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: ranbutan (Nephelium lappaceumt)

Authors: Arias De Ares, Renee; Ballard, Linda; Duke, Mary; Simpson, Sheron; Liu, Xiaofen - Fanny; Orner, Valerie; Sobolev, Victor; Scheffler, Brian; MARTINEZ-CASTILLO, JAMIE - Yucatan Center For Scientific Research

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/14/2020
Publication Date: 6/28/2020
Citation: Arias De Ares, R.S., Ballard, L.L., Duke, M.V., Simpson, S.A., Liu, X.F., Orner, V.A., Sobolev, V., Scheffler, B.E., Martinez-Castillo, J. 2020. 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: ranbutan (Nephelium lappaceumt). Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-020-00965-w.
DOI: https://doi.org/10.1007/s10722-020-00965-w

Interpretive Summary: Banks of germplasm around the world need molecular markers to correctly identify samples, determine their genetic diversity and to select core-collections that represent the genetic diversity in the collections. In addition, large number of molecular markers allow for more accurately determination of population genetic parameters. In this work we provide 1872 molecular markers that were tested in five groups of tropical plants: mangosteen, lychee, sapodilla, rambutan and bamboo. All these species produce edible fruits or shoot, and all of them have medical applications. As habitat is being lost for these species, the availability of these markers will facilitate conservation efforts.

Technical Abstract: Simple sequence repeat (SSR) enriched libraries for seven species of tropical plants were prepared and sequenced in a GS-FLX Roche 454: Manilkara zapota (sapodilla), Litchi chinensis (lychee), Garcinia cochinchinensis Choisy, Garcinia mangostana (mangosteen), Nephelium lappaceum (rambutan), Bambusa vulgaris and Guadua angustifolia (bamboo). 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 using capillary electrophoresis 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 66057 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.