Abstract:
Coconut (Cocos nucifera L.) is an important oil crop that can play a major role in the food
security of the people in most of the Asian countries including Sri Lanka. The genomic
knowledge on coconut is extremely important to increase productivity by incorporating
superior traits targeting quality end products. Simple Sequence Repeats (SSR) are DNA-based
markers which are informative for basic and applied studies such as molecular breeding.
Coconut genetic and genomic resources, especially molecular markers, have been scarce until
recently, impeding coconut breeding efforts. Comprehensive analysis of SSR has become
possible now because several coconut genomes have been sequenced. In this study the draft
genome of C. nucifera Hainan Tall (HAT) variety (accession number GCA_008124465.1) was
surveyed to determine the distribution and frequency of SSRs. The polymorphism of the
available SSRs of the HAT variety was investigated using an electronic PCR approach and,
manual analysis of each PCR product marker in five genomes: C. nucifera Chowghat Green
Dwarf variety, C. nucifera Catigan Green Dwarf variety, Phoenix dactylifera and Elaeis
guineensis and C. nucifera L. ESTs. A total of 522,524 SSRs (repeat units 1-6 bp) from the
draft genome of variety HAT with an overall density of 258.675 (SSRs/Mbp) was characterized
using the GMATA tool. Dinucleotide was the most common repeat motif with a frequency of
58.87%, followed by 28.01% mononucleotides, 7.15% trinucleotide, 4.31% tetranucleotide,
1.50% pentanucleotide and 0.16% hexanucleotide. The motif AG/CT was the most abundant
and AT/TA was the second most abundant among all identified SSR motifs by accounting for
42.01% and 32.79% respectively. A total of 245,048 unique SSR markers were developed from
the total SSR loci and a high degree of polymorphism (nearly 51 %) was found between
different genotypes. Polymorphic SSR sites of C. nucifera were mostly comprised of
dinucleotide motifs (82.91%), followed by trinucleotide motifs (10.39%), then tetranucleotide
motifs (4.15%). The findings of the present study indicate that whole-genome sequencing is an
excellent resource for developing SSR markers, and the newly identified large numbers of SSR
markers could make an important contribution to the coconut research community
