小米(Setaria italica)在傳統上是東亞許多國家的重要作物。近年來又重新受到科學界的關注，成為模式植物(model plant)。因其生長環境的高度適應力，小米成為台灣原住民的主要糧食。在時代變遷與文化衝擊下，小米逐漸被高經濟作物，如：玉米、小麥等取代，造成小米的種原不斷流失。為了維護小米基因庫與遺傳豐富度，小米的種原保存勢在必行。在種原保存工作中，探討遺傳歧異度(genetic diversity)是重要的一環。傳統上，物種的遺傳歧異度主要藉由外表性狀(phenotypic traits)的調查來進行，在植物上即是指農藝性狀(agronomic traits)。然而，隨著分子標記(molecular marker)的發展，不受生長階段(growth stage)與環境限制的基因型調查(genotype)更是近年來常用的調查方式。微衛星序列(microsatellite)，因其具有共顯性(codominant)遺傳、多對偶基因性(multiallelism)、高度多型性(high polymorphism)、高度再現性(high reproducibility)與易以聚合酵素連鎖反應(PCR)偵測等多項優點，是目前廣泛運用於遺傳歧異度評估的分子標記。因此，本篇研究目標為藉由外表性狀與基因型調查，深入了解台灣小米種原遺傳歧異度，並利用微衛星分子標記來探討台灣小米的傳播與分布。此外，針對結果，深入分析各原住民族的遷徙、文化交流與小米族群遺傳歧異度的關聯。
本研究以324個採集自台灣各原住民部落的小米品系與兩個來自中國的外群進行實驗。首先，進行隨機完全區集設計(RCBD)田間試驗，調查33個農藝性狀，並針對調查結果加以統計分析。以非加權配對算數平均法(UPGMA)進行群聚分析，結果將小米分成三大群，最主要的分群依據為質量性狀。事實上，農藝性狀的表現易受生長條件影響，尤其是數量性狀。相較之下，以穩定性較高的基因型進行分析，更能深入探討台灣小米族群的遺傳歧異度。首先，利用500組隨機引子擴增具有多型性的DNA片段(RAPD-PCR)，以構築小米的小片段隨機基因組基因庫。利用雙鹼基短片段重複序列(dinucleotide repeat)進行聚合酵素連鎖反應，在3095個選殖株(clone)中，得到約570個具正向結果(positive)的選殖株(clone)。經核酸定序(sequencing)後，得到134個微衛星序列，並設計引子對，為了提高後續分析的豐富度，另外從Genbank上搜尋小米微衛星序列，設計引子。最後，總共得到86個表現出多型性的引子對。其中佔最高比例分別為雙核苷酸重複(72.09%，AC/TG為主)與三核苷酸重複(19.77%，ATG/TAC為主)的微衛星序列。接著隨機挑選出40對引子，對324個採集群進行遺傳歧異度分析，平均每個微衛星基因座具有2.4個等位基因(allele)。在多型性(polymorphism information content, PIC)分析中，平均每個微衛星體基因座PIC值為0.381。其中十一個基因座具有高於0.5的PIC值，可作為十分有效的多型性分析工具。而平均觀測異質度(HObs)與平均理論異質度(HExp)分別為0.190與0.354。經由哈溫平衡偏離(deviation of Hardy-Weinberg equilibrium)測試，顯示出87.5％的微衛星序列具有顯著偏離（p < 0.05）哈溫定律的傾向。在無效等位基因頻率的測試上，40個基因座具有接近於0的無效等位基因頻度，代表無效等位基因存在機率很低。接著，經由非加權配對算數平均法(UPGMA)與主成分分析(PCA)對微衛星序列的分析，兩者皆將台灣地區的小米區分為三大群：北部族群、中部族群與南部族群。經比對發現，各小米分群與地理區域具有一致性。再對照原住民歷史紀錄，可從中看出小米族群的基因流動、遺傳分群與原住民遷徙、原住民間文化交流有強烈關聯。
本研究證實台灣小米族群的遺傳歧異度和原住民遷徙與文化交流有密切關係。所開發出的微衛星體序列中，含有雙鹼基及三鹼基重覆序列，分別以AC/TG及ATG/TAC所佔比例最高，不僅提供了小米種原保存的珍貴資源，研究結果亦可應用於未來小米及相近物種遺傳與種原研究。

As an important traditional crop, foxtail millet (Setaria italica) has aroused international attention in recent years. The ability to thrive in harsh condition had made this small seeded grain to be the main food resources of the indigenous people in Taiwan for a long time. However, the modernization of crop production and pop culture had led to species origins declined recently. To prevent the germplasm from extinction, the preservation of foxtail millet is necessary. To maintain a crop species, the genetic diversity must be revealed, which is useful for germplasm conservation. Traditionally, species divesity was investigated by phenotypic traits. As the development of molecular markers, inspection of genotypic traits is widely accepted. Microsatellite markers are considered to be one of the most powerful tools because of their abundance in the genome, co-dominant inheritance, high reproducibility, ease of manipulation, low requirement for genome DNA, and the speed of their use. Therefore, the objective of this study is to investigate the genetic diversity of foxtail millet by phenotypic and genotypic traits and to canvass the dispersal and distribution of the foxtail millets in Taiwan by microsatellites. Additionally, we will make a special effort on inspecting the correlation of the indigenous migration, cultural exchange and the genetic diversity of foxtail millets.
Three hundred and twenty-four foxtail millet landraces collected from Taiwan and two out-group landraces from mainland of China were used in this research. During four years of filed works, thirty-three agronomic traits were examined and the data was operated in UPGMA analysis. All foxtail millets are divided into three clusters, which were mainly identified by some qualitative traits. However, the agronomic traits can only reveal the differences among foxtail millet clusters. Generally speaking, the agronomic traits are sensitive to growth condition. On the contrary, the genotypic traits are much more conservative among individuals. In order to dig out the correlation between the genetic diversity of foxtail millet and the indigenous cultural exchanges, the genotypic traits investigation must be achieved.
Five hundred random primers were operated by RAPD-PCR to obtain a small DNA fragments library. Then, short dinucleotide repeat sequence fragments were manipulated as primers by PCR. Among 3095 clones, 570 clones had shown positive results. After sequencing, 134 microsatellites were obtained and 86 primer pairs had showed polymorphic pattern by PCR testing. The most common dinucleotide and trinucleotide repeat motifs are AC/TG (72.09%) and ATG (19.77%), respectively. Genetic diversity and relationships in 324 foxtail millet landraces was then analyzed by 40 randomly selected primer pairs, which showed high level of average alleles per microsatellite locus, 2.4. The PIC values ranged from 0.117 to 0.672, and had an average value of 0.381 per SSR. The average observed heterozygosity (HObs) and average expected heterozygosity (HExp) were 0.190 and 0.354, respectively. By the result of deviation from Hardy-Weinberg equilibrium test, 87.5% microsatellite loci exhibit significant result in deviation level (p < 0.05). All loci had null allele frequencies close to zero, which represent the absence of a null allele. The results of UPGMA clustering analysis and principal component analysis (PCA) using microsatellites all divided 324 foxtail millet landraces into three groups, which coincided with the geographic regions in Taiwan. In addition, the results had showed strong association with the foxtail millet and the indigenous cultural exchange.
There is a close relation between the genetic clustering of foxtail millets and the indigenous cultural exchange. According to the result in this research, we demonstrated that the genetic diversity of foxtail millets in Taiwan had close relationships with the indigenous migration and cultural exchange. The development of microsatellites contained dinucleotide and trinucleotide repeats with highest portion of AC/TG and ATG/TAC repeats, respectively. The data in this study not only provide valuable information for foxtail millet germplasm preservation, but could also benefit future work for Setaria italica and related species in breeding and germplasm studies.

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Website:

FAO statistics (http://www.fao.org/; accessed on 02/06/2012)
Human Genome Project (http://www.ornl.gov/sci/; accessed on 02/06/2012)
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