35,153 research outputs found
An integrated molecular and conventional breeding scheme for enhancing genetic gain in maize in Africa
Open Access Journal; Published online: 06 Nov 2019Maize production in West and Central Africa (WCA) is constrained by a wide range of interacting stresses that keep productivity below potential yields. Among the many problems afflicting maize production in WCA, drought, foliar diseases, and parasitic weeds are the most critical. Several decades of efforts devoted to the genetic improvement of maize have resulted in remarkable genetic gain, leading to increased yields of maize on farmersâ fields. The revolution unfolding in the areas of genomics, bioinformatics, and phenomics is generating innovative tools, resources, and technologies for transforming crop breeding programs. It is envisaged that such tools will be integrated within maize breeding programs, thereby advancing these programs and addressing current and future challenges. Accordingly, the maize improvement program within International Institute of Tropical Agriculture (IITA) is undergoing a process of modernization through the introduction of innovative tools and new schemes that are expected to enhance genetic gains and impact on smallholder farmers in the region. Genomic tools enable genetic dissections of complex traits and promote an understanding of the physiological basis of key agronomic and nutritional quality traits. Marker-aided selection and genome-wide selection schemes are being implemented to accelerate genetic gain relating to yield, resilience, and nutritional quality. Therefore, strategies that effectively combine genotypic information with data from field phenotyping and laboratory-based analysis are currently being optimized. Molecular breeding, guided by methodically defined product profiles tailored to different agroecological zones and conditions of climate change, supported by state-of-the-art decision-making tools, is pivotal for the advancement of modern, genomics-aided maize improvement programs. Accelerated genetic gain, in turn, catalyzes a faster variety replacement rate. It is critical to forge and strengthen partnerships for enhancing the impacts of breeding products on farmersâ livelihood. IITA has well-established channels for delivering its research products/technologies to partner organizations for further testing, multiplication, and dissemination across various countries within the subregion. Capacity building of national agricultural research system (NARS) will facilitate the smooth transfer of technologies and best practices from IITA and its partners
Inverse meta-modelling to estimate soil available water capacity at high spatial resolution across a farm
Geo-referenced information on crop production that is both spatially- and temporally-dense would be useful for management in precision agriculture (PA). Crop yield monitors provide spatially but not temporally dense information. Crop growth simulation modelling can provide temporal density, but traditionally fail on the spatial issue. The research described was motivated by the challenge of satisfying both the spatial and temporal data needs of PA. The methods presented depart from current crop modelling within PA by introducing meta-modelling in combination with inverse modelling to estimate site-specific soil properties. The soil properties are used to predict spatially- and temporally-dense crop yields. An inverse meta-model was derived from the agricultural production simulator (APSIM) using neural networks to estimate soil available water capacity (AWC) from available yield data. Maps of AWC with a resolution of 10 m were produced across a dryland grain farm in Australia. For certain years and fields, the estimates were useful for yield prediction with APSIM and multiple regression, whereas for others the results were disappointing. The estimates contain âimplicit informationâ about climate interactions with soil, crop and landscape that needs to be identified. Improvement of the meta-model with more AWC scenarios, more years of yield data, inclusion of additional variables and accounting for uncertainty are discussed. We concluded that it is worthwhile to pursue this approach as an efficient way of extracting soil physical information that exists within crop yield maps to create spatially- and temporally-dense dataset
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
Dominance and GĂE interaction effects improvegenomic prediction and genetic gain inintermediate wheatgrass (Thinopyrumintermedium)
Genomic selection (GS) based recurrent selection methods were developed to accelerate the domestication of intermediate wheatgrass [IWG, Thinopyrum intermedium (Host) Barkworth & D.R. Dewey]. A subset of the breeding population phenotyped at multiple environments is used to train GS models and then predict trait values of the breeding population. In this study, we implemented several GS models that investigated the use of additive and dominance effects and GĂE interaction effects to understand how they affected trait predictions in intermediate wheatgrass. We evaluated 451 genotypes from the University of Minnesota IWG breeding program for nine agronomic and domestication traits at two Minnesota locations during 2017â2018. Genet-mean based heritabilities for these traits ranged from 0.34 to 0.77. Using fourfold cross validation, we observed the highest predictive abilities (correlation of 0.67) in models that considered GĂE effects. When GĂE effects were fitted in GS models, trait predictions improved by 18%, 15%, 20%, and 23% for yield, spike weight, spike length, and free threshing, respectively. Genomic selection models with dominance effects showed only modest increases of up to 3% and were trait-dependent. Crossenvironment predictions were better for high heritability traits such as spike length, shatter resistance, free threshing, grain weight, and seed length than traits with low heritability and large environmental variance such as spike weight, grain yield, and seed width. Our results confirm that GS can accelerate IWG domestication by increasing genetic gain per breeding cycle and assist in selection of genotypes with promise of better performance in diverse environments
Using numerical plant models and phenotypic correlation space to design achievable ideotypes
Numerical plant models can predict the outcome of plant traits modifications
resulting from genetic variations, on plant performance, by simulating
physiological processes and their interaction with the environment.
Optimization methods complement those models to design ideotypes, i.e. ideal
values of a set of plant traits resulting in optimal adaptation for given
combinations of environment and management, mainly through the maximization of
a performance criteria (e.g. yield, light interception). As use of simulation
models gains momentum in plant breeding, numerical experiments must be
carefully engineered to provide accurate and attainable results, rooting them
in biological reality. Here, we propose a multi-objective optimization
formulation that includes a metric of performance, returned by the numerical
model, and a metric of feasibility, accounting for correlations between traits
based on field observations. We applied this approach to two contrasting
models: a process-based crop model of sunflower and a functional-structural
plant model of apple trees. In both cases, the method successfully
characterized key plant traits and identified a continuum of optimal solutions,
ranging from the most feasible to the most efficient. The present study thus
provides successful proof of concept for this enhanced modeling approach, which
identified paths for desirable trait modification, including direction and
intensity.Comment: 25 pages, 5 figures, 2017, Plant, Cell and Environmen
Local Motion Planner for Autonomous Navigation in Vineyards with a RGB-D Camera-Based Algorithm and Deep Learning Synergy
With the advent of agriculture 3.0 and 4.0, researchers are increasingly
focusing on the development of innovative smart farming and precision
agriculture technologies by introducing automation and robotics into the
agricultural processes. Autonomous agricultural field machines have been
gaining significant attention from farmers and industries to reduce costs,
human workload, and required resources. Nevertheless, achieving sufficient
autonomous navigation capabilities requires the simultaneous cooperation of
different processes; localization, mapping, and path planning are just some of
the steps that aim at providing to the machine the right set of skills to
operate in semi-structured and unstructured environments. In this context, this
study presents a low-cost local motion planner for autonomous navigation in
vineyards based only on an RGB-D camera, low range hardware, and a dual layer
control algorithm. The first algorithm exploits the disparity map and its depth
representation to generate a proportional control for the robotic platform.
Concurrently, a second back-up algorithm, based on representations learning and
resilient to illumination variations, can take control of the machine in case
of a momentaneous failure of the first block. Moreover, due to the double
nature of the system, after initial training of the deep learning model with an
initial dataset, the strict synergy between the two algorithms opens the
possibility of exploiting new automatically labeled data, coming from the
field, to extend the existing model knowledge. The machine learning algorithm
has been trained and tested, using transfer learning, with acquired images
during different field surveys in the North region of Italy and then optimized
for on-device inference with model pruning and quantization. Finally, the
overall system has been validated with a customized robot platform in the
relevant environment
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