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政府計畫
計畫名稱(中文) 探勘臺灣小米地方種之米質基因
計畫名稱(英文)
文獻分類 其它
計畫編號 MOST104-2313-B002-014-MY3
計畫主辦人 林彥蓉
計畫主管機關 科技部
計畫執行機構 國立臺灣大學農藝學系暨研究所
全程計畫年 2017年 ~ 2018年
中文關鍵字 小米;糯性基因;快速黏度特性譜;高通量基因型分析;全基因體關連性分析
英文關鍵字 foxtail millet; Waxy gene; parameters of rapid visco analyzer; high throughput genotying; genome wide association mapping (GWAS)
中文摘要 小米(foxtail millet, Setaria italic, 2n=2x=18)是公認的耐旱的作物之一,和其他禾本科之穀類作物和能源作 物之親緣性近,因其基因體小(~500 Mb)、生命週期短、遺傳歧異度大,隨著兩個中國的品種Yugul和Zhang gu的全基因體解序與基因註解,成為新興的C4模式作物。在臺灣,小米之產量於2012年後產量有逐漸上升 的趨勢,仍是供不應求,2013年的進口量達4,000公噸。小米一般認為是原住民的傳統食物之一,為一種特 用作物,用於特殊用途,如釀酒、小米製品和營養保健的全穀類,因此,小米的米質研究除了累積對於基因 與環境影響米質特性之數量性狀基因座之遺傳研究外,後續亦可應用於小米育種,促進小米產業,並可活化 休耕地、提升糧食自給率。 臺灣的小米大都為由不同的原住民部落依其栽培管理、食用與祭祀等原因保留很大的遺傳歧異度,根 據插入的轉座子類型及插入位點的不同,前人研究43個臺灣地方種小米,四種Wx基因型,依米質大略分 為糖性、低直鏈性澱粉、非糖性三大類。小米總計有10個不同的Wx等位基因,為DNA transposon或 retrotransposn造成,這些跳躍子造成的突變是否穩定?臺灣原住民的小規模的栽培、保種下,是否會因 genetic drift和selection的影響,而有尚未發現的新的Wx等位基因?而這些不同的Wx等位基因是否可以 轉錄出全長的mRNA?可以轉錄出具有功能的mRNA的量為何?轉譯出的GBSS酵素的活性為何?這 些都是尚未報導,但是值得探討之課題。除Wx之外,但仍有其他參與澱粉合成相關的基因亦參與最終的 米質,是以,將以黏度特性為分析小米米質的指標,並探勘影響小米米質之相對應重要的基因。為了回答 上述之問題,本實驗室已經蒐集120個臺灣地方種小米,仍持續進行蒐集中,於此研究將150地方品系進 行研究。本研究計晝的架構如:(一)調查臺灣小米種原之Wx基因型和mRNA表現量,以及GBSSI酵 素活性測定(二)重要農藝性狀調查:每個品系種植約6株,採完全隨機(complete randomize design, CRD) 種植,並於2016年春、秋作種植在臺灣大學農場和屏東枋寮,並收穫種子,在本實驗室進行黏度特性的分 析。(三)MSG文庫建構:小米基因體約500 Mb,是以將採用此修正適於高粱MSG文庫建構的方法。 (四)高通量SNP基因型分析:MSG文庫將委外以IlluminaHi-seq 2500儀器進行100-bp paired end定 序。(五)以GWAS分析黏度特性之數量性狀基因座(QTLs) : TASSEL由康乃爾大學Dr. Ed Buckler 是第一個針對植物(以玉米為例)開發的GWAS分析的軟體,本研究也採取此方法(六)以候選基因策略 選殖黏度特性的基因:我們以此策略成功找到稻米黏度特性的基因。在執行本三年計晝中之第二年和第三 年,預計分別將臺灣小米地方品系之Wx基因型分析和族群結構分析結果於國際和國?會議論文宣讀並發 表各一篇中文期刊,在計晝結束之後,會寫成1~2篇完整的報告投稿至SCI期刊。
英文摘要 Foxtail millet (Setaria italic, 2n=2x=18) is well known as one of drought tolerance crops. Foxtail millet is genetically close to several cereal crops and biofuel crops. Because of its small genome size with an estimation of 500 Mb, short-life cycle, highly genetic diversity, and available whole genome sequences and gene annotation of two Chinese varieties, Yugu1 and Zhang gu, foxtail millet is becoming a new model C4 crop. In Taiwan, even the production of foxtail millet was increased since 2012, importation of foxtail millet is required to meet demands as 4,000 tons were imported in 2013. In Taiwan, foxtail is known as traditional food for aboriginal peoples. Foxtail is used for brewing wine, pastry, and supplements of whole grains. In this proposal, we propose to study how QTLs/genes and environments influencing grain quality of foxtail millet. In addition to publish in scientific journals, the results are expected to apply to breeding program of foxtail millet. New varieties of foxtail millet are expected to promote industry of foxtail millet, activate fallow lands, and increase food self-sufficiency ratio. The genetic diversity of Taiwan’s foxtail landraces is relative high because aboriginal peoples preserve seeds according to various cultivation practice, food process and worships. Based on different transposons and transposition sites, 4 different Wx alleles were identified among 43 landraces which were classified as waxy, low amylose content, and non-waxy as reported previously. A total of 10 Wx alleles were dated in foxtail millet. However, are all alleles stable because of Wx alleles arisen by transposon and retrotransposon? Are there any uncovered novel Wx alleles because the aboriginal peoples preserve small scales of seeds leading to genetic drift and selection? How many w:x alleles are able to transcribe full-length mRNA? How about activities of GBSS enzyme for different genotypes? All mentioned questions are not answered yet and worth for deep investigation. In addition to Wx, the other genes participating starch synthesis also confer grain quality. Thus, parameters of rapid visco analyzer (RVA) will be used an indicators for grain quality to mine QTLs/genes regulating the grain quality of foxtail millet. We collected 120 landraces of green foxtail until now and going to collect more landraces. In this study, we are going to use 150 landraces for the following experiments. The scheme of this research proposal is divided 6 aspects as: (1) Identification of Wx genotypes, estimation of mRNA gene expression levels and activity of GBSS; (2) measure important agronomy traits, RVA parameters, for which 6 individuals of each landraces will be planted according to complete randomize design, CRD, in NTU farm and Pingtung in spring and fall seasons 2016; (3) Construct MSG library that we adopt sorghum MSG protocol because of genome size of 500 Mb; (4) high throughput SNP genotyping that MSG libraries will be sequenced by applied 100-bp paired end using IlluminaHi-seq 2500; (5) apply GWAS to uncover QTLs regarding to RVA for which TASSEL is the first method used in plant; (6) apply candidate gene approach to find out genes conferring grain quality which was successfully applied to identify paste properties of cooked rice grain in our lab. We expect to announce the Wx haplotypes and genetic structure of the Taiwan’s foxtail millet landraces in domestic and international conferences and publish in domestic journals in year 2 and 3. The intact results will be elucidated for one ~two SCI manuscripts which are expected to be submitted after the end of protects.
其他研究人員 林彥蓉
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