作物学报 ›› 2020, Vol. 46 ›› Issue (9): 1340-1350.doi: 10.3724/SP.J.1006.2020.91076
徐婷婷(
), 汪巧玲, 邹淑琼, 狄佳春, 杨欣, 朱银, 赵涵, 颜伟*(
)
XU Ting-Ting(
), WANG Qiao-Ling, ZOU Shu-Qiong, DI Jia-Chun, YANG Xin, ZHU Yin, ZHAO Han, YAN Wei*(
)
摘要:
分子标记是遗传研究的基础工具, 广泛应用于遗传多样性研究、种质鉴定、遗传图谱构建和基因定位等领域。本研究基于大麦的全基因组重测序数据鉴定出的二态性SNP位点, 开发出遍布全基因组的118对InDel引物。以49份不同地理来源的大麦种质检测其有效性, 筛选出2个等位基因的共显性InDel标记72对, 进一步对288份大麦种质进行遗传距离分析及构建系统发育树。结果显示, 筛选到32个有效性的核心InDel标记, 覆盖大麦7条染色体上, 平均PIC为0.44, 平均MAF为0.34; 基于InDel标记位点的供试大麦的系统发育树结果揭示供试大麦具有丰富的遗传多样性, 且能够将具有相同地理来源的多数品种聚为一类。表明开发的32个二态性InDel标记可有效地用于鉴定品种间的亲缘关系, 且丰富了大麦品种鉴定的分子标记。上述核心InDel标记在大麦品种鉴定、大麦资源亲缘关系分析以及群体划分方面具有一定的理论意义和应用价值。
| [1] | Heun M, Kennedy A E, Anderson J A, Lapitan N L V, Sorrells M E, Tanksley S D. Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome, 1991,34:437-447. |
| [2] | Van Hintum T J. Comparison of marker system and construction of a core collection in pedigree of European spring barley. Theor Appl Genet, 1994,89:991-997. |
| [3] | Davila J A, Sanchez M P, Loarce Y, Ferrer E. The use of random amplified microsatellite polymorphic DNA and coefficients of parentage to determine genetic relationships in barley. Genome, 1998,41:477-486. |
| [4] | Hanif Z, Swatiz A, Khan I, Hassant G, Marwat K B, Ali S, Ishfaq Khan M. RAPD and SSR analysis of wild oats (Avena species) from north west frontier province of Pakistan. Albrecht Von Graaes Archiv Für Ophthalmol, 2008,245:1229-1231. |
| [5] | 黄祥斌, 杨华林. 采用PCR-RAPD技术鉴定16种北美啤酒大麦. 啤酒科技, 2003, (10):52-54. |
| Huang X B, Yang H L. Identification of 16 North American beer barley by PCR-RAPD. Beer Sci Technol, 2003, (10):52-54. | |
| [6] | 吴亚君, 王斌, 韩建勋, 张振民, 杨海荣, 陈颖. 采用RAPD-毛细管芯片电泳法鉴定啤酒大麦品系. 食品与发酵工业, 2012,38(2):174-180. |
| Wu Y J, Wang B, Han J X, Zhang Z M, Yang H R, Chen Y. Identification of beer barley strain by RAPD-capillary chip electrophoresis. Food Ferment Ind, 2012,38(2):174-180. | |
| [7] | 谷方红, 张五九, 冯景章, 林智平. 酿造大麦品种鉴定技术的研究. 啤酒科技, 2003, (11):27-29. |
| Gu F H, Zhang W J, Feng J Z, Lin Z P. Study on identification techniques of brewed barley varieties. Beer Sci Technol, 2003, (11):27-29. | |
| [8] | 初雷. 酿酒大麦种质资源AFLP分子指纹图谱构建. 大连工业大学硕士论文, 辽宁大连, 2011. pp 37-42. |
| Chu L. Construction of AFLP Molecular Fingerprints of Wine Barley Germplasm Resources. MS Thesis of Dalian University of Technology, Dalian, Liaoning, China, 2011. pp 37‒42 (in Chinese with English abstract). | |
| [9] | Russel J R, Fuller J D, Macaulay M. Direct comparisons of level of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs, and RAPD. Theor Appl Genet, 1997,95:714-722. |
| [10] | 朱彩梅, 张京. 应用SSR标记分析中国糯大麦种质的遗传多样性. 植物遗传资源学报, 2010,11:57-64. |
| Zhu C M, Zhang J. Genetic diversity analysis of waxy barley in China based on SSR markers. J Plant Genet Resour, 2010,11:57-64 (in Chinese with English abstract). | |
| [11] | 王艳平, 沈奇, 张继红, 李华勇, 吴燕. 大麦DUS测试标准品种的遗传多样性分析及指纹图谱的构建. 麦类作物学报, 2013,33:273-278. |
| Wang Y P, Shen Qi, Zhang J H, Li H Y, Wu Y. Genetic diversity analysis and building of DNA fingerprints of barley standard varieties in DUS testing based on SSR markers. J Triticeae Crops, 2013,33:273-278 (in Chinese with English abstract). | |
| [12] | 杨振华. 啤酒大麦SSR分子标记PCR反应体系的建立与优化. 黑龙江农业科学, 2015, (5):26-29. |
| Yang Z H. Establishment and optimization of SSR molecular marker PCR reaction system for beer barley. Heilongjiang Agric Sci, 2015, (5):26-29. | |
| [13] | 张利莎, 董国清, 扎桑, 卓嘎, 王德良, 谷方红, 袁兴淼, 张京, 郭刚刚. 基于EST-SSR和SNP标记的大麦麦芽纯度检测. 作物学报, 2015,41:1147-1154. |
| Zhang L S, Dong G Q, Zha sang, Zhuo ga, Wang D L, Gu F H, Yuan X M, Zhang J, Guo G G. EST-SSR and SNP markers based barley malt purity detection. Acta Agron Sin, 2015,41:1147-1154 (in Chinese with English abstract). | |
| [14] | Pattemore J A, Rice N, Marshall D F, Waugh R, Henry R J. Cereal variety identification using MALDI-TOF mass spectrometry SNP genotyping. J Cereal Sci, 2010,52:356-361. |
| [15] | 徐东东, 张利莎, 董国清, 谷方红, 王德良, 袁兴淼, 张京, 郭刚刚. SNP标记分型与品质分析联合的麦芽纯度及品种真实性鉴定. 啤酒科技, 2015, (1):28-31. |
| Xu D D, Zhang L S, Dong G Q, Gu F H, Wang D L, Yuan X M, Zhang J, Guo G G. Identification of malt purity and variety authenticity combined with SNP marker typing and quality analysis. Beer Sci Technol, 2015, (1):28-31. | |
| [16] | 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 . 水稻 InDel和SSR标记多态性的比较分析. 分子植物育种, 2005,3:725-730. |
| Feng F J, Luo L J, Li Y, Zhou L G, Xu X Y, Wu J H, Chen H W, Chen L, Mei H W. Comparative analysis of polymorphism InDel and SSR markers in Rice. Mol Plant Breed, 2005,3:725-730 (in Chinese with English abstract). | |
| [17] | 杨德卫, 曾美娟, 卢礼斌, 叶宁, 刘成德, 郑向华, 叶新福. 一个水稻矮秆突变体的遗传分析及基因定位. 植物学报, 2011,46:617-624. |
| Yang D W, Zeng M J, Lu L B, Ye N, Liu C D, Zheng X H, Ye X F. Genetic analysis and gene mapping of a rice dwarf mutant. Acta Bot Sin, 2011,46:617-624. | |
| [18] | 葛敏, 蒋璐, 张晓林, 赵涵, 张体付. 利用Insertion/Deletion (InDel)分子标记检测玉米互交种混杂的原理及应用. 分子植物育种, 2013,11:37-47. |
| Ge M, Jiang L, Zhang X L, Zhao H, Zhang T F. The principle of distinguishing maize hybrids of direct and reciprocal crosses using Insertion/Deletion (InDel) markers and its application. Mol Plant Breed, 2013,11:37-47 (in Chinese with English abstract). | |
| [19] | 张体付, 葛敏, 韦玉才, 赵涵. 玉米功能性Insertion/Deletion (InDel)分子标记的挖掘及其在杂交种纯度鉴定中的应用. 玉米科学, 2012,20(2):64-68. |
| Zhang T F, Ge M, Wei Y C, Zhao H. Discovery for maize function Insertion/Deletion (InDel) polymorphic marker and its implication in purity identification of maize hybrid seeds. J Maize Sci, 2012,20(2):64-68 (in Chinese with English abstract). | |
| [20] | 周玲, 梁帅强, 林峰, 吕远大. 玉米二态性InDel位点的鉴定和分子标记开发. 江苏农业学报, 2016,32:1223-1231. |
| Zhou L, Liang S Q, Lin F, Lyu Y D. Biallelic InDel loci detection and molecular marker development in maize. Jiangsu J Agric Sci, 2016,32:1223-1231 (in Chinese with English abstract). | |
| [21] | 陈吉宝, 景蕊莲, 员海燕, 卫波, 昌小平. 小麦TaDREB1基因的单核苷酸多态性分析. 中国农业科学, 2005,38:2387-2394. |
| Chen J B, Jing R L, Yuan H Y, Wei B, Chang X P. Study on single nucleotide polymorphism of TaDREB1 gene in wheat. Sci Agric Sin, 2005,38:2387-2394 (in Chinese with English abstract). | |
| [22] | 尚世界. 小麦抗病基因类似序列(RGA)标记开发及其利用. 中国农业科学院研究生院硕士学位论文, 北京, 2009. pp 36-41. |
| Shang S J. Development and Application of RGA Markers in Wheat. MS Thesis of Chinese Academy of Agricultural Sciences, Beijing, China, 2009. pp 25-27 (in Chinese with English abstract) | |
| [23] | 刘栓桃, 张志刚, 王荣花, 王立华, 李巧云, 赵智中. 基于InDel标记的大白菜育种材料分子身份证构建. 中国蔬菜, 2019, (2):34-41. |
| Liu S T, Zhang Z G, Wang R H, Wang L H, Li Q Y, Zhao Z Z. Molecular ID card construction of Chinese cabbage breeding materials based on InDel marker. China Veget, 2019, (2):34-41. | |
| [24] | 兰青阔, 张桂华, 王永, 赵新, 朱珠, 杜胜利, 程奕. 基于InDel标记快速检测黄瓜津优38种子纯度. 种子, 2011,30(6):19-23. |
| Lan Q K, Zhang G H, Wang Y, Zhao X, Zhu Z, Du S L, Cheng Y. Detecting seed purity quickly by InDel molecular of cucumber Jinyou-38. Seed, 2011,30(6):19-23 (in Chinese with English abstract). | |
| [25] | 张圣平, 苗晗, 程周超, 张忠华, 武剑, 孙日飞, 顾兴芳. 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, 2011,19:649-653. |
| Zhang S P, Miao H, Cheng Z C, Zhang Z H, Wu J, Sun R F, Gu X F. The insertion-deletion (InDel) marker linked to the fruit bitterness gene (Bt) in cucumber. J Agric Biotechnol, 2011,19:649-653 (in Chinese with English abstract). | |
| [26] | 李斯更, 沈镝, 刘博, 邱杨, 张晓辉, 张忠华, 王海平, 李锡香. 基于黄瓜基因组重测序的InDel标记开发及其应用. 植物遗传资源学报, 2013,14:278-283. |
| Li S G, Shen W, Liu B, Qiu Y, Zhang X H, Zhang Z H, Wang H P, Li X X. Development and application of cucumber InDel markers based on genome re-sequencing. J Plant Genet Resour, 2013,14:278-283 (in Chinese with English abstract). | |
| [27] | Mayer K F, Waugh R, Brown J W, Schulman A, Langridge P. A physical, genetic and functional sequence assembly of the barley genome. Nature, 2012,544:427-433. |
| [28] | Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok S O, Wicker T, Radchuk V, Dockter C, Hedley P E, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X. Q, Zhang Q, Barrero R A, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke J K, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland J A, Bellgard M I, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer G J, Clark M D, Caccamo M, Schulman A H, Mayer K F X, Platzer M, Close T J, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. A chromosome conformation capture ordered sequence of the barley genome. Nature, 2017,491:711-716. |
| [29] | Lü Y D, Liu Y H, Zhao H. mInDel: a high-throughput and efficient pipeline for genome-wide InDel marker development. BMC Genomics, 2016,17:290. |
| [30] | 陆海燕, 程璐, 王显生, 赵涵, 沈奇. 基于高通量测序的棉花InDel标记开发及其应用. 棉花学报, 2019,31:297-306. |
| Lu H Y, Chen L, Wang X S, Zhao H, Shen Q. Development and application of cotton InDel markers based on high throughput sequencing. Cotton Sci, 2019,31:297-306 (in Chinese with English abstract). | |
| [31] | Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol, 1987,4:406-425. |
| [32] | 张英虎, 沈会权, 臧慧, 栾海业, 乔海龙, 陶红, 陈健, 陈和. 1982-2011年江苏大麦育成品种亲本分析. 江苏农业科学, 2016,44(4):141-145. |
| Zhang Y H, Shen H Q, Zang H, Luan H Y, Qiao H L, Tao H, Chen J, Chen H. Analysis of parents of Jiangsu barley breeding varieties from 1982 to 2011. Jiangsu Agric Sci, 2016,44(4):141-145. |
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