苦瓜長片段基因體組裝與馴化訊號研究

Long-read based genome assembly and signatures of domestication in Momordica charantia

蕭閔建(Min-Chien Hsiao)

指導教授 ： 李承叡

國立臺灣大學/生命科學院/生態學與演化生物學研究所/碩士(2019年)

https://doi.org/10.6342/NTU201903262

摘要

Momordica charantia （苦瓜）為常見蔬菜並可藥用，在熱帶與亞熱帶被廣為栽種。本研究以兩組雜交子代之基因圖譜，將PacBio 定序之鷹架基因組，組裝至染色體層次。另外，為了更進一步探討苦瓜在馴化的過程中基因多樣性的變化，我們定序了42 個栽培品系，18 個野生種，和一個外群來調查這些品系間的族群結構，我們觀察到，這些品系分別為野生，東南亞，與東亞族群，透過雜合性以及連鎖不平衡下降的趨勢可得知東南亞族群內有最低多樣性，而東亞族群次之。人擇訊號方面，本研究使用四種偵測選擇位點的方法，Composite likelihood ratio(CLR)， cross population composite likelihood ratio (XP-CLR)， reduction of diversity(ROD)，fixation index (FST)，在基因本體（gene ontology, GO）分析中，人擇位點在代謝途徑這個基因分類群上，有不同之分佈，顯示人類在馴化苦瓜的過程中，人擇顯著作用於代謝途徑之相關基因。而在栽培種相關性狀的全基因體關聯分析（GWAS）中，我們觀察到東亞與東南亞族群分別使用不同的基因使果實長度增加。

關鍵字

苦瓜 ； 基因體組裝 ； 馴化 ； 人擇 ； 族群遺傳

並列摘要

Momordica charantia (bitter gourd) is a vegetable and medicinal plant of the family Cucurbitaceae, widely distributed in tropical and subtropical Asia. In this study, we constructed a chromosome-level genome assembly with two linkage maps and PacBio scaffolds. Furthermore, to study genetic variation contributing to domestication, we sequenced 42 cultivars, 18 wild accessions, and an outgroup to investigate the population structure. Three major genetic groups were identified: wild, South Asia (SA), and Southeast Asia (SEA), with signs of introgression among groups. The heterozygosity and linkage disequilibrium (LD) decay depicted the lowest diversity in SEA population, followed by SA and wild populations. Composite likelihood ratio (CLR), crosspopulation composite likelihood ratio (XP-CLR), reduction of diversity (ROD), and fixation index (FST) were further employed to detect selective sweep. Gene ontology metabolic process terms display different pattern between the sweep region and genomic background, indicating the artificial selection has worked on the metabolic process. Genome-wide association study (GWAS) was also implemented to identify genomic regions associated with domestication traits. By analyzing the trait-increasing alleles under GWAS peaks, we observed that SA and SEA population respectively had alleles for making fruit longer.

並列關鍵字

Momordica charantia ； genome assembly ； domestication ； artificial selection ； population genetics

參考文獻

References

1. Zaman, M.Y. and S.S. Alam, Karyotype Diversity in Three Cultivars of Momordica charantia L. 2009. 74(4): p. 473-478.

2. Urasaki, N., Okinawa Prefectural Agricultural Research Center, Itoman, Okinawa (Japan), et al., Comparison of genome size among seven crops cultivated in Okinawa. mar2015.

3. Urasaki, N., et al., Draft genome sequence of bitter gourd (Momordica charantia), a vegetable and medicinal plant in tropical and subtropical regions. DNA Res, 2017. 24(1): p. 51-58.

4. Tan, S.P., et al., Bitter melon (Momordica charantia L.) bioactive composition and health benefits: A review. Food Reviews International, 2016. 32(2): p. 181- 202.