Data and analysis code for "Aboveground Predictors of Perenniality in the S3011 Diploid Perennial Sorghum Population"

This repository contains the analysis-ready phenotypic and genotypic datasets and R analysis code associated with the manuscript “Aboveground Predictors of Perenniality in the S3011 Diploid Perennial Sorghum Population.” The study evaluates relationships among aboveground plant architecture, rhizome vigor, and overwinter regrowth in an interspecific diploid sorghum population. The archived materials include plant-level and analysis-ready phenotype data, genotype data, and R scripts supporting genotype quality control, phenotype processing, BLUP estimation, genome-wide association analysis, trait-correlation and trait-decoupling analyses, QTL-dosage-index analysis, window-based ancestry contrasts, candidate-interval evaluation, candidate-gene annotation, and figure generation. Window-based ancestry contrasts represent differences in mean ancestry scores between accessions in the upper and lower phenotypic quartiles. These contrasts are descriptive allele-dosage summaries and should not be interpreted as phased local-ancestry assignments or formal statistical tests of ancestry enrichment. File descriptions, software dependencies, and the recommended analysis sequence are provided in the README included with the code archive. Funding: This work was supported by the Perennial Agriculture Project, in conjunction with the Malone Family Land Preservation Foundation and The Land Institute.