Biology subjects

Ainsworth, E.

Publications and source records attributed to Ainsworth, E..

5 recordsLinked to original sources

bioRxiv2026

A century of soybean breeding increased photosynthetic capacity but not NPQ relaxation

Accelerating photoprotective regulation to improve carbon assimilation is a promising strategy to increase crop productivity. Although rapid non-photochemical quenching (NPQ) relaxation has been validated as a target through metabolic engineering, it remains unclear whether conventional breeding has improved this trait. Here, we investigated whether more than a century of soybean breeding enhanced NPQ relaxation alongside light-saturated carbon assimilation and seed traits. We evaluated a historical panel of 24 soybean genotypes across vegetative and reproductive developmental stages by integrating NPQ relaxation, gas exchange parameters, xanthophyll-cycle pigment profiles, expression of key photoprotective genes (VDE, PsbS, and ZEP), seed number and seed weight. NPQ relaxation parameters were not consistently associated with genotype release year, seed number, or seed weight at either developmental stage. The only exception was the amplitude of the rapidly relaxing NPQ component (AqE), which was negatively correlated with all three variables during the reproductive stage. In contrast, genotype release year was positively associated with maximum net CO2 assimilation rate (Amax), maximum carboxylation rate of Rubisco (Vcmax), maximum electron transport rate (Jmax), seed number, and seed weight, while Amax and Vcmax were positively correlated with seed number and seed weight. These findings indicate that the greater photosynthetic capacity of modern genotypes was not accompanied by faster photoprotective response. Thus, photoprotective regulation has not kept pace with gains in photosynthetic capacity under field conditions. We conclude that rapid NPQ relaxation remains an important target for synchronizing photoprotection with the high photosynthetic capacity of modern soybean lines.

plant biology↗

bioRxiv2026

Natural leaf shape variation reveals diverse transcriptional targets of GmJAG1 during soybean leaf development

The JAGGED transcription factor family regulates lateral organ development across angiosperms. In soybean (Glycine max Merr.), a D9H mutation in the EAR repression motif of GmJAG1 causes a narrow leaflet phenotype and explains over 70% of phenotypic variance in leaf shape. Because this mutation does not affect the zinc finger DNA-binding domain, both alleles bind identical targets but differ in repressor recruitment. Previous studies mapped GmJAG1 binding sites, but the functional targets controlling leaf morphology are uncharacterized. Here, we used comparative transcriptomics across four soybean genotypes with contrasting leaf shape, spanning a developmental time series from shoot apex to mature leaf, and identified 1,567 candidate target genes. GmJAG1 expression was confined to the shoot apex, yet 99.1% of candidate targets maintained differential expression throughout development. We found that neither Kip-Related Protein (KRP) cell cycle inhibitors nor Cyclin-Dependent Kinases (CDKs) showed differential expression despite binding evidence in Arabidopsis. However, D-type cyclins were upregulated in narrow-leaf genotypes suggesting cyclin-mediated rather than KRP-mediated cell cycle regulation in soybean. Pathway analysis revealed enrichment of auxin (1.8-fold, P = 0.02) and salicylic acid (4-fold, P = 0.016) genes among JAG1D9H targets. Filtering by differential expression, binding data, phenotype correlation, and co-expression network membership identified 79 high-confidence targets, including orthologs of NPH3 (phototropin-mediated leaf flattening), MIK2 (cell wall integrity sensing), RD22 (ABA-responsive stress signaling), and SCL23 (GRAS transcription factor in bundle sheath development). These candidates provide targets for functional validation and breeding in legumes.

plant biology↗

bioRxiv2025

Elevated CO2 induces phyllosphere community changes in soybean

Plant-associated microbiomes play significant roles in determining their hosts responses to stress, which is increasingly common in a rapidly changing world. For example, foliar endophytes can increase tolerance to drought and decrease herbivory. Global atmospheric changes, such as increased atmospheric carbon dioxide concentration ([CO2]), have the potential to directly and indirectly alter microbiome community structure in ways that affect host plants underscoring our need to understand how microbial communities in planta will change under global change. Here, we used a metabarcoding approach to assess community composition and network structure of bacterial and fungal phyllosphere microbiomes within soybean (Glycine max) exposed to ambient and elevated [CO2] in the field. We found that fungal community composition differed between soybean grown in elevated and ambient [CO2], while bacterial communities did not. Additionally, co-occurrence networks for both fungi and bacteria in elevated [CO2] exhibited marked changes compared to the ambient networks including the composition of hub taxa. Overall, our findings suggest that anthropogenic change, such as elevated [CO2], can cause profound shifts in community assembly of microbes within their plant hosts. Our findings may aid those developing agro-ecological strategies using microbes to improve crop traits, which necessitates understanding the drivers of microbiome community structure. HighlightLeaf-associated microbes benefit plants, but how climate change affects these communities remains unclear. We found that elevated CO2 shifted fungal and bacterial community composition and network structure within soybean leaves.

ecology↗

bioRxiv2025

Bigger is not always better: Optimizing leaf area index with narrow leaf shape in soybean

Modern soybean varieties have higher than optimal leaf area index (LAI), which could divert resources from reproductive growth. Altering leaf shape could be a simple strategy to reduce LAI. To test this, we developed 204 near-isogenic soybean lines differing in leaf morphology by introgressing narrow-leaf alleles from donor parents PI 612713A and PI 547745 into the elite, broad-leaf cultivar LD11-2170. We evaluated the lines across two locations and two row spacings (38-cm and 76-cm) to assess how reduced investment in leaf area influences canopy architecture, crop physiology, and yield. Narrow-leaf lines showed 13% lower peak LAI and 3% lower digital biomass compared to broad-leaf counterparts yet maintained yield parity (5,756 vs. 5.801 kg ha-1, p = 0.43) across environmental conditions. Photosynthetic capacity remained largely unchanged, with narrow-leaf lines showing modest increases in electron transport rate and leaf mass per area. Narrow-leaf lines achieved similar canopy closure timing despite lower LAI, suggesting architectural compensation mechanisms. The most striking difference appeared in seed packaging, with narrow-leaf lines producing 34% four-seeded pods compared to only 1.8% in broad-leaf lines. There was a nonlinear relationship between peak LAI and yield, with optimal LAI values of 9-11 varying by environment. These findings show that the single-gene GmJAG1-controlled narrow-leaf trait offers a tractable strategy for reducing LAI and maintaining high productivity. This could reduce the metabolic costs associated with excessive canopy development and support sustainable agriculture under increasing climate variability.

plant biology↗

bioRxiv2024

Nutrient Challenges in a Changing Atmosphere: Investigating Biomass Growth and Mineral Concentration Changes in Soybean Plants under Elevated CO2

Rising atmospheric CO2 levels, projected to reach [~]650 ppm by 2050, threaten the nutritional value of food crops. This rise is expected to increase biomass yield in C3 plants through enhanced photosynthesis and water-use efficiency. However, elevated CO2 (eCO2) reduces protein, nitrogen, and essential minerals like zinc (Zn) and iron (Fe) in plant leaves and seeds, posing a global nutrition risk. We conducted an experiment using Open Top Chambers to examine the response of three soybean cultivars (Clark, Flyer, and Loda) to ambient ([~]410 ppm) and eCO2 ([~]610 ppm) conditions. These cultivars were selected due to their contrasting responses to eCO2. Measurements of physiological parameters (i.e., biomass, and nutrient concentration) were taken at different growth stages. Our results showed that eCO2 increased carbon assimilation, leading to higher aboveground biomass and seed yield (through increased seed number) while root biomass remained unchanged. eCO2 also reduced stomatal conductance and transpiration. There was a significant decrease in seed nutrient concentration at maturity, particularly iron (Fe), phosphorous (P), potassium (K), and magnesium (Mg), in plants grown in eCO2. These findings suggest that increased yield, reduced transpiration, and unchanged root biomass are key drivers of nutrient dilution in seeds under eCO2.

plant biology↗