Genetic data of 326 diverse common beans and genetic and phenotypic data of two RIL populations segregating for pod shattering

Here, we investigate the loss of seed dispersal via pod shattering during common bean (Phaseolus vulgaris L.) domestication. We identified PvMYB26 mutations in all three main gene pools of common bean, including an 8 kb deletion in Middle American lines eliminating the gene’s transcription start site and promoter; a frameshift/truncation deletion in the independently domesticated Andean population; and another frameshift/truncation insertion in the genetic background of the \"undomesticated\" debouckii population. Mutants with the 8 kb deletion express PvMYB26 at <1% of the level of wild types and produce 44% less pod lignin. RNA in situ hybridization and fluorescence microscopy show that PvMYB26 is expressed in the lignified fiber layer of pods, while mutants show no visible expression and have a greatly reduced fiber layer. Sequencing of 327 accessions revealed that the mutation is nearly diagnostic for domestication status among Middle American common bean and identified a 125 kb ha..., , # Genetic data of 326 diverse common beans and genetic and phenotypic data of two RIL populations segregating for pod shattering

Dataset DOI: [10.5061/dryad.bnzs7h4qs](https://doi.org/10.5061/dryad.bnzs7h4qs)

## Description of the data and file structure

This data deposition includes 1) a vcf of 110,095 genome-wide SNPs of 326 diverse common beans; and 2) genetic and phenotypic data of two RIL populations, which segregate for pod shattering, used for QTL mapping in ASMap and R/qtl. 

Dataset 1: Genome-wide SNPs are presented as a vcf, aligned to the 5-593 genome. All 326 samples of common bean were sequenced at 12x-16x depth with 150 bp paired-end sequencing on a Novaseq 6000.  Information for the reference sequence can be found here: [https://phytozome-next.jgi.doe.gov/info/Pvulgaris5_593_v1_1 \\](https://phytozome-next.jgi.doe.gov/info/Pvulgaris5_593_v1_1%C2%A0%5C)\
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FASTA for that reference sequence is stored in Pvulgaris5_593_696_v1.0.fa.gz available at: [https://data.jgi.doe.go..., , **Changes after Jan 16, 2026:** We have added sample metadata for the domestication status and gene pool of origin at *PvMYB26* in the Celebioglu_et_al._VCF_sample_domestication_status_and_gene_pool.xlsx