DOI: 10.5061/dryad.bnzs7h4qs
title: Genetic data of 326 diverse common beans and genetic and phenotypic data of two RIL populations segregating for pod shattering

description: 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 &lt;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 hard selective sweep, indicating the gene’s
 importance in domestication. The main Andean frameshift mutation is found
 in 84.5% of Andean domesticates but 0% of wild lines, while the debouckii
 truncation was identified in six domesticated lines of Race Peru,
 suggesting a third proto-domestication of common bean may have occurred in
 Ecuador and/or northern Peru. Wild haplotypes most like Middle American
 domesticates are found in eastern Jalisco, Mexico, strongly suggesting
 West-Central Mexico as the site of common bean domestication and the rise
 of agriculture in Middle America.
description: # 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)\ \ FASTA for that reference sequence is stored in Pvulgaris5_593_696_v1.0.fa.gz available at: [https://data.jgi.doe.gov/refine-download/phytozome?organism=Pvulgaris5-593&expanded=696&phytozome_version=14&_gl=1*1wkerk2*_ga*MTQ3Mzg4ODIyLjE3NTkxNjIyNDM.*_ga_YBLMHYR3C2*czE3NjE4NTc2NzgkbzE2JGcwJHQxNzYxODU3Njc4JGo2MCRsMCRoMA](https://data.jgi.doe.gov/refine-download/phytozome?organism=Pvulgaris5-593&expanded=696&phytozome_version=14&_gl=1*1wkerk2*_ga*MTQ3Mzg4ODIyLjE3NTkxNjIyNDM.*_ga_YBLMHYR3C2*czE3NjE4NTc2NzgkbzE2JGcwJHQxNzYxODU3Njc4JGo2MCRsMCRoMA) SNPs were extracted using mpileup, varscan, and GATK. \ \ Dataset 2: The data used for QTL mapping were derived from the Khufu method of skim sequencing, conducted by the Hudson-Alpha Institute. Two biparental populations were involved, one descended from a cross between Canario 707 and PI 638850; the other population was descended from a cross between Orca and PI 638850.  The populations were used to conduct QTL mapping of pod shattering and the related trait of pod twists. ### Files and variables **File: PodShatteringAndTwistQTLmappingData.xlsx** **Description:** Genotype and phenotype data for two populations, Canario 707 x Wild PI 638850 ("CxW"); and Orca x Wild PI 638850 ("OxW"), on separate tabs. Files are ready to read into ASMAP / Rqtl. ##### Variables * Pod shattering phenotypes (two-year averages) * Pod twist phenotypes (two-year averages) * RIL name * Genome-wide SNP data **File: Final-Pv-326-geno-110095-SNP.vcf** **Description:** VCF (Variant Call Format) file of 110,095 genome-wide SNPs of 326 diverse accessions of P. vulgaris. 
 
 **File:
 Celebioglu_et_al._VCF_sample_domestication_status_and_gene_pool.xlsx**
 Description: Sample metadata for Final-Pv-326-geno-110095-SNP.vcf,
 describing the domestication status and gene pool of origin at *PvMYB26*.
 #### Code/software For QTL mapping of the RIL populations, these are
 formatted for ASMAP and Rqtl. The VCF file can be opened with a wide
 variety of bioinformatics software. #### Access information Other publicly
 accessible locations of the data: * None