稻米(Oryza sativa) 廣泛種植於亞洲地區，主要可分為日本稻 (ssp. japonica)及印度稻 (ssp. indica)兩亞種，為全球主要的糧食作物。如同達爾文所述，作物馴化過程可視為植物的演化模式之一，藉由篩選野生稻(O. rufipogon) 的特定性狀以符合人類需求的行為，加速了栽培稻與野生稻在外部形態及遺傳結構上的差異。隨著栽培稻全基因組定序的完成，提供大量資料來鑑定與馴化相關的基因，並利用栽培稻遺傳變異的組成與分布，來顯現過去馴化的歷史足跡。而在不同緯度的地理區，光週期所帶來的影響，決定了人類選擇栽培稻的方向。本研究利用野生稻與不同種類的栽培稻為樣本，挑選四個光週期主要決定基因phyB、Hd1、Hd3a與Ehd1進行親緣分析，並探討這些基因在馴化過程中所受到的選汰效應。結果顯示在栽培稻的光週期基因中，相較於野生稻，phyB與Ehd1皆具有較低的遺傳多樣性。而Hd1則顯現不論在序列長度或基因多型性，都具有高度的變異，在Hd1中性測試結果下，栽培稻受到方向性天擇的影響，且累積過多的非同義置換突變，推測是來自近代人為的照料減輕栽培稻所受的負向選汰壓力（relaxation of selective constraint）；而在兩基因間的相關表現分析中，Hd1-Hd3a與Hd1-Ehd1的基因組合在印度稻及日本稻的分布上具有顯著差異。在各基因多型性的分布則顯示，日本稻與印度稻因栽種的緯度不同，這些功能基因上的突變扮演著重要的角色。同樣，台灣的兩栽培稻亦藉由基因多型性的分布顯示彼此存在著基因交流；而非洲的日本稻則在Hd1基因中具有新的插入序列存在，與其它栽培稻相比，具有高度的基因連鎖不平衡效應。

Rice, broadly cultivated in Asia, is one of the staple crops in the world and consists of two genetically divergent cultivated rice, subspecies indica and japonica. As noted by Charles Darwin, domestication can serve as a model of evolution. This process usually accompanies the extremely selective force on the desired traits in their wild progenitors (O. rufipogon). Completion of the rice whole genome provided the opportunity for identifying the domesticated-related genes and revealed the recent selective evidence by the distribution of the genetic variation and their composition. The impact of the photoperiod from tropical to temperate zones determines the direction of the artificial selection on cultivated rice. Among the genes of the photoperiod pathway, phyB、Hd1、Hd3a and Ehd1were chosen to be the target genes in this study. The primary objectives were to estimate the relationship of the phylogeny and the pattern of potentially adaptive factors in the cultivated rice and wild progenitor. The results of the genetic variation showed that phyB and Ehd1 have lower genetic diversity in cultivated rice than in wild rice. The high diversity both in the DNA length and polymorphism were detected in the Hd1 gene. The neutrality test showed Hd1 suffered the directional selection because of the significantly negative Tajima’D and Fu and Li’s D* values. An excess of non-synonymous polymorphisms found in Hd1 is considered as a signal of the relaxation of selective constraint and suggested that it is possible to experience recent population demography with human assistance. The gene association of the pair of the Hd1-Hd3a and Hd1-Ehd1 showed the significant differentiation in two subspecies. The distributions of the polymorphisms found in each gene play an important role in the adaptation of the different latitudes. Those polymorphisms also showed a remarkable gene flow through hybridization in Taiwan cultivars. The observation of the high linkage disequilibrium in Africa japonica is due to the emergence of the new insertion event in the Hd1 gene.

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