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Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity

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Abstract

Being an economical and nutritional crop, Capsicum appeases people’s peppery taste and is found to be widely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.

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Acknowledgements

The authors express sincere thanks to Council of Scientific and Industrial Research (CSIR) and Indian Council of Medical Research (ICMR) for providing Junior Research Fellow (JRF). We are also grateful to UGC-UPE programme and Bioinformatics Infrastructure Facilities (BIF), University of Rajasthan for providing research facilities. CSIR-Research Associate programme is also acknowledged for providing fellowship. Our thanks are extended to Ms Raini Verma, Ms Prerna Dhingra and Ms Rakhi Poonia for their assistance in technical work.

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  1. Department of Botany, University of Rajasthan, Jaipur, 302 004, India

    Vibha Gupta, Pradeep Kumar Jatav, Shamshad Ul Haq, Varsha Khurana Kaul & Sumita Kachhwaha

  2. Amity Institute of Biotechnology, Amity University, Jaipur, 302 004, India

    Kumar Sambhav Verma & S. L. Kothari

  3. Bioinformatics Infrastructure Facility, University of Rajasthan, Jaipur, 302 004, India

    Sumita Kachhwaha

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  1. Vibha Gupta
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Gupta, V., Jatav, P.K., Haq, S.U. et al. Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity. J Genet 98, 61 (2019). https://doi.org/10.1007/s12041-019-1095-0

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