利用水稻 3K 資料庫探勘雜草化性狀的遺傳組成

Abstract

栽培稻 (Oryza sativa L.) 是在馴化過程中歷經人為選拔而逐漸演變成為現今世界上最重要的糧食作物之一。然而，作為同ㄧ生物種而言，雜草稻似乎在演化過程中選擇有別於栽培稻馴化的道路，一般也被稱為去馴化 (de-domestication)。雜草稻在外觀特性上時常具有較長的芒、較高的落粒性以及紅色種皮，對世界許多產稻國家造成重大危害。本研究利用一些主要區分雜草稻與栽培稻的性狀分析其背後的遺傳結構，進而了解這些雜草化性狀在（去）馴化過程中所扮演的角色。透過3,000水稻基因體計劃 (3K Rice Genome Project) 的公開資料，我們針對1,378個來自不同次族群的水稻品系的五個性狀（芒的顏色、種皮顏色、落粒性、脫粒性以及株高）進行全基因體關聯性分析（Genome-Wide Association Studies）並且找到一些與目標相關之變異。水稻種皮顏色主要由已知的 Rc 基因在不同次族群內的對偶基因所調控，而與水稻中芒的有無相關之變異則分屬各次族群間特有。在利用雜草稻資料來交叉驗證在水稻 3K 資料庫中所獲得之顯著位點後，我們發現栽培稻與雜草稻中調控芒的基因不盡相同。本研究之結果表明了去馴化性狀的複雜性可能是導致栽培稻與雜草稻中觀察到相異結果的主要原因。

Rice (Oryza sativa L.) had gone through the process of domestication under human selection and became one of the most important staple crops around the world. Weedy rice, the conspecific counterpart of cultivated rice, seems to have escaped domestication for another rapid evolutionary process, also known as the de-domestication. Weedy rice is commonly characterized by long awn, shattering panicles and red pericarp and causes great damages in rice producing countries. This study focused on traits that mainly differed weedy rice from cultivated rice in order to dissect the genetic architecture underlied which may help in a better understanding of the role of 'weedy' traits during (de)-domestication process. We used publicly available data from the 3K Rice Genome Project (3K RGP) and have conducted genome- wide association studies (GWAS) on a subset of 1,378 accessions, selected based on sub-populations. We focused on awn color, pericarp color, panicle shattering degree, panicle threshability and seedling height. Several variants associated to target traits were identified. Pericarp color was mainly regulated by the well established Rc gene and varied among sub- populations. Variants associated with awn presence/absence appeared to be sub-population specific. We cross-checked significant variants identified in 3K RGP using data from weedy rice and found that different genes seemed to be involved in the control of awn presence/absence. Our results suggests that the complexity of de-domestication traits might account for the discrepancy observed between weedy rice and cultivated rice.