Discovery and characterization of new microsatellite loci in Dipteryx alata Vogel (Fabaceae) using next-generation sequencing data
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2017
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The use of next-generation sequencing (NGS) technologies provides a great volume of genome sequence data even for non-model species. The development of microsatellite markers using these data is a relatively quick and easy process. Dipteryx alata Vogel (Fabaceae) is an arboreal species from the Cerrado biome and is considered an important plant genetic resource. Here, we report the development of microsatellite markers for D. alata using NGS data. DNA samples from four individuals were sequenced using the Illumina MiSeq platform and high-quality reads were assembled into contigs of the D. alata genome sequence. Microsatellite regions were identified using the IMEX webserver and primer pairs were designed using the Primer3 software. The amplification settings for each locus were optimized. Fluorescent-labeled primers were developed and used to genotype individuals derived from three natural populations of D. alata. Fifty-four microsatellite regions were identified, from which
27 were elected to primer design. Among the amplified loci, 11 were
polymorphic, with the number of alleles ranging from 2 to 10. The
expected heterozygosity under Hardy-Weinberg Equilibrium (HWE)
per locus varied from 0.191 to 0.807. Genotype and allele frequencies
for all loci agreed with those expected under HWE and linkage
disequilibrium was not significant for all pairs of loci. The probabilities
of exclusion of paternity and of combined identity were equal to 0.993
and 5.65 x 10-8, respectively. The markers developed in this study are
useful to several types of population genetic studies with D. alata and,
eventually, for closely related species.
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Baru, Illumina MiSeq, SSR, Cerrado
Citação
GUIMARÃES, R. A.; TELLES, M. P. C.; ANTUNES, A. M.; CORRÊA, K. M.; RIBEIRO, C.V. G.; COELHO, A. S. G.; SOARES, T. N. Discovery and characterization of new microsatellite loci in Dipteryx alata Vogel (Fabaceae) using next-generation sequencing data. Genetics and Molecular Research, Ribeirão Preto, v. 16, n. 2, p. 1-6, 2017. DOI: 10.4238/gmr16029639. Disponível em: https://pubmed.ncbi.nlm.nih.gov/28453176/. Acesso em: 24 mar. 2023.