植物無法透過播遷等方式改變棲息的位置，因此演化出一系列特徵以利於其適應環境中的極端逆境，葉背角質蠟層便是植物抵抗環境逆境最重要的特徵之一。過去二十年間葉背角質蠟層的功能與生合成機制受到植物學家的廣泛關注，相比之下葉背角質蠟層遺傳架構的探討則較為缺乏，研究多集中於模式物種與作物，非模式物種則鮮有相關研究。本研究以殼斗科物種為研究對象，探討非模式物種葉背角質蠟層的遺傳架構與天擇訊號。我首先利用全基因組重定序 (whole genome re-sequencing) 獲得臺灣中北部30個白背櫟複合群 (Q. salicina species complex) 個體的基因組序列，並以全基因組關聯性分析、族群分化指數與功能性註釋，定位及辨別葉背角質蠟層變異的候選基因座位置及功能，接著使用族群分化指數與序列分化程度關聯性、基因座的核苷酸多態性與基因樹總分支長等指標辨別候選基因座的族群尺度天擇訊號。為了進一步揭示不同物種間候選基因座的天擇訊號，我利用實驗室未發表的68個殼斗科物種的轉錄組序列，重建葉背角質蠟層的演化歷史並分析序列的同義/非同義突變比例。研究結果顯示第五號染色體上具有兩個相鄰的候選區域，並且首個候選區域中存在六個與葉背角質蠟層變異高度相關的ABCC3候選基因座。關聯區域內族群分化指數與序列分化程度的高度正相關，以及候選基因座顯著上升的核甘酸多態性與總分支長則支持候選區域存在族群尺度的平衡選汰訊號。葉背角質蠟層的祖徵重建顯示蠟質層最早出現於石櫟屬 (Lithocarpus)、石柯屬(Notholithocarpus) 與櫟屬 (Quercus) 的共祖中，相當於古新世晚期至始新世早期階段。同義/非同義突變比例顯示六個ABCC3候選基因座受到淨化選擇，然而ABCC3-4基因表現出淨化選擇減弱的訊號。以上結果支持野生殼斗科植物透過運輸蛋白影響葉背角質蠟層的表型，而結合組徵重建結果與物種尺度的天擇訊號，ABCC3基因可能在古新世晚期至始新世早期獲得運輸蠟質產物的新功能，以應對此時期快速上升的昆蟲植食壓力。族群尺度的平衡選擇訊號則顯示頻率依賴選擇可能決定了族群中葉背角質蠟層的頻率，進一步導致了候選基因座表現出平衡選擇訊號。

Plants are not able to relocate their growth sites, thus heavily rely on a series of traits to withstand environmental extremes. The abaxial epicuticular wax layer is considered one of the most important traits for plant adaptation, playing significant roles in drought and temperature tolerance, as well as resistance against pathogens and herbivores. While extensive research has focused on the biofunctions and biosynthesis pathways of the wax layer over the past two decades, investigations into the genetic architecture underlying wax layer variation, especially in non-model organisms, remain relatively limited. In this study, I obtained whole-genome resequencing data from 30 individuals of the Quercus salicina species complex from central-northern Taiwan, exploring the genetic architecture of wax variation in this species complex and detecting selection signals at candidate loci. I further accessed transcriptome sequences from 68 Fagaceae species, reconstructing the evolution of the epicuticular wax layer trait and detecting species-level selection signals in orthologs of candidate genes. The results discovered two candidate regions on chromosome 5, and identified six ABCC3 genes encoding ABC-type transporter proteins as the candidate loci underlying epicuticular wax variation. Additionally, a positive correlation between FST and Dxy, along with distinct elevated nucleotide diversity and total branch lengths of ABCC3 genes, suggests balancing selection signals at the population level for these candidate loci. Ancestral state reconstruction indicates the earliest occurrence of the epicuticular wax layer in the common ancestor of Lithocarpus, Notholithocarpus, and Quercus, which can be dated back to the late Paleocene to early Eocene origin. CODEML analyses further reveal a low but higher ω ratio in the foreground branches of ABCC3 orthologs, supporting a relaxation from purifying selection for this gene. These results demonstrate that the transporter proteins modulates epicuticular wax variation in wild oaks. The evolution of the wax layer in the late Paleocene to early Eocene matched the period with increased insect herbivory. Together with the relaxation from purifying selection suggests that ABCC3 gained wax transportation functionality in response to positive selection from sharply increased insect herbivory during this period. Furthermore, the population-level balancing selection signals suggest that frequency-dependent selection determines the frequency of the wax layer to maintain an effective defense system against various herbivores.

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