Investigation of Persian black cumin (Bunium persicum Boiss.) transcriptome in the granulation stage and identification of genomic microsatellites in this plant

Document Type : Research Paper

Authors

1 Ph.D candidate, Plant Production and Genetic Engineering Department, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran.

2 Corresponding Author. Prof., Plant Production and Genetic Engineering Department, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran.

3 Prof., Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, I.R. Iran.

4 Prof. La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, VIC 3086, Australia.

5 Prof., Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia.

Abstract

Persian black cumin is one of the most important endemic plants to Iran. Its seed is used in the daily diet of Iranians and also has medicinal properties and aromatic compounds. Unfortunately, there is little information about its genome and molecular markers. In this study, the transcriptome of Iranian black cumin was sequenced in the granulation stage and after extracting the microsatellites (SSR markers) related to this growth stage, their interpretation was done. After RNA extraction, the inflorescences and stems were sequenced. Sequencing depth and length were 6 GB and 150 bp pair-end, respectively. Sequencing data were analyzed using different softwares. De-novo assembly of Persian black cumin was performed by Trinity software. Microsatellite markers were extracted using MISA software. Finally, the functional interpretation of the microsatellite-containing sequences was performed by the WEGO database. The GC content of different samples was 47 to 50%. 8389 microsatellite markers were obtained from 45146 unigenes. At least 11% of unigenes contained microsatellites. A/T and AG/CT nucleotides had the highest percentage of microsatellite markers. Among the three nucleotide repeats, ATC/ATG and AAG/CTT had the highest frequency of microsatellites. The results of functional interpretation showed that unigenes containing microsatellite markers cover a wide range of biological activities of Persian black cumin and the genes involved in seed development and growth have a high level of expression. This study is the first report of microsatellite markers of Persian black cumin. The results of the present study can be useful in finding different markers for breeding programs and developing cultivars with different goals.

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References

  • Bharti, R., Kumar, S., and Parekh, MJ., 2018. Development of genomic simple sequence repeat (gSSR) markers in cumin and their application in diversity analyses and cross-transferability. Industrial Crops and Products, 111: 158-164.
  • Emamipoor, Y. and Maziah, M. 2014. An efficient method in breaking of dormancy from Bunium persicum (Boiss) Fedtsch seeds: a valuable herb of Middle East and Central Asia. Asian Pac J Trop Biomed; 4(8): 642-649.
  • Fungtammasan, A., Guruprasad, A., Suzanne, E., Marcia, S., Chen, S., Robert, H., Paul, M,. Kristin, E., and Kateryna, D., 2015. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Research 25: 736-749.
  • Grubisha, L., Bailey A., Nicholas, J., Steven, L and Matthew, R., 2014. Characterization of microsatellite markers for pinedrops, Pterospora andromedea (Ericaceae), from Illumina MiSeq sequencing. Applications in Plant Sciences 2:
  • Hui, L., Defang, L., Anguo, Ch, Huijuan, T., Jianjun, L. and Siqi, Huang., 2016. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers. Polos One.11: 230-247.
  • Hosseini, S., Ismaili, A., Nazarian Firouz-Abadi, F., Fallahi, H. and Rezaeinejad, A., 2018. Development of est-ssr microsattelite markers related to drought tolerance in lentile (Lens culinaris). Crop Biotechnology. 8:43-57 (In Persian).
  • Soltani Howyzeh, M., Seyed Ahmad, S., Vahid, S. and Mahboubeh, A., 2018. Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi Scientific reports 8: 1-19.
  • Jafari, H. and Saadatfar, S., 2020. Genetic relationship and phytochemical assessment among populations of Bunium persicum (Boiss.) B. Fedtsch. in the natural habitats of Yazd and Kerman. Iranian Journal of Medicinal and Aromatic Plants. 36: 306-316 ( In Persian).
  • Jie, Ch., Runqing, Y., Lijun, L., Bo, W. and Dingxiang, P., 2016. Large‑scale developing of simple sequence repeat markers and probing its correlation with ramie (Boehmeria nivea L.) fiber quality. Molecular Genetics and Genomics. 291:753–761.
  • Kumpatla, S. and Mukhopadhyay S., 2005. Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48: 985-998.
  • Li, Y., Abraham, B., Tzion, F., Avigdor, B. and Eviatar, N., 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular ecology 11: 2453-2465.
  • Mittal, R., Chahota, S. and Katna, G., 2006. Genetic variability and component analysis in kalazira (Bunium persicum) in dry temperate areas of North-western Himalayas. Crop Improvement-India- 33,
  • Pezhmanmehr, M., Hasani, M,. Jahansouz, F., Najafi, A., Sefidkon, F. and Pirseyedi, M., 2009. Assessment of genetic diversity in some Iranian populations of Bunium persicum using RAPD and AFLP markers.  Iranian Journal of Biotechnology 7: 93-100.
  • Sadeghi, D., Mortazavian, M. and Bakhtiyarizadeh, M., 2018. Transcriptome analysis of cumin (Cuminum cyminum) using RNA-Seq. Agricultural Biotechnology Journal 9: 101-116.
  • Senthilvel, S., Jayashree, B., Mahalakshmi, V., Sathish, P. and Hash, C., 2008. Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biology 8: 1-9.
  • Sheidai, M., Ahmadian, P. and Poorseyedy, S., 1996. Cytological studies in Iran zira from three genus: Bunium, Carum and Cuminum. Cytologia 61: 19-25.
  • Singh, S. and Kumar, V., 2021. Biology, genetic improvement and agronomy of Bunium persicum (Boiss.) Fedtsch. A comprehensive review. Journal of Applied Research on Medicinal and Aromatic Plants,
  • Sofi, P., Zeerak, A. and Singh, P., 2009. Kala zeera (Bunium persicum): a Kashmirian high value crop. Turkish Journal of Biology 33: 249-258.
  • Sohrabi, S., Ismaili, A., Nazarian Firouz-Abadi, F. and Fallahi, H., 2018. Discovery of EST-SSRs Markers in Lentil (Lens culinaris) under cold stress. Crop Biotechnology. 8:1-14 (In Persian).
  • Varshney, R., Thomas, T., Nils, S., Langridge, P. and Graner, A., 2002. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cellular and Molecular Biology Letters 7: 537-546.
  • Wei, W., Xiaoqiong, W., Linhai, Z., Yanxin, H., Wei, Z. and Xiurong, x., 2011. Characterization of the sesame (Sesamum indicum) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC genomics 12: 1-13.
  • Zhang, H., Wei, L. and Miao, H., 2012. Development and validation of genic-SSR markers in sesame by RNA-seq. BMC genomics 13: 1-11.

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