%0 Journal Article %A LI Ming-na %A LONG Rui-cai %A FENG Zi-rong %A LIU Feng-qi %A SUN Yan %A ZHANG Kun %A KANG Jun-mei %A WANG Zhen %A CAO Shi-hao %T Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq %D 2018 %R 10.1016/S2095-3119(17)61749-0 %J Journal of Integrative Agriculture %P 184-196 %V 17 %N 01 %X 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. %U https://www.chinaagrisci.com/Jwk_zgnykxen/EN/10.1016/S2095-3119(17)61749-0