9,359 research outputs found
TasselNet: Counting maize tassels in the wild via local counts regression network
Accurately counting maize tassels is important for monitoring the growth
status of maize plants. This tedious task, however, is still mainly done by
manual efforts. In the context of modern plant phenotyping, automating this
task is required to meet the need of large-scale analysis of genotype and
phenotype. In recent years, computer vision technologies have experienced a
significant breakthrough due to the emergence of large-scale datasets and
increased computational resources. Naturally image-based approaches have also
received much attention in plant-related studies. Yet a fact is that most
image-based systems for plant phenotyping are deployed under controlled
laboratory environment. When transferring the application scenario to
unconstrained in-field conditions, intrinsic and extrinsic variations in the
wild pose great challenges for accurate counting of maize tassels, which goes
beyond the ability of conventional image processing techniques. This calls for
further robust computer vision approaches to address in-field variations. This
paper studies the in-field counting problem of maize tassels. To our knowledge,
this is the first time that a plant-related counting problem is considered
using computer vision technologies under unconstrained field-based environment.Comment: 14 page
Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum.
The ability to connect genetic information between traits over time allow Bayesian networks to offer a powerful probabilistic framework to construct genomic prediction models. In this study, we phenotyped a diversity panel of 869 biomass sorghum (Sorghum bicolor (L.) Moench) lines, which had been genotyped with 100,435 SNP markers, for plant height (PH) with biweekly measurements from 30 to 120 days after planting (DAP) and for end-of-season dry biomass yield (DBY) in four environments. We evaluated five genomic prediction models: Bayesian network (BN), Pleiotropic Bayesian network (PBN), Dynamic Bayesian network (DBN), multi-trait GBLUP (MTr-GBLUP), and multi-time GBLUP (MTi-GBLUP) models. In fivefold cross-validation, prediction accuracies ranged from 0.46 (PBN) to 0.49 (MTr-GBLUP) for DBY and from 0.47 (DBN, DAP120) to 0.75 (MTi-GBLUP, DAP60) for PH. Forward-chaining cross-validation further improved prediction accuracies of the DBN, MTi-GBLUP and MTr-GBLUP models for PH (training slice: 30-45 DAP) by 36.4-52.4% relative to the BN and PBN models. Coincidence indices (target: biomass, secondary: PH) and a coincidence index based on lines (PH time series) showed that the ranking of lines by PH changed minimally after 45 DAP. These results suggest a two-level indirect selection method for PH at harvest (first-level target trait) and DBY (second-level target trait) could be conducted earlier in the season based on ranking of lines by PH at 45 DAP (secondary trait). With the advance of high-throughput phenotyping technologies, our proposed two-level indirect selection framework could be valuable for enhancing genetic gain per unit of time when selecting on developmental traits
Digital phenotyping and genotype-to-phenotype (G2P) models to predict complex traits in cereal crops
The revolution in digital phenotyping combined with the new layers of omics and envirotyping tools offers great promise to improve selection and accelerate genetic gains for crop improvement. This chapter examines the latest methods involving digital phenotyping tools to predict complex traits in cereals crops. The chapter has two parts. In the first part, entitled “Digital phenotyping as a tool to support breeding programs”, the secondary phenotypes measured by high-throughput plant phenotyping that are potentially useful for breeding are reviewed. In the second part, “Implementing complex G2P models in breeding programs”, the integration of data from digital phenotyping into genotype to phenotype (G2P) models to improve the prediction of complex traits using genomic information is discussed. The current status of statistical models to incorporate secondary traits in univariate and multivariate models, as well as how to better handle longitudinal (for example light interception, biomass accumulation, canopy height) traits, is reviewe
Leveraging Image Analysis for High-Throughput Plant Phenotyping
The complex interaction between a genotype and its environment controls the biophysical properties of a plant, manifested in observable traits, i.e., plant’s phenome, which influences resources acquisition, performance, and yield. High-throughput automated image-based plant phenotyping refers to the sensing and quantifying plant traits non-destructively by analyzing images captured at regular intervals and with precision. While phenomic research has drawn significant attention in the last decade, extracting meaningful and reliable numerical phenotypes from plant images especially by considering its individual components, e.g., leaves, stem, fruit, and flower, remains a critical bottleneck to the translation of advances of phenotyping technology into genetic insights due to various challenges including lighting variations, plant rotations, and self-occlusions. The paper provides (1) a framework for plant phenotyping in a multimodal, multi-view, time-lapsed, high-throughput imaging system; (2) a taxonomy of phenotypes that may be derived by image analysis for better understanding of morphological structure and functional processes in plants; (3) a brief discussion on publicly available datasets to encourage algorithm development and uniform comparison with the state-of-the-art methods; (4) an overview of the state-of-the-art image-based high-throughput plant phenotyping methods; and (5) open problems for the advancement of this research field
PREDICTION OF CROP YIELDS ACROSS FOUR CLIMATE ZONES IN GERMANY: AN ARTIFICIAL NEURAL NETWORK APPROACH
This paper shows the ability of artificial neural network technology to be used for the approximation and prediction of crop yields at rural district and federal state scales in different climate zones based on reported daily weather data. The method may later be used to construct regional time series of agricultural output under climate change, based on the highly resolved output of the global circulation models and regional models. Three 30-year combined historical data sets of rural district yields (oats, spring barley and silage maize), daily temperatures (mean, maximum, dewpoint) and precipitation were constructed. They were used with artificial neural network technology to investigate, simulate and predict historical time series of crop yields in four climate zones of Germany. Final neural networks, trained with data sets of three climate zones and tested against an independent northern zone, have high predictive power (0.83global change, agriculture, artificial neural networks, yield prediction
A Mixed Data-Based Deep Neural Network to Estimate Leaf Area Index in Wheat Breeding Trials
Remote and non-destructive estimation of leaf area index (LAI) has been a challenge in
the last few decades as the direct and indirect methods available are laborious and
time-consuming. The recent emergence of high-throughput plant phenotyping platforms has
increased the need to develop new phenotyping tools for better decision-making by breeders. In
this paper, a novel model based on artificial intelligence algorithms and nadir-view red green blue
(RGB) images taken from a terrestrial high throughput phenotyping platform is presented. The
model mixes numerical data collected in a wheat breeding field and visual features extracted from
the images to make rapid and accurate LAI estimations. Model-based LAI estimations were
validated against LAI measurements determined non-destructively using an allometric
relationship obtained in this study. The model performance was also compared with LAI estimates
obtained by other classical indirect methods based on bottom-up hemispherical images and gaps
fraction theory. Model-based LAI estimations were highly correlated with ground-truth LAI. The
model performance was slightly better than that of the hemispherical image-based method, which
tended to underestimate LAI. These results show the great potential of the developed model for
near real-time LAI estimation, which can be further improved in the future by increasing the
dataset used to train the model
Soil Nitrogen: research and extension
These are the proceedings of the 4th QLIF workshiop with contributions of several European soil and nitrogen researchers
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