Page 12 - Molecular Plant Breeding

Molecular Plant Breeding 2011, Vol.2, No.12, 83-91
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3.4 Diversity parameters
The amplified SSR markers were scored as present (1)
or absent (0), and then recorded into a binary matrix
as discrete variables (Lynch, 1994). The loci were
eliminated from the analysis if they were not
consistently amplified or with doubtful interpretation.
We evaluated the genetic polymorphisms for different
geographical regions of coconuts by calculating the
number of alleles per locus (N), polymorphic loci (Np ),
percentage of polymorphic loci (P), expected
heterozygosity (He), heterozygosity statistics for all
loci (Ho), and Wright F statistics (F is, Fst, Fit) (Nei,
1978). Based on the average expected and observed
heterozygosities, the apparent outcrossing rate (t) was
calculated from the inbreeding coefficient f (Ellstrand
et al., 1978). All parameters of genetic diversity were
calculated by the PopGene program (version 1.31).
3.5 Bayesian assignment tests
F statistics provided an overall assessment of
differentiation among accessions. F statistics was
examined more precisely by using a Bayesian
assignment test. Individuals were be randomly
assigned to any accession once no differentiation was
observed. Therefore, deviation from randomness was
the evidence of differentiation in one or more
accessions. Geneclass 2 (Piry et al., 2004) was used,
and 10 studied samples were used as the reference
data. All individuals were tested and assigned to the
most probable accession. In order to avoid systematic
bias resulting from rare alleles, the “leave one out”
option of Geneclass 2 was used: the tested individual
was excluded from the reference dataset. Moreover,
Bayesian assignment could also be used to identify
populations demonstrating affinities with the local
genotypes. In fact, the likelihood L of a population is
the probability of obtaining the tested genotype in the
population. Likewise, the probability of obtaining all
Hainan Tall (HNT) genotypes is the product of the
likelihoods. We used the sum of the scores issued by
Geneclass 2 ( -log L) as a dissimilarity measure.
3.6 Cluster analysis
A total of 45 coconut plants from Hainan (China) were
studied via cluster analysis to determine their
relationships. Cavalli-Sforza's distance rather than
Nei's distance was used in this study because the role
of genetic drift, migration and selection is more
important than mutation in the evolution of this group.
The weighted pair group method with arithmetic mean
dendrogram was produced by the DARwin software
(version 5.0.158) and the NTSYS software (version 2.1).
Authors’ contributions
XLL conceived the overall study, performed the experiment designs, and
drafted the manuscript. HT and LHH took part to the data analysis and the
writing. XLL obtained and analyzed the DDL data and was involved in the
writing. All authors read and approved the final manuscript.
Acknowledgements
This research was supported by the National Natural Science Foundation
(No. 30560092 and 31060259) and National Nonprofit Institute Research
Grant of CATAS-ITBB. The authors thank the coconut farmers from the six
cities for their assistance.
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