Generation of EST SSR markers in coconut and their validation in assessment of genetic diversity in coconut cultivars

Abstract

In this study, we have focused on developing and characterizing informative S newlineSR markers newlinefrom a larger collection of ESTs, representing leaf transcriptome of coconut. A total of newline3,18,528 potential SSRs could be identified, which is testimony to the high frequency of newlineSSRs in transcribed regions of coconut genome. Di-nucleotide repeats were the dominant type followed by tri-nucleotide repeats. Among the di-nucleotide repeat motifs, the dominant repeat was AG/CT, followed by AT/AT and AC/GT. The dominant trinucleotide repeat was AAG/CTT. A total of 523 primers were designed from flankin g SSR region EST SSR newlinesimilarity searches were done by using BLASTx program against oil palm and date palm newlinesequences. The genetic diversity assessment of 193 palms, comprising of 25 each of tall and newlinedwarf coconut accessions, representing diverse geographic locations, was carried out using newline10 highly polymorphic primers. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. All the loci showed 100% polymorphism with respect to the samples screened. The number of alleles observed ranged from seven to 22. The mean PIC value was 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. Clustering of the palms based on molecular data revealed that t all accessions from the same newlinegeographic regions were grouped together. Among dwarfs, Niu Leka Green Dwarf (from Fiji) newlineformed a distinct cluster. These EST SSRs were also utilized for authenticating hybrids from newlineselect crosses. The transferability of coconut specific EST SSR markers to other cultivated newlinepalms viz., date palm, oil palm and arecanut, was also investigated. Out of 50 EST SSRs newlineselected for transferability study, 35 (70%) primers amplified with oil palm, 20 (40%) newlineprimers gave amplification with date palm and 31 (62%) primers amplified with arecanut. A newline Coconut EST SSR Marker Database was also created to provide researchers with access to newlinecoconut EST SSR data which allow users to access data via search. These new polymorph