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CHARACTERIZATION AND DEVELOPMENT OF MICROSATELLITE MARKERS IN COCONUT (Cocos nucifera L.) BASED ON DE NOVO ASSEMBLED TRANSCRIPTOME DATA
Cecille Ann L. Osio, Wilson F. Aala Jr., Ma. Carmina C. Manuel, Maria Genaleen Q. Diaz, and Rita P. Laude
To develop microsatellite markers using available RNA-Seq data, microsatellite loci were identified from the transcriptome of ‘Laguna Tall’, ‘Makapuno’, and ‘Lono’ coconut endosperm samples. ‘Laguna Tall’ had the highest percentage of microsatellite-containing contigs (10%), followed by ‘Makapuno’ (8.8%) and ‘Lono’ (7.1%). All the detected microsatellite loci have perfect repeat motifs. Class II (12-19 bp) SSR (71.6%) were more prevalent than class I (≥20 bp) SSR (28.4%). Trinucleotide repeats were most abundant (31.8%), followed by dinucleotide (26.3%), tetranucleotide (6.0%), hexanucleotide (2.0%), and pentanucleotide (1.8%) SSR. The most dominant motifs were AG/CT (18.8%), AGG/CCT (7.8%), AAAT/ATTT (1.5%), AAAAG/CTTTT (0.5%), and AGGCGG/CCGCCT (0.1%). A total of 15,033 primer pairs were designed, in which 50 were selected for validation of amplification and assessment of polymorphism in 22 coconut varieties. A total of 46 markers yielded amplification products, of which 31 were potentially polymorphic. Analysis of the 31 SSR revealed that the number of alleles per locus ranged from 2 to 5 and the polymorphism information content (PIC) ranged from 0.34 to 0.68. The identified transcriptome-derived microsatellite markers may be used to study genetic and functional diversity, genetic mapping, comparative mapping with related genera, and population differentiation related to local adaptation of coconut varieties.