Biology subjects

Sekhon, R. S.

Publications and source records attributed to Sekhon, R. S..

7 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

Gene-by-Environment Interaction Significantly Drives Bacterial Endophyte Communities in Maize Stalks

1.BackgroundMany microbes are known to boost the performance of crop plants, and their use as crop treatments ("biologicals") is an active area of research and commercialization. Although many identified microbes can boost plant production under laboratory settings, most fail to translate to field settings, and even the ones that are commercialized are often unreliable. While many factors likely underlie these issues, one that has been underexplored is the idea that interactions between plants and microbes can vary across both different host genetics and different environments, and that specific combinations of host and environment can result in very different microbial outcomes. ResultsTo quantify how a plant microbiome can change across host genotype and environment and to determine the relative importance of these factors, we sampled maize stalks from 20 specific hybrid varieties grown at 15 locations in the United States. Using 16S rRNA gene sequencing, we find that the stalk microbiome is highly variable, with a handful of bacterial taxa conserved at broader taxonomic levels (Phylum, Class) and almost none at finer levels (Genus, Species). Local environment and gene-by-environment interactions both had consistently large and significant effects on the microbial community (measured by alpha-and beta-diversity summary statistics, individual taxa, and inferred functional capacity), whereas host genotype had little to no consistent effect across environments. We also identified specific soil factors (pH and potassium) as the most significant environmental drivers of the community, even though these communities were living inside the stalks. ConclusionsTaken together, our results indicate that while host genetics can significantly affect the stalk microbial community, these effects are almost entirely predicated on interactions with the environment. These results imply that reliable deployment of microbes for crop production will require significant investment in trials across many locations and genetic backgrounds, either to estimate the GxE effects directly or to screen for microbes whose effects are less dependent on these two factors.

microbiology↗

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

Temporal analysis of physiological phenotypes identifies novel metabolic and genetic underpinnings of senescence in maize

Leaf senescence induces extensive metabolome reprogramming to optimize nutrient recycling, enhance resilience to abiotic and biotic stress, and improve productivity. However, the characterization of these metabolic shifts and the identification of key metabolites and pathways remains limited. We generated a temporal map of physiological and metabolic diversity in genetically diverse maize inbred lines varying for the staygreen trait. Combinatorial analysis of physiological and metabolic changes revealed substantial metabolic perturbations and identified 84 leaf metabolites associated with senescence. Non-staygreen inbred lines exhibited higher accumulation of primary metabolites including sugar alcohols such as mannitol and erythritol, and amino acids such as phenylalanine and arginine. In contrast, the staygreen inbred lines showed higher abundance of secondary metabolites, primarily phenylpropanoids, including caffeic acid, chlorogenic acid, and eriodictyol. Linking metabolome to the genome identified 56 novel candidate genes expressed in adult maize leaf that regulate metabolic flux during senescence. Reverse genetic analysis validated the role of naringenin chalcone and eriodictyol in both maize and Arabidopsis, demonstrating a conserved function of these phenylpropanoids in leaf senescence across monocots and dicots. Our study provides valuable insights into the coordinated physiological and metabolic changes driving leaf senescence and identifies novel genes underlying this complex developmental process.

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

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↗