Biology subjects

Studer, A. J.

Publications and source records attributed to Studer, A. J..

9 recordsLinked to original sources

bioRxiv2026

Cloning and characterization of a novel maize leaf area modifier and its effects across elite germplasm

Plant architecture is a crucial component of maize productivity. Tailoring architectural component traits like leaf area and angle can increase productivity by promoting deeper light penetration into the canopy and better resource utilization. Novel genetic variants can increase the rate of gain for optimized plant architecture. Here, we map a moderate-effect mutation denoted reduced leaf area1 (rdla1) to the RAGGED5 (RGD5) locus and characterize it as a transposon insertion allele. Mutant leaf area reductions were most extreme in mid-upper canopy positions. Photosynthetic gas exchange rates were not significantly impacted in rdla1 relative to wild-type, indicating that mutant leaf structure, but not function, is altered. Functional annotations of RDLA1 were supported by metabolite profiles suggesting a role in cuticular wax biosynthesis. Introgression of the rdla1 allele into 27 commercially relevant genetic backgrounds identified differences in effect size across genotypes, revealing modifier effects that could serve as targets for modulating plant architecture.

plant biology↗

bioRxiv2026

The Role of Phosphoenolpyruvate Carboxylase-Protein Kinase in C4 Photosynthesis: Insights from Zea mays Mutant Analysis

Understanding the regulation of enzyme activity involved in photosynthesis is essential for engineering enhanced carbon fixation in crops. In C4 plants, the enzyme phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) is one of the most abundant leaf enzymes and plays an essential role in photosynthetic carbon dioxide (CO2) fixation. The enzyme also plays a key role in central metabolism (e.g., providing intermediates to the citric acid cycle) and therefore must be highly regulated to coordinate its activity. The regulation of PEPC activity can occur allosterically by glucose 6-phosphate activation and malate inhibition, which is in part influenced by reversible phosphorylation. A specific light-dependent phosphorylation of PEPC at an N-terminal serine residue by the PEPC-protein kinase (PEPC-PK) can regulate its sensitivity to this allosteric regulation. However, the impact of this PEPC phosphorylation has not been tested in a C4 crop. Therefore, we created PEPC-PK mutant lines in Zea mays to assess the impact of PEPC phosphorylation on its allosteric regulation, photosynthesis, and growth. While the maximum PEPC activity was unchanged, PEPC in the PEPC-PK mutant plants was not phosphorylated under light and was more sensitive to malate inhibition. However, gas exchange, electron transport, and field biomass analyses showed no differences in the PEPC-PK mutant plants. These results demonstrate that in Z. mays PEPC phosphorylation affects enzyme sensitivity to malate in vitro but does not substantially alert photosynthetic performance or growth under field conditions suggesting additional regulation of PEPC activity in planta.

plant biology↗

bioRxiv2025

A spontaneous mutation in a key C4 pathway gene significantly alters leaf δ13C uncoupling its relationship with WUE and photosynthetic performance in Zea mays

Increases in global temperature and drought are negatively impacting the yields of major crops. Therefore, targeted improvements to intrinsic water use efficiency (WUEi) are needed to reduce the water required for agricultural production. While it is very time-consuming to directly measure WUEi, stable carbon isotope ratios ({delta}13C) are a reliable high throughput proxy trait for quantifying WUEi in C3 species. While genetic studies have improved our understanding of the relationship between WUEi and {delta}13C in C4 species, the knowledge needed to implement {delta}13C in breeding schemes is incomplete. Using a Zea mays line with an extremely negative {delta}13C value, a quantitative genetics approach was used to identify a large deletion in carbonic anhydrase1 (cah1). Carbonic anhydrase is the first enzymatic step of the C4 photosynthetic pathway and is known to affect {delta}13C. Surprisingly, the line with the mutant allele has significantly higher carbonic anhydrase activity with a concurrent reduction in {delta}13C, opposite of what would be expected based on C4 carbon isotope fractionation theory. These observed decouple {delta}13C and WUEi, which calls for further investigation into carbon isotope discrimination in C4 species.

plant biology↗

bioRxiv2025

Investigating the role of stomatal dynamics on agronomic traits using a slac1-2 Zea mays mutant

The production of staple food crops is becoming increasingly difficult due to the amount of freshwater needed to realize food security for a growing global population. Climate projections show hotter and drier growing seasons in traditionally productive agricultural regions, which will increase the demand for limited water resources. Thus, strategies to improve water use efficiency will only become more important for sustainable agriculture. At the leaf level, stomatal conductance has a large influence on transpirational water loss and therefore water use efficiency. The anion channel SLAC1 has been shown in several plant species to function as the primary mechanism for stomatal closure, which allows stomatal aperture to change dynamically in response to environmental stimuli. Given that slac1 is a single gene that can significantly alter stomatal conductance, it has the potential to serve as a control point for improving water use efficiency. Here we fully characterize a Zea mays slac1-2 mutant in multiple field environments. Interestingly, homozygous slac1-2 hybrids did not show improved net CO2 assimilation or increased grain yield despite having greater stomatal conductance compared to a wild-type hybrid. Net CO2 assimilation and grain yield were either lower or similar in slac1-2 compared to wild-type across environments. Furthermore, the slac1-2 hybrid did not have increased nitrogen uptake. These results suggest that the C4 carbon concentrating mechanism removes any stomatal conductance limitations to CO2 assimilation, even in highly productive wild-type Z. mays hybrids. Because the slac1-2 hybrids eliminate stomatal conductance as a major variable for modulating water loss, future studies will be able to investigate alternate regulators of plant water potential to identify novel mechanisms for increasing water use efficiency.

physiology↗

bioRxiv2023

Differences in stomatal sensitivity to COC2 and light influences variation in water use efficiency and leaf carbon isotope composition in two genotypes of the C4 plant Zea mays.

The ratio of net CO2 uptake (Anet) and stomatal conductance (gs) is an intrinsic measurement of leaf water use efficiency (WUEi) however its measurement can be challenging for large phenotypic screens. Measurements of leaf carbon isotope composition ({delta}13Cleaf) may be a scalable tool to approximate WUEi for screening because it in part reflects the competing influences of Anet and gs on the CO2 partial pressure (pCO2) inside the leaf over time. However, in C4 photosynthesis the CO2 concentrating mechanism complicates the relationship between {delta}13Cleaf and WUEi. Despite this complicated relationship, several studies have shown genetic variation in {delta}13Cleaf across C4 plants. Yet there has not been a clear demonstration of whether Anet or gs are the causal mechanisms controlling WUEi and {delta}13Cleaf. Our approach was to characterize leaf photosynthetic traits of two Zea mays recombinant inbred lines (Z007E0067 and Z007E0150) which consistently differ for {delta}13Cleaf even though they have minimal confounding genetic differences. We demonstrate that these two genotypes contrasted in WUEi driven by differences in the speed of stomatal responses to changes in pCO2 and light that lead to unproductive leaf water loss. These findings provide support that differences in {delta}13Cleaf in closely related genotypes do reflect greater WUEi and further suggests that differences in stomatal kinetic response to changing environmental conditions is a key target to improve WUEi.

plant biology↗

bioRxiv2023

Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response

Popcorn is an important crop in the United States; however, genetic analyses of popcorn are limited and tend to utilize relatively few markers that cannot capture the total genomic variation. To improve the genomic resources in popcorn, a panel of 362 popcorn accessions was evaluated using 417,218 single nucleotide polymorphisms generated using a genotyping-by-sequencing approach. Using this genomic data, a model-based clustering analysis identified two populations. The first comprised North American Yellow Pearl Popcorns and several accessions of the Chilean Curagua landrace. The second, the Pointed and Latin American Popcorns, included all remaining North American (pointed and early popcorns), Latin American, and global accessions. The two populations exhibited large differences in population structure and genetic diversity. The North American Yellow Pearl Popcorns constitute a highly inbred population with limited genetic diversity compared to the Pointed and Latin American Popcorns. Additionally, phenotypic differences between the two populations were observed in kernel color and nicosulfuron sensitivity. A filtered set of SNPs was curated and used for genome-wide association studies and popcorn-specific candidate genes for nicosulfuron tolerance were identified. The genomic characterization described here can be used by breeding programs to accelerate the rate of genetic gain and incorporate genetic diversity into elite popcorn germplasm. Core IdeasO_LINorth American Popcorn is composed of two distinct populations that differ genetically and phenotypically. C_LIO_LINorth American Yellow Pearl Popcorns contain limited genetic diversity and are highly inbred. C_LIO_LIPointed and Latin American Popcorns exhibit considerable genetic diversity and rapid linkage disequilibrium decay. C_LIO_LIKernel color does not affect nicosulfuron sensitivity and instead reflects differences between the populations. C_LIO_LIPopcorn-specific candidate genes for nicosulfuron tolerance are distinct from dent corn. C_LI

genetics↗

bioRxiv2021

Demonstration of local adaptation of maize landraces by reciprocal transplantation

Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness, as well as reported highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparison between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. While population genetic structure largely recapitulates drift during post-domestication dispersal, landrace phenotypes reflect adaptations to native elevation. Quantitative trait QST was greater than neutral FST for many traits, signaling divergent directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in our Mexican sites. Highland populations expressed generally higher anthocyanin pigmentation than lowland populations, and more so in the highland site than in the lowland site. Macrohair density was largely non-plastic, and Mexican landraces and highland landraces were generally more pilose. Analysis of{delta} 13C indicated that lowland populations may have lower WUE. Each population demonstrated garden-specific correlations between highland trait expression and fitness, with stronger positive correlations in the highland site. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.

evolutionary biology↗

bioRxiv2020

The Genetic Architecture of Leaf Stable Carbon Isotope Composition in Zea mays and the Effect of Transpiration Efficiency on Elemental Accumulation

With increased demand on freshwater resources for agriculture, it is imperative that more water-use efficient crops are developed. Leaf stable carbon isotope composition, {delta}13C, is a proxy for transpiration efficiency and a possible tool for breeders, but the underlying mechanisms effecting {delta}13C in C4 plants are not known. It has been suggested that differences in specific leaf area, which potentially reflects variation in internal CO2 diffusion, can impact leaf {delta}13C. However, at this point the relationship has not been tested in maize. Furthermore, although it is known that water movement is important for elemental uptake, it is not clear how manipulation of transpiration for increased water-use efficiency may impact nutrient accumulation. Here we characterize the underlying genetic architecture of leaf {delta}13C and test its relationship to specific leaf area and the ionome in four biparental populations of maize. Five significant QTL for leaf {delta}13C were identified, including both novel QTL as well as some that were identified previously in maize kernels. One of the QTL regions contains an Erecta-like gene, the ortholog of which has been shown to regulate transpiration efficiency and leaf {delta}13C in Arabidopsis. Our data does not support a relationship between {delta}13C and specific leaf area, and of the 19 elements analyzed, only a weak correlation between molybdenum and {delta}13C was detected. Together these data begin to build a genetic understanding of leaf {delta}13C in maize and suggest the potential to improve plant water use without significantly influencing elemental homeostasis. Article SummaryQuantitative genetics approaches were used to investigate the genetic architecture of leaf stable carbon isotope discrimination ({delta}13C) in maize. Developing a better understanding of leaf {delta}13C could facilitate its use in breeding for reduced transpirational water loss. Several genomic regions were identified that contribute to the variation observed in leaf {delta}13C. Furthermore, contrary to what has been observed in other species, leaf {delta}13C was not correlated with specific leaf area. Finally, a leaf ionomic analysis indicates that a reduction in transpiration, and thus mass flow, would not result in a decrease in nutrient accumulation.

plant biology↗

bioRxiv2018

Stable Carbon Isotopes in Zea mays

The increasing demand for food production and predicted climate change scenarios highlight the need for improvements in crop sustainability. The efficient use of water will become increasingly important for rainfed agricultural crops even in fertile regions that have historically received ample precipitation. Improvements in water-use efficiency in Zea mays have been limited, and warrants a renewed effort aided by molecular breeding approaches. Progress has been constrained by the difficulty of measuring water-use in a field environment. The stable carbon isotope composition ({delta}13C) of the leaf has been proposed as an integrated signature of carbon fixation with a link to stomatal conductance. However, additional factors affecting leaf {delta}13C exist, and a limited number of studies have explored this trait in Z. mays. Here we present an extensive characterization of leaf {delta}13C in Z. mays. Significant variation in leaf {delta}13C exists across diverse lines of Z. mays, which we show to be heritable across several environments.\n\nFurthermore, we examine temporal and spatial variation in leaf {delta}13C to determine the optimum sampling time to maximize the use of leaf {delta}13C as a trait. Finally, our results demonstrate the relationship between transpiration and leaf {delta}13C in the field and the greenhouse. Decreasing transpiration and soil moisture are associated with decreasing leaf {delta}13C. Taken together these results outline a strategy for using leaf {delta}13C and reveal its usefulness as a measure of transpiration efficiency under well-watered conditions rather than a predictor of performance under drought.\n\nSignificance StatementThis study identifies sources of variation in stable carbon isotopes of maize leaves and establishes the framework for connecting leaf {delta}13C and transpiration efficiency.

plant biology↗