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Cross-genera amplification of Cajanus spp. specific SSR markers in Clitoria ternatea (L.) and their application in genetic diversity studies

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Abstract

Clitoria ternatea (L.) is a medicinal leguminous plant and is cultivated to cater the need of herbal industries and asthetic purposes. The unavailability of steady molecular marker impedes the genetic improvement of C. ternatea. In the present study, transferability of 98 pairs of Cajanus spp. specific SSR primers were assessed among 14 genotypes of C. ternatea, varied for their flower color, floral architecture and bio-metabolite (taraxerol and delphinidin) content, and out of them 43 had successfully amplified the fragments. Among them, 36 pairs of primers showed 100% transferability, whereas rest seven varied from 42.86 to 92.85% transferability. The transferable 43 pairs of SSR primers generated 196 alleles across the 14 genotypes and the AMOVA analysis showed moderate genetic variation (55.1%) among the genotypes of C. ternatea, which was also reinforced by Nei’s genetic distance and gene identity estimates derived haplotype matrix. Similarly, both the principal coordinate analysis and dendrogram grouped these 14 genotypes of C. ternatea into two major clusters based on SSR allele distribution and frequency, and the clustering pattern is in accordance with petal color but in contrast to floral architecture. MCheza based outlier analysis revealed 16 alleles for balancing selection, which are putatively involved in the maintenance of genetic polymorphism in C. ternatea. Moreover, the estimates of molecular diversity and bio-metabolite content revealed the possible use of these genotypes in future breeding programme of this species.

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Abbreviations

AMOVA:

Analysis of molecular variance

CTAB:

Cetyl trimethyl ammonium bromide

EMR:

Effective multiplex ratio

HPLC:

High performance liquid chromatography

HPTLC:

High performance thin layer chromatography

MI:

Marker Index

PCoA:

Principal coordinate analysis

PIC:

Polymorphic information content

Rp:

Resolving power

SSR:

Simple sequence repeat

UPGMA:

Un-weighted pair group method with arithmetic mean

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Acknowledgements

The authors are profoundly grateful to the SERB, Govt. of India, New Delhi, for financial assistance through an R&D project (EMR/2016/006351) to the corresponding author (JP) and the DST, Government of Odisha for providing Biju Patnaik Research Fellowship to the author (AN) for pursuing the doctoral degree, and acknowledge the Vice-Chancellor, Khallikote University, Berhampur for providing laboratory facilities.

Funding

Science and Engineering Research Board, Govt. of India; Grant no. EMR/2016/006351.

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Authors and Affiliations

  1. Department of Bioscience and Bioinformatics, Khallikote University, Konishi, Berhampur, Odisha, 761008, India

    Aparupa Naik, Gopal K. Soren, Aditya K. Panda & Jogeswar Panigrahi

  2. Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768019, India

    Aparupa Naik, Sujit K. Mishra, Atul Nag & Jogeswar Panigrahi

  3. Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Ajmer, Rajasthan, 305817, India

    Sanjib K. Panda

  4. Department of Zoology, Centurion University of Technology and Management, Bhubaneswar, Odisha, India

    Sujit K. Mishra

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  1. Aparupa Naik
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  2. Sujit K. Mishra
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  3. Atul Nag
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Contributions

JP—conceived and designed the experiments, fund acquisition; AN,SKM and GKS—performed the experiments; JP, AP, AN and SKP—analysed the data, deduced interpretations and performed statistical and computational analysis; JP, AN and AKP—wrote the manuscript including Tables and Figures; All authors have reviewed the manuscript and have given approval to the final version.

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Correspondence to Jogeswar Panigrahi.

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Naik, A., Mishra, S.K., Nag, A. et al. Cross-genera amplification of Cajanus spp. specific SSR markers in Clitoria ternatea (L.) and their application in genetic diversity studies. Physiol Mol Biol Plants 26, 2371–2390 (2020). https://doi.org/10.1007/s12298-020-00907-x

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