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Genetic characterization of coconut (Cocos nucifera L.) varieties conserved in Vietnam through SCoT marker-based polymorphisms

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Abstract

Coconut (Cocos nucifera L.) production sustains millions of smallholder farmers and their families around the globe, and also powers a thriving industry of climate-adaptive nutrition and biomaterials. Demand for high-quality planting materials has risen sharply in recent years, calling for greater understanding and potential utilization of the genetic diversity in coconut populations. Genetic diversity among several conserved coconut varieties in Vietnam was investigated to assess the suitability of 15 start codon targeted (SCoT) primers for future selective breeding programs. Amplification of 15 SCoT primers in 57 individuals from 19 coconut varieties revealed high intra-varietal diversity (Nei’s genetic diversity index = 0.237, Shannon’s Information index = 0.352), especially among the Vietnamese Dwarfs. Intriguingly, inter-varietal differentiation accounted for only 9.41% of total genetic variation. The designated SCoT primers were moderately informative. On average, each primer had 9.5 reproducible polymorphic bands per reaction. Polymorphism Information Content (PIC) per locus ranged between 0.217 and 0.390, with Resolving power (Rp) between 0.271 and 0.599. Principal Coordinate Analysis (PCoA) and Unweighted Pair Group Method with Arithmetic mean (UPGMA) analyses revealed distinct clusters for non-native Dwarf, native Dwarf, and Tall varieties. This paper represents the first-of-its-kind attempt to shed light on coconut genetic diversity in Vietnam using molecular markers.

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Data availability

Data supporting the findings of this study are available from the corresponding authors (Nguyen Bao Quoc and Nguyen Phuong Thao) upon reasonable request.

Abbreviations

SCoT :

Start codon targeted

QTL :

Quantitative trait locus

PIC :

Polymorphism information content

Rp :

Resolving power

PCoA :

Principal coordinate analysis

UPGMA :

Unweighted pair group method with arithmetic mean

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Acknowledgements

We are grateful to the Dong Go Coconut Research Center for generous provision of leaf materials and information.

Funding

This research was funded by the Ministry of Science and Technology (MOST, Vietnam) under grant number ĐTĐL.CN-12/19.

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Authors and Affiliations

  1. Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam

    Nguyen Hoang Minh Khang, Nguyen Thien Quang & Nguyen Phuong Thao

  2. Vietnam National University, Linh Trung Ward, Thu Duc, Ho Chi Minh, 700000, Vietnam

    Nguyen Hoang Minh Khang, Nguyen Thien Quang & Nguyen Phuong Thao

  3. Research Institute for Biotechnology and Environment, Nong Lam University, Linh Trung ward, Thu Duc, Ho Chi Minh, Vietnam

    Hoang Ngoc Xuan Mai, Nguyen Doan Nguyen Phuong & Nguyen Bao Quoc

Authors
  1. Nguyen Hoang Minh Khang
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  2. Nguyen Thien Quang
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  3. Hoang Ngoc Xuan Mai
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  4. Nguyen Doan Nguyen Phuong
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  5. Nguyen Phuong Thao
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  6. Nguyen Bao Quoc
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Contributions

Conceptualization: NBQ, Data curation: NHMK, HNXM, NDNP, NBQ, Formal analysis: NHMK, Funding acquisition: NPT, Investigation: NHMK, NTQ, HNXM, NDNP, NPT and NBQ, Methodology: NBQ, NHMK, Validation: NBQ, NPT, Writing—original draft: NHMK, NBQ, Writing—review and editing: NBQ, NPT, NTQ.

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Correspondence to Nguyen Phuong Thao or Nguyen Bao Quoc.

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Khang, N.H.M., Quang, N.T., Mai, H.N.X. et al. Genetic characterization of coconut (Cocos nucifera L.) varieties conserved in Vietnam through SCoT marker-based polymorphisms. Genet Resour Crop Evol 69, 385–398 (2022). https://doi.org/10.1007/s10722-021-01237-x

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