Sustainable food production for a growing world population will pose a central challenge in the coming decades. Organic farming is among the feasible approaches to achieving this goal if the yield gap to conventional farming can be decreased. However, uncertainties exist to which extend—and for which phenotypes in particular—organic and conventional agro-ecosystems require differentiated breeding strategies. To answer this question, a heterogeneous spring barley population was established between a wild barley and an elite cultivar to examine this question. This initial population was divided into two sets and sown one in organic and the other in conventional managed agro-ecosystems, without any artificial selection for two decades. A fraction of seeds harvested each year was sown the following year. Various generations, up to the 23th were whole-genome pool-sequenced to identify adaptation patterns towards ecosystem and climate conditions in the allele frequency shifts. Additionally, a meta-data analysis was conducted to link genomic regions’ increased fitness to agronomically related traits. This long-term experiment highlights for the first time that allele frequency pattern difference between the conventional and organic populations grew with subsequent generations. Further, the organic-adapted population showed a higher genetic heterogeneity. The data indicate that adaptations towards new environments happen in few generations. Drastic interannual changes in climate are manifested in significant allele frequency changes. Particular wild form alleles were positively selected in both environments. Clustering these revealed an increased fitness associated with biotic stress resistance, yield physiology, and yield components in both systems. Additionally, the introduced wild alleles showed increased fitness related to root morphology, developmental processes, and abiotic stress responses in the organic agro-ecosystem. Concluding the genetic analysis, we demonstrate that breeding of organically adapted varieties should be conducted in an organically managed agro-ecosystem, focusing on root-related traits, to close the yield gap towards conventional farming.

为不断增长的世界人口提供可持续粮食生产将成为未来几十年的主要挑战。如果可以缩小与传统农业的产量差距，有机农业是实现这一目标的可行方法之一。然而，有机和传统农业生态系统在何种程度上需要差异化育种策略，尤其是对于哪些表型，存在不确定性。为了回答这个问题，在野生大麦和优良品种之间建立了异质春大麦群体来研究这个问题。这个最初的种群被分成两组，一组播种在有机农业生态系统中，另一组播种在传统管理的农业生态系统中，二十年来没有任何人工选择。每年收获的一小部分种子在第二年播种。对直至第 23 代的各代进行了全基因组库测序，以确定等位基因频率变化对生态系统和气候条件的适应模式。此外，还进行了元数据分析，将基因组区域的适应性增强与农艺相关性状联系起来。这项长期实验首次强调，传统种群和有机种群之间的等位基因频率模式差异随着后代的增加而增加。此外，有机适应群体表现出更高的遗传异质性。数据表明，对新环境的适应需要几代人的时间。气候的剧烈年际变化表现为显着的等位基因频率变化。在两种环境中都积极选择了特定的野生型等位基因。对这些进行聚类揭示了两个系统中与生物胁迫抗性、产量生理学和产量组成相关的适应性的增加。此外，引入的野生等位基因显示出与有机农业生态系统中根部形态、发育过程和非生物胁迫反应相关的适应性增强。在遗传分析的结论中，我们证明有机适应品种的育种应在有机管理的农业生态系统中进行，重点关注与根系相关的性状，以缩小与传统农业的产量差距。