TABLE 1.
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** |
***, P < 0.001; **, P < 0.01; *, P < 0;05; NS, not significant (P > 0.05).
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).
HW, Nei's mean index of gene diversity within populations.
FST estimates were calculated for eight and three geographical groups (with 10 or more members) composed of pathotype A and A* strains, respectively.
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.
Parameters were calculated for 225 strains, as 7 pathotype A*/Aw strains did not produce any amplicon for the XL5 locus.
Strains originally described as pathotype Aw (68) were included in the pathotype A* group for data derived from all three genotyping techniques.