A cost-effective oligo-based barcode system for chromosome identification in longan and lychee

Abstract

Oligonucleotide (Oligo)-based fluorescence in situ hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan (Dimocarpus longan Lour., 2n = 2x = 30). For this system, each synthesized oligo contained two chromosome-specific sequences that spanned a distance of over 200 kb, and a PCR-based flexible amplification method coupled with nested primers was used for probe labeling. The use of these oligo-based barcodes enabled the marking of 36 chromosomal regions, which allowed for the unambiguous distinction of all 15 chromosomes in both longan and lychee (Litchi chinensis Sonn., 2n = 2x = 30) species. Based on the identification of individual chromosomes, we constructed karyotypes and detected genome assembly errors involving the 35S ribosomal RNA gene (35S rDNA) in longan and lychee. Developing oligo-based barcodes offers considerable promise for advancing cytogenetic research in longan, lychee, and their related species. Furthermore, this cost-effective synthesis system can be referred to the development of new oligo libraries among other species.

Acknowledgements

This work was supported by Natural Science Foundation of Hainan Province Youth Fund Project (320QN322); Young Talent Start-up Fund of South Subtropical Crop Research Institution CATAS; The Natural Science Foundation of Fujian Province, China (2021 J011048); The Guangxi Natural Science Foundation (2024GXNSFBA010352); The Sugarcane Research Foundation of Guangxi University (Grant No. 2022GZB007); and the fellowship of China Postdoctoral Science Foundation (2022MD723761).

Author contributions

J. Z., Y. H., and F. Y. designed the research. Z. Y., Y. Q., Y. W., and G. Z. performed the experiments. Z. Y., Y. L., B. W., X. H., Y. H., Y. X., Q. X., Z. D., and J. Z. analyzed the results and wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

Data availability

All relevant data are included in the article and its supporting materials.

Conflict of interests

The authors declare no conflict of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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