Hostname: page-component-848d4c4894-2pzkn Total loading time: 0 Render date: 2024-05-22T22:19:06.670Z Has data issue: false hasContentIssue false

Mining, characterization and application of transcriptome-based SSR markers in Chinese jiaotou

Published online by Cambridge University Press:  05 February 2018

Chan Liu*
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
Qing Tang
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
Chaohua Cheng
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
Ying Xu
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
Zemao Yang
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
Zhigang Dai
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
Jianguang Su*
Affiliation:
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
*
*Corresponding author. E-mail: 53385141@qq.com, jgsu@vip.163.com
*Corresponding author. E-mail: 53385141@qq.com, jgsu@vip.163.com

Abstract

Chinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembled de novo by a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

Type
Research Article
Copyright
Copyright © NIAB 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Aggarwal, RK, Hendre, PS, Varshney, RK, Bhat, PR, Krishnakumar, V and Singh, L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theoretical and Applied Genetics 114: 359372.Google Scholar
Cloutier, S, Niu, Z, Datla, R and Duguid, S (2009) Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theoretical and Applied Genetics 119: 5363.Google Scholar
Ding, X, Jia, Q, Luo, X, Zhang, L, Cong, H, Liu, G and Bai, C (2015) Development and characterization of expressed sequence tag-derived simple sequence repeat markers in tropical forage legume Stylosanthes guianensis (Aubl.) Sw. Molecular Breeding 35: 202.Google Scholar
Guo, R, Mao, Y, Cai, J, Wang, J, Wu, J and Qiu, Y (2014) Characterization and cross-species transferability of EST–SSR markers developed from the transcriptome of Dysosma versipellis (Berberidaceae) and their application to population genetic studies. Molecular Breeding 34: 17331746.Google Scholar
Hou, B, Feng, S and Wu, Y (2017) Systemic identification of Hevea brasiliensis EST-SSR markers and primer screening. Journal of Nucleic Acids 2017: 6590902.Google Scholar
Iseli, C, Jongeneel, C and Bucher, P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In Proceedings of International Conference on Intelligent Systems for Molecular Biology, Menlo Park, CA: AAAI Press, pp. 138148.Google Scholar
Li, F, Ma, C, Chen, Q, Liu, T, Shen, J, Tu, J, Xing, Y and Fu, T (2012) Comparative mapping reveals similar linkage of functional genes to QTL of yield-related traits between Brassica napus and Oryza sativa. Journal of Genetics 91: 163170.Google Scholar
Li, Y, Korol, A, Fahima, T and Nevo, E (2004) Microsatellites within genes: structure, function, and evolution. Molecular Biology and Evolution 21: 9911007.Google Scholar
Liu, T, Mao, D, Zhang, S, Xu, C and Xing, Y (2009) Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza Sativa). Theoretical and Applied Genetics 118: 15091517.Google Scholar
Liu, T, Shao, D, Kovi, M and Xing, Y (2010a) Mapping and validation of quantitative trait loci for spikelets per panicle and 1000-grain weight in rice (Oryza sativa L.). Theoretical and Applied Genetics 120: 933942.Google Scholar
Liu, T, Zhang, Y, Xue, W, Xu, C, Li, X and Xing, Y (2010b) Comparison of quantitative trait loci for 1,000-grain weight and spikelets per panicle across three connected rice populations. Euphytica 175: 383394.Google Scholar
Liu, T, Zhang, Y, Zhang, H and Xing, Y (2011a) Quantitative trait loci for the number of grains per panicle dependent on or independent of heading date in rice (Oryza Sativa L.). Breeding Science 61: 142150.Google Scholar
Liu, T, Li, L, Zhang, Y, Xu, C, Li, X and Xing, Y (2011b) Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations. Journal of Genetics 90: 377382.Google Scholar
Liu, T, Zhu, S, Tang, Q, Chen, P, Yu, Y and Tang, S (2013a) De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). BMC Genomics 14: 125.Google Scholar
Liu, T, Zhu, S, Fu, L, Tang, Q, Yu, Y, Chen, P, Luan, M, Wang, C and Tang, S (2013b) Development and characterization of 1,827 expressed sequence tag-derived simple sequence repeat markers in ramie (Boehmeria nivea L. Gaud). PLoS ONE 8: e60346.Google Scholar
Liu, T, Zhu, S, Tang, Q, Yu, Y and Tang, S (2013c) Identification of drought stress-responsive transcription factors in ramie (Boehmeria nivea L. Gaud). BMC Plant Biology 13: 130.Google Scholar
Liu, T, Zhu, S, Tang, Q and Tang, S (2014a) QTL mapping for fiber yield-related traits by constructing the first genetic linkage map in ramie (Boehmeria nivea L. Gaud). Molecular Breeding 34: 883892.Google Scholar
Liu, T, Zhu, S, Tang, Q and Tang, S (2014b) Identification of 32 full-length NAC transcription factors in ramie (Boehmeria nivea L. Gaud) and characterization of the expression pattern of these genes. Molecular Genetics and Genomics 289: 675684.Google Scholar
Liu, T, Tang, S, Zhu, S, Tang, Q and Zheng, X (2014c) Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud). Plant Molecular Biology 86: 8592.Google Scholar
Liu, T, Zeng, L, Zhu, S, Chen, X, Tang, Q, Mei, S and Tang, S (2015a) Large-scale development of expressed sequence tag-derived simple sequence repeat markers by deep transcriptome sequencing in garlic (Allium sativum L.). Molecular Breeding 35: 204.Google Scholar
Liu, T, Zhu, S, Tang, Q and Tang, S (2015b) Identification of a CONSTANS homologous gene with distinct diurnal expression patterns in varied photoperiods in ramie (Boehmeria nivea L. Gaud). Gene 560: 6370.Google Scholar
Liu, T, Zhu, STang, Q and Tang, S (2015c) Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress. Gene 558: 131137.Google Scholar
Mann, L and Stearn, W (1960) Rakkyo or ch'iao t'ou (Allium chinense G. Don, syn. A. bakeri Regel) a little known vegetable crop. Economic Botany 14: 6383.Google Scholar
Mao, D, Liu, T, Xu, C, Li, X and Xing, Y (2011) Epistasis and complementary gene action adequately account for the genetic bases of transgressive segregation of kilo-grain weight in rice. Euphytica 180: 261271.Google Scholar
Mei, S, Liu, T and Wang, Z (2016) Comparative transcriptome profile of the cytoplasmic male sterile and fertile floral buds of radish (Raphanus sativus L.). International Journal of Molecular Sciences 17: 42.Google Scholar
Ohri, D, Fritsch, R and Hanetl, P (1998) Evolution of genome size in Allium (Alliaceae). Plant Systematics and Evolution 210: 5786.Google Scholar
Peng, JH and Lapitan, NL (2005) Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Functional & Integrative Genomics 5: 8096.Google Scholar
Rohlf, FJ (2002) NTSYS-pc. Numerical taxonomy and multivariate analysis system, version 2.10. Exeter Software, New York.Google Scholar
Thiel, T (2003) MISA – Microsatellite identification tool. http://www.pgrc.ipk-gatersleben.de/misa/.Google Scholar
Untergasser, A, Nijveen, H, Rao, X, Bisseling, T, Geurts, R and Leunissen, J (2007) Primer3plus, an enhanced web interface to Primer3. Nucleic Acids Research 35: W71W74.Google Scholar
Wang, H, Jiang, J, Chen, S, Qi, X, Peng, H, Li, P, Song, A, Guan, Z, Fang, W, Liao, Y and Chen, F (2013) Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery. PLoS ONE 8: e62293.Google Scholar
Wu, KS and Tanksley, SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Molecular Genetics and Genomics 241: 225235.Google Scholar
Xu, Z, Um, Y, Kim, C, Lu, G, Guo, D, Liu, H, Bah, A and Mao, A (2008) Effect of plant growth regulators, temperature and sucrose on shoot proliferation from the stem disc of Chinese jiaotou (Allium chinense) and in vitro bulblet formation. Acta Physiologiae Plantarum 30: 521528.Google Scholar
Ye, J, Fang, L, Zheng, H, Zhang, Y, Chen, J, Zhang, Z, Wang, J, Li, S, Li, R, Bolund, L and Wang, J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Research 34: W293W297.Google Scholar
Young, M, Wakefield, M, Smyt, G and Oshlack, A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11: R14.Google Scholar
Yu, Y, Zeng, L, Yan, Z, Liu, T, Sun, K, Zhu, T and Zhu, A (2015) Identification of ramie genes in response to Pratylenchus coffeae infection challenge by digital gene expression analysis. International Journal of Molecular Sciences 16: 2198922007.Google Scholar
Zeng, L, Shen, A, Chen, J, Yan, Z, Liu, T, Xue, Z and Yu, Y (2016) Transcriptome analysis of ramie (Boehmeria nivea L. Gaud.) in response to ramie moth (Cocytodes coerulea Guenée) infestation. BioMed Research International 2016: 3702789.Google Scholar
Zhai, L, Xu, L, Wang, Y, Cheng, H, Chen, Y, Gong, Y and Liu, L (2014) Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.). Molecular Breeding 33: 611624.Google Scholar
Zhang, L, Li, Y, Tao, A, Fang, P and Qi, J (2015) Development and characterization of 1,906 EST-SSR markers from unigenes in jute (Corchorus spp.). PLoS ONE 10: e0140861.Google Scholar
Zheng, X, Pan, C, Diao, Y, You, Y, Yang, C and Hu, Z (2013) Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae). BMC Genomics 14: 490.Google Scholar
Zheng, X, Tang, S, Zhu, S, Dai, Q and Liu, T (2016a) Identification of an NAC transcription factor family by deep transcriptome sequencing in onion (Allium cepa L.). PLoS ONE 11: e0157871.Google Scholar
Zheng, X, Zhu, S, Tang, S and Liu, T (2016b) Identification of drought, cadmium and root-lesion nematode infection stress-responsive transcription factors in ramie. Open Life Science 11: 191199.Google Scholar
Zhu, S, Tang, S, Tang, Q and Liu, T (2014) Genome-wide transcriptional changes of ramie (Boehmeria nivea L. Gaud) in response to root-lesion nematode infection. Gene 552: 6774.Google Scholar
Zhu, S, Zheng, X, Dai, Q, Tang, S and Liu, T (2016) Identification of quantitative trait loci for flowering time traits in ramie (Boehmeria nivea L. Gaud). Euphytica 210: 367374.Google Scholar
Zhu, S, Tang, S, Tan, Z, Yu, Y, Dai, Q and Liu, T (2017a) Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium. BMC Genomics 18: 60.Google Scholar
Zhu, S, Liu, T, Dai, Q, Wu, D, Zheng, X, Tang, S and Chen, J (2017b) Genetic structure and relationships of an associated population in ramie (Boehmeria nivea L. Gaud) evaluated by SSR markers. Biotechnology & Biotechnological Equipment 31: 3644.Google Scholar
Supplementary material: File

Liu et al. supplementary material

Liu et al. supplementary material 1

Download Liu et al. supplementary material(File)
File 152 KB
Supplementary material: File

Liu et al. supplementary material

Liu et al. supplementary material 2

Download Liu et al. supplementary material(File)
File 408 KB
Supplementary material: File

Liu et al. supplementary material

Liu et al. supplementary material 3

Download Liu et al. supplementary material(File)
File 27.6 KB