%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