Processed genotype, phenotype, and analysis scripts for the S3011 perennial sorghum GWAS study

This repository contains the datasets and analysis pipeline supporting the genome-wide association study (GWAS) of the S3011 diploid perennial sorghum population derived from an interspecific cross between Sorghum bicolor and Sorghum halepense. The repository includes the processed genotype matrix, accession-level genotype data, phenotype data, marker metadata, complete R scripts used for data processing, quality control, BLUP estimation, GWAS, local ancestry and linkage disequilibrium analyses, figure generation, and reproducibility documentation. Reproducibility files include session information, package versions, file checksums, and analysis metadata, together with a README describing the repository structure and workflow. These resources enable reproduction of the analyses presented in the associated manuscript investigating the genetic architecture of rhizome development and overwinter regrowth in diploid perennial sorghum.