基于PCR技术的谷子分子标记遗传图谱构建

doi:10.3864/j.issn.0578-1752.2014.17.017

摘要/Abstract

摘要： 【目的】构建一张基于PCR技术的谷子分子标记遗传图谱。【方法】以谷子高146A和K103杂交自交F2分离群体为作图群体，以分布于谷子9条染色体上的81个SSR标记为主要参考标记，采用来自谷子、水稻、珍珠粟和高羊茅的SSR、STS、SNP、SV和ACGM标记共1 733个，在亲本间筛选多态性标记，并进一步在F2群体间进行验证，利用MAPMAKER VERSION 3.0软件进行连锁分析，采用MapDraw V2软件绘制遗传连锁图谱。【结果】构建了一张包含192个不同类型分子标记的谷子遗传图谱，新定位标记33个，其中32个来自谷子，另1个来自珍珠粟。遗传图谱包含9个连锁群，覆盖基因组全长2 082.5 cM，连锁群长度介于119.5—475.2 cM，平均长度231.39 cM，标记间平均距离10.85 cM，每个连锁群上的标记数介于10—37个。部分连锁群上标记存在偏分离现象，在定位的192个标记中，共有36个标记发生偏分离，占图谱总标记的18.75%，其中，在LG2、LG6和LG7上分别聚集分布了10、15和7个偏分离标记，出现了偏分离热点区域，而在LG1、LG4、LG5和LG8上仅有零星分布，LG3和LG9上则没有偏分离标记。对来自不同作物的分子标记在谷子上的可转移性分析发现，来自谷子的1 235个PCR标记中有205个标记在双亲及其F2群体间有多态性，多态率为16.60%，而来自珍珠粟、高羊茅和水稻的498个PCR标记，在该群体上仅发现1个多态性标记。【结论】利用不同物种中的分子标记构建了一张覆盖基因组长度为2 082.5 cM的谷子遗传连锁图谱，其分子标记主要来自于谷子。

关键词: 谷子 , 分子标记 , 多态性 , 遗传图谱 , 可转移性

Abstract: 【Objective】 This study aims to construct a genetic map of foxtail millet (Setaria italica (L.) Beauv.) using PCR- based molecular markers. 【Method】 With 81 SSR markers distributed in nine chromosome of foxtail millet as reference markers, a total of 1 733 markers including SSR, STS, SNP, and SV from foxtail millet and ACGM and SSR from pearl millet, tall fescue and rice were used to screen polymorphic markers between Gao 146A and K103, and the polymorphic markers were tested in the F2 segregation populations derived from cross Gao 146A / K103. MAPMAKER VERSION 3.0 and MapDraw V2 were used for linkage analysis and integrated genetic map drawing.【Result】A genetic linkage map of foxtail millet containing 192 different kinds of markers was constructed, and 33 markers were newly mapped, of which 32 were from foxtail millet and 1 from pearl millet. The map consisted of nine linkage groups and covered the genome length 2 082.5 cM. Each linkage group was between 119.5-475.2 cM and the average distance of each linkage group spanned 231.39 cM. The number of markers on each linkage group ranged from 10 to 37 and the average distance between different markers was 10.85 cM. There were 36 markers accounted for 18.75% of 192 ones distributed in different linkage group and appeared segregation disorder. There appeared segregation disorder hotspots on LG2, LG6 and LG7, including 10, 15 and 7 segregation markers, respectively, and segregation disorder scattered on LG1, LG4, LG5 and LG8, however, no segregation disorder occurred on LG3 and LG9. According to transferability of molecular markers from different crops, there were 205 polymorphic markers of 1 235 ones from foxtail millet between parents and F2 population and the polymorphism rate was 16.60%, however there was only one polymorphic marker of 498 ones from pearl millet, tall fescue and rice.【Conclusion】A genetic linkage map of foxtail millet, covering the genome length 2 082.5 cM, was constructed using molecular markers from different species and most of the markers in this map were from foxtail millet.

Key words: foxtail millet , molecular marker , polymorphism , genetic map , transfer ability

王智兰，王军，袁峰，杜晓芬，杨慧卿，郭二虎. 基于PCR技术的谷子分子标记遗传图谱构建[J]. 中国农业科学, 2014, 47(17): 3492-3500.

WANG Zhi-lan, WANG Jun, YUAN Feng, DU Xiao-fen, YANG Hui-qing, GUO Er-hu. Construction of Genetic Map of Foxtail Millet (Setaria italica (L.) Beauv.) Using PCR-Based Molecular Markers[J]. Scientia Agricultura Sinica, 2014, 47(17): 3492-3500.

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参考文献

[1]王永芳, 李伟, 智慧, 李海权, 刁现民. 基于谷子测序开发的SSR标记多态性检测. 河北农业科学, 2010, 14(11): 73-76.
Wang Y F, Li W, Zhi H, Li H Q, Diao X M. Selection of SSR primers development from genome sequence of foxtail millet. Journal of Hebei Agricultural Sciences, 2010, 14(11): 73-76. (in Chinese)
[2]王晓宇, 刁现民, 王节之, 王春芳, 王根全, 郝晓芬, 梁増浩, 王雪梅, 赵芳芳. 谷子SSR分子图谱构建及主要农艺性状QTL定位. 植物遗传资源学报, 2013, 14(5): 871-878.
Wang X Y, Diao X M, Wang J Z, Wang C F, Wang G Q, Hao X F, Liang Z H, Wang X M, Zhao F F. Construction of genetic map and QTL analysis of some main agronomic traits in millet. Journal of Plant Genetic Resources, 2013, 14(5): 871-878. (in Chinese)
[3]骆晚侠, 张李, 杨凯, 李奕松, 赵波, 李明, 万平. 小豆SSR分子标记遗传连锁图谱构建. 中国农业科学, 2013, 46(17): 3534-3544.
Luo W X, Zhang L, Yang K, Li Y S, Zhao B, Li M, Wan P. Construction of genetic linkage map using SSR molecular markers in azuki bean (Vigna angularis Ohwi and Ohashi). Scientia Agicultura Sinica, 2013, 46(17): 3534-3544. (in Chinese)
[4]杨延兵, 管延安, 张华文, 徐平平, 张文兰, 陈利容, 秦岭. 谷子品种遗传差异的RAPD标记分析. 华北农学报, 2007, 22(4): 134-136.
Yang Y B, Guan Y A, Zhang H W, Xu P P, Zhang W L, Chen L R, Qin L. Genetic variation among varieties of foxtail millet (Setaria italica Beauv.) based on RAPD markers. Acta Agriculturae Boreali Sinica, 2007, 22(4): 134-136. (in Chinese)
[5]Wang Z M, Devos K M, Liu C J, Wang R Q, Gale M D. Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. Theoretical and Applied Genetics, 1998, 96: 31-36.
[6]d’Enuequin M L T, Panaud O, Toupance B, Sarr A. Assessment of genetic relationship between Setaria italica and it’s wild relative S.viridis using AFLP markers. Theoretical and Applied Genetics, 2000, 100(7): 1061-1066.
[7]Jia X P, Zhang Z B, Liu Y H, Zhang C W, Shi Y S, Song Y C, Wang T Y, Li Y. Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theoretical and Applied Genetics, 2009, 118: 821-829.
[8]Zhang G Y, Liu X, Quan Z W, Cheng S F, Xu X, Pan S K, Xie M, Zeng P, Yue Z, Wang W L, Tao Y, Bian C, Han C L, Xia Q J, Peng X H, Cao R, Yang X H, Zhan D L, Hu J C, Zhang Y X, Li H N, Li H, Li N, Wang J Y, Wang C C, Wang R Y, Guo T, Cai Y J, Liu C Z, Xiang H T, S hi Q X, Huang P, Chen Q C, Li Y R, Wang J, Zhao Z H, Wang J. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology, 2012, 30(6): 549-556.
[9]纪剑辉, 曹爱忠, 王海燕, 覃碧, 王苏玲, 孔芳, 陈佩度, 刘大钧, 王秀娥. 利用基于PCR的分子标记区分普通小麦-提莫菲维小麦渐渗系. 遗传, 2007, 29(10): 1256-1262.
Ji J H, Cao A Z, Wang H Y, Qin B, Wang S L, Kong F, Chen P D, Liu D J, Wang X E. Discrimination of the Triticum aestivum-T. timopheevii introgression lines using PCR-based molecular markers. Hereditas, 2007, 29(10): 1256-1262. (in Chinese)
[10]Xu P, Wu X H, Wang B G, Liu Y H, Ehlers J D, Close T J, Roberts P A, Diop N N , Qin D H , Hu T T, Lu Z F, Li G J. A SNP and SSR based genetic map of asparagus bean (Vigna. unguiculata ssp. Sesquipedialis ) and comparison with the broader species. PLoS One, 2011, 6(1): e15952.
[11]Hearnden P R, Eckermann P J, McMichael G L, Hayden M J, Eglinton J K, Chalmers K J. A genetic map of 1,000 SSR and DArT markers in a wide barley cross. Theoretical and Applied Genetics, 2007, 115: 383-391.
[12]Xia Z J, Tsubokura Y, Hoshi M, Hanawa M, Yano C, Okamura K, Ahmed T A, Anai T, Watanabe S, Hayashi M, Kawai T, Hossain K G, Masaki H, Asai K, Yamanaka N, Kubo N, Kadowaki K, Nagamura Y, Yano M, Sasaki T, Harada K. An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using A single F2 population. DNA Research, 2007, 14: 257-269.
[13]Ganal M W, Röder M S. Microsatellite and SNP markers in wheat breeding. Genomics Applications in Crops, 2007, 2: 1-24.
[14]赵丹, 程须珍, 王丽侠, 王素华, 马燕玲. 绿豆遗传连锁图谱的整合. 作物学报, 2010, 36(6): 932-939.
Zhao D, Cheng X Z, Wang L X, Wang S H, Ma Y L. Integration of mungbean (Vigna radiata) genetic linkage map. Acta Agronomica Sinica, 2010, 36(6): 932-939. (in Chinese)
[15]李媛媛, 沈金雄, 王同华, 傅廷栋, 马朝芝. 利用SRAP、SSRA和FLP标记构建甘蓝型油菜遗传连锁图谱. 中国农业科学, 2007, 40(6): 1118-1126.
Li Y Y, Shen J X, Wang T H, Fu T D, Ma C Z. Construction of a linkage map using SRAP, SSR and AFLP markers in Brassica napus L.. Scientia Agicultura Sinica, 2007, 40(6): 1118-1126. (in Chinese)
[16]Graham J, Smith K, MacKenzie K, Jorgenson L, Hackett C, Powell W. The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theoretical and Applied Genetics, 2004, 109: 740-749.
[17]Testolin R, Huang W G, Lain O, Messina R, Vecchione A, Cipriani G. A kiwifruit (Actinidia spp.) linkage map based on microsatellites and integrated with AFLP markers. Theoretical and Applied Genetics, 2001, 103: 30-36.
[18]Rosa R L, Angiolillo A, Guerrero C, Pellegrini M, Rallo L, Besnard G, Bervill A, Martin A, Baldoni L. A first linkage map of olive (Olea europaea L.) cultivars using RAPD, AFLP, RFLP and SSR markers. Theoretical and Applied Genetics, 2003, 106: 1273-1282.
[19]Dellaporta S L, Wood J, Hicks J B. A plant DNA minipreparation: Version Ⅱ. Plant Molecular Biology Reporter, 1983, 1(4): 19-21.
[20]Jia X P, Shi Y S, Song Y C, Wang G Y, Wang T Y, Li Y. Development of EST-SSR in foxtail millet (Setaria italica). Genetic Resources and Crop Evolution, 2007, 54(2): 233-236.
[21]Zhao W G, Lee G A, Kwon S W, Ma K H, Lee M C, Park Y J. Development and use of novel SSR markers for molecular genetic diversity in Italian millet (Setaria italica L.). Genes and Genomics, 2012, 34: 51-57.
[22]Gupta S, Kumari K, Sahu P P, Vidapu S, Prasad M. Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Report, 2012, 31: 323-327.
[23]杨坤. 谷子SSR标记连锁图谱构建及几个主要性状QTL分析[D]. 石家庄: 河北师范大学, 2006.
Yang K. Construction of genetic map using SSR markers and QTL analysis of some main agronomic traits in foxtail millet[D]. Shijiazhuang: Hebei Normal University, 2006. (in Chinese)
[24]卢泳全, 汪旭升, 黄伟素, 肖天霞, 郑燕, 吴为人. 基于水稻内含子长度多态性开发禾本科扩增共有序列遗传标记. 中国农业科学, 2006, 39(3): 433-439.
Lu Y Q, Wang X S, Huang W S, Xiao T X, Zheng Y, Wu W R. Development of amplified consensus genetic markers in gramineae based on rice intron length polymorphisms. Scientia Agiculturea Sinica, 2006, 39(3): 433-439. (in Chinese)
[25]Yu J K, Rota M L, Kantety R V, Sorrells M E. EST derived SSR markers for comparative mapping in wheat and rice. Molecular Genetics and Genomics, 2004, 271: 742-751.
[26]Senthilvel S, Jayashree B, Mahalakshmi V, Kumar P S, Nakka S, Nepolean T, Hash C. Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biology, 2008, 8: 119-127.
[27]Saha M C, Rouf Mian M A, Eujayl I, Zwonitzer J C, Wang L J, May G D. Tall fescue EST-SSR markers with transferability across several grass speciel. Theoretical and Applied Genetics, 2004, 109: 783-791.
[28]梁宏伟, 王长忠, 李忠, 罗相忠, 邹桂伟. 聚丙烯酰胺凝胶快速、高效银染方法的建立. 遗传, 2008, 30(10): 1379-1382.
Liang H W, Wang C Z, Li Z, Luo X Z, Zou G W. Improvement of the silver-stained technique of polyacrylamide gel electrophoresis. Hereditas, 2008, 30(10): 1379-1382. (in Chinese)
[29]Phadnis N, Orr H A. A single gene causes both male sterility and segregation distortion in drosophila hybrids. Science, 2009, 323: 376-379.
[30]Lin S Y, Ikehashi H, Yanagihara S, Kawashima A. Segregation distortion via male gametes in hybrids between Indica and Japonica or wide-compatibility varieties of rice (Oryza sativa L.). Theoretical and Applied Genetics, 1992, 84: 812-818.
[31]Xu Y, Zhu L, Xiao J, Huang N, McCouch S R. Chromosomal regions associated with segregation distortion of molecular markers in F2 , backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Molecular and General Genetics, 1997, 253: 535-545.
[32]Howden R, Park S K, Moore J M, Orme J, Grossniklaus U, Twell D. Selection of T-DNA tagged male and female gametophytic mutants by segregation distortion in Arabidopsis. Genetics, 1998, 149: 621-631.
[33]严建兵, 汤华, 黄益勤, 郑用琏, 李建生. 玉米F2群体分子标记偏分离的遗传分析. 遗传学报, 2003 , 30: 913-918.
Yan J B, Tang H, Huang Y Q, Zheng Y L, Li J S. Genetic analysis of segregation distortion of molecular markers in maize F2 population. Acta Genetica Sinica, 2003, 30: 913-918. (in Chinese)
[34]Lashermes P, Combes M C, Prakash N S, Trouslot P, Lorieux M, Charrier A. Genetic linkage map of Coffea canephora: Effect of segregation distortion and analysis of recombination rate in male and female meioses. Genome, 2001, 44: 589-596.
[35]Wang J, Wang Z L, Yang H Q, Yuan F, Guo E H, Tian G, Han Y H, Li H X, Wang Y W, Diao X M, Guo P Y. Genetic analysis and preliminary mapping of a highly male-sterile gene in foxtail millet (Setaria italica (L.) P. Beauv.) using SSR markers. Journal of Integrative Agriculture, 2013, 12(12): 2143-2148.
[36]Nayak S N, Zhu H Y, Varghese N, Datta S, Choi H K, Horres R, Jüngling R, Singh J, Kavi Kishor P B, Sivaramakrishnan S, Hoisington D A, Kahl G, Winter P, Cook D R, Varshney R K. Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical and Applied Genetics, 2010, 120: 1415-1441.