Year 2019, Volume 3 , Issue 4, Pages 240 - 244 2019-12-24

Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.)

Ayse INCE [1] , Mehmet KARACA [2]


New DNA sequencing techniques enable researchers obtain large quantity of sequence information, which are deposited in digital storage or could be further mined for other purposes. Sesame (Sesamum indicum L.) is one of very important oilseed crops, its seed oil contains many antioxidant properties making sesame the queen of oil crops. Today, molecular plant breeding technology is indispensable for plant breeders and seed producers. Compared to other seed oil crops the available number of microsatellite markers in sesame is still not sufficient enough for the development of polymorphic markers for breeding and genetic studies. Thus, new approaches or resources are needed for development of microsatellite markers for sesame. In the present study, we utilized a total of 45099 transcribed genomic DNA sequences/expressed sequence tags and mined these sequences for studying frequency of microsatellite motifs, ranging from di- to hexa-nucleotides with four to ten tandem repeats, and repeat numbers greater than 10. Using mined transcribed data, 42 putative microsatellite markers were developed and characterized at the sequence level. However, we did not confirm these markers and have no information about the level of their polymorphisms in sesame in vitro. We discussed the biological meaning of the motif lengths and repeat numbers in the sesame genome. 
Microsatellite, Motif length, Repeating motif, Primer pairs, Tandem repeats
  • Ali, G.M., Yasumoto, S. and Katsuta, M.S. (2007). Assessment of genetic diversity in sesame (Sesamum indicum L.) detected by amplified fragment length polymorphism. Electronic Journal of Biotechnology, 10, 12-23.
  • Ali-Al-Somain, B.H., Migdadi, H.M., Al-Faifi, S.A., Muharram, A.A., Mohammed, N.A. and Refay, Y.A. (2017). Assessment of genetic diversity of sesame accessions collected from different ecological regions using sequence-related amplified polymorphism markers. 3 Biotech, 7, 82.
  • Bilgen, M., Karaca, M., Onus, A.N. and Ince, A.G. (2004). A soft-ware program combining sequence motif searches with key-words for finding repeats containing DNA Sequences. Bioinformatics, 20, 3379-3386.
  • Cheung, S.C., Szeto, Y.T. and Benzie, I.F. (2007). Antioxidant protection of edible oils. Plant Foods Human Nutrition, 62, 39-42.
  • Cloutier, S., Niu, Z., Datla, R. and Duguid, S. (2009). Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theoretical Applied Genetic, 119, 53-63.
  • Ince, A.G., Karaca, M., Bilgen, M. and Onus, A.N. (2008). Digital differential display tools for mining microsatellite containing organism, organ and tissue. Plant Cell Tissue and Organ Culture, 94, 281-290.
  • Ince, A.G., Onus, A.N. and Karaca, M. (2010a). Polymorphic microsatellite markers transferable across Capsicum species. Plant Molecular Biology Reporter, 28, 285-291.
  • Ince, A.G., Karaca, M. and Onus, A.N. (2010b). CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Molecular Breeding, 25, 491-499.
  • Karaca, M, Bilgen, M, Onus, A.N., Ince, A.G. and Elmasulu, S.Y. (2005). Exact tandem repeats analyzer (ETRA): a new program for DNA sequence mining. Journal of Genetics, 84, 49-54.
  • Karaca, M. and Ince, A.G. (2011). New non-redundant microsatellite and CAPS-Microsatellite markers for cotton (Gossypium L.). Turkish Journal of Field Crops, 16, 172-178.
  • Karaca, M., Ince, A.G., Uygur-Göçer, E. and Aydin, A. (2017a). Microsatellite distribution and densities in promoter and gene body entities of some plant genes. The Journal of Scientific and Engineering Research, 4, 154-163.
  • Karaca, M., Ince, A.G., Uygur-Göçer, E. and Aydin, A. (2017b). Descriptive statistics and PIC values of genomicand transcriptomic-microsatellites in several plant species. The Journal of Scientific and Engineering Research, 4, 236-246.
  • Kumar, V. and Sharma, S.N. (2011). Comparative potential of phenotypic, ISSR and SSR markers for characterization of sesame (Sesamum indicum L.) varieties from India. Journal of Crop Science and Biotechnology, 14, 163-171.
  • Pham, T.D., Geleta, M., Bui, T. M., Bui, T.C., Merker, A. and Carlsson, A.S. (2011). Comparative analysis of genetic diversity of sesame (Sesamum indicum L.) from Vietnam and Cambodia using agro-morphological and molecular markers. Hereditas, 148, 28-35.
  • Weber, J.L. (1990). Informativeness of human (dC-dA)n·(dG-dT)n polymorphisms. Genomics, 7, 524-530.
  • Wei, W., Qi, X, Wang, L., Zhang, Y., Hua, W., Li, D., Lv H. and Zhang W. (2011). Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics, 12, 451.
  • Wei, X., Wang, L., Zhang, Y., Qi, X., Wang, X., Ding, X. and Zhang, J. (2014). Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey. Molecules, 19, 5150-5162.
  • Yen, G.C. (1990). Influence of seed roasting process on the changes in composition and quality of sesame (Sesamum indicum L.) oil. Journal of the Science of Food and Agriculture, 50, 563-570.
  • You, F.M., Huo, N., Gu, Y.Q., Luo, M., Ma, Y., Hane, D., Lazo, G.R., Dvorak, J. and Anderson, O.D. (2008). BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics, 9, 253.
  • Yue, W., Wei L., Zhang T., Li C., Miao H. and Zhang H. (2013). Genetic diversity and population structure of germplasm resources in sesame (Sesamum indicum L.) by SSR markers. Acta Agronomica Sinica, 38, 2286-2296.
  • Zhang, H., Wei, L., Miao, H., Zhang, T. and Wang C. (2012). Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics, 13, 316.
Primary Language en
Subjects Agriculture, Agricultural, Engineering, Agriculture, Multidisciplinary, Agriculture, Dairy and Animal Science
Published Date December 2019
Journal Section Research Articles
Authors

Orcid: 0000-0002-9015-6580
Author: Ayse INCE
Institution: AKDENİZ ÜNİVERSİTESİ
Country: Turkey


Orcid: 0000-0003-3219-9109
Author: Mehmet KARACA (Primary Author)
Institution: AKDENİZ ÜNİVERSİTESİ
Country: Turkey


Dates

Application Date : September 28, 2019
Acceptance Date : December 4, 2019
Publication Date : December 24, 2019

Bibtex @research article { jaefs651863, journal = {International Journal of Agriculture Environment and Food Sciences}, issn = {}, eissn = {2618-5946}, address = {Dicle University Faculty of Agriculture Department of Horticulture, 21280 Diyarbakir / Turkey}, publisher = {Gültekin ÖZDEMİR}, year = {2019}, volume = {3}, pages = {240 - 244}, doi = {10.31015/jaefs.2019.4.7}, title = {Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.)}, key = {cite}, author = {INCE, Ayse and KARACA, Mehmet} }
APA INCE, A , KARACA, M . (2019). Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.). International Journal of Agriculture Environment and Food Sciences , 3 (4) , 240-244 . DOI: 10.31015/jaefs.2019.4.7
MLA INCE, A , KARACA, M . "Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.)". International Journal of Agriculture Environment and Food Sciences 3 (2019 ): 240-244 <https://dergipark.org.tr/en/pub/jaefs/issue/50908/651863>
Chicago INCE, A , KARACA, M . "Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.)". International Journal of Agriculture Environment and Food Sciences 3 (2019 ): 240-244
RIS TY - JOUR T1 - Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.) AU - Ayse INCE , Mehmet KARACA Y1 - 2019 PY - 2019 N1 - doi: 10.31015/jaefs.2019.4.7 DO - 10.31015/jaefs.2019.4.7 T2 - International Journal of Agriculture Environment and Food Sciences JF - Journal JO - JOR SP - 240 EP - 244 VL - 3 IS - 4 SN - -2618-5946 M3 - doi: 10.31015/jaefs.2019.4.7 UR - https://doi.org/10.31015/jaefs.2019.4.7 Y2 - 2019 ER -
EndNote %0 International Journal of Agriculture Environment and Food Sciences Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.) %A Ayse INCE , Mehmet KARACA %T Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.) %D 2019 %J International Journal of Agriculture Environment and Food Sciences %P -2618-5946 %V 3 %N 4 %R doi: 10.31015/jaefs.2019.4.7 %U 10.31015/jaefs.2019.4.7
ISNAD INCE, Ayse , KARACA, Mehmet . "Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.)". International Journal of Agriculture Environment and Food Sciences 3 / 4 (December 2019): 240-244 . https://doi.org/10.31015/jaefs.2019.4.7
AMA INCE A , KARACA M . Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.). int. j. agric. environ. food sci.. 2019; 3(4): 240-244.
Vancouver INCE A , KARACA M . Sequence data characterization and development of DNA markers for sesame (Sesamum indicum L.). International Journal of Agriculture Environment and Food Sciences. 2019; 3(4): 244-240.