InDel标记的研究和应用进展

doi:10.17520/biods.2015205

摘要/Abstract

摘要：

InDel是指在近缘种或同一物种不同个体之间基因组同一位点的序列发生不同大小核苷酸片段的插入或缺失(insertion-deletion), 是同源序列比对产生空位(gap)的现象。InDel在基因组中分布广泛、密度大、数目众多。InDel多态性分子标记是基于插入/缺失位点两侧的序列设计特异引物进行PCR扩增的标记, 其本质仍属于长度多态性标记, 可利用便捷的电泳平台进行分型。InDel标记准确性高、稳定性好, 避免了由于特异性和复杂性导致的后续分析模糊。此外, InDel标记能扩增混合DNA样品和高度降解的微量DNA样品, 并进行有效分型。InDel标记目前已开始应用于动植物群体遗传分析、分子辅助育种以及人类法医遗传学、医学诊断等领域。随着位于功能基因上InDel标记的开发, 结合染色体步移和基因精细定位, 可将这些标记应用于相关物种经济性状的功能基因的筛选, 有利于优良基因的进一步开发和利用。

关键词: 分子标记, InDel, SNP, SSR

Abstract

InDel indicates insertions or deletions (insertion-deletion) of nucleotide fragments of different sizes at the same site in the genome sequence between the same or closely related species and is a gap in sequence derived from alignment of the homologous sequence. InDel is widely distributed across the genome and occurs in a high density and large numbers in a genome. The InDel polymorphic molecular marker is a PCR-amplified marker that is based on specific primers designed from both sides of the site of sequence of insertion / deletion. It is essentially a length polymorphic marker still, and one can use the convenient electrophoresis platform for genotyping. InDel molecular markers have the advantage of high accuracy and good stability, which help to avoid confusion in subsequent analysis due to marker specificity and complexity, as is often seen in other length polymorphic markers. Furthermore, mixed or highly degraded DNA samples can be successfully amplified with InDel markers, and effectively typed. Because of its abundance, convenient typing platform and other advantages, InDel molecular markers have been applied to genetic analyses of animal and plant populations, molecular assisted crops and farmed animal breeding, human forensic genetics, medical diagnostics and other research areas. The development of the InDel molecular marker located on functional genes, combined with chromosome walking and fine gene mapping, has enabled the application of these molecular markers in the screening of genes related to important economic traits, which is conducive to the further development and utilization of these valuable genes. In this review, on the basis of an overview of the InDel marker development and applications, we discuss some of the technical limitations of the development and limited efficiency of genetic analysis, as well as potential future applications in the fine mapping and genetic structure of large numbers of individuals.

Key words: molecular marker, InDel, SNP, SSR

杨洁, 赫佳, 王丹碧, 施恩, 杨文宇, 耿其芳, 王中生 (2016) InDel标记的研究和应用进展. 生物多样性, 24, 237-243. DOI: 10.17520/biods.2015205.

Jie Yang, Jia He, Danbi Wang, En Shi, Wenyu Yang, Qifang Geng, Zhongsheng Wang* (2016) Progress in research and application of InDel markers. Biodiversity Science, 24, 237-243. DOI: 10.17520/biods.2015205.

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2015205

https://www.biodiversity-science.net/CN/Y2016/V24/I2/237

参考文献 49

1	Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nature Reviews Genetics, 12, 363-376.
2	Barker G, Batley J, O’Sullivan H, Edwards KJ, Edwards D (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics, 19, 421-422.
3	Bastos-Rodrigues L, Pimenta JR, Pena SD (2006) The genetic structure of human populations studied through short insertion-deletion polymorphisms. Annals of Human Genetics, 70, 658-665.
4	Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA (2005) Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Human Molecular Genetics, 14, 59-69.
5	Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register JC III, Tingey SV, Rafalski A (2002) Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Molecular Biology, 48, 539-547.
6	Brandström M, Ellegren H (2007) The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus Gallus) genome: a high frequency of deletions in tandem duplicates. Genetics, 176, 1691-1701.
7	Britten RJ, Rowen L, Williams J, Cameron RA (2003) Majority of divergence between closely related DNA samples is due to indels. Proceedings of the National Academy of Sciences, USA, 100, 4661-4665.
8	Da SC, Matos S, Costa HA, Morais P, Santos RM, Espinheira R (2013) Genetic portrait of south Portugal population with InDel markers. Forensic Science International: Genetics, 7, e101-e103.
9	Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435-445.
10	Fan YH, Wang WJ, Ma GJ, Liang LJ, Shi Q, Tao SH (2007) Patterns of insertion and deletion in mammalian genomes. Current Genomics, 8, 370-378.
11	Feng FJ, Luo LJ, Li Y, Zhou LG, Xu XY, Wu JH, Chen HW, Chen L, Mei HW (2005) Comparative analysis of polymorphism of InDel and SSR markers in rice. Molecular Plant Breeding, 3, 725-730. (in Chinese with English abstract)
	[冯芳君, 罗利军, 李荧, 周立国, 徐小艳, 吴金红, 陈宏伟, 陈亮, 梅捍卫 (2005) 水稻InDel和SSR标记多态性的比较分析. 分子植物育种, 3, 725-730.]
12	Gao Q, Yue G, Li W, Wang J, Xu J, Yin Y (2012) Recent progress using high-throughput sequencing technologies in plant molecular breeding. Journal of Integrative Plant Biology, 54, 215-227.
13	Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theoretical and Applied Genetics, 113, 251-260.
14	Huang J, Luo H, Wei W, Hou Y (2014) A novel method for the analysis of 20 multi-Indel polymorphisms and its forensic application. Electrophoresis, 35, 487-493.
15	Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics, 11, 1248-1251.
16	Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiology, 129, 440-450.
17	Kondrashov AS, Rogozin IB (2004) Context of deletions and insertions in human coding sequences. Human Mutation, 23, 177-185.
18	Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. The Plant Journal, 4, 403-410.
19	Kvikstad EM, Tyekucheva S, Chiaromonte F, Makova DK (2007) A macaque’s-eye view of human insertions and deletions: differences in mechanisms. PLoS Computational Biology, 3, 1772-1782.
20	Lee TH, Chafets DM, Reed W, Wen L, Yang Y, Chen J, Utter GH, Owings JT, Busch MP (2006) Enhanced ascertainment of microchimerism with real-time quantitative polymerase chain reaction amplification of insertion-deletion polymorphisms. Transfusion, 46, 1870-1878.
21	Lehrman MA, Russell DW, Goldstein JL, Brown MS (1986) Exon-Alu recombination deletes 5 kilobases from the low density lipoprotein receptor gene, producing a null phenotype in familial hypercholesterolemia. Proceedings of the National Academy of Sciences, USA, 83, 3679-3683.
22	Li X, Gao W, Guo H, Zhang X, Fang DD, Lin Z (2014) Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping. BMC Genomics, 15, 1046-1056.
23	Liu T, Mao D, Zhang S, Xu C, Xing Y (2009) Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa). Theoretical and Applied Genetics, 118, 1509-1517.
24	Long WH, Xu MH (2002) The genetic difference between Indica rice and Japonica rice on RAPD. Journal of Yunnan Agricultural University, 17, 245-247. (in Chinese)
	[龙雯虹, 许明辉 (2002) 籼稻和粳稻品种在RAPD上的遗传差异. 云南农业大学学报, 17, 245-247.]
25	Lu BR, Cai X, Jin X (2009) Efficient Indica and Japonica rice identification based on the InDel molecular method: its implication in rice breeding and evolutionary research. Progress in Natural Science, 19, 1241-1252.
26	Lu BR, Zheng KL, Qian HR, Zhuang JY (2002) Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theoretical and Applied Genetics, 106, 101-106.
27	Lv H, Yang L, Kang J, Wang Q, Wang X, Fang Z, Liu Y, Zhuang M, Zhang Y, Lin Y, Yang Y, Xie B, Liu B, Liu J (2013) Development of InDel markers linked to Fusarium wilt resistance in cabbage. Molecular Breeding, 32, 961-967.
28	Ma JF, Nagao S, Huang CF, Nishimura M (2005) Isolation and characterization of a rice mutant hypersensitive to Al. Plant and Cell Physiology, 46, 1054-1061.
29	Manta F, Caiafa A, Pereira R, Silva D, Amorim A, Carvalho EF, Gusmão L (2012) Indel markers: genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material. Forensic Science International Genetics, 6, 658-661.
30	Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Research, 16, 1182-1190.
31	Pan CH, Wang ZB, Ma YY, Yin YJ, Zhang YF, Zuo SM, Chen ZX, Pan XB (2007) InDel and SNP markers and their application in map-based cloning of rice genes. Chinese Journal of Rice Science, 21, 447-453. (in Chinese with English abstract)
	[潘存红, 王子斌, 马玉银, 殷跃军, 张亚芳, 左示敏, 陈宗祥, 潘学彪 (2007) InDel和SNP标记在水稻图位克隆中的应用. 中国水稻科学, 21, 447-453.]
32	Pereira R, Phillips C, Alves C, Amorim A, Carracedo A, Gusmão L (2009) A new multiplex for human identification using insertion/deletion polymorphisms. Electrophoresis, 30, 3682-3690.
33	Salathia N, Lee HN, Sangster TA, Morneau K, Landry CR, Schellenberg K, Behere AS, Gunderson KL, Cavalieri D, Jander G, Queitsch C (2007) Indel arrays: an affordable alternative for genotyping. The Plant Journal, 51, 727-737.
34	Santos C, Fondevila M, Ballard D, Banemann R, Bento AM, Børsting C, Branicki W, Brisighelli F, Burrington M, Capal T, Chaitanya L, Daniel R, Decroyer V, England R, Gettings KB, Grosso TE, Haas C, Harteveld J, Hoff-Olsen P, Hoffmann A, Kayser M, Kohler P, Linacre A, Mayr-Eduardoff M, McGovern C, Morling N, O’Donnell G, Parson W, Pascalig VL, Porto MJ, Roseth A, Schneider PM, Sijen T, Stenzl V, Syndercombe Court D, Templeton JE, Turanska M, Vallone PM, van Oorchot RAH, Zatkalikova L, The RUROFORGEN-NoE Consortium, Carracedo A, Phillips C (2015) Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: results of a collaborative EDNAP exercise. Forensic Science International: Genetics, 19, 56-67.
35	Santos NPC, Ribeiro-Rodrigues EM, Ribeiro-Dos-Santos AKC, Pereira R, Gusmão L, Amorim A, Guerreiro JF, Zago MA, Matte C, Hutz MH, Santos SEB (2010) Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel. Human Mutation, 31, 184-190.
36	Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker G, Spangenberg GC, Edwards D (2005) SNPServer: a real-time SNP discovery tool. Nucleic Acids Research, 33, 493-495.
37	Schnabel RD, Kim JJ, Ashwell MS, Sonstegard TS, Van Tassell CP, Connor EE, Taylor JF (2005) Fine-mapping milk production quantitative trait loci on BTA6: analysis of the bovine osteopontin gene. Proceedings of the National Academy of Sciences, USA, 102, 6896-6901.
38	Shedlock AM, Okada N (2000) SINE insertions: powerful tools for molecular systematics. Bioessays, 22, 148-160.
39	Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiology, 135, 1198-1205.
40	Sjödin P, Bataillon T, Schierup MH (2010) Insertion and deletion processes in recent human history. PloS ONE, 5, e8650.
41	Steele KA, Ogden R, McEwing R, Briggs H, Gorham J (2008) InDel markers distinguish Basmatis from other fragrant rice varieties. Field Crops Research, 105, 81-87.
42	Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE (2005) Fine-scale structural variation of the human genome. Nature Genetics, 37, 727-732.
43	Väli U, Brandström M, Johansson M, Ellegren H (2008) Insertion-deletion polymorphisms (Indels) as genetic markers in natural populations. BMC Genetics, 9, 715-720.
44	Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends in Biotechnology, 27, 522-530.
45	Vasemägi A, Gross R, Palm D, Paaver T, Primmer CR (2010) Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics, 11, 156-166.
46	Weber JL, David D, Heil J, Fan Y, Zhao CF, Marth G (2002) Human diallelic insertion/deletion polymorphisms. American Journal of Human Genetics, 71, 854-862.
47	Xue Y, Jiang L, Su N, Wang JK, Deng P, Ma JF, Zhai HQ, Wan JM (2007) The genetic basic and fine-mapping of a stable quantitative-trait loci for aluminium tolerance in rice. Planta, 227, 255-262.
48	Yi ZH, Lu YF, Guo XQ, Hui MX, Zhang LG, Zhang MK (2012) Development of simple sequence repeat (SSR) and insertion/deletion (InDel) markers in Chinese cabbage (Brassica rapa ssp. pekinesis) and analysis of their transferability. Journal of Agricultural Biotechnology, 20, 1398-1406. (in Chinese with English abstract)
	[仪泽会, 卢有飞, 郭晓芹, 惠麦侠, 张鲁刚, 张明科 (2012) 大白菜简单序列重复(SSR)和插入/缺失(InDel)标记的开发及通用性分析. 农业生物技术学报, 20, 1398-1406.]
49	Zhang SP, Miao H, Cheng ZC, Zhang ZH, Wu J, Sun RF, Gu XF (2011) The insertion-deletion (Indel) marker linked to the fruit bitterness gene (Bt) in cucumber. Journal of Agricultural Biotechnology, 19, 649-653. (in Chinese with English abstract)
	[张圣平, 苗晗, 程周超, 张忠华, 武剑, 孙日飞, 顾兴芳 (2011) 黄瓜果实苦味(Bt)基因的插入缺失(Indel)标记. 农业生物技术学报, 19, 649-653.]

[1]	牛晓锋, 王晓梅, 张研, 赵志鹏, 樊恩源. 鲟鱼分子鉴定方法的整合应用[J]. 生物多样性, 2022, 30(6): 22034-.
[2]	张梦华, 张宪春. 中国薄叶卷柏复合群的物种划分[J]. 生物多样性, 2021, 29(12): 1607-1619.
[3]	陈向向, 盖中帅, 翟军团, 徐劲东, 焦培培, 吴智华, 李志军. 中国西北地区天然胡杨群体遗传多样性及核心保护单元的构建[J]. 生物多样性, 2021, 29(12): 1638-1649.
[4]	李媛媛, 刘超男, 王嵘, 罗水兴, 农寿千, 王静雯, 陈小勇. 分子标记在濒危物种保护中的应用[J]. 生物多样性, 2020, 28(3): 367-375.
[5]	张亚红,贾会霞,王志彬,孙佩,曹德美,胡建军. 滇杨种群遗传多样性与遗传结构[J]. 生物多样性, 2019, 27(4): 355-365.
[6]	张剑, 董路, 张雁云. 基于基因组SNPs的南极恩克斯堡岛阿德利企鹅繁殖种群的遗传结构[J]. 生物多样性, 2019, 27(12): 1291-1297.
[7]	赵颖, 马荣, 尹永香, 张志东, 田呈明. 新疆不同来源金黄壳囊孢的多样性[J]. 生物多样性, 2019, 27(10): 1122-1131.
[8]	盛芳, 陈淑英, 田嘉, 李鹏, 秦雪, 罗淑萍, 李疆. 新疆准噶尔山楂不同居群的遗传多样性[J]. 生物多样性, 2017, 25(5): 518-530.
[9]	何长欢, 周玉, 王利繁, 张立. 尚勇保护区亚洲象种群数量评估和遗传多样性分析[J]. 生物多样性, 2015, 23(2): 202-209.
[10]	张珰妮, 郑连明, 何劲儒, 张文静, 林元烧, 李阳. 基于线粒体COI和16S片段序列的北部湾北部水螅水母DNA条形码分析[J]. 生物多样性, 2015, 23(1): 50-60.
[11]	周伟, 王红. 基于DNA分子标记的花粉流动态分析[J]. 生物多样性, 2014, 22(1): 97-108.
[12]	徐刚标, 梁艳, 蒋燚, 刘雄盛, 胡尚力, 肖玉菲, 郝博搏. 伯乐树种群遗传多样性及遗传结构[J]. 生物多样性, 2013, 21(6): 723-731.
[13]	吴雪琴, 徐刚标, 梁艳, 申响保. 南岭地区观光木自然和人工迁地保护种群的遗传多样性[J]. 生物多样性, 2013, 21(1): 71-79.
[14]	向妮, 肖炎农, 段灿星, 王晓鸣, 朱振东. 利用SSR标记分析茄镰孢豌豆专化型的遗传多样性[J]. 生物多样性, 2012, 20(6): 693-702.
[15]	刘文, 梁红, 杨碧忍, 林杰文, 胡延吉. 一种高等植物小片段RNA分子标记方法[J]. 生物多样性, 2012, 20(1): 86-93.