax,” notes Associate Professor Dongliang Guo, the study’s first author. “The number of thick‑stem alleles is positively correlated with stem diameter and stem‑yield‑related traits, suggesting that QTL pyramiding could simultaneously improve stem diameter and stem yield in flax.”
“Our study provides the first systematic dissection of the genetic basis of stem diameter in flax and identifies LuMED25 / PFT1 as a key regulatory gene,” adds co-corresponding author Professor Liqiong Xie. “This discovery offers a directly applicable target gene for molecular breeding aimed at lodging resistance and high yield in flax.”
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Author contact:
Liqiong Xie
Email address: picea@xju.edu.cn
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The Crop Journal
Experimental study
Not applicable
A genome-wide association study identifies LuMED25/PFT1 as a major locus controlling stem diameter in flax (Linum usitatissimum L.)
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.