Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 626 No. 3: 23 Nov. 2023
Type: Article
Published: 2023-11-23
DOI: 10.11646/phytotaxa.626.3.3
Page range: 170-180
Abstract views: 88
PDF downloaded: 38

Development of SSR markers identification system for Carex L. based on RAD sequencing

Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
National Key Laboratory of Wheat Improvement; Peking University Institute of Advanced Agricultural Sciences; Shandong Laboratory of Advanced Agricultural Sciences in Weifang; 261325; Shandong; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
College of Landscape Architecture and Tourism; Hebei Agricultural University; 071000; Baoding; Hebei; P.R. China
Beijing Radiation Center; Beijing Academy of Science and Technology; 102300; Beijing; P.R. China
Science and technology exploitation and examination base of Mentougou District; 102300; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Beijing Key Laboratory of Greening Plants Breeding; Beijing Institute of Architecture; 100102; Beijing; P.R. China
Monocots Carex L. Restriction site-associated DNA sequencing SNP SSR Molecular identification

Abstract

In this study, we designed and evaluated an efficient set of simple sequence repeat (SSR) markers from restriction site-associated DNA (RAD) sequencing data of four widely utilized Carex L. accession across Northern China, especially in Beijing. Based on their genomic sequencing data, we developed 400 SSR markers and evaluated their amplification specificities among which a total of 17 SSR markers were identified as a core set of molecular markers for efficient assessment of diverse Carex L. accessions. Using this molecular identification system, we classified 26 Carex L. accessions into 3 genetically distinct groups. The establishment of a molecular identification system based on a core set of 17 SSR markers provides an essential basis for evaluating genetic relationships among Carex L. accessions along with a wealth of genetic resources for marker-assisted selection and breeding of Carex L..

 

References

  1. Adam-Blondon, A.F., Roux, C., Claux, D., Butterlin, G., Merdinoglu, D. & This, P. (2004) Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theoretical and Applied Genetics 109: 1017–1027. https://doi.org/10.1007/s00122-004-1704-y
  2. Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33: 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
  3. Biswas, M.K., Bagchi, M., Nath, U.K., Biswas, D., Natarajan, S., Jesse, D.M.I., Park, J.I. & Nou, I.S. (2020) Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species. Scientific reports 10: 18621. https://doi.org/10.1038/s41598-020-75553-0
  4. Bruce, A.F., Habibollah, G., Robert, F.C.N. & Julian, R.S. (2012) Phylogeny of Carex subg. Vignea (Cyperaceae) based on amplified fragment length polymorphism and nrDNA data. Systematic Botany 37: 913–925. https://doi.org/10.1600/036364412X656464
  5. Caro, R.E.S., Cagayan, J., Gardoce, R.R., Manohar, A.N.C., Canama-Salinas, A.O., Rivera, R.L., Lantican, D.V., Galvez, H.F. & Reaño, C.E. (2022) Mining and validation of novel simple sequence repeat (SSR) markers derived from coconut (Cocos nucifera L.) genome assembly. Journal of Genetic Engineering & Biotechnology 20: 71. https://doi.org/10.1186/s43141-022-00354-z
  6. Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34: i884–i890. https://doi.org/10.1093/bioinformatics/bty560
  7. Cui, F., Li, J., Ding, A., Zhao, C., Wang, L., Wang, X., Li, S., Bao, Y., Li, X., Feng, D., Kong, L. & Wang, H. (2011) Conditional QTL mapping for plant height with respect to the length of the spike and internode in two mapping populations of wheat. TAG Theoretical and Applied Genetics 122: 1517–1536. https://doi.org/10.1007/s00122-011-1551-6
  8. Daware, A., Das, S., Srivastava, R., Badoni, S., Singh, A.K., Agarwal, P., Parida, S.K. & Tyagi, A.K. (2016) An efficient strategy combining SSR markers- and advanced QTL-seq-driven QTL mapping unravels candidate genes regulating grain weight in rice. Frontiers in plant science 7: 1535. https://doi.org/10.3389/fpls.2016.01535
  9. Gu, L., Wei, B., Fan, R., Jia, X., Wang, X. & Zhang, X. (2015) Development, identification and utilization of introgression lines using Chinese endemic and synthetic wheat as donors. Journal of Integrative Plant Biology 57: 688–697. https://doi.org/10.1111/jipb.12324
  10. Han, B., Wang, C., Tang, Z., Ren, Y., Li, Y., Zhang, D., Dong, Y. & Zhao, X. (2015) Genome-wide analysis of microsatellite markers based on sequenced database in Chinese spring wheat (Triticum aestivum L.). PloS one 10:e0141540. https://doi.org/10.1371/journal.pone.0141540
  11. Hendrichs, M., Michalski, S., Begerow, D., Oberwinkler, F. & Hellwig, F. (2004a) Phylogenetic relationships in Carex, subgenus Vignea (Cyperaceae), based on ITS sequences. Plant Systematics and Evolution 246: 109–125. https://doi.org/10.1007/s00606-004-0127-1
  12. Hendrichs, M., Oberwinkler, F., Begerow, D. & Bauer, R. (2004b) Carex, subgenus Carex (Cyperaceae)—A phylogenetic approach using ITS sequences. Plant Systematics and Evolution 246: 89–107. https://doi.org/10.1007/s00606-004-0128-0
  13. Jiménez-Mejías, P., Hahn, M., Lueders, K., Starr, J.R., Brown, B.H., Chouinard, B.N., Chung, K.-S., Escudero, M., Ford, B.A., Ford, K.A., Gebauer, S., Gehrke, B., Hoffmann, M.H., Jin, X.-F., Jung, J., Kim, S., Luceño, M., Maguilla, E., Martín-Bravo, S., Míguez, M., Molina, A., Naczi, R.F.C., Pender, J.E., Reznicek, A.A., Villaverde, T., Waterway, M.J., Wilson, K.L., Yang, J.-C., Zhang, S., Hipp, A.L. & Roalson, E.H. (2016) Megaphylogenetic specimen-level approaches to the Carex (Cyperaceae) phylogeny using ITS, ETS, and matK sequences: implications for classification. Systematic Botany 41: 500–518. https://doi.org/10.1600/036364416X692497
  14. Kõressaar, T., Lepamets, M., Kaplinski, L., Raime, K., Andreson, R. & Remm, M. (2018) Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics 34: 1937–1938. https://doi.org/10.1093/bioinformatics/bty036
  15. Li, Y. & He, M. (2014) Genetic mapping and QTL analysis of growth-related traits in Pinctada fucata using restriction-site associated DNA sequencing. PloS one 9: e111707. https://doi.org/10.1371/journal.pone.0111707
  16. Liang, F., Dong, A. & Ma, Y. (2012) Resource survey of wild Carex plants and evaluation of their ornamental characteristics in Beijing. Pratacultural Science 6: 710–716.
  17. Lowe, A.J., Moule, C., Trick, M. & Edwards, K.J. (2004) Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theoretical and Applied Genetics 108: 1103–1112. https://doi.org/10.1007/s00122-003-1522-7
  18. Ma, W., Han, L. & Luo, J. (2001) A new lawn plant resource: genus Carex L. Pratacultural Science 18: 43–56.
  19. Martín-Bravo, S., Jiménez-Mejías, P., Villaverde, T., Escudero, M., Hahn, M., Spalink, D., Roalson, E.H., Hipp, A.L., Group, t.G.C., Benítez-Benítez, C., Bruederle, L.P., Fitzek, E., Ford, B.A., Ford, K.A., Garner, M., Gebauer, S., Hoffmann, M.H., Jin, X.-F., Larridon, I., Léveillé-Bourret, É., Lu, Y.-F., Luceño, M., Maguilla, E., Márquez-Corro, J.I., Míguez, M., Naczi, R., Reznicek, A.A. & Starr, J.R. (2019) A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification. Journal of Systematics and Evolution 57: 695–718. https://doi.org/10.1111/jse.12549
  20. Mohammadi, S.A., Abdollahi Sisi, N. & Sadeghzadeh, B. (2020) The influence of breeding history, origin and growth type on population structure of barley as revealed by SSR markers. Scientific reports 10: 19165. https://doi.org/10.1038/s41598-020-75339-4
  21. Murray, M.G. & Thompson, W.F. (1980) Rapid isolation of high molecular weight plant DNA. Nucleic acids research 8: 4321–4326. https://doi.org/10.1093/nar/8.19.4321
  22. Ning, H., Wang, W., Zheng, C., Li, Z., Zhu, C. & Zhang, Q. (2014a) Genetic diversity analysis of sedges (Carex spp.) in Shandong, China based on inter-simple sequence repeat. Biochemical Systematics and Ecology 56: 158–164. https://doi.org/10.1016/j.bse.2014.05.014
  23. Ning, H., Zheng, C., Wang, W., Zhu, C., Li, Z. & Zhang, Y. (2014b) Establishment and optimization of lSSR-PCR system in Carex. Molecular Plant Breeding 12: 349–355.
  24. Reznicek, A.A. (1990) Evolution in sedges (Carex cyperaceae). Canadian Journal of Botany 68: 1409–1432. https://doi.org/10.1139/b90-180
  25. Rochette, N.C. & Catchen, J.M. (2017) Deriving genotypes from RAD-seq short-read data using Stacks. Nature protocols 12: 2640–2659. https://doi.org/10.1038/nprot.2017.123
  26. Shi, J. (2007) Study on ecological adaptability of Carex giraldiana in Beijing area. Pratacultural Science 24: 98–102.
  27. Somers, D.J., Isaac, P. & Edwards, K. (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theoretical and Applied Genetics 109: 1105–1114. https://doi.org/10.1007/s00122-004-1740-7
  28. Vidak, M., Šatović, Z., Liber, Z., Grdiša, M., Gunjača, J., Kilian, A. & Carović-Stanko, K. (2021) Assessment of the origin and diversity of croatian common bean germplasm using phaseolin type, SSR and SNP markers and morphological traits. Plants 10: 665. https://doi.org/10.3390/plants10040665
  29. Wang, N., Fang, L., Xin, H., Wang, L. & Li, S. (2012) Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC plant biology 12: 148. https://doi.org/10.1186/1471-2229-12-148
  30. Xue, H., Sha, W. & Ni, H. (2005) General situation of studies on Carex L. Journal of qiqihar University 20: 789.
  31. Yang, L.J., Li, X.L., Shi, D.J. & Sa, W.J. (2000) Study on the bio-diversity of alpine plant communities in the higher altitude area of south Qinghai. Grassland and Turf 89: 32–35.
  32. Zhang, C., Zhu, X., Cai, K. & Yu, Y. (2010) Evaluation of shade tolerance of Carex species available for garden-environment planting. Journal of Beijing Forestry University 32: 207–212.