Abstract
Determinacy is a desirable trait in sesame, an important oilseed crop. We have developed an inter-specific hybrid between basally branched indeterminate cultivated Sesamum indicum genotype and wild S. prostratum with no branching yet synchronous pods on the shoot. The hybrid and a few exotic sesame germplasms were successfully screened with a determinacy (dt) gene-based DNA marker. In-silico translation of the partial coding sequences of the dt gene from the two contrasting parent genotypes revealed an SNP (V159A) in S. prostratum. The predicted cytoplasmic dt protein showed a high resemblance with flowering protein centroradialis.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Availability of data and material
Not applicable.
Code availability
Not applicable.
References
Abbas G, Hameed A, Rizwan M, Ahsan M, Asghar MJ, Iqbal N (2015) Genetic confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) inter-specific recombinants using molecular markers. Front Plant Sci 6:1107
Ashri A (1981) Increased genetic variability for sesame improvement by hybridization and induced mutations. In: Ashri A (ed.), Sesame: status and improvement. FAO Plant Production and Protection Paper 29: 141–145
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf, calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 38:W529–W533
Chen W, Taylor MC, Barrow RA, Croyal M, Masle J (2019) Loss of phosphoethanolamine n-methyltransferases abolishes phosphatidylcholine synthesis and is lethal. Plant Physiol 179:124–142. https://doi.org/10.1104/pp.18.00694
Choi Y, Chan AP (2015) PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31:2745–2747
Dossa K, Diouf D, Wang L, Wei X, Zhang Y, Niang M et al (2017) The emerging oilseed crop Sesamum indicum enters the “Omics” era. Front Plant Sci 8:1154. https://doi.org/10.3389/fpls.2017.01154
Drew ED, Janes RW (2019) 2StrucCompare: a web server for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content. Nucleic Acids Res 47:W477–W481
Dutta D, Awon VK, Gangopadhyay G (2020) Transcriptomic dataset of cultivated (Sesamum indicum), wild (S. mulayanum), and inter-specific hybrid sesame in response to induced Macrophomina phaseolina infection. Data Brief 33:106448
Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788
Islam F, Gill R A, Ali B, Farooq M A, Xu L, Najeeb U et al. (2016) Sesame, in breeding oilseed crop for sustainable production: opportunities and constraints, ed. S. K. Gupta. Academic Press, Cambridge, MA 135–147
Kulmanov M, Hoehndorf R (2020) DeepGOPlus: improved protein function prediction from sequence. Bioinformatics 15:422–429. https://doi.org/10.1093/bioinformatics/btz595
Liu YY, Yang KZ, Wei XX, Wang XQ (2016) Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. New Phytol 212:730–744. https://doi.org/10.1111/nph.14066
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C (T)) Method. Method 25:402–408
Mei H, Liu Y, Du Z, Wu K, Cui C, Jiang X, Zhang H, Zheng Y (2017) High-density genetic map construction and gene mapping of basal branching habit and flowers per leaf axil in sesame. Front Plant Sci 8:636
Nadeem MA, Nawaz MA, Shahid MQ et al (2018) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32:261–285. https://doi.org/10.1080/13102818.2017.1400401
Pathak N, Bhaduri A, Bhat KV, Rai AK (2015) Tracking sesamin synthase gene expression through seed maturity in wild and cultivated sesame species—a domestication footprint. Plant Biol 17:1039–1046. https://doi.org/10.1111/plb.12327
Prasad R, Gangopadhyay G (2011) Phenomic analyses of Indian and exotic accessions of Sesame (Sesamum indicum L.). J Plant Breed Crop Sci 3:335–351
Song YP, Jiang XB, Zhang M et al (2012) Differences of EST-SSR and genomic-SSR markers in assessing genetic diversity in poplar. Forest Stud China 14:1–7. https://doi.org/10.1007/s11632-012-0106-5
Subramanian M (2003) Wide crosses and chromosome behaviour in Sesamum. Madras Agric J 90:1–3
Uzun B, Cagirgan MI (2006) Comparison of determinate and indeterminate lines of sesame for agronomic traits. Field Crops Res 96:13–18
Uzun B, Yol E, Furat S (2013) Genetic advance, heritability and inheritance in determinate growth habit of sesame. Austral J Crop Sci 7:978–983
Venselaar H, Beek TAH, Kuipers RKP, Hekkelman ML, Vriend G (2010) Protein structure analysis of mutations causing inheritable diseases: an e-Science approach with life scientist friendly interfaces. BMC Bioinform 11:548. https://doi.org/10.1186/1471-2105-11-548
Wei W, Qi X, Wang L et al (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genom 12:451
Zahran HA, Abd-Elsaber A, Tawfeuk HZ (2020) Genetic diversity, chemical composition and oil characteristics of six sesame genotypes. OCL 27:39
Zhang D, Sun W, Singh R, Zheng Y, Cao Z, Li M, Lunde C, Hake S, Zhanga Z (2018a) GRF-interacting factor1 regulates shoot architecture and meristem determinacy in maize. Plant Cell 30:360–374
Zhang H, Miao H, Li C, Wei L, Duan Y, Ma Q, Kong J, Xu F, Chang S (2016) Ultra-dense SNP genetic map construction and identification of SiDt gene controlling the determinate growth habit in Sesamum indicum L. Sci Rep 6:31556
Zhang Y, Wang L, Gao Y, Li D, Yu J, Zhou R, Zhang X (2018b) Genetic dissection and fine mapping of a novel dt gene associated with determinate growth habit in sesame. BMC Genet 19:38
Zhao X, Zhang J, Zhang Z, Wang Y, Xie W (2017) Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers. Hereditas 154:15
Acknowledgements
We acknowledge the technical assistance of Mr Jadab Ghosh and Mrs Kaberi Ghosh in a few laboratory experiments.
Funding
GG is funded by intramural project grant of Bose Institute, Department of Science and Technology, Government of India. DD and SB are funded by the UGC, Government of India for research fellowship. The funders had no role in the design of experiments, data collection and analysis, decision to publish, or preparation of the manuscript.
Author information
Authors and Affiliations
Contributions
GG conceived the study, designed and supervised the experiments. DD performed the SSR, sequencing and in-silico experiments. SB did the validation experiments. MP did the RT-PCR and expression analysis. GG and DD wrote the manuscript. All the authors approved the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Consent to participate
Not applicable.
Ethics approval
The manuscript complies with the Ethical Rules applicable for Springer publications.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Dutta, D., Banerjee, S., Pal, M. et al. Validation of determinate (dt) gene-based DNA marker in inter-specific hybrid sesame and in-silico analysis of the predicted dt protein structures. Physiol Mol Biol Plants 28, 139–152 (2022). https://doi.org/10.1007/s12298-022-01135-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12298-022-01135-1