? Transcriptome analysis of salt-responsive genes and SSR marker exploration in <em>Carex rigescens</em> using RNA-seq
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    2018, Vol. 17 Issue (01): 184-196     DOI: 10.1016/S2095-3119(17)61749-0
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Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq
LI Ming-na1*, LONG Rui-cai2*, FENG Zi-rong1, LIU Feng-qi3, SUN Yan1, ZHANG Kun1, KANG Jun-mei2, WANG Zhen2, CAO Shi-hao1 
1 Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R.China
2 Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
3 Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, Heilongjiang 150086, P.R.China
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Abstract Carex rigescens (Franch.) V. Krecz is a wild turfgrass perennial species in the Carex genus that is widely distributed in salinised areas of northern China.  To investigate genome-wide salt-response gene networks in C. rigescens, transcriptome analysis using high-throughput RNA sequencing on C. rigescens exposed to a 0.4% salt treatment (Cr_Salt) was compared to a non-salt control (Cr_Ctrl).  In total, 57 742 546 and 47 063 488 clean reads were obtained from the Cr_Ctrl and Cr_Salt treatments, respectively.  Additionally, 21 954 unigenes were found and annotated using multiple databases.  Among these unigenes, 34 were found to respond to salt stress at a statistically significant level with 6 genes up-regulated and 28 down-regulated.  Specifically, genes encoding an EF-hand domain, ZFP and AP2 were responsive to salt stress, highlighting their roles in future research regarding salt tolerance in C. rigescens and other plants.  According to our quantitative RT-PCR results, the expression pattern of all detected differentially expressed genes were consistent with the RNA-seq results.  Furthermore, we identified 11 643 simple sequence repeats (SSRs) from the unigenes.  A total of 144 amplified successfully in the C. rigescens cultivar Lüping 1, and 69 of them reflected polymorphisms between the two genotypes tested.  This is the first genome-wide transcriptome study of C. rigescens in both salt-responsive gene investigation and SSR marker exploration.  Our results provide further insights into genome annotation, novel gene discovery, molecular breeding and comparative genomics in C. rigescens and related grass species.
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Key wordssalt stress     Carex rigescens     transcriptome     differentially expressed genes     SSR markers     
Received: 2017-04-10; Published: 2017-08-15
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This work was supported by the National Natural Science Foundation of China (31472139).

Corresponding Authors: Correspondence SUN Yan, E-mail: 02008@cau.edu.cn    
About author: LI Ming-na, E-mail: naljt4@163.com; LONG Rui-cai, E-mail: dragongodsgod@163.com;* These authors contributed equally to this study.
Cite this article:   
LI Ming-na, LONG Rui-cai, FENG Zi-rong, LIU Feng-qi, SUN Yan, ZHANG Kun, KANG Jun-mei, WANG Zhen, CAO Shi-hao. Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq[J]. Journal of Integrative Agriculture, 2018, 17(01): 184-196.
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http://www.chinaagrisci.com/Jwk_zgnykxen/EN/10.1016/S2095-3119(17)61749-0      or     http://www.chinaagrisci.com/Jwk_zgnykxen/EN/Y2018/V17/I01/184
 
[1] Bushman B S, Amundsen K L, Warnke S E, Robins J G, Johnson P G. 2016. ranscriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress. BMC Genomics, 17, 48.
[2] Chen C, Sun X, Duanmu H, Zhu D, Yu Y, Cao L, Liu A, Jia B, Xiao J, Zhu Y. 2015. GsCML27, a gene encoding a calcium-binding Ef-Hand protein from Glycine soja, plays differential roles in plant responses to bicarbonate, salt and osmotic stresses. PLoS ONE, 10, e0141888.
[3] Deinlein U, Stephan A B, Horie T, Luo W, Xu G, Schroeder J I. 2014. Plant salt-tolerance mechanisms. Trends Plant Science, 19, 371-379.
[4] Deshmukh R, Sonah H, Patil G, Chen W, Prince S, Mutava R, Vuong T, Valliyodan B, Nguyen H T. 2014. Integrating omic approaches for abiotic stress tolerance in soybean. Frontiers in Plant Science, 5, 244.
[5] Duan Y B, Li J, Qin R Y, Xu R F, Li H, Yang Y C, Ma H, Li L, Wei P C, Yang J B. 2016. Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis. Plant Molecular Biology, 90, 49-62.
[6] Gao C, Rong R, Zhang Z Q, Guo P J, Meng H. 2009. Experimental research of extracting extracorporeal anti-herpes virus. ChinaPharmaceuticals, 18, 5-6. (in Chinese)
[7] Gao H, Song A, Zhu X, Chen F, Jiang J, Chen Y, Sun Y, Shan H, Gu C, Li P, Chen S. 2012. The heterologous expression in Arabidopsis of a chrysanthemum Cys2/His2 zinc finger protein gene confers salinity and drought tolerance. Planta, 235, 979-993.
[8] Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q D, Chen Z H, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren B W, Nusbaum C, Lindblad-Toh K, Friedman N, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29, 644-652.
[9] Han G L, Wang M J, Yuan F, Sui N, Song J, Wang B S. 2014. The CCCH zinc finger protein gene AtZFP1 improves salt resistance in Arabidopsis thaliana. Plant Molecular Biology, 86, 237-253.
[10] He S, Xing Q, Yin Z. 1993. Flora of Beijing. Beijing Publishing House, China. pp. 1293-1314. (in Chinese)
[11] Hu L, Li H, Chen L, Lou Y, Amombo E, Fu J. 2015. RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. BMC Genomics, 16, 575.
[12] Jiang L, Pan L J. 2012. Identification and expression of C2H2 transcription factor genes in Carica papaya under abiotic and biotic stresses. Molecular Biology Reports, 39, 7105-7115.
[13] Jin X, Xue Y, Wang R, Xu R, Bian L, Zhu B, Han H, Peng R, Yao Q. 2013. Transcription factor OsAP21 gene increases salt/drought tolerance in transgenic Arabidopsis thaliana. Molecular Biology Reports, 40, 1743-1752.
[14] Jing P, Zou J, Kong L, Hu S, Wang B, Yang J, Xie G. 2016. OsCCD1, a novel small calcium-binding protein with one EF-hand motif, positively regulates osmotic and salt tolerance in rice. Plant Science, 247, 104-114.
[15] Jung Y J, Lee I H, Nou I S, Lee K D, Rashotte A M, Kang K K. 2013. BrRZFP1 a Brassica rapa C3HC4-type RING zinc finger protein involved in cold, salt and dehydration stress. Plant Biology, 15, 274-283.
[16] Kielbowicz-Matuk A. 2012. Involvement of plant C2H2-type zinc finger transcription factors in stress responses. Plant Science, 185-186, 78-85.
[17] Kim H, Kim S H, Seo D H, Chung S, Kim S W, Lee J S, Kim W T, Lee J H. 2016. ABA-HYPERSENSITIVE BTB/POZ PROTEIN 1 functions as a negative regulator in ABA-mediated inhibition of germination in Arabidopsis. Plant Molecular Biology, 90, 303-315.
[18] Kiyota E, Pena I A, Arruda P. 2015. The saccharopine pathway in seed development and stress response of maize. Plant Cell and Environment, 38, 2450-2461.
[19] Kudla J, Batistic O, Hashimoto K. 2010. Calcium signals: The lead currency of plant information processing. The Plant Cell, 22, 541-563.
[20] Li P, Zhang G, Gonzales N, Guo Y, Hu H, Park S, Zhao J. 2016. Ca2+-regulated and diurnal rhythm-regulated Na+/Ca2+ exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis. Plant, Cell & Environment, 39, 377-392.
[21] Li S, Fan C, Li Y, Zhang J, Sun J, Chen Y, Tian C, Su X, Lu M, Liang C, Hu Z. 2016. Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq. BMC Genomics, 17, 200.
[22] Liang F, Bai S Y, Dong A X, Wu N. 2011. Biological character comparison with the seeds of 18 plant species in Carex genus. Pratacultural science, 28, 1825-1830. (in Chinese)
[23] Liu H H, Tian X, Li Y J, Wu C A, Zheng C C. 2008. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. Rna - A Publication of the Rna Society, 14, 836-843.
[24] Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25, 402-408.
[25] Long R C, Li M N, Kang J M, Zhang T J, Sun Y, Yang Q C. 2015. Small RNA deep sequencing identifies novel and salt-stress-regulated microRNAs from roots of Medicago sativa and Medicago truncatula. Physiologia Plantarum, 154, 13-27.
[26] Ma X, Liang W, Gu P, Huang Z. 2016. Salt tolerance function of the novel C2H2-type zinc finger protein TaZNF in wheat. Plant Physiology and Biochemistry, 106, 129-140.
[27] Mohammadi-Nejad G, Singh R K, Arzani A, Rezaie A M, Sabouri H, Gregorio G B. 2010. Evaluation of salinity tolerance in rice genotypes. International Journal of Plant Production, 4, 199-207.
[28] Moulin M, Deleu C, Larher F. 2000. L-Lysine catabolism is osmo-regulated at the level of lysine-ketoglutarate reductase and saccharopine dehydrogenase in rapeseed leaf discs. Plant Physiology and Biochemistry, 38, 577-585.
[29] Munns R, Tester M. 2008. Mechanisms of salinity tolerance. Annual Review of Plant Biology, 59, 651-681.
[30] Nagaraja Reddy R, Madhusudhana R, Murali Mohan S, Chakravarthi D V N, Seetharama N. 2011. Characterization, development and mapping of unigene-derived microsatellite markers in sorghum [Sorghum bicolor (L.) Moench]. Molecular Breeding, 29, 543-564.
[31] Paul S, Kundu A, Pal A. 2011. Identification and validation of conserved microRNAs along with their differential expression in roots of Vigna unguiculata grown under salt stress. Plant Cell Tissue and Organ Culture, 105, 233-242.
[32] Postnikova O A, Shao J, Nemchinov L G. 2013. Analysis of the alfalfa root transcriptome in response to salinity stress. Plant & Cell Physiology, 54, 1041-1055.
[33] Reddy V S, Shlykov M A, Castillo R, Sun E I, Saier Jr M H. 2012. The major facilitator superfamily (MFS) revisited. FEBS Journal, 279, 2022-2035.
[34] Robinson M D, McCarthy D J, Smyth G K. 2010. edgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
[35] Sekhwal M K, Sharma V, Sarin R. 2013. Identification of MFS proteins in sorghum using semantic similarity. Theory in Biosciences, 132, 105-113.
[36] Shabala S, Cuin T A. 2008. Potassium transport and plant salt tolerance. Physiologia Plantarum, 133, 651-669.
[37] Shi H, Jiang C, Ye T, Tan D X, Reiter R J, Zhang H, Liu R, Chan Z. 2015. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin. Journal of Experimental Botany, 66, 681-694.
[38] Storey J D, Tibshirani R. 2003. Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America, 100, 9440-9445.
[39] Sun Y, Li M L, Mao P S. 2011. Study of standard germination method in Carex rigescens. Northern Horticulture, 19, 68-70. (in Chinese)
[40] Tang L, Cai H, Ji W, Luo X, Wang Z, Wu J, Wang X, Cui L, Wang Y, Zhu Y, Bai X. 2013. Overexpression of GsZFP1 enhances salt and drought tolerance in transgenic alfalfa (Medicago sativa L.). Plant Physiology and Biochemistry, 71, 22-30.
[41] NSSO (The National Soil Survey Office of China). 1998. Soil of China. China Agriculture Press, China. (in Chinese)
[42] Wang C T, Shao J M. 2012. Characterization of the ZmCK1 gene encoding a calcium-dependent protein kinase responsive to multiple abiotic stresses in maize. Plant Molecular Biology Reporter, 31, 222-230.
[43] Wang J, Li B, Meng Y, Ma X, Lai Y, Si E, Yang K, Ren P, Shang X, Wang H. 2015. Transcriptomic profiling of the salt-stress response in the halophyte Halogeton glomeratus. BMC Genomics, 16, 169.
[44] Wang L K, Feng Z X, Wang X, Wang X W, Zhang X G. 2010. DEGseq: An R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 26, 136-138.
[45] Wang X, Han H, Yan J, Chen F, Wei W. 2015. A new AP2/ERF transcription factor from the oil plant jatropha curcas confers salt and drought tolerance to transgenic tobacco. Applied Biochemistry and Biotechnology, 176, 582-597.
[46] Wang Y. 1997. Advances in research of heat shock factors. Journal of China Three Gorges University, 2, 110-114. (in Chinese)
[47] Weber H, Hellmann H. 2009. Arabidopsis thaliana BTB/ POZ-MATH proteins interact with members of the ERF/AP2 transcription factor family. FEBS Journal, 276, 6624-6635.
[48] Xie Q, Niu J, Xu X, Xu L, Zhang Y, Fan B, Liang X, Zhang L, Yin S, Han L. 2015. De novo assembly of the Japanese lawngrass (Zoysia japonica Steud.) root transcriptome and identification of candidate unigenes related to early responses under salt stress. Frontiers in Plant Science, 6, 610.
[49] Xu Z S, Chen M, Li L C, Ma Y Z. 2011. Functions and application of the AP2/ERF transcription factor family in crop improvement. Journal of Integrative Plant Biology, 53, 570-585.
[50] Yamamoto N, Takano O, Tanakay K, Ishige T, Terashima S, Endo C, Kurusu T, Yajima S, Yano K, Tada Y. 2015. Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. Frontiers in Plant Science, 6, 00241.
[51] Yang Z, Xie T, Liu Q. 2014. Physiological responses of Phragmites australisto the combined effects of water and salinity stress. Ecohydrology, 7, 420-426.
[52] Zhang F, Li L, Jiao Z, Chen Y, Liu H, Chen X, Fu J, Wang G, Zheng J. 2016. Characterization of the calcineurin B-Like (CBL) gene family in maize and functional analysis of ZmCBL9 under abscisic acid and abiotic stress treatments. Plant Science, 253, 118-129.
[53] Zhang K, Li M N, Cao S H, Sun Y. 2017. Response of Carex rigescens to different NaCl concentrations and its salinity threshold calculation. Pratacultural science, 34, 479-487. (in Chinese)
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