基于新一代高通量测序技术开发巨人半边莲 <em>Lobelia deckenii</em>的SSR标记

米奇; 龙志成; Muchuku John Kamau; 陈进明; 王青锋

doi:10.11913/PSJ.2095-0837.2015.60847

基于新一代高通量测序技术开发巨人半边莲 Lobelia deckenii的SSR标记

1.
中国科学院武汉植物园, 中国科学院水生植物与流域生态重点实验室, 武汉 430074
2. 中国科学院大学, 北京 100049

基金项目: 国家自然科学基金项目(31570220);中国科学院海外拓展工程项目(23Y323771W0777)。

详细信息

作者简介:
米奇(1990-),女,硕士研究生,研究方向为植物居群遗传学(E-mail:418468378@qq.com)。

中图分类号: Q346
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出版历程
- 收稿日期: 2015-05-28
- 发布日期: 2015-12-27

Development of SSR Markers in Giant Lobelia (Lobelia deckenii) Based on Next-generation High-throughput Sequencing

1.
Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
2. University of Chinese Academy of Sciences, Beijing 100049, China

摘要

摘要: 为了开发东非半边莲属特有植物的微卫星分子标记(SSR),本研究基于Illumina-HiSeq 2000测序平台对巨人半边莲Lobelia deckenii的基因组进行高通量测序。利用MISA软件对获得的基因组数据库进行搜索与分析,共鉴别出58 966个SSR位点,并利用Primer软件成功设计出3558对特异性的SSR引物。利用L. deckenii 3个居群的6个样品对随机挑选的40对SSR引物进行扩增效率检验,发现有32对重复性好且可扩增出清晰条带。利用筛选出的32对SSR引物对来自肯尼亚山居群的24株个体进行PCR扩增并采用荧光分型技术检测多态性,结果显示有14对可扩增出稳定的多态性条带,共有86个等位基因,各SSR位点的等位基因数(N_A)为4 ~ 9个,观测杂合度(H_o)和期望杂合度(H_e)分别为0.000~1.000和0.625~0.854。本研究结果表明,通过高通量测序技术开发东非特有植物巨人半边莲的SSR标记是一种简单而高效的途径,这些新的SSR分子标记为巨人半边莲的居群遗传多样性、遗传结构以及对其开展保护生物学研究提供了工具。
- 东非特有植物 /
- 半边莲属 /
- 高通量测序 /
- SSR标记
Abstract: To develop co-dominant microsatellite molecular markers (SSRs) for studying conservation genetics of the giant lobelia endemic to east Africa, we sequenced the genome of the giant lobelia, Lobelia deckenii, using next-generation high-throughput sequencing technology. Using the MISA program, we acquired a total of 58966 SSRs, from which we designed 3558 SSR primer pairs using Primer software. We selected 40 primer pairs at random to evaluate their application across six individuals from three L.deckenii populations (two individuals per population). Thirty-two markers were successfully amplified, yielding clear and discernible bands. Using 24 L.deckenii individuals from the Mountain Kenya population, we tested the polymorphism of the 32 SSR markers and found that 14 were polymorphic. Using these 14 polymorphic SSR markers, we detected a total of 86 alleles. The number of alleles per locus ranged from four to nine. Observed heterozygosity (H_o) and expected value (H_e) per locus varied from 0.000 to 1.000 and 0.625 to 0.854, respectively. Our results indicated that development of SSR markers from genomic data by high-throughput sequencing in the giant lobelia was valuable and effective. These newly generated SSR markers will provide novel tools for studying genetic diversity, population genetic structure and conservation biology of giant lobelias in east Africa.
- East Africa endemic plant /
- Giant lobelia /
- High-throughput sequencing /
- SSR markers

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参考文献(17)

[1]	Knox EB. The conservation status of the giant senecios and giant lobelias in eastern Africa[J]. Opera Bot, 1993, 121: 195-216.
[2]	Knox EB, Palmer JD. Chloroplast DNA evidence on the origin and radiation of the giant lobelias in eastern Africa[J]. Syst Bot, 1998, 23(2):109-149.
[3]	Magombo ZLK, Mbeiza, Ndiritu N, Ndiritu, G.G. Lobelia aberdarica. The IUCN Red List of Threa-tened Species 2004: e.T44715A10939927. http://dx.doi.org/10.2305/IUCN.UK.2004.RLTS.T44715A10939927.en
[4]	Mulugeta K, Dorothee E, Pierre T, Sileshi N, Christiana B. Phylogeography and conservation genetics of a giant lobelia (Lobelia giberroa) in Ethiopian and Tropical East African mountains[J]. Mol Ecol, 2007, 16(6): 1233-1243.
[5]	Liao YY, Yue XL, Guo YH, Gituru WR, Wang QF, Chen JM. Genotypic diversity and genetic structure of populations of the distylous aquatic plant Nymphoides peltata (Menyanthaceae) in China[J]. J Syst Evol, 2013, 51 (5): 536-544.
[6]	高洁,李巧明. 羽叶金合欢的DNA提取和SSR引物筛选[J]. 云南植物研究, 2008, 30(1): 64-68.
[7]	程小毛,黄晓霞. SSR标记开发及其在植物中的应用[J]. 中国农学通报, 2011, 27(05): 304-307.
[8]	Li R, Zhu H, Ruan J, Qian W,Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. De novo assembly of human genomes with massively parallel short read sequencing[J]. Genome Res, 2010, 20(2): 265-272.
[9]	袁阳阳,王青锋,陈进明. 基于转录组测序信息的水生植物莕菜SSR标记开发[J]. 植物科学学报, 2013, 31(5): 485-492.
[10]	Yeh FC B. Population genetic analysis of codominant and dominant markers and quantitative traits [J]. Belgian J Bot, 1997, 129: 157.
[11]	Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L. Identification characterization and utilization of EST derived genic microsatellite markers for genome analyses of coffee and related species[J]. Theor Appl Genet,2007, 114(2): 359-372.
[12]	Gupta PK, Varshney RK. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat[J]. Euphytica, 2000, 113(3): 163-185.
[13]	Wei WL, Qi XQ, Wang LH, Zhang YX, Hua W, Li DH, Lv HX, Zhang XR. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers[J]. BMC Genomics, 2011, 12(1): 451-463.
[14]	杨春霞,温强,叶金山,朱培林. 枳壳EST-SSR标记的开发[J]. 分子植物育种, 2011, 9(1): 123-127.
[15]	Kantety RV, La Rota M, Matthews DE, Sorrells ME. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat[J].Plant Mol Biol, 2002, 48(5-6): 501-510.
[16]	向华,毛盛贤. 固定指数理论及其在遗传育种中的应用[J]. 遗传, 1995, 17(S1): 63-70.
[17]	Truman PY. The comparative demography of semelparous Lobelia telekii and iteroparous Lobe-lia keniensis on Mount Kenya[J]. J Ecol, 1982, 72 (2): 637-650.

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基于新一代高通量测序技术开发巨人半边莲 Lobelia deckenii的SSR标记

作者简介: 米奇(1990-),女,硕士研究生,研究方向为植物居群遗传学(E-mail:418468378@qq.com)。

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出版历程

Development of SSR Markers in Giant Lobelia (Lobelia deckenii) Based on Next-generation High-throughput Sequencing

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出版历程

目录

作者简介:
米奇(1990-),女,硕士研究生,研究方向为植物居群遗传学(E-mail:418468378@qq.com)。