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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (10): 1767-1775.doi: 10.3724/SP.J.1006.2014.01767

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of Gene Expression Variation by cDNA-SCoT Technique at the Early Period of Arachis Artificial Allopolypoidy Evolution

HE Liang-Qiong1,2,3,XIONG Fa-Qian1,TANG Xiu-Mei1,JIANG Jing1,HAN Zhu-Qiang1,ZHONG Rui-Chun1,GAO Zhong-Kui4,Li Zhong1,HE Xin-Hua2,*,TANG Rong-Hua1,*   

  1. 1 Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; 2 Agricultural College of Guangxi University, Nanning 530004, China; 3 Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning 530007, China; 4 Guangxi Academy of Agricultural Sciences, Nanning 530007, China?
  • Received:2014-04-15 Revised:2014-07-06 Online:2014-10-12 Published:2014-07-25
  • Contact: 何新华, E-mail: honest66222@163.com; 唐荣华, E-mail: tronghua@163.com E-mail:heliangqiong@163.com
  • About author:何新华, E-mail: honest66222@163.com; 唐荣华, E-mail: tronghua@163.com

Abstract:

To explore the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, study the gene expression variation by cDNA-SCoT technique in the early period of Arachis artificial allopolypoidy evolution, using the progenitors, F1 and early polyploidy generations (S0 to S3) of the hybridization between tetraploid cultivated peanut and diploid wild peanut A. doigoi. Among 108 cDNA fragments amplified by 12 SCoT primers 80 were differentially expressed with the polymorphism frequency of 74.07%. Among 80 TDFs (transcripts derived fragments) 35 were cloned and sequenced, and the sequences of 26 TDFs shared high similarity with the genes documented in the GenBank. These genes included energy and metabolism-related genes (8), resistance-related genes (4), unknown functional protein genes (3), signal transduction-related genes (2) and retrotransposon-related genes (9). The results indicated that gene expression changes happened rapidly and drastically in the early generations during artificial allopolyploidization of peanut interspecific hybridization, and some obtained TDFs probably could be used in the research of molecular mechanism of Arachis allopolyploidization.

Key words: Peanut, Allopolyploidization, cDNA-SCoT technique, Gene expression

[1]Otto S P. The evolutionary consequences of polyploidy. Cell, 2007, 131: 452–462



[2]宋灿, 刘少军, 肖军, 何伟国, 周毅, 覃钦博, 张纯, 刘筠. 多倍体生物研究进展. 中国科学C辑(生命科学), 2012, 42: 173–184



Song C, Liu S J, Xiao J, He W G, Zhou Y, Qin Q B, Zhang C, Liu J. Polyploidy organisms. Sci China (Ser C: Life Sci), 2012, 42: 173–184 (in Chinese with English abstract)



[3]赵旭博, 李爱丽, 毛龙. 植物多倍化过程中小分子RNA调控基因表达机制研究进展. 作物学报, 2013, 39: 1331–1338



Zhao X B, Li A L, Mao L. Progress on gene regulatory mechanisms by small RNAs during plant polyploidization. Acta Agron Sin, 2013, 39: 1331–1338 (in Chinese with English abstract)



[4]Jiao Y, Wickett N J, Ayyampalayam S, Chanderbali A S, Landherr L, Ralph P E, Tomsho L P, Hu Y, Liang H, Soltis P S, Soltis D E, Clifton S W, Schlarbaum S E, Schuster S C, Ma H, Leebens-Mack J, Pamphilis C W. Ancestral polyploidy in seed plants and angiosperms. Nature, 2011, 473: 97–100



[5]Feldman M, Levy A A. Genome evolution due to allopolyploidization in wheat. Genetics, 2012, 192: 763–774



[6]Adams K L, Wendel J F. Polyploidy and genome evolution in plants. Curr Opin Plant Biol, 2005, 8: 135–141



[7]Higgins J, Magusin A, Trick M, Fraser F, Bancroft I. Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC Genomics, 2012, 13: 247



[8]彭海, 张静, 吴先军. 植物基因表达中的倍性效应: 研究进展、问题与展望. 中国科学C辑(生命科学), 2008, 38: 1–7



Peng H, Zhang J, Wu X J. The ploidy effect of plant gene expression: research progress, problem and expectation. Sci China (Ser C: Life Sci), 2008, 38: 1–7 (in Chinese with English abstract)



[9]蔡得田, 陈建国, 陈冬玲, 戴兵成, 张维, 宋兆建, 杨之帆, 杜超群, 唐志强, 何玉池, 张道生, 何光存, 朱英国. 两个具多倍体减数分裂稳定性的多倍体水稻品系的选育. 中国科学C辑(生命科学), 2007, 37: 217–226



Cai D T, Chen J G, Chen D L, Dai B C, Zhang W, Song Z J, Yang Z F, Du C Q, Tamg Z Q, He Y C, Zhang D S, He G C, Zhu Y G. Breeding of two polyploidy rice strains with meiotic stability. Sci China (Ser C: Life Sci), 2007, 37: 217–226 (in Chinese with English abstract)



[10]周汉群, 唐荣华, 周翠球, 钟瑞春, 韩柱强. 花生亲和种远缘杂交育种研究. 花生学报, 2003, 32(suppl): 155–161



Zhou H Q, Tang R H, Zhou C Q, Zhong R C, Han Z Q. Interspecific hybridization between cultivated peanut and compatible wild species in Arachis. J Peanut Sci, 2003, 32(suppl): 155–161 (in Chinese with English abstract)



[11]王纪娟, 杨淑娟, 任兰柱. 植物远缘杂交及其在小麦育种的应用. 粮食作物, 2010, (6): 109–113



Wang J J, Yang S J, Ren L Z. Wide hybridization of plant and its application in wheat breeding. Grain Crops, 2010, (6): 109–113 (in Chinese with English abstract)



[12]Lu J, Zhang C, Baulcombe D C, Chen Z J. Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds. Proc Nat Acad Sci USA, 2012, 109: 5529–5534



[13]Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, Levy A A. Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics, 2011, 188: 263–272



[14]Miller M, Zhang C, Chen Z J. Ploidy and hybridity effects on growth vigor and gene expression in Arabidopsis thaliana hybrids and their parents. Genes Genomes Genet, 2012, 2: 505–513



[15]Pumphrey M, Bai J, Laudencia-Chingcuanco D, Anderson O, Gill B S. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics, 2009, 181: 1147–1157



[16]Chen Z J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol, 2007, 58: 377–406



[17]Wang J, Tian L, Lee H S, Wei N E, Jiang H, Watson B, Madlung A, Osborn T C, Doerge R W, Comai L, Chen Z J. Genome wide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics, 2006, 172: 507–517



[18]Kashkush K, Feldman M, Levy A A. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics, 2002, 160: 1651–1659



[19]He P, Friebe B R, Gill B S, Zhou J M. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol, 2003, 52: 401–414



[20]Adams K L, Percifield R. Wendel J F. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics, 2004, 168: 2217–2226



[21]Albertin W, Balliau T, Brabant P, Chevre A M, Eber F, Malosse C, Thiellement H. Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics, 2006, 173: 1101–1113



[22]Hegarty M J, Jones J M, Wilson I D, Barker G L, Coghill J A, Sanchez-Baracaldo P, Liu G, Buggs R J, Abbott R J, Edwards K J, Hiscock S J. Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol, 2005, 14: 2493–2510



[23]Zhuang Y, Chen J F. Changes of gene expression in early generations of the synthetic allotetraploid Cucumis×hytivus Chen et Kirkbride. Genet Resour Crop Evol, 2009, 56: 1071–1076



[24]Kochert G, Halward T, Branchi W D. RFLP variability in peanut (Arachis hypogaea L.) cultivars and wild species. Theor Appl Genet, 1991, 81: 565–570



[25]Gimenes M A, Lopes C R, Valls F M. Genetic relationships among Arachis species based on AFLP. Genet Mol Biol, 2002, 25: 349–353



[26]Gimenes M A, Lopes C R, Galgaro M L, Valls J, Kochert G. RFLP analysis of genetic variation in species of section Arachis, genus Arachis (Leguminosae). Euphytica, 2002, 123: 421-429



[27]任小平, 廖伯寿, 黄家权, 张晓杰, 姜慧芳. 利用SRAP标记分析花生属花生区组种质亲缘关系. 中国油料作物学报, 2009, 31: 449–454



Ren X P, Liao B S, Huang J Q, Zhang X J, Jiang H F. Genomic affinities of Arachis section Arachis revealed by SRAP markers. Chin J Oil Crop Sci, 2009, 31: 449–454 (in Chinese with English abstract)



[28]Garcia G M, Tallury S, Kochert G S. Molecular analysis of Arachis interspecific hybrids. Theor Appl Genet, 2006, 112: 1342–1348



[29]贺梁琼, 熊发前, 钟瑞春, 韩柱强, 李忠, 唐秀梅, 蒋菁, 唐荣华, 何新华. 利用SCoT标记分析花生栽培种×A. chacoensis组合异源多倍化的早期基因组变化. 中国农业科学, 2013, 46: 1555–1563



He L Q, Xiong F Q, Zhong R C, Han Z Q, Li Z, Tang X M, Jiang J, Tang R H, He X H. Study on genome variations by using SCoT markers during allopolyploidization of the cultivated peanut × A. chacoensis. Sci Agric Sin, 2013, 46: 1555–1563 (in Chinese with English abstract)



[30]贺梁琼, 熊发前, 韩柱强, 韩柱强, 蒋菁, 唐秀梅, 李忠, 何新华, 唐荣华. 花生种间杂种异源多倍化早期世代性状和微卫星变化研究. 中国油料作物学报, 2013, 35: 499–507



He L Q, Xiong F Q, Han Z Q, Zhong R C, Jiang J, Tang X M, Li Z, He X H, Tang R H. Traits and microsatellites variation research of early generations during allopolyploidization in Arachis interspecific hybridization. Chin J Oil Crop Sci, 2013, 35: 499–507 (in Chinese with English abstract)



[31]Collard B C Y, Mackill D J. Start codon targeted (SCoT) polymorphism: A simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep, 2009, 27: 86–93



[32]Xiong F Q, Zhong R C, Han Z Q, Jiang J, He L Q, Zhuang W J, Tang R H. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep, 2011, 38: 3487–3494



[33]熊发前, 唐荣华, 陈忠良, 潘玲华, 庄伟建. 目标起始密码子多态性(SCoT): 一种基于翻译起始位点的目的基因标记新技术. 分子植物育种, 2009, 7: 635–638



Xiong F Q, Tang R H, Chen Z L, Pan L H, Zhuang W J. Start codon target polymorphism (SCoT): a novel gene targeted marker technique based on the translation start codon. Mol Plant Breed, 2009, 7: 635–638 (in Chinese with English abstract)



[34]熊发前, 蒋菁, 钟瑞春, 韩柱强, 贺梁琼, 李忠, 庄伟建, 唐荣华. 目标起始密码子多态性(SCoT)分子标记技术在花生属中的应用. 作物学报, 2010, 36: 2055–2061



Xiong F Q, Jiang J, Zhong R C, Han Z Q, He L Q, Li Z, Zhuang W J, Tang R H. Application of SCoT molecular marker in genus Arachis. Acta Agron Sin, 2010, 36: 2055–2061 (in Chinese with English abstract)



[35]陈虎, 何新华, 罗聪, 高美萍. 龙眼24个品种的SCoT遗传多样性分析. 园艺学报, 2010, 37: 1651–1654



Chen H, He X H, Luo C, Gao M P. Analysis on the genetic diversity of 24 longan (Dimocarpus longan) accessions by SCoT markers. Acta Hortic Sin, 2010, 37: 1651–1654 (in Chinese with English abstract)



[36]Luo C, He X H, Chen H, Ou S J, Gao M P, Brown J S, Tondo C T, Schnell R J. Genetic diversity of mango cultivars estimated using SCoT and ISSR markers. Biochem Syst Ecol, 2011, 39: 676–684



[37]Luo C, He X H, Chen H, Hu Y, Ou S J. Genetic relationship and diversity of Mangifera indica L.rrevealed through SCoT analysis. Genet Resour Crop Evol, 2012, 59: 1505–1515



[38]陈香玲, 苏伟强, 刘业强, 任惠, 陆玉英. 36份菠萝种质的遗传多样性SCoT分析. 西南农业学报, 2012, 25: 625–629



Chen X L, Su W Q, Liu Y Q, Ren H, Lu Y Y. Analysis on genetic diversity of 36 pineapple collections by SCoT markers. Southwest China J Agric Sci, 2012, 25: 625–629 (in Chinese with English abstract)



[39]吴建明, 李杨瑞, 王爱琴, 杨柳, 杨丽涛. 赤霉素诱导甘蔗节间伸长基因的 cDNA-SCoT差异表达分析. 作物学报, 2010, 36: 1883–1890



Wu J M, Li Y R, Wang A Q, Yang L, Yang L T. Differential expression of genes in gibberellin-induced stalk elongation of sugarcane analyzed with cDNA-SCoT. Acta Agron Sin, 2010, 36: 1883–1890 (in Chinese with English abstract)



[40]陈香玲, 李杨瑞, 杨丽涛, 吴建明, 罗聪, 熊发前, 杨柳. 低温胁迫下甘蔗抗寒相关基因的cDNA-SCoT差异显示. 生物技术通报, 2010, (8): 120–124



Chen X L, Li Y R, Yang L T, Wu J M, Luo C, Xiong F Q, Yang L. cDNA-SCoT differential display of cold resistance related genes in sugarcane under low temperature stress. Biotechnol Bull, 2010, (8): 120–124 (in Chinese with English abstract)



[41]熊发前, 刘俊仙, 王丛丛, 蒋菁, 钟瑞春, 韩柱强, 贺梁琼, 李忠, 唐秀梅, 唐荣华. mCTAB-dLiCl法高效提取花生各组织部位RNA及其验证. 南方农业学报, 2013, 44: 1781–1784



Xiong F Q, Liu J X, Wang C C, He L Q, Han Z Q, Jiang J, Zhong R C, Li Z, Tang X M, Tang R H. mCTAB-dLiCl method for efficiently extracting RNA from various tissues of cultivated peanut and its verification. J Southern Agric, 2013, 44: 1781–1784 (in Chinese with English abstract)



[42]Comai L, Tyagi A P, Winter K, Holmes-Davis R, Reynolds S H, Stevens Y, Byers B. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell, 2000, 12: 1551–1567



[43]Hegarty M J, Barker G L, Wilson I D, Abbott R J, Edwards K J, Hiscock S J. Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Curr Biol, 2006, 16: 1652–1659



[44]Auger D L, Gray A D, Ream T S, Kato A, Jr. E H C, Birchler J A. Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics, 2005, 169: 389–397



[45]Bennetzen J L. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol, 2000, 42: 251–269

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