The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species
文献类型： 外文期刊
作者： Liu, Lingyun 1 ; Fan, Xifeng 2 ; Tan, Penghui 3 ; Wu, Juying 2 ; Zhang, Hui 2 ; Han, Chao 2 ; Chen, Chao 2 ; Xun, Lulu 4 ; G 1 ;
作者机构： 1.Beijing Forestry Univ, Coll Grassland Sci, Beijing 100083, Peoples R China
2.Beijing Acad Agr & Forestry Sci, Beijing Res & Dev Ctr Grass & Environm, Beijing 100097, Peoples R China
3.Beijing Chaoyang Foreign Language Sch, Beijing 100000, Peoples R China
4.Inst Bot Shaanxi Prov, Xian Bot Garden Shaanxi Prov, Shaanxi Engn Res Ctr Conservat & Utilizat Bot Res, Xian 710000, Shaanxi, Peoples R China
5.Univ Calif Davis, Dept Plant Biol, Davis, CA 95616 USA
关键词： Carex L.; Illumina RNA-sequencing; Gene function annotation; SSR marker; Marker polymorphism; Genetic cluster
期刊名称：BMC PLANT BIOLOGY （ 影响因子：4.215； 五年影响因子：4.96 ）
ISSN： 1471-2229
年卷期： 2021 年 21 卷 1 期
页码：
收录情况： SCI
摘要： Background: Carex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order to investigate the gene function annotation of Carex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79 Carex germplasms. Results: In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei's (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What's more, the fingerprints of 79 Carex species are established in this study. Different combinations of primer pairs can be used to identify multiple Carex at one time, which overcomes the difficulties of traditional identification methods. Conclusions: The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79 Carex species. These markers can be used to investigate the evolutionary history of Carex and related species, as well as to serve as a guide in future breeding projects.
- 相关文献
作者其他论文 更多>>
-
The Importance of Soil Seed Bank Function in Studies of Grassland Degradation
作者：Chen, Chao;He, Wei;Scullion, John;Wilkinson, Mike
关键词：plant life cycle; soil permeability; dormancy; Poaceae; soil organic matter
-
In vitro induction and characterization of octaploid Schizachyrium scoparium, an ornamental grass
作者：Xiao, Zhuolin;Wei, Mingjun;Xu, Yue;Nie, Haochen;Zhang, Hui;Teng, Ke;Teng, Wenjun;Wu, Juying;Fan, Xifeng;Yue, Yuesen;Xiao, Zhuolin
关键词：
Schizachyrium scoparium ; Polyploidization; Flow cytometry; Tetraploid; Octaploid -
The Effects of Multi-Scenario Land Use Change on the Water Conservation in the Agro-Pastoral Ecotone of Northern China: A Case Study of Bashang Region, Zhangjiakou City
作者：Zhao, Ruiyang;Kan, Haiming;Xu, Hengkang;Chen, Chao;Zhang, Guofang;Pang, Zhuo;Zhang, Weiwei;Zhao, Ruiyang
关键词：water conservation capacity (WCC); land-use change scenarios; water yield (WY); sustainable agricultural development; irrigated land
-
Insights into the interlinkages between rhizosphere soil extracellular enzymes and microbiome assemblages across soil profiles in grasslands
作者：Liu, Xueqing;Fan, Xifeng;Zhang, Hui;Yue, Yuesen;Wu, Juying;Teng, Wenjun;Mu, Na;Teng, Ke;Wen, Haifeng;Zhang, Mingcai
关键词：Carex leucochlora; Rhizosphere microbe; Soil extracellular enzymes; Soil organic carbon; Soil ecosystem service
-
Miscanthus sinensis 'Gracillimus' Shows Strong Submergence Tolerance Implying Its Potential Utilization in Construction of Ecological Ditches
作者：Zhao, Chunqiao;Wu, Ting;Chang, Aoxiang;Li, Xiaona;Li, Cui;Zheng, Mei;Chen, Zebing;Zhao, Di;Guo, Qiang;Hou, Xincun;Fan, Xifeng;Zhao, Chunqiao;Wu, Ting;Chang, Aoxiang;Fan, Zhenyu;Li, Xiaona;Li, Cui;Zheng, Mei;Sun, Yu;Chen, Zebing;Zhao, Di;Guo, Qiang;Hou, Xincun;Fan, Xifeng;Wu, Ting;Chang, Aoxiang;Fan, Zhenyu;Sun, Yu;Wan, Xiuyun;Meng, Jie;Zhang, Jing
关键词：submergence; perennial grass; ecological ditch; farmland ecosystem; physiological indicators; nitrogen assimilation; biomass dry weight
-
The Evolutionary Traits of Carbon Emissions from the Planting Industry in Beijing, China
作者：Chuan, Limin;Zhang, Hui;Zhao, Jiang;Zhao, Jingjuan;Wang, Ailing
关键词：Beijing; planting industry; carbon emissions; carbon efficiency; low-carbon agriculture
-
A novel plant growth regulator B2 mediates drought resistance by regulating reactive oxygen species, phytohormone signaling, phenylpropanoid biosynthesis, and starch metabolism pathways in Carex breviculmis
作者：Shi, Jiannan;Wang, Ye;Li, Runzhi;Yu, Chunxin;Peng, Zhen;Gao, Yuerong;Liu, Ziyan;Duan, Liusheng;Fan, Xifeng;Duan, Liusheng
关键词：B2; Carex breviculmis; Drought resistance; Plant growth regulator; Transcriptome
