Data from: Predicting genotypes environmental range from genome-environment associations

Genome-environment association methods aim to detect genetic markers associated with environmental variables. The detected associations are usually analysed separately to identify the genomic regions involved in local adaptation. However, a recent study suggests that single-locus associations can be combined and used in a predictive way to estimate environmental variables for new individuals on the basis of their genotypes. Here, we introduce an original approach to predict the environmental range (values and upper and lower limits) of species genotypes from the genetic markers significantly associated with those environmental variables in an independent set of individuals. We illustrate this approach to predict aridity in a database constituted of 950 individuals of wild beets and 299 individuals of cultivated beets genotyped at 14,409 random Single Nucleotide Polymorphisms (SNPs). We detected 66 alleles associated with aridity and used them to calculate the fraction (I) of aridity-associated alleles in each individual. The fraction I correctly predicted the values of aridity in an independent validation set of wild individuals and was then used to predict aridity in the 299 cultivated individuals. Wild individuals had higher median values and a wider range of values of aridity than the cultivated individuals, suggesting that wild individuals have higher ability to resist to stress-aridity conditions and could be used to improve the resistance of cultivated varieties to aridity.

基因组-环境关联分析（Genome-environment association）方法旨在检测与环境变量相关的遗传标记。过往研究通常会单独分析所检测到的关联，以鉴定参与局部适应的基因组区域。然而，近期一项研究表明，单基因座关联可被整合并以预测性方式加以利用，基于新个体的基因型估算其所处的环境变量。本研究提出一种原创性方法，可基于独立样本群体中与上述环境变量显著相关的遗传标记，预测物种基因型的环境适配范围（包括具体数值、上下限值）。我们以一组数据库样本为例展示该方法的应用：该数据库包含950份野生甜菜与299份栽培甜菜样本，所有样本均通过14409个随机单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）完成基因分型。本研究共检测到66个与干旱程度相关的等位基因，并利用这些等位基因计算每个样本中干旱相关等位基因的占比（记为I）。该占比I可在独立的野生甜菜验证群体中准确预测干旱程度，随后被用于估算299份栽培甜菜样本的干旱程度。分析结果显示，野生甜菜样本的干旱程度中位数更高，且数值分布范围更广，这表明野生甜菜具备更强的干旱胁迫抗性，可用于改良栽培品种的耐旱性。