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