Biology subjects

Robertson, D. J.

Publications and source records attributed to Robertson, D. J..

8 recordsLinked to original sources

bioRxiv2026

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

Stalk lodging causes severe yield losses in maize (Zea mays L.) worldwide, worsening food and feed security. Stalk lodging resistance is influenced by multiple traits at various levels of biological organization, collectively referred to as intermediate traits, but their identities, genetic bases, and interrelationships remain poorly resolved. Here, evaluation of multiple geometric and structural intermediate traits in a maize diversity panel across four environments showed that macroenvironmental variation is the predominant driver of phenotype plasticity and that plasticity varies with internode position along the stalk, consistent with height-dependent mechanosensing. Major and minor diameters, moment of inertia, and rind penetration resistance, were genetically tractable and showed strong genetic correlations with stalk flexural stiffness. Multivariate analyses revealed two distinct but complementary mechanistic pathways, represented by cross-sectional geometry and rind architecture, that contribute to stalk mechanical performance. Association analyses using whole-genome resequencing data identified 705 SNPs associated with intermediate traits, fewer than 20% of which overlapped genic regions, indicating that most associated variation resides outside annotated genes. Interestingly, about 22% of SNPs were shared between at least two traits, indicating substantial shared genetic control among intermediate traits. Candidate gene analyses highlighted novel promising candidate loci associated with intermediate traits while recovering genes previously implicated in stalk lodging resistance. The predominance of noncoding associations further suggests that regulatory variation may contribute substantially to natural variation in intermediate traits underlying stalk lodging resistance.

genetics↗

bioRxiv2025

Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data

Breeding for stalk lodging resistance is of paramount importance to maintain and improve maize yield and quality and meet increasing food demand. The integration of environmental, phenotypic, and genotypic information offers the opportunity to develop genomic prediction strategies that can improve the genetic gain for complex traits such as stalk lodging. However, implementation of genomic predictions for stalk lodging resistance has been sparse primarily due to the lack of reliable and reproducible phenotyping strategies. In this study, we measured 10 traits related to stalk lodging resistance obtained from a novel phenotyping platform on approximately 31,000 individual stalks. These traits were combined with environmental information and whole-genome resequence data to investigate the predictive ability of different single and multi-environment genomic prediction models. In total, 555 maize inbred lines from the Wisconsin diversity panel were evaluated in four environments. The multi-environment models more than doubled the prediction accuracy compared to the single-environment model for most traits, particularly when predicting lines in a sparse testing design. Predictive correlations for stalk bending strength and stalk flexural stiffness, a non-destructive method for assessment of stalk lodging resistance, were moderately high and ranged between 0.32 to 0.89 and 0.26 to 0.88, respectively. In contrast, rind thickness was the most difficult trait to predict. Our results show that the use of multi-environmental data could improve genomic prediction accuracy for stalk lodging resistance and its intermediate phenotypes. This study will serve as a first step toward genetic improvement and the development of maize varieties resistant to stalk lodging. Core IdeasO_LIThe DARLING platform was successfully used to collect lodging resistance-related phenotypes C_LIO_LIProportion of variation explained by genotype by environment interaction was not negligible C_LIO_LIGenomic predictions for lodging resistance phenotypes ranged from moderate to high C_LIO_LIAccounting for genotype by environment interaction was found to be important for improved predictive performance C_LI Plain language summaryStalk lodging - when maize stalks break or fall over before harvest - can seriously reduce crop yields. Breeding maize that resists lodging is important to ensure reliable food production. We tested about 31,000 individual stalks for 10 traits related to lodging resistance using a new phenotyping system. These traits were combined with environmental information and whole-genome resequence data to investigate the predictive ability of single and multi-environment genomic prediction models. By analyzing 555 maize lines, we found that using data from multiple environments improved genomic prediction accuracy by more than twice as much as using data from a single environment. Traits such as bending strength and flexural stiffness were easier to predict, while rind thickness was more difficult. These results show that combining genetic, environmental, and phenotypic data can help breeders more accurately select maize plants with stronger stalks, leading to better, more resilient crops.

genetics↗

bioRxiv2025

High Density Phenotypic Map of Natural Variation for Intermediate Phenotypes Associated with Stalk Lodging Resistance in Maize

The world has food security needs that are currently not being met. Stalk lodging undermines crop productivity and incurs global yield losses of at least $6 billion in maize (Zea mays L.). Genetic architecture of stalk lodging resistance, a measure of the ability of the stalk to withstand lodging, remains poorly resolved, creating a bottleneck for genetic improvement. Identification of diverse plant traits at multiple length scales of biological organizations that contribute to stalk lodging resistance and characterization of natural variation for these traits is critical for improving stalk lodging resistance. We identified and evaluated 11 intermediate phenotypes, traits associated with stalk lodging resistance, in a maize diversity panel of 566 inbred lines evaluated over four environments. The identity of each of the 31,260 stalks evaluated in the study was preserved throughout the phenotyping pipeline which enabled capturing variation at the individual plant level. This high-density phenotypic dataset provided a foundation for statistical genomics, predictive modeling, and machine learning analyses to identify genes and genetic elements underlying stalk lodging resistance. Additionally, phenotypic characterization of multiple intermediate phenotypes on a diverse set of inbred lines provided excellent opportunities to understand the relative contribution of these traits to stalk lodging resistance. Besides improvement of maize for grain and animal feedstock, the inferences from this data will be valuable for improvement of stalk lodging resistance in other grass species.

plant biology↗

bioRxiv2020

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations

Stalk lodging, breakage of the stalk at or below the ear, causes substantial yield losses in maize. The strength of the stalk rind, commonly measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance RPR genetic architecture, we conducted selection mapping on populations developed by 15 cycles of divergent selection for high (C15-H) and low (C15-L) RPR. We also performed time-course transcriptome and metabolic analyses on developing stalks of high (Hrpr1) and low (Lrpr1) RPR inbred lines derived from the C15-H and C15-L populations, respectively. Divergent selection significantly altered allele frequencies at 3,656 and 3,412 single nucleotide polymorphisms (SNP) in the C15-H and C15-L populations, respectively. While the majority of the SNPs under selection were unique, 110 SNPs were common in both populations indicating the fixation of alleles with alternative effects. Remarkably, preferential selection on the genomic regions associated with lignin and polysaccharide biosynthesis genes was observed in C15-H and C15-L populations, respectively. This observation was supported by higher lignification and lower extractability of cell wall-bound sugars in Hrpr1 compared to Lrpr1. Tricin, a monolignol important for incorporation of lignin in grass cell walls, emerged as a key determinant of the different cell wall properties of Hrpr1 and Lrpr1. Integration of selection mapping with transcriptomics and previous genetic studies on RPR identified 40 novel candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, two PAL paralogues, two lichenases, ZmEXPA2, ZmIAA41, and Caleosin. Enhanced mechanistic and genetic understanding of RPR provides a foundation for improved stalk lodging resistance.

genetics↗

bioRxiv2020

The Effect of Self-Loading on the Mechano-Stability and Stalk Lodging Resistance of Plant Stems

BackgroundStalk lodging (breaking of agricultural plant stalks prior to harvest) is a multi-billion dollar a year problem. Stalk lodging occurs when bending moments induced by a combination of external loading (e.g. wind) and self-loading (e.g. the plants own weight) exceed the bending strength of plant stems. Previous biomechanical plant stem models have investigated both external loading and self-loading of plants, but have evaluated them as separate and independent phenomena. However, these two types of loading are highly interconnected and mutually dependent. The purpose of this paper is twofold: (1) to investigate the combined effect of external loads and plant weight on the displacement and stress state of plant stems / stalks, and (2) to provide a generalized framework for accounting for self-weight during mechanical phenotyping experiments used to predict stalk lodging resistance. ResultsA method of properly accounting for the interconnected relationship between self-loading and external loading of plants stems is presented. The interconnected set of equations are used to produce user-friendly applications by presenting (1) simplified self-loading correction factors for a number of common external loading configurations of plants, and (2) a generalized Microsoft Excel framework that calculates the influence of self-loading on crop stems. The effect of self-loading on the structural integrity of wheat is examined in detail. A survey of several other plants is conducted and the influence of self-loading on their structural integrity is also presented. ConclusionsThe self-loading of plants plays a potentially critical role on the structural integrity of plant stems. Equations and tools provided herein enable researchers to account for the plants weight when investigating the flexural rigidity and bending strength of plant stems.

bioengineering↗

bioRxiv2020

Are Maize Stalks Efficiently Tapered to Withstand Wind Induced Bending Stresses?

Stalk lodging (breaking of agricultural plant stalks prior to harvest) results in millions of dollars in lost revenue each year. Despite a growing body of literature on the topic of stalk lodging, the structural efficiency of maize stalks has not been investigated previously. In this study, we investigate the morphology of mature maize stalks to determine if rind tissues, which are the major load bearing component of corn stalks, are efficiently organized to withstand wind induced bending stresses that cause stalk lodging. 945 fully mature, dried commercial hybrid maize stem specimens (48 hybrids, [~]2 replicates, [~]10 samples per plot) were subjected to: (1) three-point-bending tests to measure their bending strength and (2) rind penetration tests to measure the cross-sectional morphology at each internode. The data were analyzed through an engineering optimization algorithm to determine the structural efficiency of the specimens. Hybrids with higher average bending strengths were found to allocate rind tissue more efficiently than weaker hybrids. However, even strong hybrids were structurally suboptimal. There remains significant room for improving the structural efficiency of maize stalks. Results also indicated that stalks are morphologically organized to resist wind loading that occurs primarily above the ear. Results are applicable to selective breeding and crop management studies seeking to reduce stalk lodging rates. HighlightMaize stem morphology was investigated through an optimization algorithm to determine how efficiently their structural tissues are allocated to withstand wind induced bending stresses that cause stalk lodging.

biophysics↗

bioRxiv2019

Stalk Bending Strength is Strongly Associated with Maize Stalk Lodging Incidence Across Multiple Environments

Stalk lodging in maize results in substantial yield losses worldwide. These losses could be prevented through genetic improvement. However, breeding efforts and genetics studies are hindered by lack of a robust and economical phenotyping method for assessing stalk lodging resistance. A field-based phenotyping platform that induces failure patterns consistent with natural stalk lodging events and measures stalk bending strength in field-grown plants was recently developed. Here we examine the association between data gathered from this new phenotyping platform with counts of stalk lodging incidence on a select group of maize hybrids. For comparative purposes, we examine four additional predictive phenotypes commonly assumed to be related to stalk lodging resistance; namely, rind puncture resistance, cellulose, hemicellulose, and lignin. Historical counts of lodging incidence were gathered on 47 hybrids, grown in 98 distinct environments, spanning four years and 41 unique geographical locations in North America. Using Bayesian generalized linear mixed effects models, we show that stalk lodging incidence is associated with each of the five predictive phenotypes. Further, based on a joint analysis we demonstrate that, among the phenotypes considered, stalk bending strength measured by the new phenotyping platform is the most important predictive phenotype of naturally occurring stalk lodging incidence in maize, followed by rind puncture resistance and cellulose content. This study demonstrates that field-based measurements of stalk bending strength provide a reliable estimate of stalk lodging incidence. The stalk bending strength data acquired from the new phenotyping platform will be valuable for phenotypic selection in breeding programs and for generating mechanistic insights into the genetic regulation of stalk lodging resistance.

plant biology↗

bioRxiv2019

Stalk Lodging: A Portable Device for Phenotyping Stalk Bending Strength of Maize and Sorghum

BackgroundStalk lodging (breakage of plant stems prior to harvest) is a major problem for both farmers and plant breeders. A limiting factor in addressing this problem is the lack of a reliable method for phenotyping stalk strength. Previous methods of phenotyping stalk strength induce failure patterns different from those observed in natural lodging events. This paper describes a new device for field-based phenotyping of stalk strength called \"DARLING\" (Device for Assessing Resistance to Lodging IN Grains). The DARLING apparatus consists of a vertical arm which is connected to a horizontal footplate by a hinge. The operator places the device next to a stalk, aligns the stalk with a force sensor, steps on the footplate, and then pushes the vertical arm forward until the stalk breaks. Force and rotation are continuously recorded during the test and these quantities are used to calculate two quantities: stalk flexural stiffness and stalk bending strength.\n\nResultsField testing of DARLING was performed at multiple sites. Validation was based upon three factors. First, the device induces the characteristic \"crease\" or Brazier buckling failure patterns observed in naturally lodged stalks. Second, in agreement with prior research, flexural stiffness values attained using the DARLING apparatus are strongly correlated with bending strength measurements. Finally, a paired specimen experimental design was used to determine that the flexural data obtained with DARLING is in agreement with laboratory-based flexural testing results of the same specimens. DARLING was also deployed in the field to assess phenotyping throughput (# of stalks phenotyped per hour). Over approximately 5000 tests, the average testing rate was found to be 210 stalks/hour.\n\nConclusionsThe DARLING apparatus provides a quantitative assessment of stalk strength in a field setting. It induces the same failure patterns observed in natural lodging events. DARLING can also be used to perform non-destructive flexural tests. This new technology has many applications, including breeding, genetic studies on stalk strength, longitudinal studies of stalk flexural stiffness, and risk assessment of lodging propensity.

bioengineering↗