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. 2024 Jul 17:55:110759.
doi: 10.1016/j.dib.2024.110759. eCollection 2024 Aug.

RADseq datasets of native beans from Mexico

Aragón-Magadán Marco Aurelio  1 , Cruz-Cárdenas Carlos Iván  1 , Calvillo-Aguilar Francisco Fabián  1 , Pichardo-González Juan Manuel  1 , Guzmán Luis Felipe  1
Affiliations

RADseq datasets of native beans from Mexico

Aragón-Magadán Marco Aurelio et al. Data Brief. .

Abstract

Forty-five accessions of the genus Phaseolus from the orthodox seed collection of the National Center for Genetic Resources (CNRG) of the National Institute of Forestry, Agricultural, and Livestock Research (INIFAP) of Mexico were sequenced using RADseq. The species utilized were: P. acutifolius (14), P. coccineus (12), P. lunatus (8), P. dumosus (6), P. leptostachyus (2), P. filiformis (2), and P. vulgaris (1). A variant call file (VCF) was generated using GATK with the P. vulgaris reference genome GCF_000499845.1, identifying 97,103 shared SNPs among the species. These data have the potential to be used for studies of genetic diversity intra and interspecies, phylogeny, evolution, genetic resource conservation, and agricultural improvement.

Keywords: Bioinformatics; Genotype-by-sequencing; Phaseolus; SNP; VCF.

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Figures

Fig 1
Fig. 1
Basic statistics in vcfR of the variant call.
Fig 2
Fig. 2
Read depth of variants per accession.
See this image and copyright information in PMC

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