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.

本研究针对一组洪都拉斯普通菜豆（涵盖地方品种、通过参与式植物育种（Participatory Plant Breeding，PPB）培育的品种，以及针对中北美洲选育的常规品种）的遗传多样性，以及农艺、固氮与水分利用效率性状展开分析。
遗传多样性分析：采用VCFtools软件，基于单核苷酸多态性（Single Nucleotide Polymorphism，SNP）数据集（详见配套仓库文件）计算核苷酸多样性（π值）与遗传分化（FST值）。其中，π统计量可反映群体内基于核苷酸多样性的多态性水平，塔伊马D统计量（Tajima’s D，D）可反映选择压力。本研究通过VCFtools的`--window-pi`与`--TajimaD`参数，在全基因组范围内以1 Mb为滑动窗口进行π与D值计算，每个窗口平均包含6个SNP。同时还计算了不同亚群间的成对π与D值。通过对所有滑动窗口计算结果取平均，得到各育种历史类别的全基因组π与D平均值。对地方品种与PPB品种的π值进行全基因组比较，将地方品种π值超过PPB品种π值3倍以上的区域视为高度分化区域，长度不低于25,000 bp的区域则判定为显著分化区域。为探究地方品种与PPB基因型间的分化水平，本研究计算了FST统计量：采用VCFtools的`--weir-fst-pop`参数，在全基因组范围内以100 bp为滑动窗口计算加权FST值。加权FST值的取值范围为0（无遗传分化）至1（等位基因完全固定），本研究中将FST值大于0.5的区域视为显著分化区域。
基因型概况：本研究针对整体种质群体及各育种历史类别，分析了性状多样性、基因型间的显著差异以及性状相关性。农艺性状（开花天数、成熟天数、叶片叶绿素含量、百粒重、产量）的测定分别于2014、2015年在圭尔夫大学埃洛拉研究站，以及2014-2015年在洪都拉斯约里托的低氮田间试验中完成。本研究附表全面呈现了本研究所用种质资源的详细信息。
表型数据：本研究针对整体种质群体及各育种历史类别，分析了性状多样性、基因型间的显著差异以及性状相关性。农艺性状（开花天数、成熟天数、叶片叶绿素含量、百粒重、产量）的测定分别于2014、2015年在圭尔夫大学埃洛拉研究站，以及2014-2015年在洪都拉斯约里托的低氮田间试验中完成。种子组成性状（氮同位素分馏[δ15N]、碳同位素分馏[δ13C]）通过气相色谱-质谱联用法在加拿大农业与农业食品部阿尔伯塔省莱斯布里奇研究中心完成测定。大气来源氮百分比（%Ndfa）通过标准化后的δ15N值，结合Shearer与Kohl于1988年提出的公式计算得到。
单核苷酸多态性（SNP）分析：从圭尔夫大学可控环境条件下种植的各基因型菜豆幼苗叶片组织中提取DNA，分别采用德国Macherey-Nagel公司的NucleoSpin植物II试剂盒或加拿大Qiagen公司的DNeasy植物迷你试剂盒，按照标准规程进行DNA提取。基因组DNA由麦吉尔大学蒙特利尔分校魁北克基因组创新中心使用Illumina Infinium iSelect定制基因分型芯片（BARCBEAN6K_3，含5398个SNP标记，Song等，2015）进行单核苷酸多态性分型。SNP数据与菜豆（Phaseolus vulgaris）参考基因组Pv 02版本进行比对，用于状态同一性分析与遗传多样性分析。