Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean

doi:10.1016/S1671-2927(00)8632

Journal of Integrative Agriculture ›› 2012, Vol. 12 ›› Issue (7): 1075-1085.DOI: 10.1016/S1671-2927(00)8632

Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean

LI Liang, WANG Wei-qi, HAN Tian-fu, HOU Wen-sheng

1.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Ministry of Agriculture/Institute of Crop Sciences,Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
2.Daqing Branches, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, P.R.China

收稿日期:2011-03-23 出版日期:2012-07-01 发布日期:2012-07-27
通讯作者: HOU Wen-sheng, Tel: +86-10-82108589, Fax: +86-10-82108784, E-mail: houwsh@caas.net.cn
基金资助:
This project was supported by the National Natural Science Foundation of China (30771358).

Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean

LI Liang, WANG Wei-qi, HAN Tian-fu, HOU Wen-sheng

1.National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Ministry of Agriculture/Institute of Crop Sciences,Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
2.Daqing Branches, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, P.R.China

Received:2011-03-23 Online:2012-07-01 Published:2012-07-27
Contact: HOU Wen-sheng, Tel: +86-10-82108589, Fax: +86-10-82108784, E-mail: houwsh@caas.net.cn
Supported by:
This project was supported by the National Natural Science Foundation of China (30771358).

摘要/Abstract

摘要： Soybean is planted worldwide and its productivity is significantly hampered by salinity. Development of salt tolerant cultivars is necessary for promoting soybean production. Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. A continued effort is needed to understand the salt tolerance mechanism in soybean using suitable molecular tools. To better understand the molecular basis of the responses of soybean to salt stress and to get an enrichment of critical salt stress responsive genes in soybean, suppression subtractive hybridization libraries (SSH) are constructed for the root tissue of two cultivated soybean genotypes, one was tolerant and the other was sensitive to salt stress. To compare the responses of plants in salt treatment and non-treatment, SSH1 was constructed for the salt-tolerant cultivar Wenfeng 7 and SSH2 was constructed for the salt-sensitive cultivar Union. From the two SSH cDNA libraries, a total of 379 high quality ESTs were obtained. These ESTs were then annotated by performing sequence similarity searches against the NCBI nr (National Center for Biotechnology Information protein non-redundant) database using the BLASTX program. Sixty-three genes from SSH1 and 49 genes from SSH2 could be assigned putative function. On the other hand, 25 ESTs of SSH1 which may be not the salt tolerance-related genes were removed by comparing and analyzing the ESTs from the two SSH libraries, which increased the proportion of the genes related to salt tolerance in SSH1. These results suggested that the novel way could realize low background of SSH and high level enrichment of target cDNAs to some extent.

关键词: salt stress, suppression subtractive hybridization (SSH), soybean

Abstract: Soybean is planted worldwide and its productivity is significantly hampered by salinity. Development of salt tolerant cultivars is necessary for promoting soybean production. Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. A continued effort is needed to understand the salt tolerance mechanism in soybean using suitable molecular tools. To better understand the molecular basis of the responses of soybean to salt stress and to get an enrichment of critical salt stress responsive genes in soybean, suppression subtractive hybridization libraries (SSH) are constructed for the root tissue of two cultivated soybean genotypes, one was tolerant and the other was sensitive to salt stress. To compare the responses of plants in salt treatment and non-treatment, SSH1 was constructed for the salt-tolerant cultivar Wenfeng 7 and SSH2 was constructed for the salt-sensitive cultivar Union. From the two SSH cDNA libraries, a total of 379 high quality ESTs were obtained. These ESTs were then annotated by performing sequence similarity searches against the NCBI nr (National Center for Biotechnology Information protein non-redundant) database using the BLASTX program. Sixty-three genes from SSH1 and 49 genes from SSH2 could be assigned putative function. On the other hand, 25 ESTs of SSH1 which may be not the salt tolerance-related genes were removed by comparing and analyzing the ESTs from the two SSH libraries, which increased the proportion of the genes related to salt tolerance in SSH1. These results suggested that the novel way could realize low background of SSH and high level enrichment of target cDNAs to some extent.

Key words: salt stress, suppression subtractive hybridization (SSH), soybean

LI Liang, WANG Wei-qi, HAN Tian-fu, HOU Wen-sheng. Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean[J]. Journal of Integrative Agriculture, 2012, 12(7): 1075-1085.

参考文献

[1]Ashraf M. 1994. Breeding for salinity tolerance in plants. Critical Reviews in Plant Sciences, 13, 17-42.

[2]Bailey-Serres J, Freeling M. 1990. Hypoxic stress-induced changes in ribosomes of maize seedling roots. Plant Physiology, 94, 1237-1243.

[3]Binod S B, Birendra S P. 2009. Isolation, identification and expression analysis of salt-induced genes in Suaeda maritim, a natural halophyte, using PCR-based suppression subtractive hybridization. BMC Plant Biology, 9, 69. Cho C, Lee H, Chung E, Kim K M, Heo J E, Kim J, Chung J, Ma Y, Fukui K, Lee D. 2007. Molecular characterization of the soybean L-asparaginase gene induced by low temperature stress. Molecules and Cells, 23, 280. Choi J J, Alkharouf N W, Schneider K T, Matthews B F, Frederick R D. 2008. Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. Functional and Integrative Genomics, 8, 341-359.

[4]Degenhardt J, Al-Masri A N, Kürkcüoglu S, Szankowski I, Gau A E. 2005. Characterization by suppression subtractive hybridization of transcripts that are differentially expressed in leaves of apple scab-resistant and susceptible cultivars of Malus domestica. Molecular Genetics and Genomics, 273, 326-335.

[5]Deragon J, Casacuberta J, Panaud O. 2008. Plant transposable elements. Genome Dynamics, 4, 69. Diatchenko L, Lau Y F, Campbell A P, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov E D. 1996. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proceedings of the National Academy of Sciences of the United States of America, 93, 6025.

[6]Fontaniella B, Vicente C, Legaz M E. 2000. The cryoprotective role of polyols in lichens: effects on the redistribution of RNase in Evernia prunastri thallus during freezing. Plant Physiology and Biochemistry, 38, 621-627.

[7]Gomes-Filho E, Lima C R F M, Costa J H, da Silva A C M, da Guia Silva Lima M, de Lacerda C F, Prisco J T. 2008. Cowpea ribonuclease: properties and effect of NaClsalinity on its activation during seed germination and seedling establishment. Plant Cell Reports, 27, 147-157.

[8]Guo L, Wang Z Y, Lin H, Cui W E, Chen J, Liu M, Chen Z L, Qu L J, Gu H. 2006. Expression and functional analysis of the rice plasma-membrane intrinsic protein gene family. Cell Research, 16, 277-286.

[9]He F, Zhu Y, Zhang Y. 2008. Identification and characterization of differentially expressed genes involved in pharmacological activities of roots of Panax notoginseng during plant growth. Plant Cell Reports, 27, 923-930.

[10]Huang J, Wang J F, Wang Q H, Zhang H S. 2005. Identification of a rice zinc finger protein whose expression is transiently induced by drought, cold but not by salinity and abscisic acid. Mitochondrial DNA, 16, 130-136.

[11]Hubank M, Schatz A D. 1994. Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Research, 22, 5640-5648.

[12]Kawasaki S, Borchert C, Deyholos M, Wang H, Brazille S, Kawai K, Galbraith D, Bohnert H J. 2001. Gene expression profiles during the initial phase of salt stress in rice. The Plant Cell Online, 13, 889-906.

[13]Kim J C, Lee S H, Cheong Y H, Yoo C M, Lee S I, Chun H J, Yun D J, Hong J C, Lee S Y, Lim C O. 2001. A novel coldinducible zinc finger protein from soybean, SCOF-1, enhances cold tolerance in transgenic plants. The Plant Journal, 25, 247-259.

[14]Li L G, Li S F, Tao Y, Kitagawa Y. 2000. Molecular cloning of a novel water channel from rice: its products expression in Xenopus oocytes and involvement in chilling tolerance. Plant Science, 154, 43-51.

[15]Li W Y F, Shao G, Lam H M. 2008. Ectopic expression of GmPAP3 alleviates oxidative damage caused by salinity and osmotic stresses. New Phytologist, 178, 80-91.

[16]Liang P, Pardee A B. 1992. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science, 257, 967-971.

[17]Liao H, Wong F L, Phang T H, Cheung M Y, Li WYF, Shao G, Yan X, Lam H M. 2003. GmPAP3, a novel purple acid phosphatase-like gene in soybean induced by NaCl stress but not phosphorus deficiency. Gene, 318, 103-111.

[18]Liao Y, Zhang J S, Chen S Y, Zhang W K. 2008. Role of soybean GmbZIP132 under abscisic acid and salt stresses. Journal of Integrative Plant Biology, 50, 221-230.

[19]Luo G Z, Wang H W, Huang J, Tian A G, Wang Y J, Zhang J S, Chen S Y. 2005. A putative plasma membrane cation/ proton antiporter from soybean confers salt tolerance in Arabidopsis. Plant Molecular Biology, 59, 809-820.

[20]Mano Y, Takeda K. 1997. Mapping quantitative trait loci for salt tolerance at germination and the seedling stage in barley (Hordeum vulgare L.). Euphytica, 94, 263-272.

[21]McGinness K E, Sauer R T. 2004. Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules. Proceedings of the National Academy of Sciences of the United States of America, 101, 13454-13459

[22]Monforte A J, Asins M J, Carbonell E A. 1997. Salt tolerance in Lycopersicon species VI. Genotype-by-salinity interaction in quantitative trait loci detection: constitutive and response QTLs. Theoretical and Applied Genetics, 95, 706-713.

[23]Nakagami H, Maeda K, Morishita R, Iguchi S, Nishikawa T, Takami Y, Kikuchi Y, Saito Y, Tamai K, Ogihara T. 2005. Novel autologous cell therapy in ischemic limb disease through growth factor secretion by cultured adipose tissue-derived stromal cells. Arteriosclerosis, Thrombosis, and Vascular Biology, 25, 2542-2547.

[24]Ouyang B, Yang T, Li H, Zhang L, Zhang Y, Zhang J, Fei Z, Ye Z. 2007. Identification of early salt stress response genes in tomato root by suppression subtractive hybridization and microarray analysis. Journal of Experimental Botany, 58, 507-520.

[25]Rhoades J D, Loveday J. 1990. Salinity in irrigated agriculture. In: Irrigation of Agricultural Crops. ASA/ CSSA/SSSA, Madison. pp. 1089-1142.

[26]Sakurai J, Ishikawa F, Yamaguchi T, Uemura M, Maeshima M. 2005. Identification of 33 rice aquaporin genes and analysis of their expression and function. Plant and Cell Physiology, 46, 1568-1577.

[27]Sánchez-Barrena M J, Martínez-Ripoll M, Zhu J K, Albert A. 2005. The structure of the Arabidopsis thaliana SOS3: molecular mechanism of sensing calcium for salt stress response. Journal of Molecular Biology, 345, 1253-1264.

[28]Schaffer M A, Fischer R L. 1988. Analysis of mRNAs that accumulate in response to low temperature identifies a thiol protease gene in tomato. Plant Physiology, 87, 431-436.

[29]Tozlu I, Guy C L, Moore G A. 1999. QTL analysis of Na+ and Cl-accumulation related traits in an intergeneric BC1 progeny of Citrus and Poncirus under saline and nonsaline environments. Genome, 42, 692-705.

[30]Wei W H, Chen B, Yan X H, Wang L J, Zhang H F, Cheng J P, Zhou X A, Sha A H, Shen H. 2008. Identification of differentially expressed genes in soybean seeds differing in oil content. Plant Science, 175, 663-673.

[31]Wessler S R. 2001. Plant transposable elements. A hard act to follow. Plant Physiology, 125, 149. Yu X, Peng Y H, Zhang M H, Shao Y J, Su W A, Tang Z C. 2006. Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery. Cell Research, 16, 599-608.

[32]Zhao L, Luo Q, Yang C, Han Y, Li W. 2008. A RAV-like transcription factor controls photosynthesis and senescence in soybean. Planta, 227, 1389-1399.

[33]Zhao M F. 1992. The status and research trend of soil pickled in the world. Chinese World Forestry Research, 1, 84-86. (in Chinese)

[34]Zhou Q Y, Tian A G, Zou H F, Xie Z M, Lei G, Huang J, Wang C M, Wang H W, Zhang J S, Chen S Y. 2008. Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnology Journal, 6, 486-503.

[35]Zhu C, Schraut D, Hartung W, Schaffner A R. 2005. Differential responses of maize MIP genes to salt stress and ABA. Journal of Experimental Botany, 56, 2971-2981.

Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean

Construction of Two Suppression Subtractive Hybridization Libraries and Identification of Salt-Induced Genes in Soybean

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

[1]	KONG Ling-an, WU Du-qing, HUANG Wen-kun, PENG Huan, HE Wen-ting, PENG De-liang. Assaying the potential of twenty-one legume plants in Medicago truncatula and M. sativa for candidate model plants for investigation the interactions with Heterodera glycines[J]. Journal of Integrative Agriculture, 2016, 15(3): 702-704.
[2]	LI Yan-fei, HONG Hui-long, LI Ying-hui, MA Yan-song, CHANG Ru-zhen, QIU Li-juan. The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans[J]. Journal of Integrative Agriculture, 2016, 15(2): 262-270.
[3]	ZHANG Li-wei, Til Feike, Jirko Holst, Christa Hoffmann, Reiner Doluschitz. Comparison of energy consumption and economic performance of organic and conventional soybean production - A case study from Jilin Province, China[J]. Journal of Integrative Agriculture, 2015, 14(8): 1561-1572.
[4]	ZHAO Lei, ZHANG Ya-qing. Effects of phosphate solubilization and phytohormone production of Trichoderma asperellum Q1 on promoting cucumber growth under salt stress[J]. Journal of Integrative Agriculture, 2015, 14(8): 1588-1597.
[5]	GUO Bing-fu, GUO Yong, WANG Jun, ZHANG Li-juan, JIN Long-guo, HONG Hui-long, CHANG, Ru-zheng, QIU Li-juan. Co-treatment with surfactant and sonication significantly improves Agrobacterium-mediated resistant bud formation and transient expression efficiency in soybean[J]. Journal of Integrative Agriculture, 2015, 14(7): 1242-1250.
[6]	ZHOU De, Dieter Koemle. Price transmission in hog and feed markets of China[J]. Journal of Integrative Agriculture, 2015, 14(6): 1122-1129.
[7]	CHEN Hua-tao, CHEN Xin, WU Bing-yue, YUAN Xing-xing, ZHANG Hong-mei, CUI Xiao-yan. Whole-genome identification and expression analysis of K+ efflux antiporter (KEA) and Na+/H+ antiporter (NHX) families under abiotic stress in soybean[J]. Journal of Integrative Agriculture, 2015, 14(6): 1171-1183.
[8]	WANG Xiao-guang, ZHAO Xin-hua, JIANG Chun-ji, LI Chun-hong, CONG Shan, WU Di, CHEN Yan-qiu, YU Hai-qiu, WANG Chun-yan. Effects of potassium deficiency on photosynthesis and photoprotection mechanisms in soybean (Glycine max (L.) Merr.)[J]. Journal of Integrative Agriculture, 2015, 14(5): 856-863.
[9]	WU Ting-ting, LI Jin-yu, WU Cun-xiang, SUN Shi, MAO Ting-ting, JIANG Bing-jun, HOU Wen-sheng, HAN Tian-fu. Analysis of the independent- and interactive-photo-thermal effects on soybean flowering[J]. Journal of Integrative Agriculture, 2015, 14(4): 622-632.
[10]	MA Ya-nan, CHEN Ming, XU Dong-bei, FANG Guang-ning, WANG Er-hui, GAO Shi-qing, XU Zhao-shi, LI Lian-cheng, ZHANG Xiao-hong, MIN Dong-hong, MA You-zhi. G-protein β subunit AGB1 positively regulates salt stress tolerance in Arabidopsis[J]. Journal of Integrative Agriculture, 2015, 14(2): 314-325.
[11]	QIANG Xiao-jing, YU Guo-hong, JIANG Lin-lin, SUN Lin-lin, ZHANG Shu-hui, LI Wei, CHENG Xian-guo. Thellungiella halophila ThPIP1 gene enhances the tolerance of the transgenic rice to salt stress[J]. Journal of Integrative Agriculture, 2015, 14(10): 1911-1922.
[12]	WANG Jun, LIU Lin, GUO Yong, WANG Yong-hui, ZHANG Le, JIN Long-guo, GUAN Rong-xia, LIU Zhang-xiong, WANG Lin-lin, CHANG Ru-zhen , QIU Li-juan. A Dominant Locus, qBSC-1, Controls β Subunit Content of Seed Storage Protein in Soybean (Glycine max (L.) Merri.)[J]. Journal of Integrative Agriculture, 2014, 13(9): 1854-1864.
[13]	AO Xue, GUO Xiao-hong, ZHU Qian, ZHANG Hui-jun, WANG Hai-ying, MA Zhao-hui, HAN, Xiao-ri, ZHAO Ming-hui , XIE Fu-ti. Effect of Phosphorus Fertilization to P Uptake and Dry Matter Accumulation in Soybean with Different P Efficiencies[J]. Journal of Integrative Agriculture, 2014, 13(2): 326-334.
[14]	ZHANG Gu-wen, XU Sheng-chun, HU Qi-zan, MAO Wei-hua , GONG Ya-ming. Putrescine Plays a Positive Role in Salt-Tolerance Mechanisms by Reducing Oxidative Damage in Roots of Vegetable Soybean[J]. Journal of Integrative Agriculture, 2014, 13(2): 349-357.
[15]	LI Xi-huan, WANG Yun-jie, WU Bing, KONG You-bin, LI Wen-long, CHANG Wen-suo , ZHANG Cai-ying. GmPHR1, a Novel Homolog of the AtPHR1 Transcription Factor, Plays a Role in Plant Tolerance to Phosphate Starvation[J]. Journal of Integrative Agriculture, 2014, 13(12): 2584-2593.