Abstract
Simple sequence repeat (SSR) enriched libraries for five groups of tropical perennial plants with edible fruits and shoots were prepared and sequenced in a GS-FLX Roche 454: sapodilla (Manilkara zapota (L.) P. Royen), lychee (Litchi chinensis Sonn.), mangosteen (Garcinia mangostana Linn. and G. cochinchinensis (Lour.) Choisy), rambutan (Nephelium lappaceum L.), and bamboo (Bambusa vulgaris Schrad. ex J.C. Wendl and Guadua angustifolia Kunth). For SSR development, these species were organized by their common names in five groups. A total of 3870 SSR primer sets were designed, using capillary electrophoresis 1872 nuclear SSRs were tested on 4 to 10 DNA samples within each plant group, that is 384 loci for each of the four groups of fruit trees and 336 loci for the bamboo group. Only 7.9% of the primers tested did not result in amplification. All 1872 SSRs are provided, we highlight 178 SSRs (between 26 and 47 per group) considered top-quality polymorphic SSRs that amplified all the samples, had strong fluorescence signal, presented no stutters and showed minimum non-specific amplification or background fluorescence. A total of 66,057 contig sequences were submitted to GenBank Database. Markers presented here will be useful not only for conservation efforts in banks of germplasm, but also for in-depth analysis of population genetics which usually requires evaluation of large number of loci.
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Acknowledgements
This work was supported by USDA-ARS project number 6044-21000-005-00D and the U.S. National Plant Germplasm System (NPGS). Any library/sequence information requirements can be addressed to Dr. Renee S. Arias at Renee.Arias@usda.gov. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.
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Table S1. List of 1872 SSR markers developed and tested. These correspond to 384 for each of the four tropical fruit trees (rambutan, sapodilla, lychee, mangosteen), and 336 for bamboo. Tm: melting temperature, Product size: estimated amplicon size in base pairs based on the sequencing results (DOCX 147 kb)
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Arias, R.S., Ballard, L.L., Duke, M.V. et al. Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: rambutan (Nephelium lappaceum L.), sapodilla (Manilkara zapota (L.) P. Royen), lychee (Litchi chinensis Sonn.), mangosteen (Garcinia mangostana Linn. and Garcinia cochinchinensis (Lour.) Choisy) and bamboo (Bambusa vulgaris Schrad. ex J.C. Wendl and Guadua angustifolia Kunth). Genet Resour Crop Evol 67, 1715–1731 (2020). https://doi.org/10.1007/s10722-020-00965-w
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DOI: https://doi.org/10.1007/s10722-020-00965-w