Whole Genome Shotgun Sequences for Microsatellite Discovery and Application in Cultivated and Wild <i>Macadamia</i> (Proteaceae)
2014
Catherine J. Nock | Martin S. Elphinstone | Gary Ablett | Asuka Kawamata | Wayne Hancock | Craig M. Hardner | Graham J. King
Premise of the study: Next-generation sequencing (NGS) data are widely used for single-nucleotide polymorphism discovery and genetic marker development in species with limited available genome information. We developed microsatellite primers for the Proteaceae nut crop species <i>Macadamia integrifolia</i> and assessed cross-species transferability in all congeners to investigate genetic identification of cultivars and gene flow. Methods and Results: Primers were designed from both raw and assembled Illumina NGS paired-end reads. The final 12 microsatellite markers selected were polymorphic among wild individuals of all four <i>Macadamia</i> species—<i>M. integrifolia</i>, <i>M. tetraphylla</i>, <i>M. ternifolia</i>, and <i>M. jansenii</i>—and in commercial macadamia cultivars including hybrids. Conclusions: We demonstrate the utility of raw and assembled Illumina NGS reads from total genomic DNA for the rapid development of microsatellites in <i>Macadamia</i>. These primers will facilitate future studies of population structure, hybridization, parentage, and cultivar identification in cultivated and wild <i>Macadamia</i> populations.
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