Please wait a minute...
Journal of Integrative Agriculture  2017, Vol. 16 Issue (05): 1093-1102    DOI: 10.1016/S2095-3119(16)61462-4
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
Rapid gene expression change in a novel synthesized allopolyploid population of cultivated peanut×Arachis doigoi cross by cDNA-SCoT and HFO-TAG technique
HE Liang-qiong1, TANG Rong-hua1, JIANG Jing1, XIONG Fa-qian1, HUANG Zhi-peng1, WU Hai-ning1, GAO Zhong-kui1, ZHONG Rui-chun1, HE Xin-hua2, HAN Zhu-qiang1

1 Cash Crops Research Institute/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, P.R.China

2 Guangxi University, Nanning 530004, P.R.China

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract  Allopolyploidy has played an important role in plant evolution and heterosis.  Recent studies indicate that the process of wide hybridization and (or) polyploidization may induce rapid and extensive genetic and epigenetic changes in some plant species.  To better understand the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, this study was conducted to monitor the gene expression variation by cDNA start codon targeted polymorphism (cDNA-SCoT) and cDNA high-frequency oligonucleotide-targeting active gene (cDNA-HFO-TAG) techniques, from the hybrids (F1) and newly synthesized allopolyploid generations (S0-S3) between tetraploid cultivated peanut Zhongkaihua 4 with diploid wild one Arachis doigoi. Rapid and considerable gene expression variations began as early as in the F1 hybrid or immediately after chromosome doubling.  Three types of gene expression changes were observed, including complete silence (gene from progenitors was not expressed in all progenies), incomplete silence (gene expressed only in some progenies) and new genes activation.  Those silent genes mainly involved in RNA transcription, metabolism, disease resistance, signal transduction and unknown functions.  The activated genes with known function were almost retroelements by cDNA-SCoT technique and all metabolisms by cDNA-HFO-TAG.  These findings indicated that interspecific hybridization and ploidy change affected gene expression via genetic and epigenetic alterations immediately upon allopolyploid formation, and some obtained transcripts derived fragments (TDFs) probably could be used in the research of molecular mechanism of Arachis allopolyploidization which contribute to thwe genetic diploidization of newly formed allopolyploids.  Our research is valuable for understanding of peanut evolution and improving the utilization of putative and beneficial genes from the wild peanut.
Keywords:  peanut, allopolyploidy      gene expression      start codon-targeted polymorphism      high-frequency oligonucleotide-targeting active gene  
Received: 06 May 2016   Accepted:

This project was supported by the Guangxi Academy of Agricultural Sciences Foundation, China (2015JZ08 and 2015YT57), the Guangxi Sciences Foundation, China (2011GXNSFA018079), the Modern Agro-industry Technology Research System, China (CARS-14-19) and the National Natural Science Foundation of China (31160294 and 31240059).

Corresponding Authors:  HE Xin-hua, Mobile: +86-15177169189, E-mail:; HAN Zhu-qiang, Mobile: +86-13977139289, E-mail:    
About author:  HE Liang-qiong, E-mail:

Cite this article: 

HE Liang-qiong1, TANG Rong-hua1, JIANG Jing1, XIONG Fa-qian1, HUANG Zhi-peng1, WU Hai-ning1, GAO Zhong-kui1, ZHONG Rui-chun1, HE Xin-hua2, HAN Zhu-qiang1 . 2017. Rapid gene expression change in a novel synthesized allopolyploid population of cultivated peanut×Arachis doigoi cross by cDNA-SCoT and HFO-TAG technique. Journal of Integrative Agriculture, 16(05): 1093-1102.

Adams K L, Percifield R, Wendel J F. 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics, 168, 2217-2226.
Albertin W, Balliau T, Brabant P, Chevre A M, Eber F, Malosse C, Thiellement H. 2006. Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics, 173, 1101-1113.
Amnon L, Judy A T, Wechter W P, Howard F H, Alvin M S, Umesh K R, Padma N, Zhang J F. 2013. High frequency oligonucleotides: Targeting active gene (HFO-TAG) markers revealed wide genetic diversity among Citrullus spp. accessions useful for enhancing disease or pest resistance in watermelon cultivars. Genetic Resources and Crop Evolution, 60, 427-440.
Ammon L, William P W. 2010. High-frequency oligonucleotides in watermelon expressed sequenced tag-unigenes are useful in producing polymorphic polymerase chain reaction markers among watermelon genotypes. America Society for Horticultural Science, 135, 369-378.
Auger D L, Gray A D, Ream T S, Kato A, Coe Jr E H, Birchler J A. 2005. Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics, 169, 389-397.
Baumel A, Ainouehe M, Kalendar R. 2002. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae). Molecular Biology Evolution, 19, 218-227.
Bennetzen J L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology, 42, 251-269.
Bertioli D J, Cannon S B, Froenicke L, Huang G D, Farmer A D, Cannon E K S , Liu X , Gao D Y, Clevenger J, Dash S. 2016. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics, 48, 438-446.
Bottley A, Xia G M, Koebner M D. 2006. Homoeologous gene silencing in hexaploid wheat. Plant, 47, 897-906.
Buggs R J A, Chamala S, Wu W, Tate J A, Schnable P S, Soltis D E, Soltis P S, Barbazuk W B. 2012a. Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Current Biology, 22, 248-252.
Buggs R J A, Renny-Byfield S, Chester M. 2012b. Next-generation sequencing and genome evolution in allopolyploids. American Journal of Botany, 99, 372-382.
Chen Z J. 2007. Genetic and epgenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annual Review Plant Biology, 58, 377-406.
Collard B C Y, Mackill D J. 2009. Start codon targeted (SCoT) polymorphism: A simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, 27, 86-93.
Flagel L E, Wendel J F. 2010. Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytologist, 186, 184-193.
Gaeta R T, Pires J C, Iniguez-Luy F, Leon E, Osborn T C. 2007. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. The Plant Cell, 19, 3403-3417.
Garcia G M, Tallury S, Kochert G S. 2006. Molecular analysis of Arachis interspecific hybrids. Theoretical and Applied Genetics, 112, 1342-1348.
Gimenes M A, Lopes C R, Valls F M. 2002. Genetic relationships among Arachis species based on AFLP. Genetic and Molecular Biology, 25, 349-353.
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. 2013a. Traits and microsatellites variation research of early generations during allopolyploidization in Arachis interspecific hybridization. Chinese Journal of Oil Crop Sciences, 35, 499-507. (in Chinese)
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. 2013b. Study on genome variations by using SCoT markers during allopolyploidization of the cultivated peanut×A. chacoensis. Scientia Agricultura Sinica, 46, 1555-1563. (in Chinese)
He P, Friebe B R, Gill B S, Zhou J M. 2003. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Molecular Biology, 52, 401-414.
Hegarty M J, Barker G L, Wilson I D, Abbott R J, Edwards K J, Hiscock S J. 2006. Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Current Biology, 16, 1652-1659.
Higgins J, Magusin A, Trick M, Fraser F, Bancroft I. 2012. Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC Genomics, 13, 247.
Hollister J D. 2014. Polyploidy: Adaption to the genomic environment. New Phytologist, 205, 1034-1039.
Kashkush K, Feldman M, Levy A A. 2002. Gene loss, silencing and activation in newly synthesized wheat allopolyploid. Genetics, 160, 1651-1659.
Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, Levy A A. 2011. Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics, 188, 263-272.
Lashermes P, Combes M C, Hueber Y, Severac D, Dereeper A. 2014. Genome rearangements derrived from homoeologous recombination following allopolyploidy speciation in coffee. The Plant Journal, 78, 674-685.
Lee H S, Chen Z J. 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proceedings of the National Acadamy of Sciences of the United States of America, 98, 6753-6758.
Liu B, Brubaker C L, Mergeai G, Cronn R C, Wendel J F. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome, 44, 321-330.
Miller M, Zhang C, Chen Z J. 2012. Ploidy and hybridity effects on growth vigor and gene expression in Arabidopsis thaliana hybrids and their parents. G3 - Genes Genomes Genetics, 2, 505-513.
Otto S P. 2007. The evolutionary consequences of polyploidy. Cell, 131, 452-462.
Seijo J G, Lavia G I, Fernandez A, Krapovickas A, Ducasse D, Moscone E A. 2004. Physical mapping of the 5S and 18S-25S rRNA genes by FISH as evidence that Arachis duranensis and A. ipaensis are the wild diploid progenitors of A. hypogaea (Leguminosae). American Journal of Botany, 91, 1294-1303.
Soltis D E, Buggs R J A, Doyle J J, Soltis P S. 2010. What we still don’t know about polyploidy. Taxon, 59, 1387-1403.
Soltis P S. 2005. Ancient and recent polyploidy in angiosperms. New Phytologist, 166, 5-8.
Talluny S P. 2005. Genomic affinities in Arachis section Arachis (Fabacaea): Molecular and cytogenetic evidence. Theoretical and Applied Genetics, 111, 1229-1237.
Wood T E, Takebayashi N, Barker M S, Mayrose I, Greenspoon P B, Reisberq L H. 2009. The frequency of polyploidy specification in vascular plants. Proceedings of the National Acadamy of Sciences of the United States of America, 106, 13975-13979.
Xiong F Q, Zhong R C, Han Z Q, Jiang J, He L Q, Zhuang W J, Tang R H. 2011. Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Molecular Biology Reports, 38, 3487-3494.
Zhuang Y, Chen J F. 2009. Changes of gene expression in early generations of the synthetic allotetraploid Cucumis×hytivus Chen & Kirkbride. Genetic Resources and Crop Evolution, 56, 1071-1076.
[1] ZHAO Shu-ping, DENG Kang-ming, ZHU Ya-mei, JIANG Tao, WU Peng, FENG Kai, LI Liang-jun.

Optimization of slow-release fertilizer application improves lotus rhizome quality by affecting the physicochemical properties of starch [J]. >Journal of Integrative Agriculture, 2023, 22(4): 1045-1057.

[2] ZHANG Yan-mei, AO De, LEI Kai-wen, XI Lin, Jerry W SPEARS, SHI Hai-tao, HUANG Yan-ling, YANG Fa-long. Dietary copper supplementation modulates performance and lipid metabolism in meat goat kids[J]. >Journal of Integrative Agriculture, 2023, 22(1): 214-221.
[3] JIANG Yong, MA Xin-yan, XIE Ming, ZHOU Zheng-kui, TANG Jing, CHANG Guo-bin, CHEN Guo-hong, HOU Shui-sheng. Dietary threonine deficiency affects expression of genes involved in lipid metabolism in adipose tissues of Pekin ducks in a genotype-dependent manner[J]. >Journal of Integrative Agriculture, 2022, 21(9): 2691-2699.
[4] RONG Hao, YANG Wen-jing, XIE Tao, WANG Yue, WANG Xia-qin, JIANG Jin-jin, WANG You-ping. Transcriptional profiling between yellow- and black-seeded Brassica napus reveals molecular modulations on flavonoid and fatty acid content[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2211-2226.
[5] AN Feng, ZHANG Kang, ZHANG Ling-kui, LI Xing, CHEN Shu-min, WANG Hua-sen, CHENG Feng. Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1620-1632.
[6] FAN Xiao-xue, BIAN Zhong-hua, SONG Bo, XU Hai. Transcriptome analysis reveals the differential regulatory effects of red and blue light on nitrate metabolism in pakchoi (Brassica campestris L.)[J]. >Journal of Integrative Agriculture, 2022, 21(4): 1015-1027.
[7] LIU Cong, LI De-xiong, HUANG Xian-biao, Zhang Fu-qiong, Xie Zong-zhou, Zhang Hong-yan, Liu Ji-hong. Manual thinning increases fruit size and sugar content of Citrus reticulata Blanco and affects hormone synthesis and sugar transporter activity[J]. >Journal of Integrative Agriculture, 2022, 21(3): 725-735.
[8] DUAN Yao-ke, HAN Rong, SU Yan, WANG Ai-ying, LI Shuang, SUN Hao, GONG Hai-jun. Transcriptional search to identify and assess reference genes for expression analysis in Solanum lycopersicum under stress and hormone treatment conditions[J]. >Journal of Integrative Agriculture, 2022, 21(11): 3216-3229.
[9] Kashif NOOR, Hafiza Masooma Naseer CHEEMA, Asif Ali KHAN, Rao Sohail Ahmad KHAN. Expression profiling of transgenes (Cry1Ac and Cry2A) in cotton genotypes under different genetic backgrounds[J]. >Journal of Integrative Agriculture, 2022, 21(10): 2818-2832.
[10] WANG Pei-pei, WANG Zhao-ke, GUAN Le, Muhammad Salman HAIDER, Maazullah NASIM, YUAN Yong-bing, LIU Geng-sen, LENG Xiang-peng. Versatile physiological functions of the Nudix hydrolase family in berry development and stress response in grapevine[J]. >Journal of Integrative Agriculture, 2022, 21(1): 91-112.
[11] GUO Bing-bing, LI Jia-ming, LIU Xing, QIAO Xin, Musana Rwalinda FABRICE, WANG Peng, ZHANG Shao-ling, WU Ju-you. Identification and expression analysis of the PbrMLO gene family in pear, and functional verification of PbrMLO23[J]. >Journal of Integrative Agriculture, 2021, 20(9): 2410-2423.
[12] JI Xiao-hao, WANG Bao-liang, WANG Xiao-di, WANG Xiao-long, LIU Feng-zhi, WANG Hai-bo. Differences of aroma development and metabolic pathway gene expression between Kyoho and 87-1 grapes[J]. >Journal of Integrative Agriculture, 2021, 20(6): 1525-1539.
[13] CHEN Chang-long, YUAN Fang, LI Xiao-ying, MA Rong-cai, XIE Hua. Jasmonic acid and ethylene signaling pathways participate in the defense response of Chinese cabbage to Pectobacterium carotovorum infection[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1314-1326.
[14] WANG Lu-lu, ZHAO Chun-fang, LIU Chang-jun, ZHANG Hao, LIAN Ling. Analysis of DNA methylation of CD79B in MDV-infected chicken spleen[J]. >Journal of Integrative Agriculture, 2021, 20(11): 2995-3002.
[15] WANG Xi-cheng, WU Wei-min, ZHOU Bei-bei, WANG Zhuang-wei, QIAN Ya-ming, WANG Bo, YAN Li-chun. Genome-wide analysis of the SCPL gene family in grape (Vitis vinifera L.)[J]. >Journal of Integrative Agriculture, 2021, 20(10): 2666-2679.
No Suggested Reading articles found!