Common bean (Phaseolus vulgaris) Honduran Panel (HON) genetic diversity analysis raw data, genotype description tables, raw phenotypic data, and single nucleotide polymorphism genotype data

The study examined genetic diversity and agronomic, nitrogen-fixing, and water use efficiency traits among a panel of Honduran common beans (including landraces, varieties developed through participatory plant breeding, and conventional varieties bred for Central and North America). Genetic diversity: Genetic diversity was calculated in VCFtools software using the SNP data set (see accompanying repository file) to determine nucleotide diversity (π values) and genetic differentiation (FST values). The π statistic provides an indication of polymorphism within a population as measured by nucleotide diversity, and Tajima’s D (D) provides an indication of selection pressure. Both π and D were measured in sliding windows of 1 Mb across the genome using the --window-pi and --TajimaD options in VCFtools, which resulted in an average of 6 SNPs per window. The pairwise π and D values were also calculated among different subpopulations. Genome-wide averages of π and D for each breeding history category were generated by taking the average across all windowed calculations. Landrace and PPB π values were compared across the genome, and regions where landrace π exceeded PPB π by more than 3× were considered highly differentiated, and the regions that were at least 25,000 bp in length were considered significant. To investigate the level of differentiation between the landrace and PPB genotypes the FST statistic was computed. FST was calculated using the --weir-fst-pop option in VCFtools in sliding windows of 100 bp across the genome. Weighted FST values range from 0 with no genetic differentiation, to 1 where fixation of alleles has occurred. FST values exceeding 0.5 were considered significant in our analysis. Genotype descriptions: We examined trait diversity, significant differences between genotypes, and trait correlation for the panel overall, and by breeding history category. Agronomic traits (days to flowering, days to maturity, leaf chlorophyll content, hundred seed weight, yield) were measured in low-nitrogen field trials at the University of Guelph Elora research station (2014, 2015) and at Yorito, Honduras (2014-2015). These tables present a comprehensive description of the germplasm used in this study. Phenotype data: We examined trait diversity, significant differences between genotypes, and trait correlation for the panel overall, and by breeding history category. Agronomic traits (days to flowering, days to maturity, leaf chlorophyll content, hundred seed weight, yield) were measured in low-nitrogen field trials at the University of Guelph Elora research station (2014, 2015) and at Yorito, Honduras (2014-2015). Seed composition traits (nitrogen discrimination [δ15N], carbon discrimination [δ13C]) were measured using gas-chromatography-mass-spectometry at the Agriculture-Agrifood Canada facility in Lethbridge, Alberta. Percent nitrogen derived from the atmosphere (%Ndfa) was calculated using normalized δ15N values with the formula described by Shearer and Kohl, 1988. SNPs: DNA was isolated from leaf tissue of young bean plants of each genotype grown in controlled-environment conditions at the University of Guelph. The NucleoSpin Plant II kit (Macherey-Nagel, Germany) or the DNeasy Plant Mini Kit (Qiagen, Canada) was used to extract DNA, following standard protocols. Genomic DNA was analyzed at the Genome Quebec Innovation Centre (McGill University, Montreal) for single nucleotide polymorphisms (SNPs) using the Illumina Infinium iSelect Custom Genotyping BeadChip (BARCBEAN6K_3) containing 5398 SNPs (Song et al., 2015). SNP data was aligned to Pv 02 build of the Phaseolus vulgaris genome. SNP data was used for identity by state and genetic diversity analyses.