Supplementary Tables

A Core Collectionand Mini Core Collection of Oryza sativa L. in China

Hongliang Zhang1*, Dongling Zhang1*,MeixingWang1, Junli Sun1,Yongwen Qi1, Jinjie Li1, Xinghua Wei2, Longzhi Han3, Zongen Qiu3, Shengxiang Tang2, Zichao Li1#

1Key Laboratory of Crop Genomics & Genetic Improvement of Ministry of Agriculture, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China; 2 China National Rice Research Institute, Hangzhou, Zhejiang 310006, China; 3 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; *These authors contributed equally to this work

#The communicating author:

Zichao Li, College of Agronomy and Biotechnology, ChinaAgriculturalUniversity, Beijing 100094, China; Tel: 86-10-62731414, Fax: 86-10-62731414, E-mail:

Table S1 Numbersof varieties in different ecological zones (EZ) and subspecies

Variety type1 / Subspecies / Ecological zones
indica / japonica / EZ1 / EZ2 / EZ3 / EZ4 / EZ5 / EZ6
LV / 1762 / 1870 / 1215 / 1034 / 942 / 217 / 135 / 89
MPV / 374 / 230 / 135 / 314 / 34 / 55 / 54 / 12
PTH / 56 / 18 / 1 / 67 / 1 / 0 / 3 / 2

1 LV local varieties, MPV modern pureline varieties, PTH parents of trilinear hybrids

Table S2 Numbers of varieties in clusters (POP) determinedby STRUCTURE for the primary core collection and other level collections selected using the optimum sampling scheme

Core set2 / Size / LV1 / MPV / PTH
POP1 / POP2 / POP3 / POP4 / POP5 / POP6 / POP1 / POP2 / POP1 / POP2 / POP3 / POP4
MCC / 189 / 27 / 25 / 24 / 27 / 28 / 28 / 12 / 11 / 2 / 2 / 1 / 2
C500 / 500 / 70 / 67 / 62 / 72 / 74 / 76 / 32 / 28 / 6 / 5 / 4 / 4
CC / 932 / 131 / 125 / 117 / 134 / 137 / 141 / 59 / 53 / 8 / 10 / 8 / 9
C1500 / 1500 / 211 / 201 / 188 / 216 / 221 / 227 / 96 / 85 / 8 / 17 / 14 / 16
C2000 / 2000 / 281 / 268 / 251 / 288 / 295 / 302 / 128 / 113 / 8 / 21 / 27 / 18
PCC / 4310 / 460 / 835 / 569 / 747 / 416 / 605 / 364 / 240 / 8 / 21 / 27 / 18

1 LV local varieties, MPV modern pureline varieties, PTH parents of trilinear hybrids

2 MCC mini core collection, C500 core set with 500 accessions, CC core collection, C1500 core set with 1,500 accessions, C2000 core set with 2,000 accessions, PCC Primary Core Collection

Table S3 SSR markers used in this study

Locus / Chr. / Forward primer / Reverse primer / No. of alleles / PIC
RM23 / 1 / cattggagtggaggctgg / Gtcaggcttctgccattctc / 13 / 0.7007
RM5 / 1 / tgcaacttctagctgctcga / gcatccgatcttgatggg / 20 / 0.8425
RM81A / 1 / gagtgcttgtgcaagatcca / cttcttcactcatgcagttc / 13 / 0.7504
RM211 / 2 / ccgatctcatcaaccaactg / cttcacgaccatctcaaagg / 15 / 0.4911
RM262 / 2 / cattccgtctcggctcaact / cagagcaaggtggcttgc / 13 / 0.7049
RM71 / 2 / ctagaggcgaaaacgagatg / gggtgggcgaggtaataatg / 13 / 0.4921
RM231 / 3 / ccagattatttcctgaggtc / cacttgcatagttctgcattg / 18 / 0.8295
RM251 / 3 / gaatggcaatggcgctag / atgcggttcaagattcgatc / 30 / 0.7943
RM60 / 3 / agtcccatgttccacttccg / atggctactgcctgtactac / 3 / 0.1524
RM241 / 4 / gagccaaataagatcgctga / tgcaagcagcagatttaggtg / 23 / 0.8974
RM255 / 4 / tgttgcgtgtggagatgtg / cgaaaccgctcagttcaac / 17 / 0.7181
RM335 / 4 / gtacacacccacatcgagaag / gctctatgcgagtatccatgg / 25 / 0.8633
RM164 / 5 / tcttgcccgtcactgcagatatcc / gcagccctaatgctacaattcttc / 14 / 0.8512
RM249 / 5 / ggcgtaaaggttttgcatgt / atgatgccatgaaggtcagc / 23 / 0.7226
RM267 / 5 / tgcagacatagagaaggaagtg / agcaacagcacaacttgatg / 15 / 0.6791
RM190 / 6 / ctttgtctatctcaagacac / ttgcagatgttcttcctgatg / 16 / 0.7770
RM225 / 6 / tgcccatatggtctggatg / gaaagtggatcaggaaggc / 15 / 0.7553
RM253 / 6 / tccttcaagagtgcaaaacc / gcattgtcatgtcgaagcc / 21 / 0.8543
RM134 / 7 / acaaggccgcgagaggattccg / gctctccggtggctccgattgg / 5 / 0.3033
RM18 / 7 / ttccctctcatgagctccat / gagtgcctggcgctgtac / 17 / 0.8213
RM82 / 7 / tgcttcttgtcaattcgcc / cgactcgtggaggtacgg / 6 / 0.2608
RM223 / 8 / gagtgagcttgggctgaaac / gaaggcaagtcttggcactg / 22 / 0.8721
RM25 / 8 / ggaaagaatgatcttttcatgg / ctaccatcaaaaccaatgttc / 13 / 0.6928
RM42 / 8 / atcctaccgctgaccatgag / tttggtctacgtggcgtaca / 11 / 0.8276
RM219 / 9 / cgtcggatgatgtaaagcct / catatcggcattcgcctg / 25 / 0.8888
RM242 / 9 / ggccaacgtgtgtatgtctc / tatatgccagcacggatggg / 21 / 0.8887
RM296 / 9 / cacatggcaccaacctcc / gccaagtcattcactact / 6 / 0.4124
RM216 / 10 / gcatggccgatggtaaag / tgtataaaaccacacggcca / 16 / 0.7635
RM244 / 10 / ccgactgttcgtccttatca / ctgctctcgggtgaacgt / 8 / 0.7277
RM258 / 10 / tgctgtatgtagctcgcacc / tggccttaaagctgtcgc / 18 / 0.7035
RM206 / 11 / cccatgcgtttaactattct / cgttccatcgatccgtatgg / 28 / 0.9344
RM224 / 11 / atcgatcgatcttcacgagg / tgctataaaaggcattcggg / 21 / 0.8852
RM254 / 11 / agccccgaataaatccacct / ctggaggagcatttggtagc / 13 / 0.7734
RM235 / 12 / agaagctagggctaacgaac / tcacctggtcagcctctttc / 24 / 0.8763
RM247 / 12 / tagtgccgatcgatgtaacg / catatggttttgacaaagcg / 32 / 0.8313
RM270 / 12 / ggccgttggttctaaaatc / tgcgcagtatcatcggcgag / 12 / 0.6572

Table S4Duncan’s homogenous test of allele retentions (RT) and Nei’s gene diversity (He) among different sampling methods

Sampling
Methoda / RT / He
Mean / Sig.b / Mean / Sig.b
AVT / VTS / 0.896 / a / 0.744 / c
VTP / 0.895 / a / 0.747 / a
VTL / 0.889 / b / 0.745 / b
VTG / 0.888 / b / 0.743 / cd
VTC / 0.884 / c / 0.743 / d
GR / SS / 0.895 / a / 0.746 / a
PS / 0.894 / a / 0.746 / a
EZ / 0.882 / b / 0.742 / b
AGR / P / 0.894 / a / 0.746 / a
S / 0.891 / b / 0.746 / a
G / 0.890 / b / 0.744 / b
L / 0.889 / bc / 0.744 / b
C / 0.888 / c / 0.743 / c
CGR / CR / 0.896 / a / 0.750 / a
CM / 0.887 / b / 0.747 / b
R / 0.885 / c / 0.739 / c

a Here, AVT refers to the methods of allocating sampling scales among three variety types, including VTC, VTG, VTL, VTP and VTS, in which the last symbol representing respectively: C constant number, G proportion to Nei’s gene diversity index of the group in the basic collection, Lproportion to the logarithmic group size in the basic collection, P proportional to the group size in the basic collection, S proportional to the square-rooted group size in the basic collection. GR refers to the grouping methods within each variety type according to ecological zones (EZ), two subspecies (Indica and Japonica) (SS) and population structure (PS). AGRrefers to the methods of allocating sampling scales among groups within each variety type, including C, G, L, P and S,which are same to those among variety types. CGR refers to the methods choosing varieties from each second level group:R random sampling, CR clustering-based random sampling, CM clustering-based most representative sampling.

bItems with the same letterare notsignificantly different at P=0.05

Table S5Duncan’s homogenous test of allele retentions for rare alleles (RA) and inferior alleles (IA) among different sampling methods

Sampling method / RA / IA
Mean / Sig. a / Mean / Sig. a
AVT / VTP / 0.94 / a / 0.39 / a
VTS / 0.93 / a / 0.38 / a
VTL / 0.92 / b / 0.37 / a
VTG / 0.91 / c / 0.38 / a
VTC / 0.91 / c / 0.37 / a
GR / SS / 0.93 / a / 0.40 / a
PS / 0.93 / a / 0.38 / b
EZ / 0.91 / b / 0.36 / c
AGR / P / 0.93 / a / 0.39 / a
L / 0.92 / ab / 0.38 / ab
S / 0.92 / ab / 0.38 / ab
G / 0.92 / ab / 0.38 / ab
C / 0.92 / b / 0.37 / b
CGR / CR / 0.93 / a / 0.40 / a
CM / 0.92 / b / 0.36 / b
R / 0.91 / c / 0.36 / b

a, bsame to Table S4

Table S6 The percentage of the variation range of 16 traits in CC and MCC relative to those in PCC, and the variances and coefficients of variation of those traits in PCC, CC and MCC

Traits / Covering of range / Variances / Coefficients of variation
CC / MCC / PCC / CC / MCC / PCC / CC / MCC
Plant height / 96.52% / 88.70% / 0.13 / 0.15 / 0.20 / 14.39 / 15.36 / 17.370
Days to flowering / 86.82% / 79.07% / 423.91 / 441.69 / 426.41 / 21.73 / 21.91 / 21.754
Panicle weight per plant / 100.00% / 97.89% / 116.75 / 154.48 / 264.87 / 54.45 / 62.08 / 78.688
Length of penultimate ligule / 85.98% / 75.25% / 0.28 / 0.28 / 0.32 / 28.83 / 28.88 / 30.877
Length of penultimate leaf / 99.21% / 95.36% / 203.39 / 219.94 / 243.09 / 26.26 / 27.12 / 28.625
Width of penultimate leaf / 93.33% / 90.00% / 0.07 / 0.07 / 0.07 / 20.15 / 19.45 / 19.204
Number of secondary branches / 93.73% / 90.40% / 123.69 / 136.17 / 143.49 / 33.19 / 34.19 / 35.065
Grain length / 100.00% / 78.87% / 0.66 / 0.75 / 0.78 / 10.20 / 10.82 / 11.040
Grain width / 95.00% / 55.00% / 0.15 / 0.18 / 0.16 / 12.07 / 13.27 / 12.329
Length of flag leaf / 89.70% / 73.36% / 83.90 / 88.17 / 91.05 / 23.46 / 23.79 / 23.979
Width of flag leaf / 85.47% / 85.47% / 0.10 / 0.10 / 0.10 / 18.89 / 18.96 / 19.065
Ratio of full seed / 96.59% / 88.44% / 0.02 / 0.03 / 0.02 / 22.26 / 22.87 / 22.875
Length of panicles / 91.64% / 63.76% / 11.94 / 11.33 / 10.02 / 14.23 / 13.80 / 12.988
Number of primary branches / 92.54% / 91.04% / 4.18 / 4.41 / 4.90 / 18.33 / 18.57 / 19.483
Number of panicles per plant / 96.49% / 93.33% / 18.88 / 18.98 / 23.19 / 43.97 / 44.48 / 49.969
100-grain weight / 100.00% / 80.91% / 1160.06 / 1148.15 / 1084.67 / 23.81 / 23.32 / 22.781
Average / 93.94% / 82.93% / 134.26 / 139.05 / 143.33 / 24.14 / 24.93 / 26.63

PCC, primary core collection; CC, core collection; MCC, mini core collection