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. 2008 Dec 16;75(4):1173–1184. doi: 10.1128/AEM.02245-08

TABLE 1.

Genetic diversity parameters for X. citri pv. citri strains estimated by using MLVA (14 VNTR loci), AFLP (4 conditions), and IS-LM-PCR (4 conditions)a

Method Locus(i) or primer combination(s) No. of allelesb Total no. of fragments No. of haplotypes HT HWc FSTd RSTe
MLVA XL1 19 0.92 0.84 0.11*** 0.23NS
XL2 29 0.93 0.58 0.38*** 0.84***
XL3 11 0.87 0.70 0.25*** 0.37NS
XL4 22 0.93 0.77 0.21*** 0.78***
XL5f 15 0.89 0.73 0.19*** 0.49**
XL6 26 0.93 0.83 0.15*** 0.56***
XL7 18 0.89 0.60 0.27*** 0.17NS
XL8 10 0.73 0.44 0.33*** 0.22NS
XL9 14 0.74 0.49 0.33*** 0.60NS
XL10 10 0.83 0.47 0.43*** 0.50NS
XL11 6 0.33 0.23 0.49*** 0.53NS
XL13 11 0.47 0.31 0.39*** 0.80*
XL14 23 0.94 0.62 0.35*** 0.86***
XL15 18 0.86 0.70 0.19*** 0.51**
All X. citri loci 232 0.80 0.59 0.27*** 0.62***
Loci from pathotype A strains (167 strains) 172.6 0.77 0.64 0.13*** 0.38***
Loci from pathotype A* strains (65 strains)g 137.6 0.79 0.48 0.54*** 0.92***
Biallelic-marker methods
    AFLP analysis SacI+C/MspI+A 26 31 0.07 0.02 0.71**
SacI+C/MspI+T 39 29 0.09 0.03 0.76**
SacI+C/MspI+C 66 45 0.07 0.02 0.80**
SacI+C/MspI+G 51 44 0.06 0.03 0.55**
All combinations 182 94 0.07 0.02 0.73**
Combinations for pathotype A strains (167 strains) 154 59 0.03 0.02 0.28**
Combinations for pathotype A* strains (65 strains)g 158 36 0.13 0.02 0.78**
    IS-LM-PCR analysis pMsp/ISXac1-D3 80 88 0.13 0.03 0.78**
pMsP/ISXac1-GF 95 92 0.12 0.03 0.76**
pMsP/ISXac2-D3 96 80 0.06 0.03 0.63**
pMsp/ISXac3-IRF 65 32 0.08 0.02 0.83**
All combinations 336 146 0.10 0.03 0.78**
Combinations for pathotype A strains (167 strains) 216 110 0.05 0.03 0.39**
Combinations for pathotype A* strains (65 strains)g 249 35 0.20 0.03 0.87**
a

***, P < 0.001; **, P < 0.01; *, P < 0;05; NS, not significant (P > 0.05).

b

Number of alleles observed at each locus. Allelic richness for both pathotypes was calculated using the rarefaction method (n [corresponding to the number of individuals in the smallest group] = 65).

c

HW, Nei's mean index of gene diversity within populations.

d

FST estimates were calculated for eight and three geographical groups (with 10 or more members) composed of pathotype A and A* strains, respectively.

e

RST estimates from VNTR data were calculated for eight and three geographical groups (with 10 or more members) composed of pathotype A and A* strains, respectively.

f

Parameters were calculated for 225 strains, as 7 pathotype A*/Aw strains did not produce any amplicon for the XL5 locus.

g

Strains originally described as pathotype Aw (68) were included in the pathotype A* group for data derived from all three genotyping techniques.