31 32 33 2 The environment has constantly shaped plant genomes, but the genetic bases underlying 34 how plants adapt to environmental influences remain largely unknown. We constructed a 35 high-density genomic variation map by re-sequencing genomes of 263 geographically 36 representative peach landraces and wild relatives. A combination of whole-genome 37 selection scans and genome-wide environmental association studies (GWEAS) was 38 performed to reveal the genomic bases of peach local adaptation to diverse climates 39 comprehensively. A total of 2,092 selective sweeps that underlie local adaptation to both 40 mild and extreme climates were identified, including 339 sweeps conferring genomic 41 pattern of adaptation to high altitudes. Using GWEAS, a total of 3,496 genomic loci strongly 42 associated with 51 specific environmental variables were detected. The molecular 43 mechanism underlying adaptive evolution of high drought, strong UV-B, cold hardiness, 44 sugar content, flesh color, and bloom date were revealed. Finally, based on 30 years of 45 observation, a candidate gene associated with bloom date advance, representing peach 46 responses to global warming, was identified. Collectively, our study provides insights into 47 molecular bases of how environments have shaped peach genomes by natural selection 48 and adds valuable genome resources and candidate genes for future studies on 49 evolutionary genetics, adaptation to climate changes, and future breeding.50 51 Environmental adaptation is fundamental to species survival and conservation of biodiversity, 52 especially under threats of climate change (Blanquart et al. 2013). Unlike animals, which can 53 escape from hostile environments, plants are sessile and have to adapt by shaping and/or fixing 54 genetic variants that are conducive for survival. Generally, climate is the major selective pressure 55 driving adaptive evolution, resulting in different ecotypes within a single species (Hancock et al. 56 2011; Fournier-Level et al. 2011). However, the mechanisms underlying how climate shapes plant 57 genomes remain largely unclear. Recently, identifying adaptive variants and understanding 58 molecular mechanism of adaptation across a genome have become tractable due to the advances 59 of sequencing technologies. Recent studies have sought to elucidate genetic bases of adaptation 60 through genome-wide identification of regions under positive selection and/or loci that control 61 adaptive traits in Arabidopsis thaliana (Fournier-Level et al. 2011), rice (Yan et al. 2013), sorghum 62 (Lasky et al. 2015), and poplar (Wang et al. 2018). However, no study has focused on genetic 63 bases of adaptation in domesticated perennial fruit crops. Domesticated crops have adapted to 64 diverse climates during domestication and subsequent spread, and show local adaptation through 65 long-term natural selection. Landraces and wild relatives harbor great genetic diversity and an 66abundance of resistance genes, which provide excellent resources for breeding initiatives. This ...