小米多樣性種原之遺傳歧異度分析與抽穗期之全基因體關聯性分析

Genetic Diversity Analysis and Genome-Wide Association Study of Heading Date in the Foxtail Millet (Setaria italica) Diversity Panel

陳彥麇(Yen-Chiun Chen)

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/NTU202000588

摘要

小米 (Setaria italica (L.) P. Beauv.) 是目前世界粟類作物中栽培量第二大宗者，也是栽培歷史悠久的作物之一，為半乾旱地區的重要糧食與飼料來源。小米在臺灣栽培歷史可追溯至約五千年前，為原住民之傳統糧食與文化象徵，依照部落活動、祭祀及飲食習慣差異，其獨特的作物文化互動模式造成各地原住民對小米亦有不同的偏好天擇，在此特殊的互動中，保留了與原住民文化息息相關的種原特性，因此臺灣小米地方種成為良好的遺傳研究題材與育種參考對象，深入了解臺灣小米之遺傳歧異度與重要農藝性狀研究有其必要性。然而關於臺灣小米種原之族群遺傳研究與開花基因研究目前仍相當有限，因此本次研究透過 genotype-by-sequencing (GBS ) 方法對211個小米多樣性種原 (diversity panel) 進行探勘多型性，成功獲得13,720個SNP (single nucleotide polymorphism) 分子標誌，並從211個樣本中選取核心族群共153個進行遺傳歧異度與抽穗期之全基因組關聯性分析 (genome wide association study, GWAS)。遺傳歧異度分析結果顯示，此小米多樣性種原可分為三個主要的次族群與樣本之原採集點與育種歷史有明顯關聯，其中大多數現有栽培種與來自臺灣東部的樣本主要屬於 Group A1 次族群；來自臺灣中部的樣本主要屬於Group A2 次族群，並對現有栽培種之遺傳背景貢獻較少；而曾因育種計畫而引進之印度種原則多屬於遺傳背景差異較大之 Group B 族群。本次研究中觀察到明顯的親緣地理關聯，多數遺傳背景較混雜的個體多位於區域交界處。此外，來自蘭嶼的種原呈現獨特的遺傳背景，其成因極可能與當地的栽培歷史與利用方式相關。而抽穗期方面Group A (包涵Group A1 和 A2) 與 Group B 次族群間具明顯差異，其中 Group A 抽穗所需日數平均約46.39日，而 Group B 則平均約為39.85日，多數品系較Group A早抽穗。抽穗期數量性狀基因座 (quantitative trait locus, QTL) 分別以核心族群與Group A兩種族群獨立分析，以一般線性模型 (general linear model, GLM) 與混合線性模型 (mix linear model, MLM) 進行GWAS分析。結果顯示，以 GLM 方法對核心族群進行分析共可偵測62個與抽穗期顯著關聯之 SNP (P < 0.001)，以 MLM 方法則有28個；以 Group A 為分析對象時，則僅從GLM中測得1個顯著之SNP。抽穗期顯著相關之 SNP 位點，可供設計前景選拔之分子標誌，其餘不顯著之位點亦可作為背景選拔分子標誌參考。本次研究對臺灣小米地方種、栽培種及育種材料進行遺傳歧異度分析與抽穗期之全基因組關聯性分析，將提供臺灣小米遺傳研究與育種利用的良好參考資訊，可供未來挑選雜交親本及分子輔助育種使用，另亦可挑選適當之抽穗期候選基因進行後續分析，使臺灣現有小米種原獲得更有效率地應用。

關鍵字

小米 ； 抽穗期 ； 遺傳歧異度分析 ； 族群結構 ； 全基因體關聯性分析

並列摘要

Foxtail millet (Setaria italica (L.) P. Beauv.), one of the oldest cultivated crops, ranks as the second-largest millet and is an important cereal and forage resource in semiarid regions. In Taiwan, foxtail millet is a symbolic food for indigenous peoples, which has been cultivated for more than 5,000 years and closely associated with cultural activities. The high genetic diversity of landraces, which was reflected by natural selection to adapt diverse environment and artificial selection as unique interaction between foxtail millet and various indigenous cultural activities, provides a scarce opportunity for genetic studies and breeding utilization. However, a detail genetic assessment among the foxtail millet landraces and cultivars in Taiwan is still limited. In this study, a diversity panel of 211 foxtail millet accessions, including 154 Taiwan landraces, 8 Taiwan cultivars, and 49 India landraces were sequenced by the genotype-by-sequencing (GBS) method, and 13,720 high-quality SNPs were obtained. A core population of 153 accessions was further selected for genetic diversity analysis and genome-wide association study (GWAS) of heading date. The analyses of population structure and genetic diversity revealed three major genetic groups in concordance with geographical regions and the accessible breeding histories. Most of Taiwan cultivars and eastern Taiwan landraces were belonged to the Group A1, whereas landraces from central Taiwan were mainly belonged to Group A2, representing an unexploited group of Taiwan landraces. Most Indian accessions and few Taiwan accessions were clustered in Group B. An obvious phylogeographic relationship and gene flow could be observed in our study, the samples collected from boundary regions were admixed. Furthermore, the accessions from Lanyu showed a unique genetic background, which might be related to Tao’s cultivation history. For heading date QTL analysis, the heading dates of Group A (A1 and A2) and Group B accessions were highly different, that most of the Group B accessions flowered in average of 39.85 days, whereas Group A flowered in average of 46.39 days. A total of 62 and 28 significant SNPs were identified from core population using general linear model (GLM) and mix linear model (MLM), respectively. For Group A subpopulation, only one significant SNPs was identified by using GLM method. Those significant SNPs potentially associated with heading date could be employed to foreground selection, and the other SNPs evenly distributed on the genome could be served for background selection. The population structure, genetic diversity analysis, and SNPs associated with heading date in this study provide useful information for germplasm utilization, further developing new varieties with various heading date for shifting production in Taiwan.

並列關鍵字

foxtail millet ； Setaria italica ； heading date ； flowering time ； genetic diversity ； population structure ； genome-wide association study (GWAS)

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