激光生物学报, 2020, 29 (6): 538, 网络出版: 2021-02-05  

拟南芥全基因组精细插入及缺失分子标记

Genome-wide Fine Insertion/Deletion of Gene Markers in Arabidopsis thaliana
作者单位
1 河南大学生命科学学院,开封 475004
2 华南师范大学生物光子学研究院,激光生命科学教育部重点实验室,广州 510631
3 华南师范大学生物光子学研究院,广东省激光生命科学重点实验室,广州 510631
摘要
为了开发精细可靠且易用的拟南芥(Arabidopsis thaliana)分子标记,通过比较基因组学,分析拟南芥哥伦比亚(Columbia)和兰兹伯格(Landsberg erecta)2个生态型的全基因组序列,从 10 449个不小于 6个碱基的插入 /缺失(INDEL)DNA片段中筛选得到 2 321个新的 INDEL标记。针对每个标记位点,设计一对或多对引物序列(共计 4 764对)。在此基础上选择相对均匀分布在拟南芥 5条染色体的 20个初定位分子标记,它们能够在统一的反应体系和扩增条件下获得稳定的聚合酶链式反应(PCR)和琼脂糖凝胶电泳结果。该研究能够方便研究者找到合适的分子标记,在常规的仪器条件和较低的试验成本下,快速进行突变体基因定位,提高基因图位克隆效率。
Abstract
To develop the.ne and reliable molecular markers in Arabidopsis thaliana, this work analyzed the whole ge-nome sequence of Columbia and Landsberg erecta with comparative genomics. From total 10 449 insertion/deletion (IN-DEL) DNA fragments that have no less than six bases, we screened 2 321 INDEL molecular markers. For each marker, at least one pair of primers (a total of 4 764) were designed. Based on this, we randomly selected 20.rst-pass mapping molecular markers that are relatively evenly distributed in.ve chromosomes of Arabidopsis thaliana. When using these molecu-lar markers, we were able to obtain stable polymerase chain reaction (PCR) and agarose gel electrophoresis results under uni-form reaction system and ampli.cation conditions. This study will facilitate researchers to.nd suitable molecular markers, and under the common instrument conditions and lower experimental costs, to quickly locate the mutant gene and improve the e.ciency of gene map-based cloning.
参考文献

[1] lecular marker techniques and their applications in plant sciences[J]. Plant Cell Reports, 2008, 27(4): 617-631.

[2] WILLIAMS J G K, KUBELIK A R, LIVAK K J, et al. DNA poly-morphisms amplified by arbitrary primers are useful as genetic markers[J]. Nucleic Acids Research, 1990, 18(22): 6531-6535.

[3] BELL C J, ECKER J R. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis[J]. Genomics, 1994, 19(1): 137-144.

[4] CHANG C, BOWMAN J L, DEJOHN A W, et al. Restriction frag-ment length polymorphism linkage map for Arabidopsis thaliana[J]. Proceedings of the National Academy of Sciences, 1988,85(18): 6856-6860.

[5] DRENKARD E, RICHTER B G, ROZEN S, et al. A simple proce-dure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis[J]. Plant Physiology, 2000,124(4): 1483-1492.

[6] HRUBA M. dCAPS method: advantages, troubles and solution[J]. Plant Soil and Environment, 2007, 53(9): 417.

[7] HOU X, LI L, PENG Z, et al. A platform of high-density INDEL/ CAPS markers for map-based cloning in Arabidopsis[J]. The Plant Journal, 2010, 63(5): 880-888.

[8] AUSTIN R S, VIDAURRE D, STAMATIOU G, et al. Next-gener-ation mapping of Arabidopsis genes[J]. The Plant Journal, 2011,67(4): 715-725.

[9] 尹润竹,于静芳,周俊.氧化应激下植物线粒体自噬分析[J].激光生物学报, 2019, 28(2): 109-113. YIN Runzhu, YU Jingfang, ZHOU Jun. Analysis the mitophagy in plant response to oxidative stress[J]. Acta Laser Biology Sinica, 2019, 28(2): 109-113.

[10] 于静芳,尹润竹,周俊.拟南芥不同组织细胞对 DAPI染色的差异分析[J].激光生物学报, 2020, 29(2): 148-152. YU Jingfang, YIN Runzhu, ZHOU Jun. Analysis of DAPI staining in di.erent tissues of Arabidopsis[J]. Acta Laser Biology Sinica, 2020, 29(2): 148-152.

[11] YIN R, LIU X, YU J, et al. Up-regulation of autophagy by low concentration of salicylic acid delays methyl jasmonate-induced leaf senescence[J]. Scienti.c Reports, 2020, 10(1): 1-10.

[12] ZENG L, YANG X, ZHOU J. The xanthophyll cycle as an early pathogenic target to deregulate guard cells during Sclerotinia sclerotiorum infection[J]. Plant Signaling & Behavior, 2020,15(1): 1691704.

[13] ZENG L, WANG Y, ZHOU J. Spectral analysis on origination of the bands at 437 nm and 475.5 nm of chlorophyll.uorescence ex-citation spectrum in Arabidopsis chloroplasts[J]. Luminescence, 2016, 31(3): 769-774.

[14] MEINKE D W, MEINKE L K, SHOWALTER T C, et al. A se-quence-based map of Arabidopsis genes with mutant phenotypes[J]. Plant Physiology, 2003, 131(2): 409-418.

[15] PAN C, LIA, DAI Z, et al. InDel and SNP markers and their ap-plications in map-based cloning of rice genes[J]. Rice Science, 2008, 15(4): 251-258.

[16] COLLARD B C Y, MACKILL D J. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century[J]. Philosophical Transactions of the Royal Society B: Biological Sciences, 2008, 363(1491): 557-572.

[17] MCNALLY K L, CHILDS K L, BOHNERT R, et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice[J]. Proceedings of the National Academy of Sci-ences, 2009, 106(30): 12273-12278.

[18] CHEN H, XIE W, HE H, et al. A high-density SNP genotyping ar-ray for rice biology and molecular breeding[J]. Molecular Plant, 2014, 7(3): 541-553.

[19] LYUY, CUI X, LI R, et al. Development of genome-wide inser-tion/deletion markers in rice based on graphic pipeline platform[J]. Journal of Integrative Plant Biology, 2015, 57(11): 980-991.

[20] Zhoujun. At_InDel_Marker[EB/OL]. https://github.com/ zhoujun1988/AtMarker/blob/master/At_InDel_Marker, 2020-08-01/2020-08-04.

施亚磊, 于静芳, 吴珂, 周俊. 拟南芥全基因组精细插入及缺失分子标记[J]. 激光生物学报, 2020, 29(6): 538. SHI Yalei, YU Jingfang, WU Ke, ZHOU Jun. Genome-wide Fine Insertion/Deletion of Gene Markers in Arabidopsis thaliana[J]. Acta Laser Biology Sinica, 2020, 29(6): 538.

关于本站 Cookie 的使用提示

中国光学期刊网使用基于 cookie 的技术来更好地为您提供各项服务,点击此处了解我们的隐私策略。 如您需继续使用本网站,请您授权我们使用本地 cookie 来保存部分信息。
全站搜索
您最值得信赖的光电行业旗舰网络服务平台!