Data and analysis code for "Genomic Analysis of a Diploid Sorghum bicolor × S. halepense Prebreeding Population Reveals Partial Separation of Perenniality and Shoot Architecture"

This repository contains the final audited, analysis-ready phenotypic and genotypic datasets, ancestry-proxy data, supporting metadata, and R analysis code associated with the manuscript: “Genomic Analysis of a Diploid Sorghum bicolor × S. halepense Prebreeding Population Reveals Partial Separation of Perenniality and Shoot Architecture.” The study evaluates relationships among plant height, lateral branching, rhizome vigor, and overwinter regrowth in an interspecific diploid-extraction population derived from Sorghum bicolor × Sorghum halepense. The repository supports trait-specific BLUP estimation, phenotype correlations, PC+K genome-wide association analyses, candidate-interval evaluation, candidate-gene annotation, descriptive SNP-dosage analyses, and window-based ancestry-proxy analyses. The primary GWAS uses 43,317 SNPs and trait-specific sample sizes of 121 accessions for plant height and lateral branching and 124 accessions for rhizome vigor and overwinter regrowth. Chromosome 3 and chromosome 4 perenniality candidate regions are treated as prespecified secondary regions rather than threshold-defined rhizome-vigor GWAS loci. Candidate-region ancestry-proxy analyses are provided separately from descriptive SNP-dosage analyses. The archive includes a SHA-256 manifest, repository inventory, release audit, and complete R reproduction workflow. Candidate-gene annotation uses BTx623 v3.1 genomic coordinates with the corresponding v3.1.1 gene annotation. File descriptions, analytical distinctions, software dependencies, and the recommended analysis sequence are documented within the repository. Funding: This work was supported by the Perennial Agriculture Project, in conjunction with the Malone Family Land Preservation Foundation and The Land Institute.