Root Phenotypic Plasticity Calculation for Crop Breeding

This document presents a method to quantify root phenotypic plasticity using the Relative Distance Plasticity Index (RDP1), enabling breeders to assess root trait adaptability under environmental stress. It details the implementation of RDP1 via R and RStudio, including required packages—tidyverse, agricolae, psych, Plastcity, and ggradar. The guide provides step-by-step instructions for data preparation with columns for trait, environment, genotype, and trait value. The rdp1_matrix function computes pairwise distances, and RDP1 is calculated as the mean of these distances with standard error. The formula is derived from relative distances between trait values. Results are stored in a data frame and visualized using spider plots (ggradar) and dot charts to compare plasticity across genotypes and traits. The method supports breeding programs targeting drought, heat, or nutrient stress resilience, with applications in both lab and field conditions.