Supplemental

Table S3 Details for SSR markers used in the study

Locus / Chr / An / Gd / Gn / Ho / PIC
rm23 / 1 / 16 / 0.8401 / 65 / 0.3183 / 0.8220
rm5 / 1 / 25 / 0.8783 / 102 / 0.5107 / 0.8664
rm81a / 1 / 20 / 0.8480 / 67 / 0.6119 / 0.8323
rm211 / 2 / 20 / 0.7751 / 68 / 0.4679 / 0.7556
rm262 / 2 / 19 / 0.8707 / 36 / 0.0349 / 0.8574
rm71 / 2 / 28 / 0.6043 / 70 / 0.4398 / 0.5706
rm231 / 3 / 19 / 0.8105 / 66 / 0.3116 / 0.7896
rm251 / 3 / 53 / 0.9653 / 320 / 0.5478 / 0.9643
rm60 / 3 / 10 / 0.2821 / 19 / 0.1530 / 0.2705
rm241 / 4 / 34 / 0.9504 / 180 / 0.3892 / 0.9481
rm255 / 4 / 29 / 0.8849 / 97 / 0.2857 / 0.8751
rm335 / 4 / 25 / 0.9401 / 175 / 0.5737 / 0.9369
rm164 / 5 / 17 / 0.8403 / 43 / 0.1114 / 0.8246
rm249 / 5 / 29 / 0.9474 / 153 / 0.3318 / 0.9448
rm267 / 5 / 21 / 0.8913 / 97 / 0.5174 / 0.8818
rm190 / 6 / 14 / 0.4277 / 23 / 0.3262 / 0.3848
rm225 / 6 / 24 / 0.9174 / 106 / 0.4184 / 0.9118
rm253 / 6 / 29 / 0.9368 / 158 / 0.5377 / 0.9332
rm134 / 7 / 11 / 0.5775 / 18 / 0.3330 / 0.4979
rm18 / 7 / 32 / 0.9324 / 99 / 0.1901 / 0.9285
rm82 / 7 / 17 / 0.6630 / 41 / 0.3453 / 0.6055
rm223 / 8 / 27 / 0.9179 / 117 / 0.2745 / 0.9126
rm25 / 8 / 18 / 0.8185 / 77 / 0.4184 / 0.8019
rm42 / 8 / 16 / 0.8750 / 70 / 0.4139 / 0.8623
rm219 / 9 / 23 / 0.9169 / 92 / 0.2171 / 0.9109
rm242 / 9 / 22 / 0.7082 / 72 / 0.2925 / 0.6833
rm296 / 9 / 10 / 0.3204 / 21 / 0.2328 / 0.3072
rm216 / 10 / 19 / 0.8558 / 86 / 0.5557 / 0.8405
rm244 / 10 / 9 / 0.6715 / 22 / 0.1170 / 0.6172
rm258 / 10 / 23 / 0.8895 / 102 / 0.3825 / 0.8804
rm206 / 11 / 36 / 0.9533 / 187 / 0.2925 / 0.9513
rm224 / 11 / 22 / 0.7447 / 87 / 0.4409 / 0.7307
rm254 / 11 / 24 / 0.8885 / 87 / 0.3735 / 0.8783
rm235 / 12 / 26 / 0.8157 / 103 / 0.2362 / 0.7976
rm247 / 12 / 24 / 0.9140 / 133 / 0.4477 / 0.9080
rm270 / 12 / 26 / 0.8872 / 110 / 0.3105 / 0.8769
Mean / 22.69 / 0.8045 / 93.58 / 0.3545 / 0.7878

Notes: An = number of alleles; Gd = genetic diversity; Gn = genotype number; Ho = observed heterozygosity; PIC = polymorphism information content. The primer sequences for these markers were available at url http://www.gramene.org/microsat/microsats.txt

Table S4. Stepwise mutation index of 36 SSR loci

Marker / SMI / Marker / SMI
rm251 / 0.6238 / rm231 / 0.8704
rm296 / 1.0000* / rm249 / 0.7465
rm134 / 0.5804 / rm219 / 0.5278
rm71 / 0.9618* / rm241 / 0.5284
rm216 / 0.9265* / rm262 / 0.6487
rm267 / 0.9994* / rm164 / 0.7037
rm190 / 1.0000* / rm42 / 0.6441
rm270 / 1.0000* / rm242 / 0.9809*
rm25 / 0.9994* / rm244 / 0.6354
rm82 / 0.4653 / rm255 / 0.6522
rm60 / 0.9358* / rm223 / 0.9936*
rm247 / 1.0000* / rm23 / 0.9994*
rm206 / 0.6007 / rm254 / 0.8779
rm18 / 1.0000* / rm211 / 0.7216
rm81a / 0.5891 / rm335 / 0.9994*
rm224 / 0.7691 / rm258 / 0.6094
rm225 / 0.6586 / rm253 / 0.9867*
rm235 / 0.9080* / rm5 / 0.9954*

Notes: SMI - Stepwise mutation index of SSR loci. * the SSR loci which SMI >0.9000, and used as stepwise mutation type.


Table S5 Genetic differentiation index between indica and japonica for each SSR locus

Marker / D / Marker / D
rm251 / 0.1511 / rm225 / 0.0636
rm296 / 0.3312 / rm235 / 0.0641
rm134 / 0.0758 / rm231 / 0.0292
rm71 / 0.3925 / rm249 / 0.0124
rm216 / 0.1169 / rm219 / 0.0753
rm267 / 0.3504 / rm241 / 0.1708
rm190 / 0.1091 / rm262 / 0.1854
rm270 / 0.0880 / rm164 / 0.0484
rm25 / 0.3085 / rm42 / 0.0836
rm82 / 0.1275 / rm242 / 0.0043
rm60 / 0.1176 / rm244 / 0.0001
rm247 / 0.0213 / rm255 / 0.0661
rm206 / 0.0184 / rm223 / 0.1906
rm18 / 0.1416 / rm23 / 0.0065
rm81a / 0.0593 / rm254 / 0.1851
rm224 / 0.0589 / rm211 / 0.0265
rm335 / 0.1945 / rm258 / 0.0359
rm253 / 0.0428 / rm5 / 0.0976

Notes: D - differentiation index between indica and japonica


Table S6 Significance of differences for each estimator of genetic diversity among model-based CWR subpopulations

Sample size / An / Gd / Gn / Ho
GD-GX1 / 114 / b / a / b / a
GX2 / 479 / a / b / a / b
FJ / 49 / e / d / d / c
YN / 46 / c / c / d / d
HuN2 / 25 / f / f / e / g
JX-HuN1 / 44 / d / e / d / e
GD-GX1 / 132 / c / e / c / f

Notes: An = number of alleles; Gd = genetic diversity; Gn = genotype number; Ho = observed heterozygosity.


Table S7 Allelic richness of model-based CWR subpopulations

6 loci / 10 loci / 12 loci / 18 loci
HN / 4.34 / 6.09 / 6.79 / 8.46
GD-GX1 / 4.08 / 5.67 / 6.31 / 7.84
FJ / 3.82 / 5.10 / 5.59 / 6.75
HuN2 / 3.37 / 4.50 / 4.95 / 6.04
JX-HuN1 / 3.12 / 4.01 / 4.35 / 5.16
GX2 / 3.14 / 3.94 / 4.23 / 4.90
YN / 1.51 / 1.73 / 1.83 / 2.07

Notes: 6 loci, 10 loci,12 loci and 18 loci showed the sample size of locus bootstrap.

Figure S1 LnP(D) at different K values in structure analysis

Figure S2 (to be continued)

(Figure S2 being countinued)

Figure S2 Patterns of CWR structure according to 10 independent repeats of structure analysis results at each K value from 2 to 9. Percentage value indicated the percentage of that structure pattern in ten simulations. Letters represent provinces: a - Guangdong; b - Guangxi; c - Hainan; d - Fujian; e - Hunan; f - Jiangxi; g -Yunnan

Figure S3 Relationships between genetic distance (Nei, 1983) and geographical distance of CWR accessions in latitude-longitude sections.

Figure S4 Map of Zhujiang River and the counties along with them

Figure S5 Cluster analysis using CWR groups from counties in Zhujiang River in Guangdong and Guangxi based on Nei’s (1983 ) genetic distance

Figure S6 Regression between japonica specific allele frequency in CWR and latitude