Development of EST-SSR Markers in Tomato (Solanum Lycopersicum L)
Abstract
The present study focuses on the development of EST-SSR (Expressed Sequence Tag-Simple Sequence Repeat) markers in tomato from the transcriptomic sequences. A database of the genes linked with ripening of tomatoes has also been developed. Transcriptome sequences SSR36311, SSR363117, SSR363118, SSR363119, SSR363120, SSR363121 and SSR363122 were retrieved from European Nucleotide Archive databases. After performing quality check using FastQC, the downstream analysis was done using Tuxedo pipeline. With the assembled transcriptomic sequences, ESTs (Expressed Sequence Tag) were identified using EST trimmer of MicroSatellite identification (MISA) tool. A total of 582 EST-SSR primers were designed using WebSat. Among them 20 SSR primers were synthesized and validated using six tomato varieties such as Pusa Ruby, Pusa Gaurav, Pusa Sheetal , F1 Roman , Vellayani Vijaya and S-22. The study would add information on the genetic resources of tomatoes thus helping in improving new cultivars.
Genbank Submission: MH370148.1, MH370149.1, MH370150.1, MH370151.1
Keywords
Full Text:
PDFReferences
Benor, S., Zhang, M., Wang, Z., & Zhang, H. (2008). Assessment of genetic variation in tomato (Solanum lycopersicum L.) inbred lines using SSR molecular markers. Journal of Genetics and Genomics, 35(6), 373-379.
Bird, C. R., Smith, C. J. S., Ray, J. A., Moureau, P., Bevan, M. W., Bird, A. S., Hughes, S., Morris, P.C., Grierson, D. & Schuch, W. (1988). The tomato polygalacturonase gene and ripening-specific expression in transgenic plants. Plant molecular biology, 11, 651-662.
Campoy, J. A., Ruiz, D., Egea, J., Rees, D. J. G., Celton, J. M., & Martínez-Gómez, P. (2011). Inheritance of flowering time in apricot (Prunus armeniaca L.) and analysis of linked quantitative trait loci (QTLs) using simple sequence repeat (SSR) markers. Plant Molecular Biology Reporter, 29, 404-410.
Caruso, A. G., Bertacca, S., Parrella, G., Rizzo, R., Davino, S., & Panno, S. (2022). Tomato brown rugose fruit virus: A pathogen that is changing the tomato production worldwide. Annals of Applied Biology, 181(3), 258-274. https://doi.org/10.1111/aab.12788
Fan, J., Lou, Y., Shi, H., Chen, L., & Cao, L. (2019). Transcriptomic analysis of dark-induced senescence in bermudagrass (Cynodon dactylon). Plants, 8(12), 614. https://doi.org/10.3390/plants8120614 .
Gharsallah, C., Abdelkrim, A. B., Fakhfakh, H., Salhi-Hannachi, A., & Gorsane, F. (2016). SSR marker-assisted screening of commercial tomato genotypes under salt stress. Breeding science, 66(5), 823-830. doi: 10.1270/jsbbs.16112.
Grube, R. C., Radwanski, E. R., & Jahn, M. (2000). Comparative genetics of disease resistance within the Solanaceae. Genetics, 155(2), 873-887.
Hoogstrate, S. W., van Bussel, L. J., Cristescu, S. M., Cator, E., Mariani, C., Vriezen, W. H., & Rieu, I. (2014). Tomato ACS4 is necessary for timely start of and progression through the climacteric phase of fruit ripening. Frontiers in Plant Science, 5, 466.
https://doi.org/10.4238/2015.October.29.7
Ko, K., Granell, A., Bennett, J., & Cashmore, A. R. (1990). Isolation and characterization of cDNAs from Lycopersicon esculentum and Arabidopsis thaliana encoding the 33 kDa protein of the photosystem II-associated oxygen-evolving complex. Plant molecular biology, 14, 217-227. doi: 10.1007/BF00018562.
Korir, N. K., Diao, W., Tao, R., Li, X., Kayesh, E., Li, A., Zhen.,W & Wang, S. (2014). Genetic diversity and relationships among different tomato varieties revealed by EST-SSR markers. Genet. Mol. Res, 13(1), 43-53. http://dx.doi.org/10.4238/2014.
KÖSE, M. A., Çetinsağ, N., & Gürcan, K. A. H. R. A. M. A. N. (2017). De novo transcriptome assembly and SSR marker development in apricot (Prunus armeniaca). Turkish Journal of Agriculture and Forestry, 41(4), 305-315
Martí, R., Roselló, S., & Cebolla-Cornejo, J. (2016). Tomato as a source of carotenoids and polyphenols targeted to cancer prevention. Cancers, 8(6), 58. doi: 10.3390/cancers8060058.
Sax, K. (1923). The association of size differences with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics, 8(6), 552.
Singh, R. (2021). Lycopene Content of Different Tomato Germplasms Grown under Irrigated and Water-stress Conditions. Pesticide Research Journal, 33(2), 120-125. http://dx.doi.org/10.5958/2249-524X.2021.00045.8
Sitrit, Y., & Bennett, A. B. (1998). Regulation of tomato fruit polygalacturonase mRNA accumulation by ethylene: a re-examination. Plant Physiology, 116(3), 1145-1150. doi: 10.1104/pp.116.3.1145.
Vidya, Venugopal, Duraisamy Prasath, Mohandas Snigdha, Ramasamy Gobu, Charles Sona, and Chandan Suravi Maiti.. (2021). Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.). PLoS One, 16(10), e0259146. https://doi.org/10.1371/journal.pone.0259146
Yeats, T. H., Huang, W., Chatterjee, S., Viart, H. M. F., Clausen, M. H., Stark, R. E., & Rose, J. K. (2014). T omato C utin D eficient 1 (CD 1) and putative orthologs comprise an ancient family of cutin synthase‐like (CUS) proteins that are conserved among land plants. The Plant Journal, 77(5), 667-675. doi: 10.1111/tpj.12422.
Zhou, R., Wu, Z., Cao, X., & Jiang, F. L. (2015). Genetic diversity of cultivated and wild tomatoes revealed by morphological traits and SSR markers. Genet. Mol. Res, 14(4), 13868-13879.
Refbacks
- There are currently no refbacks.
Informatics Studies: ISSN: 2583-8994 (Online), 2320-530X (Print)