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Microsatellite Analysis of Genetic Diversity and Relationships in 1027 Sugarcane Accessions

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Abstract

Genetic diversity is the foundation for genetic improvement in any plant breeding programme. Understanding genetic diversity and relationships in germplasm collections is critically important for improving desired traits. However, in sugarcane breeding, breeders often select parental accessions based mainly on phenotypes without knowledge of their genetic relationships. In this study, 12 polymorphic microsatellites were selected and used to analyse the genetic relationships between 1027 sugarcane accessions collected in Indonesia using an automated DNA sequencer ABI3730xl. A total of 171 alleles were detected at 12 microsatellite loci. The genetic similarities between accessions ranged from 0.55 to 0.99. The principal coordinate analysis showed that some accessions were closely related while others were genetically quite different. These data suggest that there are substantial genetic variations in the 1027 accessions. A matrix of genetic similarities was obtained for all 1027 sugarcane accessions. A phylogenetic tree based on the genetic similarities was constructed for the 1027 accessions. Taken together, these data obtained in the present study, especially the matrix of genetic similarities and the phylogenetic tree, can be used to guide the setup of breeding programmes to accelerate genetic improvement.

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Acknowledgements

We would like to thank our former laboratory member Lai CC for technical support and our institute’s sequencing facility for genotyping all microsatellites using ABI3730xl DNA sequencers.

Funding

This study is supported by PT Gunung Madu Plantation (GMP), and the internal funding of the Temasek Life Sciences Laboratory, Singapore.

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Author notes

  1. Shadame Yeo and May Lee have contributed equally to this work.

Authors and Affiliations

  1. Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore

    Shadame Yeo, May Lee, L. Wang & G. H. Yue

  2. Research and Development, PT Gunung Madu Plantations, KM 90 Terusan Nunyai, Central Lampung, Lampung, 34167, Indonesia

    S. Endah & N. A. Alhuda

  3. Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore

    G. H. Yue

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  1. Shadame Yeo
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Contributions

GHY and SE contributed to resources; GHY and EA contributed to resources; SY, ML, NAA, and GHY contributed to methodology; SY, ML, and GHY contributed to formal analysis; SY, ML, and GHY contributed to writing—original draft preparation; SY, ML, SE, NAA, and GHY contributed to writing—review and editing; GHY and SE contributed to funding acquisition. All authors have read and approved the final manuscript.

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Correspondence to G. H. Yue.

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Yeo, S., Lee, M., Wang, L. et al. Microsatellite Analysis of Genetic Diversity and Relationships in 1027 Sugarcane Accessions. Sugar Tech 25, 1082–1091 (2023). https://doi.org/10.1007/s12355-023-01278-9

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