Selection of nitrogen responsive root architectural traits in spinach using machine learning and genetic correlations

Abstract

The efficient acquisition and transport of nutrients by plants largely depend on the root architecture. Due to the absence of complex microbial network interactions and soil heterogeneity in a restricted soilless medium, the architecture of roots is a function of genetics defined by the soilless matrix and exogenously supplied nutrients such as nitrogen (N). The knowledge of root trait combinations that offer the optimal nitrogen use efficiency (NUE) is far from being conclusive. The objective of this study was to define the root trait(s) that best predicts and correlates with vegetative biomass under differed N treatments. We used eight image-derived root architectural traits of 202 diverse spinach lines grown in two N concentrations (high N, HN, and low N, LN) in randomized complete blocks design. Supervised random forest (RF) machine learning augmented by ranger hyperparameter grid search was used to predict the variable importance of the root traits. We also determined the broad-sense heritability (H) and genetic (rg) and phenotypic (rp) correlations between root traits and the vegetative biomass (shoot weight, SWt). Each root trait was assigned a predicted importance rank based on the trait’s contribution to the cumulative reduction in the mean square error (MSE) in the RF tree regression models for SWt. The root traits were further prioritized for potential selection based on the rg and SWt correlated response (CR). The predicted importance of the eight root traits showed that the number of root tips (Tips) and root length (RLength) under HN and crossings (Xsings) and root average diameter (RAvdiam) under LN were the most relevant. SWt had a highly antagonistic rg (− 0.83) to RAvdiam, but a high predicted indirect selection efficiency (− 112.8%) with RAvdiam under LN; RAvdiam showed no significant rg or rp to SWt under HN. In limited N availability, we suggest that selecting against larger RAvdiam as a secondary trait might improve biomass and, hence, NUE with no apparent yield penalty under HN.

Genetic dissection of nitrogen induced changes in the shoot and root biomass of spinach

“…The seeds of each accession were sown in triplicate in turface (Turface Athletics MVP, PROFILE Products LLC, Buffalo Grove, Illinois, USA) in small pots (10.2 cm × 10.2 cm and 8.9 cm deep) following a randomized complete block design. Additional details of the experimental set-up are detailed previously 11 . Plants were fertilized with two concentrations of N, low N (LN; 50 ppm), and high N (HN; 200 ppm) using Peters® professional ready mix (5-11-26, hydroponics special water-soluble fertilizer, Everris NA Inc., Ohio, U.S.A.) after seedling emergence.…”

“…Enhancing the NUE in spinach by exploiting genetic diversity in the leaf traits has been proposed 9 , 10 . We have previously shown that using a uniform soil-less matrix allowed us to use the supervised machine learning algorithm to predict the importance of root traits in spinach 11 . Biomass allocation among above (leaves) and below-ground (roots) organs is influenced by N uptake and distribution, which have crucial impacts on plant growth and development.…”

Enhancing Sorghum Yield Through Efficient Use of Nitrogen – Challenges and Opportunities

“…Roots architecture is crucial for uptake and supply N and other nutrients. Indeed, root traits such as root length, root tips, root average diameter, root weight, and specific root length were crucial determinants for NUE under low N conditions in wheat and spinach ( Awika et al, 2021 ; Puccio et al, 2021 ). However, information on different root trait combinations related to NUE in sorghum warrants further research.…”

Environmental and Cultivation Factors Affect the Morphology, Architecture and Performance of Root Systems in Soilless Grown Plants

“…The phenotypic consequence of a change in nutrient supply in a given genotype depends on exact nutrient concentration, nutrient distribution and gradients, concentrations of other nutrients, developmental stage of the plant, and environmental factors [43]. Awika et al [44] tested baby spinach accessions in small pots to determine phenotypic and genetic correlations between root traits and the shoot fresh weights under low and high nitrogen concentrations. They also found that, in a restricted soilless medium, the architecture of roots is a function of genetics defined by the soilless matrix and exogenously supplied nutrients.…”