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Research Project: Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources

Location: Sustainable Perennial Crops Laboratory

Title: Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm

Author
item Wang, Boyi - Yunnan Agricultural University
item Tan, Hua-wei - Nanjing Agricultural University
item Fang, Wanping - Nanjing Agricultural University
item Meinhardt, Lyndel
item Mischke, Barbara
item Matsumoto Brower, Tracie
item Zhang, Dapeng

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2014
Publication Date: 1/14/2015
Citation: Wang, B., Tan, H., Fang, W., Meinhardt, L.W., Mischke, B.S., Matsumoto Brower, T.K., Zhang, D. 2015. Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm. Horticulture Research. DOI:10.1038/hortres.2014.65.

Interpretive Summary: Longan (Dimocarpus longan Lour.) is a widely-distributed, important tropical fruit tree in the Sapindaceae (soapberry) family. Like many tropical perennial tree crops, longan germplasm is maintained in field genebanks and varieties are subject to vegetative propagation during the process of germplasm exchange. But records and labels of the varieties have not always been properly maintained and accessions often arrive bearing limited information about their correct identity. In the present study, we developed a set of single nucleotide polymorphism (SNP) markers and tested their efficacy in a panel of longan germplasm accessions, including both cultivated varieties and wild longan germplasm. The validation led to the designation of 25 SNP markers that unambiguously identified all tested longan varieties. Multiple trees belonging to same clone were verified and off-type trees were identified. Diversity analysis further revealed a large difference between the wild population and cultivated varieties, demonstrating the untapped genetic diversity for longan germplasm utilization. This information will be used by researchers, longan producers and longan industry for to improve the accuracy in germplasm management, breeding, and plant material propagation.

Technical Abstract: Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst = 0.266; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification.