An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs

Citation
B. Teulat et al., An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs, THEOR A GEN, 100(5), 2000, pp. 764-771
Citations number
24
Categorie Soggetti
Plant Sciences","Animal & Plant Sciences
Journal title
THEORETICAL AND APPLIED GENETICS
ISSN journal
00405752 → ACNP
Volume
100
Issue
5
Year of publication
2000
Pages
764 - 771
Database
ISI
SICI code
0040-5752(200003)100:5<764:AAOGDI>2.0.ZU;2-H
Abstract
Genetic diversity in 31 individuals from 14 coconut populations across the entire geographic range (2-3 individuals per population) was assessed using sequence-tagged microsatellites (or simple sequence re pears, SSRs) and am plified fragment length polymorphism (AFLP). From the 39 SSR primer sets te sted, only two gave patterns that could not be scored and used in the data analysis. The remainder included five SSRs that pave double-locus profiles in which one locus could still be scored separately. The 37 SSRs revealed b etween 2 and 16 alleles per locus and a total of 339 alleles in the 14 popu lations. Gene diversity (D = 1-Sigma p(i)(2)) ranged from 0.47 to 0.90. Two of the four Dwarf populations were homozygous at all 37 loci, which is con sistent with their autogamous (self-fertilising) reproduction. One Dwarf po pulation was heterozygous at one locus but the other (Niu Leka Dwarf), whic h is known to be cross-pollinating, showed high levels of heterozygosity. G enerally, diversity was higher in populations from the South Pacific and So uth East Asia. Three SSR loci (CNZ46, CN2A5, CN11E6) gave distinct genotype s for all but two populations. The East African populations had higher hete rozygosities than those from West Africa, and the populations from Tonga an d Fiji generally had distinct alleles from those of the South Pacific. AFLP analysis with 12 primer combinations gave a total of 1106 bands, of which 303 were polymorphic (27%). Similarity matrices were constructed from the t wo data sets using the pro-portion of shared alleles for SSRs and a Jaccard coefficient for AFLPs. In each case cluster and principal coordinates anal yses were performed, with the resultant dendrograms and plots revealing sim ilar relationships among the populations for both approaches. There was gen erally a good separation of populations, and phenetic relationships were in agreement with those previously shown by RFLPs. The use of SSRs and AFLPs in genetic-diversity analysis for the establishment of germplasm collection s is discussed.