SNP分子标记及其在木本植物遗传育种的应用

doi:10.3969/j.issn.1009-7791.2018.02.018

亚热带植物科学 ›› 2018, Vol. 47 ›› Issue (02): 187-193.DOI: 10.3969/j.issn.1009-7791.2018.02.018

SNP分子标记及其在木本植物遗传育种的应用

周琳，段玉，文博，马媛春，朱旭君，王玉花，房婉萍

(1.南京农业大学茶叶科学研究所, 江苏南京 210095；2.上海市农业科学院林木果树研究所, 上海 201106)

收稿日期:2018-01-24 修回日期:2018-02-06 出版日期:2018-06-30 发布日期:2018-06-30
通讯作者: 房婉萍
作者简介:周琳，博士，从事多年生植物分子育种研究。
基金资助:
中央高校基本科研业务费资助项目(KYZ201841, KYZ201842)；国家茶叶产业技术体系(CARS-19)；江苏省现代茶叶技术体系(SXGC[2017]279)；江苏省农业科技自主创新资金项目(CX[17]2018)

Research and Application of SNP Molecular Markers in Ligneous Plants Genetics and Breeding

ZHOU Lin, DUAN Yu, WEN Bo, MA Yuan-chun, ZHU Xu-jun, WANG Yu-hua, FANG Wan-ping

(1.Tea Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangshu China; 2.Forestry and Pomology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China)

Received:2018-01-24 Revised:2018-02-06 Online:2018-06-30 Published:2018-06-30
Contact: FANG Wan-ping

摘要/Abstract

摘要： 木本植物因其生命周期长、基因组杂合度高、基因组较大、遗传背景不清晰等特性，制约了其研究进程。随着现代生物技术的发展，DNA分子标记技术在木本植物研究领域的应用越来越多，其中单核苷酸多态性(SNP)作为第三代分子标记技术以其高效、快速、稳定、可靠等诸多优点得到广泛应用。本文简述SNP标记的特点、开发方法、检测方法及其在木本植物遗传多样性和亲缘关系分析、品种鉴定、连锁图谱构建和辅助育种等方面的研究进展，为更好地应用SNP技术开展木本植物研究提供参考。

关键词: 木本植物, SNP标记, 遗传多样性分析, 品种鉴定, 指纹图谱构建, 辅助育种

Abstract: Research progress of ligneous plants was restricted for their long life cycle, high heterozygosity, large genome and unclear genetic background. With the development of modern biotechnology, DNA molecular markers were applied in research of ligneous plants. Single nucleotide polymorphism (SNP), the third generation of molecular markers, has many advantages, such as high efficiency, rapidity, stability, reliability and so on, so it has been widely used. In order to provide a reference for better application of SNP technology in ligneous plant research, SNP markers characteristics, development methods, detection methods and its applications in genetic diversity and genetic relationship analysis, cultivar identification, genetic linkage map construction and molecular assisted breeding for ligneous plants were summarized.

Key words: ligneous plant, SNP marker, genetic diversity analysis, cultivar identification, fingerprinting construction, assisted breeding

中图分类号:

Q789

周琳,段玉,文博,马媛春,朱旭君,王玉花,房婉萍. SNP分子标记及其在木本植物遗传育种的应用[J]. 亚热带植物科学, 2018, 47(02): 187-193.

ZHOU Lin,DUAN Yu,WEN Bo,MA Yuan-chun,ZHU Xu-jun,WANG Yu-hua,FANG Wan-ping. Research and Application of SNP Molecular Markers in Ligneous Plants Genetics and Breeding[J]. Subtropical Plant Science, 2018, 47(02): 187-193.

参考文献

[1] Patwardhan A, Ray S, Roy A. Molecular markers in phylogenetic studies-a review[J]. Journal of Phylogenetics & Evolutionary Biology, 2014,2(2): 1000131.
[2] Gupta P K, Rustgi S, Kulwal P L. Linkage disequilibrium and association studies in higher plants: present status and future prospects[J]. Plant Molecular Biology, 2005,57(4): 461—485.
[3] 万志兵,戴晓港,尹佟明. 林木遗传育种基础研究热点述评[J]. 林业科学, 2012,48(2): 150—154.
[4] Vignal A, Milan D, SanCristobal M, Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics[J]. Genetics Selection Evolution, 2002,34(3): 275.
[5] Wang D G, Fan J B, Siao C J, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome[J]. Science, 1998,280(5366): 1077—1082.
[6] 杨永强,王巍杰,徐长波. 单核苷酸多态性研究进展[J]. 化学与生物工程, 2009,26(8): 19—21.
[7] Loots G G, Locksley R M, Blankespoor C M, Wang Z E, Miller W, Rubin E M, Frazer K A. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons[J]. Science, 2000,288(5463): 136—140.
[8] Snowdon R J, Luy F L I. Potential to improve oilseed rape and canola breeding in the genomics era[J]. Plant Breeding, 2012,131(3): 351—360.
[9] Liu L Z, Qu C M, Wittkop B, Yi B, Xiao Y, He Y J, Snowdon R J, Li J N. A high-density SNP map for accurate mapping of seed fiber QTL in Brassica napus L.[J]. PLoS One, 2013,8(12): e83052.
[10] 刘列钊,李加纳. 利用甘蓝型油菜高密度SNP遗传图谱定位油酸、亚麻酸及芥酸含量QTL位点[J]. 中国农业科学, 2014,47(1): 24—32.
[11] Wang N, Li F, Chen B Y, Xu K, Yan G X, Qiao J W, Li J, Gao GZ, Bancroft I, Meng J L, King G J, Wu X M. Genome-wide investigation of genetic changes during modern breeding of Brassica napus[J]. Theoretical and Applied Genetics, 2014,127(8): 1817—1829.
[12] 桑世飞,王会,梅德圣,刘佳,付丽,王军,汪文祥,胡琼. 利用全基因组 SNP芯片分析油菜遗传距离与杂种优势的关系[J]. 中国农业科学, 2015,48(12): 2469—2478.
[13] Cabezas J A, Ibá?ez J, Lijavetzky D, Vélez D, Bravo G, Rodríguez V, Carre?o I, Jermakow A M, Carre?o J, Ruiz-García L, Thomas M R. A 48 SNP set for grapevine cultivar identification[J]. BMC Plant Biology, 2011,11(1): 153.
[14] Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley C T, Gasic K, Micheletti D, Rosyara U R, Cattonaro F, Vendramin E, Main D. Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm[J]. PLoS One, 2012,7(4): e35668.
[15] Chen C, Mitchell S E, Elshire R J, Buckler E S, El-Kassaby Y A. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform[J]. Tree Genetics & Genomes, 2013,9(6):1537—1544.
[16] Jiang D, Ye Q L, Wang F S, Li C A. The mining of citrus EST-SNP and its application in cultivar discrimination[J]. Agricultural Sciences in China, 2010,9(2): 179—190.
[17] Fang W P, Meinhardt L W, Tan H W, Zhou L, Mischke S, Zhang D. Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers[J]. Horticulture Research, 2014,1: 14035.
[18] Wang B, Tan H W, Fang W, Meinhardt L W, Mischke S, Matsumoto T, Zhang D. Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm[J]. Horticulture Research, 2015,2(1): 14065.
[19] Zhou L, Vega F E, Tan H, Lluch A E, Meinhardt L W, Fang W, Mischke S, Irish B, Zhang D. Developing single nucleotide polymorphism (SNP) markers for the identification of coffee germplasm[J]. Tropical Plant Biology, 2016, 9(2): 82—95.
[20] 洪彦彬,李杏瑜,梁炫强. 植物SNP的开发研究进展[J]. 分子植物育种, 2011,9: 1807—1817.
[21] Li L, Paulo M J, Strahwald J, Lübeck J, Hofferbert H R, Tacke E, Junghans H, Wunder J, Draffehn A, van Eeuwijk F, Gebhardt C. Natural DNA variation at candidate loci is associated with potato chip color, tuber starch content, yield and starch yield[J]. Theoretical and Applied Genetics, 2008,116(8): 1167—1181.
[22] Westermeier P, Wenzel G, Mohler V. Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.)[J]. Theoretical and Applied Genetics, 2009,119(7): 1301—1311.
[23] Chao S, Zhang W, Akhunov E, Sherman J, Ma Y, Luo M C, Dubcovsky J. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars[J]. Molecular Breeding, 2009,23: 23—33.
[24] Weirather J L, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang X J, Buck D, Au K F. Comprehensive comparison of pacific biosciences and oxford nanopore technologies and their applications to transcriptome analysis[J]. F1000Research, 2017(3): 6.
[25] Schmidt M H, Vogel A, Denton A, Istace B, Wormit A, van de Geest H, Bolger M E, Alseekh S, Mass J, Pfaff C, Schurr U. Reconstructing the gigabase plant genome of Solanum pennellii using nanopore sequencing[J]. Biorxiv, 2017(1): 129148.
[26] Tsuchihashi Z, Dracopoli N C. Progress in high throughput SNP genotyping methods[J]. The Pharmacogenomics Journal, 2002,2(2): 103—110.
[27] Thiel T, Kota R, Grosse I, Stein N, Graner A. SNP 2 CAPS: a SNP and INDEL analysis tool for CAPS marker development[J]. Nucleic Acids Research, 2004,32(1): e5.
[28] Drenkard E, Richter B G, Rozen S, Stutius L M, Angell N A, Mindrinos M, Cho R J, Oefner P J, Davis R W, Ausubel F M. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis[J]. Plant Physiology, 2000,124(4): 1483—1492.
[29] Helyar S J, Limborg M T, Bekkevold D, Babbucci M, Van Houdt J, Maes G E, Bargelloni L, Nielsen R O, Taylor M I, Ogden R, Cariani A. SNP Discovery using next generation transcriptomic sequencing in atlantic herring (Clupea harengus)[J]. PLoS ONE, 2012,7(8): e42089.
[30] Boutet G, Carvalho S A, Falque M, Peterlongo P, Lhuillier E, Bouchez O, Lavaud C, Pilet-Nayel M L, Rivière N, Baranger A. SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population[J]. BMC Genomics, 2016,17(1): 121.
[31] Distefano G, La Malfa S, Gentile A, Wu S B. EST-SNP genotyping of citrus species using high-resolution melting curve analysis[J]. Tree Genetics & Genomes, 2013,9(5): 1271—1281.
[32] Pootakham W, Chanprasert J, Jomchai N, Sangsrakru D, Yoocha T, Therawattanasuk K, Tangphatsornruang S. Single nucleotide polymorphism marker development in the rubber tree, Hevea brasiliensis (Euphorbiaceae)[J]. American Journal of Botany, 2011, 98(11): e337—e338.
[33] Ji K, Zhang D, Motilal L A, Boccara M, Lachenaud P, Meinhardt L W. Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by single nucleotide polymorphism (SNP) markers[J]. Genetic Resources and Crop Evolution, 2013,60(2): 441—453.
[34] Ferguson M E, Hearne S J, Close T J, Wanamaker S, Moskal W A, Town C D, de Young J, Marri P R, Rabbi I Y, de Villiers E P. Identification, validation and high-throughput genotyping of transcribed gene SNPs in cassava[J]. Theoretical and Applied Genetics, 2012,124(4): 685—695.
[35] 赵俊生,杨晓燕,曾祥有,钟声,方静,罗剑斌,曾运友,向旭. 利用SNP分子标记分析化橘红种质资源[J]. 分子植物育种, 2016,14(5):1203—1211.
[36] Karam M J, Lefèvre F, Dagher-Kharrat M B, Pinosio S, Vendramin G G. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq[J]. Molecular Ecology Resources, 2015,15(3): 601—612.
[37] Ogden R, McGough H N, Cowan R S, Chua L, Groves M, McEwing R. SNP-based method for the genetic identification of ramin Gonystylus spp. timber and products: applied research meeting CITES enforcement needs[J]. Endangered Species Research, 2008,9(3): 255—261.
[38] 孙清明,李永忠,向旭,陈道明,杨晓燕,方静,吴绪波,周东辉,马帅鹏,马文朝. 利用SNP和EST-SSR分子标记鉴定荔枝新种质御金球[J]. 分子植物育种, 2013,11(3): 403—414.
[39] 杨润婷,吴波,李翀,曾培,曾继吾,钟云,姜波,周碧容,钟广炎. 两种SNP分型方法的比较及其在柚品种鉴定中的应用[J]. 园艺学报, 2013,40(6): 1061—1070.
[40] Hakim I R, Kammoun N G, Makhloufi E, Reba? A. Discovery and potential of SNP markers in characterization of Tunisian olive germplasm[J]. Diversity, 2009,2(1): 17—27.
[41] Jones E S, Sullivan H, Bhattramakki D, Smith J S. A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.)[J]. Theoretical and Applied Genetics, 2007,115(3): 361—371.
[42] Saha T, Priyadarshan P M. Genomics of Hevea rubber[M]// Schnell R J, Priyadarshan P M. Genomics of Tree Crops. New York : Springer New York, 2012: 261—298.
[43] 张晓红. 桉树EST-SNP的开发及EST图谱构建[D]. 南京: 南京林业大学硕士学位论文, 2009.
[44] 蒋俊. 桃高密度SNP图谱构建于果实质地和酸度全基因组关联分析[D]. 杭州: 浙江大学硕士学位论文, 2016.
[45] Septiningsih E M, Pamplona A M, Sanchez D L, Neeraja C N, Vergara G V, Heuer S, Ismail A M, Mackill D J. Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond[J]. Annals of Botany, 2009,103(2): 151—160.
[46] Naidoo R, Watson G M, Derera J, Tongoona P, Laing M D. Marker-assisted selection for low phytic acid (lpa1-1) with single nucleotide polymorphism marker and amplified fragment length polymorphisms for background selection in amaize backcross breeding programme[J]. Molecular Breeding, 2012,30(2): 1207—1217.
[47] Rahman M U, Asif M, Shaheen T, Tabbasam N, Zafar Y, Paterson A H. Marker-assisted breeding in higher plants[J]. Alternative Farming Systems, Biotechnology, Drought Stress and Ecological Fertilisation Sustainable Agriculture Reviews, 2011(6): 39—76.
[48] 刘肖. 蓝莓抗寒性、需冷量SNP分析与分子辅助育种研究[D]. 北京: 北京林业大学硕士学位论文, 2013.

编辑推荐

Metrics

闽ICP备11008787号-5　

SNP分子标记及其在木本植物遗传育种的应用

Research and Application of SNP Molecular Markers in Ligneous Plants Genetics and Breeding

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 6

编辑推荐

Metrics

[1]	肖家亮，吴林芳，李荣生，黄萧洒，覃俏梅. 广东始兴南山木本植物群落特征研究[J]. 亚热带植物科学, 2021, 50(01): 51-56.
[2]	郭学民,刘建珍,刘永军,肖啸,高荣孚. 木本植物抗寒性概述(综述)[J]. 亚热带植物科学, 2014, 43(04): 329-338.
[3]	曾焕忱,李文斌,张建文,韩锡君,温汉华,张璐. 广东东莞银瓶山自然保护区乡土木本植物资源及其引种潜力分析[J]. 亚热带植物科学, 2013, 42(04): 345-349.
[4]	单家林,余琳,郑学勤. 海南岛土著药用木本植物区系及其应用现状调查[J]. 亚热带植物科学, 2008, 37(02): 53-56.
[5]	唐宇力,章银柯,黎念林,包志毅. 浙江省木本植物区系特征及其与引种驯化的关系[J]. 亚热带植物科学, 2006, 35(01): 60-63.
[6]	黄梓良. 福建省南平茫荡山木本植物区系研究[J]. 亚热带植物科学, 1996, 25(02): 28-33.