A two-stage approach for the spatio-temporal analysis of high-throughput phenotyping data

High throughput phenotyping (HTP) platforms and devices are increasingly used for the characterization of growth and developmental processes for large sets of plant genotypes. Such HTP data require challenging statistical analyses in which longitudinal genetic signals need to be estimated against a background of spatio-temporal noise processes. We propose a two-stage approach for the analysis of such longitudinal HTP data. In a first stage, we correct for design features and spatial trends per time point. In a second stage, we focus on the longitudinal modelling of the spatially corrected data, thereby taking advantage of shared longitudinal features between genotypes and plants within genotypes. We propose a flexible hierarchical three-level P-spline growth curve model, with plants/plots nested in genotypes, and genotypes nested in populations. For selection of genotypes in a plant breeding context, we show how to extract new phenotypes, like growth rates, from the estimated genotypic growth curves and their first-order derivatives. We illustrate our approach on HTP data from the PhenoArch greenhouse platform at INRAE Montpellier and the outdoor Field Phenotyping platform at ETH Zürich.BERC 2018-2021 BCAM Severo Ochoa accreditation SEV-2017-0718) EU H2020 grant agreement ID 731013 (EPPN2020) PhenoCOOL (project no. 169542)

Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud

Improving crop water use efficiency, the amount of carbon assimilated as biomass per unit of water used by a plant, is of major importance as water for agriculture becomes scarcer. In rice, the genetic bases of transpiration efficiency, the derivation of water use efficiency at the whole-plant scale, and its putative component trait transpiration restriction under high evaporative demand remain unknown. These traits were measured in 2019 in a panel of 147 African rice (Oryza glaberrima) genotypes known to be potential sources of tolerance genes to biotic and abiotic stresses. Our results reveal that higher transpiration efficiency is associated with transpiration restriction in African rice. Detailed measurements in a subset of highly contrasted genotypes in terms of biomass accumulation and transpiration confirmed these associations and suggested that root to shoot ratio played an important role in transpiration restriction. Genome wide association studies identified marker-trait associations for transpiration response to evaporative demand, transpiration efficiency, and its residuals, with links to genes involved in water transport and cell wall patterning. Our data suggest that root-shoot partitioning is an important component of transpiration restriction that has a positive effect on transpiration efficiency in African rice. Both traits are heritable and define targets for breeding rice with improved water use strategies.This work was supported by the Institut de Recherche pour le Développement, the CGIAR Research Program (CRP) on rice-agrifood systems (RICE, 2017-2022) and the Agence Nationale de la Recherche (grant ANR-17-MPGA-0011 to VV). Financial support by the Access to Research Infrastructures activity in the Horizon 2020 Programme of the EU (EPPN2020 Grant Agreement 731013) is gratefully acknowledged. PA was supported by a doctoral fellowship from the French Ministry of Higher Education. BEE was supported by the Centre National de la Recherche Scientifique et Technologique of Gabon. The authors acknowledge the IRD iTrop HPC (South Green Platform) at IRD Montpellier for providing HPC resources (https://bioinfo.ird.fr, http://www.southgreen.fr)

Carbon stable isotope analysis of cereal remains as a way to reconstruct water availability: preliminary results

Reconstructing past water availability, both as rainfall and irrigation, is important to answer questions about the way society reacts to climate and its changes and the role of irrigation in the development of social complexity. Carbon stable isotope analysis of archaeobotanical remains is a potentially valuable method for reconstructing water availability. To further define the relationship between water availability and plant carbon isotope composition and to set up baseline values for the Southern Levant, grains of experimentally grown barley and sorghum were studied. The cereal crops were grown at three stations under five different irrigation regimes in Jordan. Results indicate that a positive but weak relationship exists between irrigation regime and total water input of barley grains, but no relationship was found for sorghum. The relationship for barley is site-specific and inter-annual variation was present at Deir ‘Alla, but not at Ramtha and Khirbet as-Samra

Effects of Soil Water and Nitrogen on Growth and Photosynthetic Response of Manchurian Ash (Fraxinus mandshurica) Seedlings in Northeastern China

Soil water and nitrogen (N) are considered to be the main environmental factors limiting plant growth and photosynthetic capacity. However, less is known about the interactive effects of soil water and N on tree growth and photosynthetic response in the temperate ecosystem. seedlings. The seedlings were exposed to three water regimes including natural precipitation (CK), higher precipitation (HW) (CK +30%) and lower precipitation (LW) (CK −30%), and both with and without N addition for two growing seasons. We demonstrated that water and N supply led to a significant increase in the growth and biomass production of the seedlings. LW treatment significantly decreased biomass production and leaf N content, but they showed marked increases in N addition. N addition could enhance the photosynthetic capability under HW and CK conditions. Leaf chlorophyll content and the initial activity of Rubisco were dramatically increased by N addition regardless of soil water condition. The positive relationships were found between photosynthetic capacity, leaf N content, and SLA in response to water and N supply in the seedling. Rubisco expression was up-regulated by N addition with decreasing soil water content. Immunofluorescent staining showed that the labeling for Rubisco was relatively low in leaves of the seedlings under LW condition. The accumulation of Rubisco was increased in leaf tissues of LW by N addition. seedlings, which may provide novel insights on the potential responses of the forest ecosystem to climate change associated with increasing N deposition

What can crop stable isotopes ever do for us? An experimental perspective on using crop carbon stable isotope values for reconstructing water availability in semi-arid and arid environments

This study re-assesses and refines the use of crop carbon stable isotopes (Δ13C) to reconstruct past water availability. Durum wheat, six-row barley, and sorghum were experimentally grown at three crop growing stations in Jordan for up to three years under five different irrigation regimes: 0% (rainfall only), 40%, 80%, 100%, and 120% of the crops’ optimum water requirements. Results show large variation in carbon stable isotopes for crops that received similar amounts of water, either as absolute water input or as percentage of crop requirements. We conclude that C3 crop carbon stable isotope composition can therefore be best interpreted in terms of extremely high values showing an abundance of water versus low values indicating water-stress. Values in between these extremes are problematic and best interpreted in conjunction with other proxies. C4 crop isotopes were not found to be useful for the reconstruction of water availability

Stable Isotope Biogeochemistry of Seabird Guano Fertilization: Results from Growth Chamber Studies with Maize (Zea Mays)

Stable isotope analysis is being utilized with increasing regularity to examine a wide range of issues (diet, habitat use, migration) in ecology, geology, archaeology, and related disciplines. A crucial component to these studies is a thorough understanding of the range and causes of baseline isotopic variation, which is relatively poorly understood for nitrogen (δ(15)N). Animal excrement is known to impact plant δ(15)N values, but the effects of seabird guano have not been systematically studied from an agricultural or horticultural standpoint.This paper presents isotopic (δ(13)C and δ(15)N) and vital data for maize (Zea mays) fertilized with Peruvian seabird guano under controlled conditions. The level of (15)N enrichment in fertilized plants is very large, with δ(15)N values ranging between 25.5 and 44.7‰ depending on the tissue and amount of fertilizer applied; comparatively, control plant δ(15)N values ranged between -0.3 and 5.7‰. Intraplant and temporal variability in δ(15)N values were large, particularly for the guano-fertilized plants, which can be attributed to changes in the availability of guano-derived N over time, and the reliance of stored vs. absorbed N. Plant δ(13)C values were not significantly impacted by guano fertilization. High concentrations of seabird guano inhibited maize germination and maize growth. Moreover, high levels of seabird guano greatly impacted the N metabolism of the plants, resulting in significantly higher tissue N content, particularly in the stalk.The results presented in this study demonstrate the very large impact of seabird guano on maize δ(15)N values. The use of seabird guano as a fertilizer can thus be traced using stable isotope analysis in food chemistry applications (certification of organic inputs). Furthermore, the fertilization of maize with seabird guano creates an isotopic signature very similar to a high-trophic level marine resource, which must be considered when interpreting isotopic data from archaeological material