Phenotypic plasticity, stalk geometry, and noncoding variation underpin stalk lodging resistance in maize

Maize stalk lodging leads to significant yield losses across the globe, exacerbating food and feed insecurity. To better understand stalk lodging resistance, researchers examined various geometric and structural traits across diverse maize lines in four different environments. They discovered that environmental factors, particularly macro-environmental changes, drive phenotypic plasticity, with this variation differing along the stalk's internode positions, likely due to height-dependent mechanosensing mechanisms.

Several structural traits, including major and minor diameters, moment of inertia, and rind penetration resistance, were found to be genetically responsive and closely linked to stalk flexural stiffness. Through multivariate analyses, the team identified two complementary pathways responsible for stalk mechanical performance: cross-sectional geometry and rind architecture.

Utilizing whole-genome resequencing data, researchers identified 705 SNPs linked to intermediate traits, but a mere 20% of these overlaps with genic regions, suggesting that most genetic variation lies outside known gene regions.

Remarkably, around 22% of the identified SNPs impacted multiple traits, indicating substantial shared genetic control among them. Through candidate gene analyses, the study revealed novel candidate loci associated with intermediate traits while reconfirming genes previously linked to stalk lodging resistance. The prevalence of noncoding associations in the findings further implies that regulatory variation may play a significant role in the natural variation of intermediate traits contributing to stalk lodging resistance in maize.