Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq

LI Ming-na; LONG Rui-cai; FENG Zi-rong; LIU Feng-qi; SUN Yan; ZHANG Kun; KANG Jun-mei; WANG Zhen; CAO Shi-hao

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Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq

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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, 57742546 and 47063488 clean reads were obtained from the Cr_Ctrl and Cr_Salt treatments, respectively. Additionally, 21954 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 downregulated. 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 11643 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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《农业科学学报（英文版）》 |2018年第1期|184-196|共13页
作者
LI Ming-na; LONG Rui-cai; FENG Zi-rong; LIU Feng-qi; SUN Yan; ZHANG Kun; KANG Jun-mei; WANG Zhen; CAO Shi-hao;
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Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing 100193,P.R.China;

Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China;

Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing 100193,P.R.China;

Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, Heilongjiang 150086, P.R.China;

Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing 100193,P.R.China;

Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing 100193,P.R.China;

Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China;

Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China;

Grassland Science Department, College of Animal Science and Technology, China Agricultural University, Beijing 100193,P.R.China;

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Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq

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