Adaptive root plasticity in pearl millet – PlastiMil

To identify plastic anatomical traits, we developed statistical models to quantify the genetic, genotype × year, and genotype × treatment components of variation for each anatomical trait. Traits influenced by the genotype × treatment interaction were then selected both for a detailed analysis of the plastic response and for the identification of the genetic determinants controlling this plasticity.

For the detailed study of plasticity, a subset of pearl millet genotypes contrasting in their plastic responses was selected and grown either in greenhouse conditions or in vitro. The dynamics of the plastic response to water stress (in the greenhouse) or osmotic stress (in vitro) were monitored over time, either on newly formed roots or on already developed roots. Root anatomical traits were tracked using laser ablation tomography. Anatomical changes were then related to plant hydraulics. The relationship between plasticity and yield maintenance under stress was also investigated.

To identify the genetic determinants controlling plasticity, three approaches were implemented: single-locus and multi-locus Genome-Wide Association Study (GWAS) models were used to identify associations specific to a given environment (year and treatment); multi-environment meta-analysis models (MetaGE), incorporating the effect of water treatment, were used to detect associations for which the effect of SNP markers on the trait depends on the treatment; and single-locus and multi-locus GWAS models were applied to plasticity indices (ratio and slope from the Finlay–Wilkinson regression). Associations common to these three approaches were prioritized. Within these regions, annotated genes were identified, and their potential role in controlling the trait of interest was considered for candidate gene selection. To further refine candidate gene identification, two pearl millet lines contrasting in plasticity were selected for transcriptome-wide gene expression analysis during the plastic response.

Field phenotyping revealed a significant positive relationship between xylem vessel area and grain yield maintenance under water stress. This result, robust as it was observed over both years of the study, suggests that a larger xylem vessel area is associated with improved yield under early water stress. In a subset of lines contrasting for xylem vessel area, we showed that genotypes with larger vessels exhibit earlier restriction of transpiration under water stress conditions, which may be associated with water-saving during soil drying.

Among the anatomical traits measured, only those related to xylem vessels—such as vessel number, mean vessel area, and total vessel area—showed a proportion of their variance explained by the Genotype × Treatment (G×T) interaction (5–10%). Several association genetics approaches were therefore used to identify the genetic determinants controlling these traits and their plasticity, revealing robust associations detected across multiple traits and GWAS models. The analysis of genes located in these regions is ongoing.

A detailed analysis of the plasticity of xylem vessel area suggests that once formed, vessel area remains stable within the root. In contrast, this trait appears to be affected in newly developing roots under water stress conditions. The plastic response to different stress intensities also appears to be non-linear, with plasticity emerging beyond a certain threshold of water stress. However, no significant correlation was observed between the ratio and slope of the Finlay–Wilkinson relationship for xylem vessel area and yield maintenance under stress.

This project opens particularly promising perspectives for a better understanding of the role of xylem vessel size in plant hydraulics and mechanisms of tolerance to water stress. From a genetic perspective, the candidate genes identified could be subject to functional validation. In addition, biparental populations contrasting for vessel area and its plasticity will enable validation of the QTLs identified in this project and the generation of genetic material useful for a detailed study of the role of xylem vessel plasticity in plant hydraulics, as well as for field validation of their role in water stress tolerance. This project also opens interesting perspectives regarding the developmental mechanisms controlling these responses.

Pearl millet is a key cereal for food security in arid and semi-arid regions of West Africa and India. However, climate change is predicted to increase the frequency of extreme events such as dry spells (strong episodes of rain interrupted by long drought periods) that will affect its yield. In this context, improving pearl millet adaptation to drought caused by rainfall uncertainty is needed. Roots represent a target to improve pearl millet adaptation to drought because they are responsible for water uptake and can greatly adapt their development in response to new environments. The changes in phenotypic traits in response to a new environment are called phenotypic plasticity. Such plasticity can be adaptive if it improves the plant ability to adapt to the new environment, for instance by stabilizing other important agronomical traits. Therefore, developing pearl millet varieties that can respond to drought by developing root systems better adapted to water capture and transport water represent an interesting perspective. However, the mechanisms associated with root plasticity remain elusive in pearl millet as well as in other cereals.

The PlastiMil project aims at identifying the genetic determinants and physiological mechanisms associated with root plasticity in response to drought in pearl millet. The Project will use root phenotyping datasets (architecture and anatomy) from a panel of 150 fully-sequenced pearl millet inbred lines obtained during two years of field experiments under irrigated and drought stress conditions. These data will be exploited in order to identify plastic root traits that are variable between lines in response to drought (controlled by the interaction between genotypes and environment) and precisely quantify plasticity of these traits. Root plasticity will be associated with agronomical performance as well as the geographical and climatic origin of each lines in order to infer the adaptive value of the plastic response. Plastic root traits showing variability, heritability and adaptive value will be further associated with the genotypes of each lines in order to identify genetic regions controlling plasticity. Whole gene expression at key steps of the most interesting root plastic response will be studied in order to identify genes controlling plasticity of the corresponding root trait. Two candidate genes for the considered plastic root response will be disrupted and root plasticity will be evaluated in the resulting mutated plants in comparison to wild type line. Mutated plants affected in their plastic response will be used to study the impact of the plastic root trait on pearl millet hydraulics under drought stress by considering root water transport, transpiration and plant water use efficiency.

PlastiMil is an interdisciplinary four years project that will look for plastic root traits in response to drought using approaches coming from the fields of evolution, genetics, functional genomics and physiology. It will provide QTLs/genes useful for breeders to develop new pearl millet varieties better adapted to rainfall uncertainties caused by climate change. This project will be coordinated by Alexandre Grondin in collaboration with young scientists from the University of Nottingham and the Institut Sénégalais des Recherches Agricoles. It will contribute to strengthen an international network of collaborations and establish AG as a scientific leader in the field of crop improvement using root traits.