Genome studio software version 1

A total of 384 SNPs, previously identified for P. vulgaris (Müller et al., 2015 ) polymorphic
between BAT 93 (Mesoamerican) and JALO EEP558 (Andean) lines, was genotyped by Vera
Code^® technology with Bead X press platform (Illumina) and selected to
compose the oligopool assay (OPA).
Three oligonucleotides were used for each of the variations of the same SNP and the
third specific-locus binding to the 3’ region of the DNA fragment containing the
target SNP, generating a unique allele-specific fragment. Subsequently, this fragment
was amplified using Taq DNA polymerase enzyme Titanium (Clontech®)
and complementary primers labeled with Cy3 and Cy5
fluorophores.
Genotyping was realized by Genome Studio software version 1.8.4 (Illumina, EUA) using
Call Rate values ranging from 0.80 to 0.90 and GenTrain ≥ 0.26 for SNP grouping.
Automated analyses were performed to cluster the SNP alleles of each line, based on
the signal intensity for Cy3 and Cy5 fluorophores,
resulting in three genotype classes, AA, BB, and AB. Groups were adjusted
individually and manually by determining the best clusters based on the parental
profile.

SNP genotyping was conducted using the technology Vera Code^® BeadXpress platform (Illumina) at the Biotechnology Laboratory of Embrapa (Goiania, GO, Brazil). A set of 384 SNP markers, validated by a previously identified Prelim file (https://icom.illumina.com/Custom/UploadOpaPrelim/) for Phaseolus vulgaris [36 ], a derivative of polymorphisms between strains BAT477 and Pérola of Mesoamerican origins, was selected to compose the Oligo Pool Assay (OPA) SNP marker panel. Three oligonucleotides were used for each of the variants of the same SNP and the third specific-locus binding to the 3′ region of the DNA fragment containing the target SNP, generating a unique allele-specific fragment. Subsequently, this fragment was amplified using Taq DNA polymerase enzyme Titanium (Clontech^®) and complementary primers labeled with Cy3 and Cy5 fluorophores. Genotyping was performed using Genome Studio software version 1.8.4 (Illumina, EUA) using Call Rate values ranging from 0.80 to 0.90 and GenTrain ≥ 0.26 for SNP grouping. Automated analyses were performed to cluster the SNP alleles of each line, based on signal intensities of Cy3 and Cy5 fluorophores. Groups were adjusted manually by determining the best clusters based on parental profiles.

DNA samples were genotyped using the Vera Code1 BeadXpress platform (Illumina) at the Biotechnology Laboratory of Embrapa (Goiania, GO, Brazil). A set of 384 SNP markers, validated by a previously identified Prelim file (https://icom.illumina.com/Custom/UploadOpaPrelim/) for Phaseolus vulgaris, was selected to compose the Oligo Pool Assay (OPA) SNP marker panel. During the procedure for SNP detection, three oligonucleotides were used for each of the variants of the same SNP and the third specific-locus binding to the 3’ region of the DNA fragment containing the target SNP, generating a unique allele-specific fragment. Genotype call was performed using Genome Studio software version 1.8.4 (Illumina, City, State, USA), with Call Rate values ranging from 0.80 to 0.90 and GenTrain ≥ 0.26 for SNP clustering. Analyses were performed to cluster the SNP alleles of each line, based on signal intensities of Cy3 and Cy5 fluorophores. The phenotypic and genotypic data sets are freely accessible at https://zenodo.org/record/1120366#.WjqyZkxFzmQ.