Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant

Crop wild relatives possess desirable traits that confer resilience to various environmental stresses. We applied landscape genomics, that associates environment with genomic variation to understand the genetic basis of their adaptation. In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hotspot of these wild relatives. Further, we explored the correlation between the genetic variations and the bio-climatic and soil conditions at their collection sites. Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected also candidate SNPs associated with ten environmental factors. Some of these SNPs signal genes involved in pathways that help with adaptation to environmental stresses such as drought, heat, cold, salinity, pests, and diseases.

作物野生近缘种（Crop wild relatives）具备多项优良性状，可赋予其抵御多种环境胁迫的能力。我们采用景观基因组学（landscape genomics）方法——一种将环境与基因组变异相关联以解析适应性遗传基础的研究手段——开展本研究。本研究针对来自非洲（该类野生近缘种的主要分布热点区域）的153份野生茄子近缘种种质材料，利用景观基因组学方法分析了其15416个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点的等位基因频率差异。此外，我们还探究了遗传变异与采集位点的生物气候及土壤条件之间的相关性。研究结果表明，在控制种群结构的前提下，相较于采集位点间的地理距离，环境对茄子野生近缘种种群的遗传变异具有更为显著的影响。上述发现揭示了环境在长期塑造茄子野生近缘种遗传变异过程中的重要作用。我们还鉴定出了与10种环境因子相关的候选SNPs位点，其中部分位点关联的基因参与了应对干旱、高温、低温、盐渍化、虫害及病害等环境胁迫的调控通路。