Abstract
Olive is an ancient oil-producing tree, widely cultivated in Mediterranean countries, and now spread to other areas of the world, including China. Recently, several molecular databases were constructed in different countries and platforms for olive identification using simple sequence repeats (SSRs) or single-nucleotide polymorphisms (SNPs). However, comparing their results across laboratories was difficult. Herein, hundreds of polymorphic single-copy nuclear sequence markers were developed from the olive genome. Using the advantage of multiplex PCR amplification and high-throughput sequencing, a fingerprint database was constructed for the majority of olives cultivated in China. We used 100 high-quality sequence loci and estimated the genetic diversity and structure among all these varieties. We found that compared with that based on SSRs, the constructed fingerprint database based on these 100 sequences or a few of them, could provide a reliable olive variety identification platform in China, with high discrimination among different varieties using the principle of BLAST algorithm. An example of such identification platform based on this study was displayed on the web for the olive database in China (http://olivedb.cn/jianding). After resolving redundant genotypes, we identified 126 olive varieties with distinct genotypes in China. These varieties could be divided into two clusters, and it was revealed that the grouping of the varieties has a certain relationship with their origin. Herein, it is concluded that these single-copy orthologous nuclear sequences could be used to construct a universal fingerprint database of olives across different laboratories and platforms inexpensively. Based on such a database, variety identification can be performed easily by any laboratory, which would further facilitate olive breeding and variety exchange globally.
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Data availability
All raw sequence data have been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences under the BioProject accession number PRJCA013968 and the Biosample number SAM103582.
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Acknowledgements
We thank two anonymous reviewers for their helpful comments and suggestions, Na li and Haiyun Zhao from the National Improved Olive Variety Breeding Base in Dawan’gou, Longnan city, Gansu province for their help on olive sampling.
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This work was supported by the National Key R&D Program of China (No. 2019YFD1000602).
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The study was designed by YZ and JZ. Material preparation, data collection, and analysis were performed by LH, JL, YZ, YD, and GS. The manuscript was written by LH and YZ, and all authors read and approved the final manuscript.
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Online Resource method:Sequence typing method using OBItools3 software. Online Resource 1 Sampling information of 168 olive accessions. Online Resource 2: The information on primer pairs for 462 loci. Online Resource 3 Tag combinations in primer pair. Online Resource 4 The information on primer pairs for 282 loci. Online Resource 5 The identification results of the variety repetitive pair. Online Resource 6 The identification results of olive accessions. Online Resource 7 The structure results from K = 3 to K = 10. Online Resource 8 The flowchart summarizing the improved protocol (DOCX 18 kb)
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Huang, L., Zeng, Y., Li, J. et al. One hundred single-copy nuclear sequence markers for olive variety identification: a case of fingerprinting database construction in China. Mol Breeding 43, 86 (2023). https://doi.org/10.1007/s11032-023-01434-9
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DOI: https://doi.org/10.1007/s11032-023-01434-9