Isolation and characterization of polymorphic microsatellites in Cocos nucifera L.

Abstract

Microsatellites or simple sequence repeats (SSRs) were isolated from coconut (Cocos nucifera) and tested for polymorphism on restricted germplasm. Sequencing of 197 clones from a cv. Tagnanan Tall-enriched genomic library showed that 75% contained a microsatellite, of which 64% were dinucleotide (GA/CT, CA/GT and GC/CG), 6% were trinucleotide, and 30% were compound repeats. Of 41 primer pairs tested on Tagnanan Tall genomic DNA, 38 gave the expected size product, two amplified two loci, and another gave a multilocus pattern. On 20 coconut samples, the 38 SSRs detected 198 alleles (average: 5.2 alleles per microsatellite). Genetic diversity (D = 1 - sigma pi2) values ranged from 0.141 to 0.809. Heterozygotes were present at high frequencies among some dwarf samples. Analysis of similarity matrices based either on shared alleles at each locus (simple matching coefficient) or on allele bands across all loci (Jaccard coefficient) showed similar results. Dwarfs grouped separately from talls and showed less genetic diversity. In a wider test on 40 samples, 8 SSRs detected 64 alleles (average: eight alleles per microsatellite). These results indicate the high potential of microsatellites to detect genetic diversity in coconut germplasm.

Genetic Fidelity Testing Using SSR Marker Assay Confirms Trueness to Type of Micropropagated Coconut (Cocos nucifera L.) Plantlets Derived from Unfertilized Ovaries

“…The selected primers recorded the highest levels of polymorphism for coconut populations [16] including Sri Lanka Tall, Sri Lanka Green dwarf and San Ramon tall which are the three parents in the two coconut hybrids tested. The selected primers have been developed by Perera et al [17], and Rivera et al [18], and were purchased from Integrate DNA Technologies (IDT), Singapore ( Table 1).…”

Floating, Boating and Introgression: Molecular techniques and the ancestry of coconut palm populations on Pacific Islands

“…RFLP (Restriction fragment length polymorphism) Lebrun et al 1998Lebrun et al , 1999Rohde et al1992 SSR (Simple sequence repeat or microsatellite DNA) Duran et al 1997;Karp 1999;Perera et al 1999Perera et al , 2000Rivera et al 1999;Teulat et al 2000 Mainly dominant markers detected RAPD (Random amplified polymorphic DNA) Anzizar et al 1998;Ashburner & Harries 1999;Ashburner & Rohde 1994;Ashburner et al 1997;Banks 1994;Cardeña et al 1999;Duran et al 1997;Rohde et al 1999;Upadhyay et al 2002;Wadt et al 1999 AFLP (Amplified fragment length polymorphism) Perera et al 1998;Rohde et al 1999;Teulat et al 2000 ISTR (Internal sequence tagged repeat) Anzizar et al 1998;Duran et al 1997;Rohde et al 1995Rohde et al , 1999 STS (Sequence tagged site amplification) Rohde et al 1999 and the Ancestry of Coconut Palm Populations on Pacific Islands.…”

Genetic and phylogenetic relationships of coconut populations from Amini and Kadmat Islands, Lakshadweep (India)

“…Characterizing of coconut diversity, earlier undertaken through morphological traits, has now given way to the use of molecular markers, especially microsatellites, which are preferred because of their co-dominant and multi-allelic nature and their capacity to detect high polymorphism (Rivera et al, 1999;Perera et al, 2000;Rajesh et al, 2008a,b ' and 11°1 6' N latitude and 72°45' and 72°48' E longitude, having a land area of 3.20 sq km). The variability in fruit shapes among LCT and LMT (Figures 1, 2) was reported earlier by Samsudeen et al (2006).…”