以候選基因關聯性分析探究小米抽穗期變異

Study of Heading Date Variation Associated with Candidate Genes in Foxtail Millet (Setaria italica)

鍾雨晴(Yee Ching Choong)

指導教授 ： 林彥蓉

國立臺灣大學/生物資源暨農學院/農藝學研究所/碩士(2020年)

https://doi.org/10.6342/NTU202001766

摘要

小米 (Setaria italica (L.) P. Beauv.) 具有高度的適應性，能在溫帶和熱帶地區種植，其抗旱及耐其他逆境的特性也使小米可在極端的環境下存活。然而，小米的開花時間研究仍處於基因定位階段，其遺傳調控機制仍有待了解。開花時間反映了作物對環境的適應性和調節能力，是影響作物產量的關鍵性狀之一。在作物馴化的過程中，開花時間也是人為選拔的目標性狀。研究人員可以透過比較基因體從演化角度探討開花調控機制在不同物種間的關係。本研究透過比較小米 (Yugu1) 品系和開花研究成果相對豐富的模式植物阿拉伯芥 (Arabidopsis thalian) 和水稻 (Oryza sativa) 的基因體，探究小米在開花過程中可能參與的基因及調控機制。本實驗首先評估九個蒐集系在三個不同環境的抽穗時間，並分析造成抽穗期差異的環境因素。另外，利用四個主要開花基因包括開花激素 (florigen)， Flowering Locus T (FT) / Heading date 3a (Hd3a) 和反應環境變化的光週期基因，包括CONSTANS (CO) / Heading date 1 (Hd1)、Early heading date 1 (Ehd1) 和 Grain number, plant height, and heading date 7 (Ghd7)，分別於高粱(Sorghum bicolor)、狗尾草 (Setaria viridis) 和小米基因體中鑑定同源基因。實驗結果顯示抽穗期受到遺傳、環境及遺傳與環境間交感作用共同影響，並發現溫度與抽穗期顯著相關。小米在上述四個開花基因中共鑑定出39個同源基因，說明這些開花基因在小米具有高度的保守性。從鑑定的同源基因中選擇在物種之間具有高相似度的基因進行多型性的分析，比較臺灣和印度種原中的全基因序列變異。其中，SiFT11 (Seita.5G317600) 在178個臺灣和印度種原中的序列多型性和抽穗期具有相關性。綜合分析結果，本實驗利用候選基因關聯性分析結果顯示SiGhd7-2 (Seita.9G020100)，SiGhd7-3 (Seita.7G007800) 和 SiFT11 (Seita.5G317600) 的序列變異和抽穗期顯著相關，可能為小米抽穗之候選基因。雖然仍不清楚種原間影響開花時間差異的分子機制，未來仍然可以經由對開花候選基因的驗證，將其納入小米的分子標誌輔助育種。

關鍵字

小米 ； 開花時間 ； 抽穗期 ； 同源基因 ； 候選基因

並列摘要

Foxtail millet (Setaria italica (L.) P. Beauv.) is a highly adaptable crop, and the ability of drought and stress tolerance allows foxtail millet to survive even in an extreme environment. However, the research on the flowering of foxtail millet is at the initial stage of gene mapping, and its genetic regulatory mechanism is still unclear. Flowering time reflects the adaptation and regulation of crops against the environment; it is one of the key traits for yield potential. Comparing the foxtail millet genome (accession Yugu1) with the dicot model plant Arabidopsis (Arabidopsis thaliana) and the monocot model plant rice (Oryza sativa) whose flowering pathways are well studied would assist gene prediction and sequence annotation of flowering-related genes in foxtail millet. Besides, we examined the heading date of nine accessions of foxtail millet in three locations and evaluated the effect of environmental factors on heading date variation. Also, we selected four genes including the florigen gene, Flowering Locus T (FT) / Heading date 3a (Hd3a) and the photoperiod gene, CONSTANS (CO) / Heading date 1 (Hd1), Grain number, plant height, and heading date 7 (Ghd7) and Early heading date 1 (Ehd1) from Arabidopsis or rice, and identifying their homologs in sorghum (Sorghum bicolor), green foxtail (Setaria viridis) and foxtail millet. Selected homologs in foxtail millet were used to investigate the genetic variation in nine accessions. The heading date variations were observed across three locations. Heading dates varied via accessions (gene, G), locations (environment, E), and accessions × locations (G × E). The temperature was the major factor contributing to the heading date variation in three locations. A total of 39 putative orthologs were identified in foxtail millet suggested the well-conserved of these four flowering genes. Interestingly, the natural variation that discovered in SiFT11 (Seita.5G317600), and 178 accessions were found to be correlated to the heading date. Out of 39 homologs, SiGhd7-2 (Seita.9G020100), SiGhd7-3 (Seita.7G007800), and SiFT11 (Seita.5G317600) were identified as a potential candidate of the flowering-related gene in multiple approaches. Although the differences of flowering time between accessions and the underlying molecular mechanism were unclear, the predicted candidate flowering genes can be further verified and incorporated into molecular breeding of foxtail millet.

並列關鍵字

foxtail millet ； flowering time ； heading date ； homolog ； candidate gene

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