基于EST-SSR及SRAP标记构建苦荬菜品种(系)DNA指纹图谱

doi:10.11686/cyxb2017072

摘要/Abstract

摘要： 苦荬菜是优良的一年生菊科青饲牧草,为构建苦荬菜品种(系)DNA指纹图谱,筛选出24对EST-SSR引物、32对SRAP引物组合构建指纹图谱。24对EST-SSR多态性引物对收集的14份苦荬菜品种(系)共扩增出270个清晰条带,多态性条带223个, PIC均值0.834,基因多样性指数变幅为0.2464~0.4288,Shannon指数变幅为0.3597~0.6148,可区分品种3~14个;32对SRAP引物检测到多态性条带367个,PIC均值0.826,基因多样性指数变幅为0.2006~0.3898,Shannon指数为0.3167~0.5716,可区分品种2~12个。7个引物在9个品种(系)上能扩增出特征谱带,综合各项遗传多样性指标筛选出IpSSR102、IpSSR80、IpSSR91、Me10+Em5、Me9+Em17,共5个核心引物的40个多态性条带构建苦荬菜品种(系)DNA指纹图谱,每个品种(系)都有一个特异分子身份指纹编码。

关键词: 苦荬菜, EST-SSR, SRAP, 核心引物, DNA指纹图谱

Abstract: Ixeris polycephala is a member of the Asteraceae family with an annual growth habit and excellent forage quality. In order to construct DNA fingerprinting of 14 I. polycephala varieties, 24 EST-SSR primers and 32 SRAP primers were screened for clear bands and high polymorphic imformation. A total of 270 bands including 223 polymorphic bands were amplified from the 24 EST-SSR primers, and the polymorphism information content values were up to 0.834. The Nei’s gene diversity (H) values ranged from 0.2464 to 0.4288, and values for Shannon’s information index (I) ranged from 0.3597 to 0.6148, while the number of distinguished varieties ranged from 3 to 14. For the 32 SRAP primers, 367 polymorphic bands were detected, and the average polymorphism information content was 0.826. The Nei’s gene diversity (H) values ranged from 0.2006 to 0.3898, and values for Shannon’s information index (I) ranged from 0.3167 to 0.5716, while the number of distinguished varieties ranged from 2 to 12. Nine varieties produced unique bands from 7 primers. With more detailed consideration of each genetic diversity index, a total of 40 polymorphic bands were obtained from 5 core primers (IpSSR102, IpSSR80, IpSSR91, Me10+Em5, Me9+Em17), and for DNA fingerprinting of the 14 I. polycephala varieties each variety had a specific molecular or DNA fingerprint.

Key words: Ixeris polycephala, EST-SSR marker, SRAP marker, core primer, DNA fingerprinting

班骞,谢彩云,范国华,黄琳凯,张新全. 基于EST-SSR及SRAP标记构建苦荬菜品种(系)DNA指纹图谱[J]. 草业学报, 2018, 27(4): 111-122.

BAN Qian, XIE Cai-yun, FAN Guo-hua, HUANG Lin-kai, ZHANG Xin-quan. DNA fingerprinting of Ixeris polycephala varieties based on EST-SSR and SRAP markers[J]. Acta Prataculturae Sinica, 2018, 27(4): 111-122.

参考文献

[1] Qiang H P, Yu G H, Liu H Q, et al. Genetic diversity and population structure of Chinese and American alfalfa (Medicago Sativa L.) germplasm assessed by SSR markers. Scientia Agricultura Sinica, 2014, 47(14): 2853-2862.
强海平, 余国辉, 刘海泉, 等. 基于SSR标记的中美紫花苜蓿品种遗传多样性研究. 中国农业科学, 2014, 47(14): 2853-2862.
[2] Dracatos P M, Cogan N O, Sawbridge T I, et al. Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.). BMC Plant Biology, 2008, 9(1): 62.
[3] Singh N, Dang T T M, Vergara G V, et al. Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A. Theoretical and Applied Genetics, 2010, 121(8): 1441-1453.
[4] Shang G F, Re F H, Sai Y, et al. Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species. Gene, 2015, 567(2): 182-188.
[5] Archak S. Plant DNA fingerprinting: an overview. AgBiotechNet, 2000, 2: https://www.researchgate.net/publication/228559903.
[6] Nybom H, Weising K, Rotter B.DNA fingerprinting in botany: past, present, future. Investigative Genetics, 2014, 5(1): 1-35.
[7] Chen S Y, Ma X, Zhang X Q, et al. The transferability of SSR and EST-SSR markers of different origins in Elymus and Roegneria in the Triticeae (Poaceae). Acta Prataculturae Sinica, 2016, 25(2): 132-140.
陈仕勇, 马啸, 张新全, 等. 不同来源SSR和EST-SSR在披碱草属和鹅观草属物种中的通用性分析. 草业学报, 2016, 25(2): 132-140.
[8] Caruso M, Federici C T, Roose M L.EST-SSR markers for Asparagus genetic diversity evaluation and cultivar identification. Molecular Breeding, 2008, 21(2): 195-204.
[9] Li L, He W M, Ma L P, et al. Construction Chinese cabbage (Brassica rapa L.) core collection and its EST-SSR fingerprint database by EST-SSR molecular markers. Genomics and Applied Biology, 2009, 28(1): 76-88.
李丽, 何伟明, 马连平, 等. 用EST—SSR分子标记技术构建大白菜核心种质及其指纹图谱库. 基因组学与应用生物学, 2009, 28(1): 76-88.
[10] Yu L Q, Liu R X, Su D, et al. Genetic diversities of fall SSR and dormancy alfalfa based on EST——SSR. Chinese Journal of Grassland,2009, 31(6): 52-58.
于林清, 刘荣霞, 苏东, 等. 利用SSR和EST-SSR技术研究不同秋眠级苜蓿遗传多样性. 中国草地学报, 2009, 31(6): 52-58.
[11] Xu C, Zhao B H.The development and application of SRAP molecular markers. Life Science Instruments, 2009, 7(4): 24-27.
徐操, 赵宝华. SRAP分子标记的研究进展及其应用. 生命科学仪器, 2009, 7(4): 24-27.
[12] Mao W W, Sun J D, Chen X H.Establishment of finger-print for a hybrid of Brassica campestris L.ssp. Chinensis var.utilis by ISSR and SRAP markers. Journal of Changjiang Vegetables, 2010, (20): 18-20.
冒维维, 孙敬东, 陈学好. 菜薹杂交种ISSR和SRAP的指纹图谱构建. 长江蔬菜, 2010, (20): 18-20.
[13] Tang Y J, Cao W J, Wu K L.Genetic diversity analysis and molecular identification card construction of Chinese Cymbidium germplasms based on SRAP markers. Scientia Agricultura Sinica, 2015, 48(9): 1795-1806.
唐源江, 曹雯静, 吴坤林. 基于SRAP标记的国兰种质资源遗传多样性分析及分子身份证构建. 中国农业科学, 2015, 48(9): 1795-1806.
[14] Guo H L, Guo A G, Zong J Q, et al. Identification analysis of eight centipedegrass materials by SRAP molecular markers. Acta Agrestia Sinica, 2014, 22(1): 203-207.
郭海林, 郭爱桂, 宗俊勤, 等. SRAP标记对8份假俭草材料的鉴定分析. 草地学报, 2014, 22(1): 203-207.
[15] Liang X Y.Germplasm evaluation, molecular marker development and genetic linkage map construction of chicory. Ya’an: Sichuan Agriculture University, 2013.
梁小玉. 菊苣种质资源评价、分子标记开发及遗传连锁图谱构建. 雅安: 四川农业大学, 2013.
[16] Li G, Quiros C F.Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics, 2001, 103(2/3): 455-461.
[17] Manoj M K, Sandhyarani N, Jayarama. Molecular identification and genetic relationships among coffee species (Coffea L.) inferred from ISSR and SRAP marker analyses. Archives of Biological Sciences, 2011, 63(3): 667-679.
[18] Yeh F C, Yang R C, Boyle T.Popgene, Version 1.31//Microsoft window-based freeware for population genetic analysis, quick user-guide. University of Alberta: Center for International Forestry Research, 1999.
[19] Nei M.Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, 1973, 70(12): 3321-3323.
[20] Chen C W, Cao K,Wang L R, et al. Molecular ID establishment of main China peach varieties and peach related species. Scientia Agricultura Sinica, 2011, 44(10): 2081-2093.
陈昌文, 曹珂, 王力荣, 等. 中国桃主要品种资源及其野生近缘种的分子身份证构建. 中国农业科学, 2011, 44(10): 2081-2093.
[21] Eujayl I, Sorrells M E, Baum M, et al. Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Tag. Theoretical & Applied Genetics, 2002, 104(2/3): 399-407.
[22] Bi Q, Mao J F, Guan W.Efficiently developing a large set of polymorphic EST-SSR markers for Xanthoceras sorbifolium by mining raw reads from high-throughput sequencing. Conservation Genetics Resources, 2015, 7(2): 423-425.
[23] Wang Q B, Zhang Y Y, Zhuang M, et al. EST-SSR fingerprinting of fifty cabbage representative varieties from China. Scientia Agricultura Sinica, 2014, 47(1): 111-121.
王庆彪, 张扬勇, 庄木. 中国50个甘蓝代表品种EST-SSR指纹图谱的构建. 中国农业科学, 2014, 47(1): 111-121.
[24] Varshney R K, Sigmund R, Börner A, et al. Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Science, 2005, 168(1): 195-202.
[25] Zhang L J, Guo Z D, Fang W X, et al. Genetic diversity analysis and cultivar identification of blueberry (Vaccinium spp.) using SRAP marker. Molecular Plant Breeding, 2015, 13(12): 2794-2802.
张鲁杰, 郭照东, 房文秀, 等. 蓝莓品种的SRAP遗传多样性分析及品种鉴别. 分子植物育种, 2015, 13(12): 2794-2802.
[26] Gao Y, Liu F Z, Wang K, et al. Establishment of molecular identity card for Malus Mill. originated from China based on the fingerprints of TP-M13-SSR. Journal of Plant Genetic Resources, 2015, 16(6): 1290-1297.
高源, 刘凤之, 王昆, 等. 基于TP-M13-SSR指纹图谱的中国原产苹果属植物分子身份证的建立. 植物遗传资源学报, 2015, 16(6): 1290-1297.
[27] Tang H, Yu H Y, Zhang X M, et al. Analysis on the diversity of DNA fingerprinting of the example varieties used for the test of rice new varieties. Journal of Plant Genetic Resources, 2015, 16(1): 100-106.
唐浩, 余汉勇, 张新明, 等. 水稻新品种测试的标准品种DNA指纹图谱多样性分析. 植物遗传资源学报, 2015, 6(1): 100-106.
[28] Miao H B, Chen F D, Zhao H B, et al. Genetic diversity and construction of fingerprinting of Chrysanthemum cultivars by ISSR markers. Scientia Agricultura Sinica, 2008, 41(11): 3735-3740.
缪恒彬, 陈发棣, 赵宏波, 等. 应用ISSR对25个小菊品种进行遗传多样性分析及指纹图谱构建. 中国农业科学, 2008, 41(11): 3735-3740.
[29] Qi L, Wang W Q, Zhang Z W, et al. DNA fingerprinting analysis of 18 Cassava varieties using sequence-related amplified polymorphism markers. Acta Agronomica Sinica, 2010, 36(10): 1642-1648.
齐兰, 王文泉, 张振文, 等. 利用SRAP标记构建18个木薯品种的DNA指纹图谱. 作物学报, 2010, 36(10): 1642-1648.
[30] Liu H Y, Wu K, Yang M M, et al. DNA fingerprinting of sesame (Sesamum indicum L.) varieties (lines) from recent national regional trials in China. Acta Agronomica Sinica, 2012, 38(4): 596-605.
刘红艳, 吴坤, 杨敏敏, 等. 国家芝麻区域试验新品种(系)的DNA指纹分析. 作物学报, 2012, 38(4): 596-605.
[31] Wang J Y, Chen Y Y, Huang B Z, et al. Establishment of fingerprinting for bananas (Musa nana) by SSR marker. Journal of Fruit Science, 2009, 26(5): 733-738.
王静毅, 陈业渊, 黄秉智, 等. 部分香蕉品种SSR指纹图谱的构建. 果树学报, 2009, 26(5): 733-738.
[32] Nie X H, You C Y, Li X F, et al. Construction of DNA fingerprinting and analysis of genetic diversity for Xinluzao cotton varieties. Acta Agronomica Sinica, 2014, 40(12): 2104-2117.
聂新辉, 尤春源, 李晓方, 等. 新陆早棉花品种DNA指纹图谱的构建及遗传多样性分析. 作物学报, 2014, 40(12): 2104-2117.