? 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

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.
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
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