identifier: G19833.gnm2.mrk.Bassett_Kamfwa_2021

synopsis: "Marker SNPs developed via Genotyping by Sequencing (GBS) of the Andean Diversity Panel; reads were mapped to the Phaseolus vulgaris G19833 v2.1 reference assembly."

scientific_name: Phaseolus vulgaris

scientific_name_abbrev: phavu

taxid: 3885

genotype: 
  - G19833

description: "This study reports an association study regarding bean taste characteristics, evaluated against a collection of 430 genotypes of the Andean Diversity Panel. Cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture."

genotyping_platform: ADP_GBS_Bassett_Kamfwa_2021

genotyping_method: "The Andean Diversity Panel was genotyped using Genotyping by Sequencing (GBS). Two GBS libraries were constructed at 364-plex and 137-plex and the raw sequencing data are available at the NCBI BioProject database (accession number PRJNA290028). The raw sequence data were cleaned of adapters, trimmed for both a quality score and minimum length ≥ 30, demultiplexed using the Next Generation Sequencing Eclipse Plugin (NGSEP) pipeline, and aligned to the Phaseolus vulgaris v2.1 genome. NGSEP was used to conduct variant calling and annotation, SNPs with more than 90% missing data were removed, and they finally imputed any missing data which remained. There were 31,273 resulting SNPs found across the 430 Andean genotypes evaluated that spanned 20 dry-bean seed types. The number of SNPs used in GWAS at each location was 29,926 in Hawassa, Ethiopia; 29,545 in Kabwe, Zambia; and 31,484 in Lusaka, Zambia."

publication_doi: 10.1007/s00122-020-03745-3

publication_title: Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

contributors: Bassett A, Kamfwa K, Ambachew D, Cichy K

citation: "Bassett A, Kamfwa K, Ambachew D, Cichy K. Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.). Theor Appl Genet. 2021 Mar;134(3):959-978. doi: 10.1007/s00122-020-03745-3. Epub 2021 Jan 3. PMID: 33388888; PMCID: PMC7925484."

data_curators: Scott Kalberer

public_access_level: Public

license: Open

keywords: flavor, taste