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LEAF-E: a tool to analyze grass leaf growth using function fitting

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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
In grasses, leaf growth is often monitored to gain insights in growth processes, biomass accumulation, regrowth after cutting, etc. To study the growth dynamics of the grass leaf, its length is measured at regular time intervals to derive the leaf elongation rate (LER) profile over time. From the LER profile, parameters such as maximal LER and leaf elongation duration (LED), which are essential for detecting inter-genotype growth differences and/or quantifying plant growth responses to changing environmental conditions, can be determined. As growth is influenced by the circadian clock and, especially in grasses, changes in environmental conditions such as temperature and evaporative demand, the LER profiles show considerable experimental variation and thus often do not follow a smooth curve. Hence it is difficult to quantify the duration and timing of growth. For these reasons, the measured data points should be fitted using a suitable mathematical function, such as the beta sigmoid function for leaf elongation. In the context of high-throughput phenotyping, we implemented the fitting of leaf growth measurements into a user-friendly Microsoft Excel-based macro, a tool called LEAF-E. LEAF-E allows to perform non-linear regression modeling of leaf length measurements suitable for robust and automated extraction of leaf growth parameters such as LER and LED from large datasets. LEAF-E is particularly useful to quantify the timing of leaf growth, which forms an important added value for detecting differences in leaf growth development. We illustrate the broad application range of LEAF-E using published and unpublished data sets of maize, Miscanthus spp. and Brachypodium distachyon, generated in independent experiments and for different purposes. In addition, we show that LEAF-E could also be used to fit datasets of other growth-related processes that follow the sigmoidal profile, such as cell length measurements along the leaf axis. Given its user-friendliness, ability to quantify duration and timing of leaf growth and broad application range, LEAF-E is a tool that could be routinely used to study growth processes following the sigmoidal profile.
Keywords
MAIZE LEAVES, EXPANSION, Leaf elongation rate, Non-linear regression, Leaf length, Cell length, Growth zone, BRACHYPODIUM-DISTACHYON, NONLINEAR-REGRESSION, ELONGATION RATE, CELL-DIVISION, MODELING APPROACH, EVAPORATIVE DEMAND, TEMPERATURE, MISCANTHUS

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Citation

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Chicago
Voorend, Wannes, Peter Lootens, Hilde Nelissen, Isabel Roldàn-Ruiz, Dirk Inzé, and Hilde Muylle. 2014. “LEAF-E: a Tool to Analyze Grass Leaf Growth Using Function Fitting.” Plant Methods 10.
APA
Voorend, W., Lootens, P., Nelissen, H., Roldàn-Ruiz, I., Inzé, D., & Muylle, H. (2014). LEAF-E: a tool to analyze grass leaf growth using function fitting. PLANT METHODS, 10.
Vancouver
1.
Voorend W, Lootens P, Nelissen H, Roldàn-Ruiz I, Inzé D, Muylle H. LEAF-E: a tool to analyze grass leaf growth using function fitting. PLANT METHODS. 2014;10.
MLA
Voorend, Wannes, Peter Lootens, Hilde Nelissen, et al. “LEAF-E: a Tool to Analyze Grass Leaf Growth Using Function Fitting.” PLANT METHODS 10 (2014): n. pag. Print.
@article{5787171,
  abstract     = {In grasses, leaf growth is often monitored to gain insights in growth processes, biomass accumulation, regrowth after cutting, etc. To study the growth dynamics of the grass leaf, its length is measured at regular time intervals to derive the leaf elongation rate (LER) profile over time. From the LER profile, parameters such as maximal LER and leaf elongation duration (LED), which are essential for detecting inter-genotype growth differences and/or quantifying plant growth responses to changing environmental conditions, can be determined. As growth is influenced by the circadian clock and, especially in grasses, changes in environmental conditions such as temperature and evaporative demand, the LER profiles show considerable experimental variation and thus often do not follow a smooth curve. Hence it is difficult to quantify the duration and timing of growth. For these reasons, the measured data points should be fitted using a suitable mathematical function, such as the beta sigmoid function for leaf elongation. 
In the context of high-throughput phenotyping, we implemented the fitting of leaf growth measurements into a user-friendly Microsoft Excel-based macro, a tool called LEAF-E. LEAF-E allows to perform non-linear regression modeling of leaf length measurements suitable for robust and automated extraction of leaf growth parameters such as LER and LED from large datasets. LEAF-E is particularly useful to quantify the timing of leaf growth, which forms an important added value for detecting differences in leaf growth development. We illustrate the broad application range of LEAF-E using published and unpublished data sets of maize, Miscanthus spp. and Brachypodium distachyon, generated in independent experiments and for different purposes. In addition, we show that LEAF-E could also be used to fit datasets of other growth-related processes that follow the sigmoidal profile, such as cell length measurements along the leaf axis. 
Given its user-friendliness, ability to quantify duration and timing of leaf growth and broad application range, LEAF-E is a tool that could be routinely used to study growth processes following the sigmoidal profile.},
  articleno    = {37},
  author       = {Voorend, Wannes and Lootens, Peter and Nelissen, Hilde and Rold{\`a}n-Ruiz, Isabel and Inz{\'e}, Dirk and Muylle, Hilde},
  issn         = {1746-4811},
  journal      = {PLANT METHODS},
  keyword      = {MAIZE LEAVES,EXPANSION,Leaf elongation rate,Non-linear regression,Leaf length,Cell length,Growth zone,BRACHYPODIUM-DISTACHYON,NONLINEAR-REGRESSION,ELONGATION RATE,CELL-DIVISION,MODELING APPROACH,EVAPORATIVE DEMAND,TEMPERATURE,MISCANTHUS},
  language     = {eng},
  pages        = {13},
  title        = {LEAF-E: a tool to analyze grass leaf growth using function fitting},
  url          = {http://dx.doi.org/10.1186/1746-4811-10-37},
  volume       = {10},
  year         = {2014},
}

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