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)

Renee S. Arias, USDA-ARS Plant Germplasm Introduction and Testing Research Unit & USDA-ARS Genomics and Bioinformatics Research Unit
Linda L. Ballard, USDA-ARS Plant Germplasm Introduction and Testing Research Unit & USDA-ARS Genomics and Bioinformatics Research Unit
Mary V. Duke, USDA-ARS Plant Germplasm Introduction and Testing Research Unit & USDA-ARS Genomics and Bioinformatics Research Unit
Sheron A. Simpson, USDA-ARS Plant Germplasm Introduction and Testing Research Unit & USDA-ARS Genomics and Bioinformatics Research Unit
Xiaofen F. Liu, USDA-ARS Plant Germplasm Introduction and Testing Research Unit & USDA-ARS Genomics and Bioinformatics Research Unit
Valerie A. Orner, USDA-ARS National Peanut Research Laboratory & USDA-ARS Plant Germplasm Introduction and Testing Research Unit
Victor S. Sobolev, USDA-ARS National Peanut Research Laboratory & USDA-ARS Plant Germplasm Introduction and Testing Research Unit
Brian E. Scheffler, USDA ARS
Jaime Martínez-Castillo, Centro de Investigación Científica de Yucatán A.C., Unidad de Recursos Naturales, Mérida, Mexico

Document Type Article

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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 ampli- fication 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.