Dataset Information

Biomechanical phenotyping pipeline for stalk lodging resistance in maize.

ABSTRACT: Stalk lodging (structural failure crops prior to harvest) significantly reduces annual yields of vital grain crops. The lack of standardized, high throughput phenotyping methods capable of quantifying biomechanical plant traits prevents comprehensive understanding of the genetic architecture of stalk lodging resistance. A phenotyping pipeline developed to enable higher throughput biomechanical measurements of plant traits related to stalk lodging is presented. The methods were developed using principles from the fields of engineering mechanics and metrology and they enable retention of plant-specific data instead of averaging data across plots as is typical in most phenotyping studies. This pipeline was specifically designed to be implemented in large experimental studies and has been used to phenotype over 40,000 maize stalks. The pipeline includes both lab- and field-based phenotyping methodologies and enables the collection of metadata. Best practices learned by implementing this pipeline over the past three years are presented. The specific instruments (including model numbers and manufacturers) that work well for these methods are presented, however comparable instruments may be used in conjunction with these methods as seen fit.•Efficient methods to measure biomechanical traits and record metadata related to stalk lodging.•Can be used in studies with large sample sizes (i.e., > 1,000).

SUBMITTER: Tabaracci K

PROVIDER: S-EPMC10825676 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature

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Biomechanical phenotyping pipeline for stalk lodging resistance in maize.

Tabaracci Kaitlin K Bokros Norbert T NT Oduntan Yusuf Y Kunduru Bharath B DeKold Joseph J Mengistie Endalkachew E McDonald Armando A Stubbs Christopher J CJ Sekhon Rajandeep S RS DeBolt Seth S Robertson Daniel J DJ

MethodsX 20240109

Stalk lodging (structural failure crops prior to harvest) significantly reduces annual yields of vital grain crops. The lack of standardized, high throughput phenotyping methods capable of quantifying biomechanical plant traits prevents comprehensive understanding of the genetic architecture of stalk lodging resistance. A phenotyping pipeline developed to enable higher throughput biomechanical measurements of plant traits related to stalk lodging is presented. The methods were developed using pr ...[more]

PMID: 38292308

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Project description:BackgroundStalk fracture caused by strong wind can severely reduce yields in maize. Stalks with higher stiffness and flexibility will exhibit stronger lodging resistance. However, stalk flexibility is rarely studied in maize. Stalk fracture of the internode above the ear before tasseling will result in the lack of tassel and pollen, which is devastating for pollination in seed production. In this study, we focused on stalk lodging before tasseling in two maize inbred lines, JING724 and its improved line JING724A1 and their F2:3 population.ResultsJING724A1 showed a larger stalk fracture angle than JING724, indicating higher flexibility. In addition, compared to JING724, JING724A1 also had longer and thicker stalks, with a conical, frustum-shaped internode above the ear. Microscopy and X-ray microcomputed tomography of the internal stalk architecture revealed that JING724A1 had more vascular bundles and thicker sclerenchyma tissue. Furthermore, total soluble sugar content of JING724A1, especially the glucose component, was substantially higher than in JING724. Using an F2:3 population derived from a JING724 and JING724A1 cross, we performed bulk segregant analysis for stalk fracture angle and detected one QTL located on Chr3: 14.00-19.28 Mb. Through transcriptome data analysis and ∆ (SNP-index), we identified two candidate genes significantly associated with high stalk fracture angle, which encode a RING/U-box superfamily protein (Zm00001d039769) and a MADS-box transcription factor 54 (Zm00001d039913), respectively. Two KASP markers designed from these two candidate genes also showed significant correlations with stalk fracture angle.ConclusionsThe internode shape and glucose content are possibly correlated with stalk flexibility in maize. Two genes in the detected QTL are potentially associated with stalk fracture angle. These novel phenotypes and associated loci will provide a theoretical foundation for understanding the genetic mechanisms of lodging, and facilitate the selection of maize varieties with improved flexibility and robust lodging resistance.

Project description:BackgroundThe stalk traits stalk diameter, stalk length, rind penetrometer resistance and dry matter content are important indicators for measuring lodging resistance.ResultsIn this study, 377 inbred lines were used as the basic materials, and four stalk-related traits including stalk diameter, stalk length, rind penetrometer resistance and dry matter content of the third segment of maize, were investigated at the tasseling, grain filling, and maturity stages. 461,053 high-quality SNPs which were obtained by whole genome resequencing were used for genome-wide association study. As a result of mixed linear model analysis (P < 9.77 × 10-6), 29 significant SNPs related to traits were detected, accounting for 7.19% -15.03% of phenotypic variation, among which 4, 1, 4 and 20 SNPs were found related to rind penetrometer resistance, stalk diameter, stalk length, and dry matter content respectively. Most candidate genes are related to plant element structure, signal transduction mechanisms, inorganic ion transport and metabolism, nucleotide transport and metabolism, and transporter enzyme families. Comparing mixed linear model with generalized linear model, a total of 12 candidate genes were detected repeatedly, during which the candidate gene Zm00001d014449 were detected 5 times, with a phenotypic variation interpretation rate of 9.95% -10.84%. This gene is mainly expressed in cells with active cell division and tissue differentiation, and is involved in the formation of stalk vascular bundles and the synthesis of cell walls. Another candidate gene, Zm00001d005300, encodes the transcription factor MYB44, which regulates the dependence of salt stress signal phosphorylation, can effectively inhibit the accumulation of destructive reactive oxygen species, and has a certain resistance to non-biotic stress. In addition, this study also found that 10 unknown functional genes can be further Functional verification.ConclusionsThis study helps to deepen the understanding of the genetic basis of traits related to maize stalk lodging resistance, and provides theoretical guidance for future maize lodging resistance breeding.

Project description:BackgroundStalk lodging (breaking of agricultural plant stalks prior to harvest) is a multi-billion dollar a year problem. Rind penetration resistance tests have been used by plant scientists and breeders to estimate the stalk lodging resistance of maize for nearly a hundred years. However, the rind puncture method has two key limitations: (1) the predictive power of the test decreases significantly when measuring elite or pre-commercial hybrids, and (2) using rind penetration measurements as a breeding metric does not necessarily create stronger stalks. In this study, we present a new rind penetration method called the Integrated Puncture Score, which uses a modified rind penetration testing protocol and a physics-based model to provide a robust measure of stalk lodging resistance.ResultsTwo datasets, one with a diverse array of maize hybrids and one with only elite hybrids, were evaluated by comparing traditional rind penetration testing and the Integrated Puncture Score method to measurements of stalk bending strength. When evaluating the diverse set of hybrids, both methods were good predictors of stalk bending strength (R2 values of 0.67). However, when evaluating elite hybrids, the Integrated Puncture Score had an R2 value of 0.74 whereas the traditional method had an R2 value of 0.48. Additionally, the Integrated Puncture Score was able to differentiate between the strongest and weakest hybrids in the elite hybrid data set whereas the traditional rind penetration method was not. Additional experiments revealed strong evidence in favor of the data aggregation steps utilized to compute the Integrated Puncture Score.ConclusionsThis study presents a new method for evaluating rind penetration resistance that highly correlates with stalk bending strength and can possibly be used as a breeding index for assessing stalk lodging resistance. This research lays the foundation required to develop a field-based high-throughput phenotyping device for stalk lodging resistance.

Project description: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 plant's own weight) exceed the stalk bending strength of plant stems. Previous studies have investigated external loading and self-loading of plants 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 flexural response of plant stems, and (2) to provide a generalized framework for accounting for self-weight during mechanical phenotyping experiments used to predict stalk lodging resistance.ResultsA mathematical methodology for properly accounting for the interconnected relationship between self-loading and external loading of plants stems is presented. The method was compared to numerous finite element models of plants stems and found to be highly accurate. The resulting interconnected set of equations from the derivation were used to produce user-friendly applications by presenting (1) simplified self-loading correction factors for common loading configurations of plants, and (2) a generalized Microsoft Excel framework that calculates the influence of self-loading on crop stems. Results indicate that ignoring the effects of self-loading when calculating stalk flexural stiffness is appropriate for large and stiff plants such as maize, bamboo, and sorghum. However, significant errors result when ignoring the effects of self-loading in smaller plants with larger relative grain sizes, such as rice (8% error) and wheat (16% error).ConclusionsProperly accounting for self-weight can be critical to determining the structural response of plant stems. Equations and tools provided herein enable researchers to properly account for the plant's weight during mechanical phenotyping experiments used to determine stalk lodging resistance.

Dataset Information

Biomechanical phenotyping pipeline for stalk lodging resistance in maize.

Publications

Biomechanical phenotyping pipeline for stalk lodging resistance in maize.

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