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Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane

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Abstract

Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using FST analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.

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Data availability statement

The sequencing data can be found under the Bioproject accession: PRJDB15041.

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Acknowledgements

We would like to thank our former laboratory member Lai CC for technical support and scientists in GMP for collecting field data and leaf samples. We are grateful to our sequencing facilities for supporting the DNA sequencing and genotyping.

Funding

This study is supported by PT Gunung Madu Plantation (GMP) (Grant no. 9350) and the internal funding of the Temasek Life Sciences Laboratory, Singapore.

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Author notes

  1. Wang Le, Yeo Shadame, and Lee May contributed equally to this work.

Authors and Affiliations

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

    Le Wang, Shadame Yeo, May Lee & 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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Contributions

GHY and SE conceived the experiment. SY, ML, NAA, SE, and LW performed the research on phenotyping and genotyping. LW analyzed the sequence data and conducted GWAS. LW and GHY drafted the manuscript. All authors read and approved the final manuscript.

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Correspondence to G. H. Yue.

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Communicated by Bing Yang.

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Wang, L., Yeo, S., Lee, M. et al. Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane. Mol Genet Genomics 298, 1107–1120 (2023). https://doi.org/10.1007/s00438-023-02040-2

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