Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq
文献类型： 外文期刊
作者：
Li Ming-na
1
;
Long Rui-cai
2
;
Feng Zi-rong
1
;
Liu Feng-qi
3
;
Sun Yan
1
;
Zhang, Kun
1
;
Kang Jun-mei
2
;
Wang Zhen
2
;
C
1
;
作者机构： 1.China Agr Univ, Grassland Sci Dept, Coll Anim Sci & Technol, Beijing 100193, Peoples R China
2.Chinese Acad Agr Sci, Inst Anim Sci, Beijing 100193, Peoples R China
3.Heilongjiang Acad Agr Sci, Inst Pratacultural Sci, Harbin 150086, Heilongjiang, Peoples R China
关键词： salt stress;Carex rigescens;transcriptome;differentially expressed genes;SSR markers
期刊名称：JOURNAL OF INTEGRATIVE AGRICULTURE （ 影响因子：2.848； 五年影响因子：2.979 ）
ISSN： 2095-3119
年卷期： 2018 年 17 卷 1 期
页码：
收录情况： SCI
摘要： 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 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 11 643 simple sequence repeats (SSRs) from the unigenes. A total of 144 amplified successfully in the C. rigescens cultivar Luping 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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