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Haplotype analysis from unmanned aerial vehicle imagery of rice MAGIC population for the trait dissection of biomass and plant architecture.

ABSTRACT: Unmanned aerial vehicles (UAVs) are popular tools for high-throughput phenotyping of crops in the field. However, their use for evaluation of individual lines is limited in crop breeding because research on what the UAV image data represent is still developing. Here, we investigated the connection between shoot biomass of rice plants and the vegetation fraction (VF) estimated from high-resolution orthomosaic images taken by a UAV 10 m above a field during the vegetative stage. Haplotype-based genome-wide association studies of multi-parental advanced generation inter-cross (MAGIC) lines revealed four quantitative trait loci (QTLs) for VF. VF was correlated with shoot biomass, but the haplotype effect on VF was better correlated with that on shoot biomass at these QTLs. Further genetic characterization revealed the relationships between these QTLs and plant spreading habit, final shoot biomass and panicle weight. Thus, genetic analysis using high-throughput phenotyping data derived from low-altitude, high-resolution UAV images during early stages of rice growing in the field provides insights into plant growth, architecture, final biomass, and yield.

SUBMITTER: Ogawa D

PROVIDER: S-EPMC8006554 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Agricultural subsurface drainage systems are commonly installed on farmland to remove the excess water from poorly drained soils. Conventional methods for drainage mapping such as tile probes and trenching equipment are laborious, cause pipe damage, and are often inefficient to apply at large spatial scales. Knowledge of locations of an existing drainage network is crucial to understand the increased leaching and offsite release of drainage discharge and to retrofit the new drain lines within the existing drainage system. Recent technological developments in non-destructive techniques might provide a potential alternative solution. The objective of this study was to determine the suitability of unmanned aerial vehicle (UAV) imagery collected using three different cameras (visible-color, multispectral, and thermal infrared) and ground penetrating radar (GPR) for subsurface drainage mapping. Both the techniques are complementary in terms of their usage, applicability, and the properties they measure and were applied at four different sites in the Midwest USA. At Site-1, both the UAV imagery and GPR were equally successful across the entire field, while at Site-2, the UAV imagery was successful in one section of the field, and GPR proved to be useful in the other section where the UAV imagery failed to capture the drainage pipes' location. At Site-3, less to no success was observed in finding the drain lines using UAV imagery captured on bare ground conditions, whereas good success was achieved using GPR. Conversely, at Site-4, the UAV imagery was successful and GPR failed to capture the drainage pipes' location. Although UAV imagery seems to be an attractive solution for mapping agricultural subsurface drainage systems as it is cost-effective and can cover large field areas, the results suggest the usefulness of GPR to complement the former as both a mapping and validation technique. Hence, this case study compares and contrasts the suitability of both the methods, provides guidance on the optimal survey timing, and recommends their combined usage given both the technologies are available to deploy for drainage mapping purposes.

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Project description:Plant nitrogen concentration (PNC) is a critical indicator of N status for crops, and can be used for N nutrition diagnosis and management. This work aims to explore the potential of multispectral imagery from unmanned aerial vehicle (UAV) for PNC estimation and improve the estimation accuracy with hyperspectral data collected in the field with a hyperspectral radiometer. In this study we combined selected vegetation indices (VIs) and texture information to estimate PNC in rice. The VIs were calculated from ground and aerial platforms and the texture information was obtained from UAV-based multispectral imagery. Two consecutive years (2015 & 2016) of experiments were conducted, involving different N rates, planting densities and rice cultivars. Both UAV flights and ground spectral measurements were taken along with destructive samplings at critical growth stages of rice (Oryza sativa L.). After UAV imagery preprocessing, both VIs and texture measurements were calculated. Then the optimal normalized difference texture index (NDTI) from UAV imagery was determined for separated stage groups and the entire season. Results demonstrated that aerial VIs performed well only for pre-heading stages (R2 = 0.52-0.70), and photochemical reflectance index and blue N index from ground (PRIg and BNIg) performed consistently well across all growth stages (R2 = 0.48-0.65 and 0.39-0.68). Most texture measurements were weakly related to PNC, but the optimal NDTIs could explain 61 and 51% variability of PNC for separated stage groups and entire season, respectively. Moreover, stepwise multiple linear regression (SMLR) models combining aerial VIs and NDTIs did not significantly improve the accuracy of PNC estimation, while models composed of BNIg and optimal NDTIs exhibited significant improvement for PNC estimation across all growth stages. Therefore, the integration of ground-based narrow band spectral indices with UAV-based textural information might be a promising technique in crop growth monitoring.

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Haplotype analysis from unmanned aerial vehicle imagery of rice MAGIC population for the trait dissection of biomass and plant architecture.

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