水稻是全球最重要的糧食作物之一，全球一半以上人口，約有30億人口以稻米為主食，廣泛種植於亞洲各國，隸屬於禾本科植物的水稻屬 (Oryza)，全球約計有24種。近年來由於工業導致的環境污染日益嚴重，其中重金屬對土地的污染最為嚴重，鎘汙染是台灣主要的環境重金屬污染之一，台灣地區因為過去的工業污染，至今仍有許多的高濃度鎘汙染地的殘留，這些對代謝非必要的重金屬離子對植物體而言是生長的限制因子，根據野外調查，僅有少數種類可以在污染地存活並繁衍後代，植物螯合蛋白合成酶(phytochelatin synthase, PCS)基因與植物中抗重金屬的植物螯合蛋白的合成有關，而螯合蛋白主要功能在於與鎘結合形成複合物，並將其帶入細胞的液泡中。本研究主要探討水稻屬PCS基因家族PCS1以及PCS2基因所受到的天擇效應以及演化力量，並選取其它物種PCS基因序列進行PCS基因的親緣分析。結果顯示單雙子葉植物、蕨類以及線蟲中PCS基因都各自呈現單一系群(monoplyly)，而水稻屬中的兩不同基因座的基因則各自形成單一系群，進一步發現水稻屬PCS1基因遭受到平衡性天擇效應，而PCS2基因卻遭受到負向天擇效應，導致在PCS1基因具有較高遺傳多型性。針對PCS1基因，可以發現Oryza sativa ssp. japonica以及O. sativa ssp. indica族群是由兩個不同的古老支系的個體所組成，因此造成Tajima’s D呈現正值，而非受到平衡性天擇的影響，野生稻兩物種卻是受到方向性天擇的影響。然而在PCS2基因中，不論在栽培稻或野生稻都受到方向性天擇影響，其中O. sativa ssp. indica所受到的是正向天擇，其餘則為負向天擇。進一步探討兩基因連鎖不平衡效應(LD)效應，顯示PCS1基因受到較低程度的LD，這主要是因為PCS1基因所受到的平衡性天擇效應以及多次的重組事件，因此造成PCS1相對PCS2有較低的LD。

Rice, one of the staple crops in the world, is cultivated widely in Asia. Oryza, a genus of the Poaceae, consists of three sections and 24 species. Since last century, the industrial pollution has been seriously contaminating environments. Among various pollutants, heavy metals in the soil influences the crop growth to a great extent. Of them, cadmium is toxic to most animals and flowering plants. To vascular plants, cadmium is a nonessential metal; only species or populations that are tolerant to cadmium can survive in the wild. Phytochelatin (PC) proteins, which are synthesized from glutathione via a transpeptidation reaction mediated by the phytochelatin synthase (PCS), enable plants to tolerate heavy-metal ions. This study focuses on molecular evolution and selection effects of the PCS gene family in Oryza. Phylogenetic analysis revealed that monocots, dicots, and pteridophytes each formed a monophyletic group. Reciprocal monophyly of PCS1 and PCS2 paralogs in the Oryza was supported. As directional selection as an evolutionary force shaping the PCS1 gene was detected in other species, PCS1 gene mediated by maintaining the ancestreal lineages in cultivated rice, resulting positive Tajima’s D values. In contrast, PCS2 genes evolved under a negative selection in the genus. Linkage disequilibrium (LD) decayed slowly. Compared to the PCS2 gene, a lower level of LD in PCS1 gene was detected. The possible explanations are that the balancing selection and high-frequency recombination events of PCS1 have led to such lower LD.

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