Title: Development of low temperature germinability markers for evaluation of rice (Oryza sativa L.) germplasm
Authors:Do Yoon Hyun1, Gi An Lee1, Man Jung Kang1, Diana Burkart-Waco2,3, Sang Ic Kim3,¶, Jae Yoon Kim4, MyungChul Lee1, Jae Gyun Gwag1, YeonGyu Kim1, Thomas H. Tai2,3,*
1 National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, Suwon, Republic of Korea
2 USDA-ARS Crops Pathology and Genetics Research Unit, Davis, CA 95616, USA
3 Department of Plant Sciences, University of California, Davis, CA 95616, USA
4Division of Biotechnology, Korea University, Seoul, Republic of Korea
*Corresponding author, email , tel. 1-530-752-4342, fax 1-530-752-4361
¶ Present address: Dupont Crop Protection, Stine Haskell Research Center, Newark, DE 19711, USA
Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.
Supplementary Data
Table S1. Germplasm accessions used in this study and LTG data
Table S2. Distribution of SNP markers identified by reduced representation sequencing and used in the LTG association analysis
Fig. S1. Phenotypic variation of the germplasm for LTG after 14 days at 13℃
Fig. S2. Classification of germplasm for low temperature germinability
Fig. S3. Dot graph for comparison of the germination rate by origin
Fig. S4. Distribution of qLTG3-1 alleles by country of origin
Fig. S5. Average germination rate of germplasm by qLTG3-1 alleles
Fig. S6. Manhattan plot for association between marker and LTG trait.
Fig. S7. Positions of LTG markers identified by association analysis.
Table S1. Germplasm accessions used in this study and LTG data
No. / Name / Origin / VRa / GRb(13°C) / GR(28°C) / LTGc1 / DPKR 036M 11767 / PRK / 3.7 / 68.3 / 100 / T
2 / DPKR 036M 1177 / PRK / 8.3 / 10.0 / 100 / S
3 / DPKR 036M 1404 / PRK / 5.7 / 63.3 / 98.3 / M
4 / DPKR 036M 2090 / PRK / 4.3 / 90.0 / 100 / T
5 / DPKR 036M 2137 / PRK / 4.3 / 81.7 / 96.7 / T
6 / DPKR 036M 3983 / PRK / 9.0 / 3.3 / 96.7 / S
7 / DPKR 036S 432 / PRK / 3.7 / 85.0 / 100 / T
8 / DPKR 036S 443 / PRK / 8.3 / 8.3 / 100 / S
9 / DPKR 036S 446 / PRK / 3.0 / 91.7 / 100 / T
10 / DPKR 036S 454 / PRK / 7.7 / 16.7 / 98.3 / S
11 / DPKR 036S 89 / PRK / 3.0 / 95.0 / 100 / T
12 / DPKR 036M 1087 / PRK / 9.0 / 6.7 / 98.3 / S
13 / DPKR 036M 1147 / PRK / 9.0 / 3.3 / 98.3 / S
14 / DPKR 036M 1400 / PRK / 4.3 / 83.3 / 95.0 / T
15 / DPKR 036M 1407 / PRK / 2.3 / 91.7 / 100 / T
16 / DPKR 036M 1610 / PRK / 1.7 / 86.7 / 100 / T
17 / DPKR 036M 1654 / PRK / 7.7 / 13.3 / 100 / S
18 / DPKR 036M 2114 / PRK / 8.3 / 11.7 / 98.3 / S
19 / DPKR 036M 2186 / PRK / 8.3 / 13.3 / 100 / S
20 / DPKR 036M 2188 / PRK / 9.0 / 11.7 / 100 / S
21 / DPKR 036M 238 / PRK / 7.7 / 15.0 / 100 / S
22 / DPKR 036M 299 / PRK / 7.7 / 16.7 / 100 / S
23 / DPKR 036M 680 / PRK / 9.0 / 0.0 / 100 / S
24 / DPKR 036M 694 / PRK / 7.7 / 10.0 / 100 / S
25 / DPKR 036M 971 / PRK / 7.0 / 23.3 / 96.7 / S
26 / DPKR 036S 10288 / PRK / 3.0 / 93.3 / 100 / T
27 / DPKR 036S 11511 / PRK / 5.0 / 63.3 / 100 / M
28 / DPKR 036S 11727 / PRK / 5.0 / 73.3 / 100 / T
29 / DPKR 036S 11685 / PRK / 2.3 / 91.7 / 95.0 / T
30 / DPKR 036S 10296 / PRK / 5.0 / 90.0 / 100 / T
31 / DPKR 036S 10309 / PRK / 9.0 / 3.3 / 100 / S
32 / DPKR 036S 10312 / PRK / 8.3 / 8.3 / 100 / S
33 / DPKR 036S 10322 / PRK / 3.0 / 91.7 / 100 / T
34 / DPKR 036S 10332 / PRK / 5.0 / 78.3 / 100 / T
35 / DPKR 036S 10336 / PRK / 5.0 / 75.0 / 100 / T
36 / DPKR 036S 10338 / PRK / 5.0 / 73.3 / 100 / T
37 / DPKR 036S 10370 / PRK / 5.0 / 73.3 / 96.7 / T
38 / DPKR 036S 10454 / PRK / 5.0 / 71.7 / 100 / T
39 / DPKR 036S 10467 / PRK / 8.3 / 11.7 / 100 / S
40 / DPKR 036S 10469 / PRK / 7.7 / 10.0 / 100 / S
41 / DPKR 036S 10487 / PRK / 9.0 / 6.7 / 100 / S
42 / DPKR 036S 10491 / PRK / 5.0 / 70.0 / 100 / T
43 / DPKR 036S 10500 / PRK / 8.3 / 5.0 / 100 / S
44 / DPKR 036S 10503 / PRK / 7.7 / 15.0 / 100 / S
45 / DPKR 036S 10512 / PRK / 9.0 / 0.0 / 100 / S
46 / DPKR 036S 11487 / PRK / 7.7 / 18.3 / 100 / S
47 / DPKR 036S 11510 / PRK / 9.0 / 5.0 / 100 / S
48 / DPKR 036S 11539 / PRK / 4.3 / 83.3 / 100 / T
49 / DPKR 036S 11556 / PRK / 7.0 / 31.7 / 100 / M
50 / DPKR 036S 11666 / PRK / 9.0 / 8.3 / 100 / S
51 / DPKR 036S 11687 / PRK / 2.3 / 88.3 / 100 / T
52 / DPKR 036S 11712 / PRK / 2.3 / 90.0 / 100 / T
53 / DPKR 036S 11713 / PRK / 1.0 / 96.7 / 100 / T
54 / DPKR 036S 11721 / PRK / 3.7 / 95.0 / 100 / T
55 / DPKR 036S 11744 / PRK / 5.0 / 61.7 / 100 / M
56 / DPKR 036S 11750 / PRK / 7.7 / 10.0 / 98.3 / S
57 / DPKR 036S 11752 / PRK / 5.0 / 65.0 / 100 / M
58 / DPKR 036S 11765 / PRK / 7.0 / 18.3 / 100 / S
59 / DPKR 036S 11781 / PRK / 5.0 / 63.3 / 100 / M
60 / DPKR 036S 11782 / PRK / 3.0 / 90.0 / 100 / T
61 / DPKR 036S 1221 / PRK / 8.3 / 18.3 / 100 / S
62 / DPKR 036S 127 / PRK / 7.7 / 15.0 / 100 / S
63 / DPKR 036S 1706 / PRK / 5.0 / 66.7 / 96.7 / M
64 / Dajiaoba / JPN / 7.7 / 16.7 / 100 / S
65 / Mogumoguaoba / JPN / 8.3 / 6.7 / 100 / S
66 / Hatsumurasaki / JPN / 5.0 / 66.7 / 100 / M
67 / Kokushokuto-2 / JPN / 3.0 / 81.7 / 96.7 / T
68 / Kuroke / JPN / 5.0 / 65.0 / 100 / M
69 / Kurouruchi / JPN / 4.3 / 80.0 / 98.3 / T
70 / Motsurewase / JPN / 4.3 / 66.7 / 100 / M
71 / Norin 20 / JPN / 5.0 / 76.7 / 100 / T
72 / Hosakan / JPN / 2.3 / 95.0 / 100 / T
73 / Sasaminori / JPN / 5.0 / 63.3 / 100 / M
74 / Tokachikuromomi / JPN / 1.0 / 98.3 / 100 / T
75 / Norin 9 / JPN / 4.3 / 83.3 / 100 / T
76 / Kokushokuto / JPN / 3.7 / 80.0 / 100 / T
77 / Nagayama 77402 spontaneous mutant / JPN / 9.0 / 0.0 / 100 / S
78 / 410750 / JPN / 7.0 / 31.7 / 100 / S
79 / thick culm dwarf / JPN / 6.3 / 23.3 / 98.3 / S
80 / A-107 / JPN / 3.0 / 96.7 / 100 / T
81 / AC-34 / JPN / 4.3 / 80.0 / 100 / T
82 / Daobei 47 / JPN / 6.3 / 33.3 / 100 / S
83 / Shang yu 697 / JPN / 4.3 / 81.7 / 100 / T
84 / Hao Hai Huan (Acc.66984) / CHN / 1.7 / 96.7 / 100 / T
85 / Jiudao 55 / CHN / 6.3 / 30.0 / 100 / M
86 / Jiudao 60 / CHN / 5.7 / 46.7 / 100 / M
87 / Jiudao 39 / CHN / 6.3 / 31.7 / 100 / M
88 / Tongyu 223 / CHN / 5.0 / 43.3 / 95.0 / M
89 / Tongyu 221 / CHN / 5.0 / 70.0 / 100 / M
90 / Jijing 504 / CHN / 7.0 / 18.3 / 100 / S
91 / Jijing 91 / CHN / 5.0 / 51.7 / 100 / M
92 / Jijing 801 / CHN / 5.0 / 38.3 / 100 / M
93 / Ji 08-156 / CHN / 5.7 / 41.7 / 100 / M
94 / Nan jing 47 / CHN / 7.7 / 15.0 / 96.7 / S
95 / Wu yujing 23 / CHN / 7.7 / 23.3 / 100 / S
96 / Chang jing 08-2 / CHN / 6.3 / 50.0 / 100 / M
97 / Chang jing 09-8 / CHN / 6.3 / 41.7 / 100 / M
98 / Su jing 8 / CHN / 6.3 / 48.3 / 100 / M
99 / Xiushui 12 / CHN / 7.7 / 16.7 / 100 / S
100 / Xiushui 114 / CHN / 5.0 / 68.3 / 100 / M
101 / Xiushui 128 / CHN / 7.0 / 25.0 / 100 / S
102 / Hong mi / CHN / 8.3 / 6.7 / 100 / S
103 / Pin 6 / CHN / 3.0 / 75.0 / 100 / T
104 / Long hua 05-0501 / CHN / 6.3 / 35.0 / 100 / S
105 / Xichang li / CHN / 5.0 / 65.0 / 100 / M
106 / Sui 02-6159 / CHN / 9.0 / 1.7 / 100 / S
107 / He xuan 03-13 / CHN / 7.7 / 11.7 / 100 / S
108 / Ha 99-245 / CHN / 9.0 / 1.7 / 100 / S
109 / Long yang 2083 / CHN / 7.7 / 13.3 / 100 / S
110 / Song 5119 / CHN / 5.0 / 61.7 / 100 / M
111 / Jinlang 1 / CHN / 5.0 / 30.0 / 100 / S
112 / Xiu 02-6173 / CHN / 8.3 / 6.7 / 100 / S
113 / Mu 2002-1235 / CHN / 6.3 / 38.3 / 93.3 / M
114 / Bei 02-20 / CHN / 7.0 / 31.7 / 100 / M
115 / Long dun 301-12 / CHN / 9.0 / 3.3 / 100 / S
116 / Long pin 02-1 / CHN / 9.0 / 3.3 / 95.0 / S
117 / Long D99709 / CHN / 8.3 / 5.0 / 100 / S
118 / Ji 2005-2 / CHN / 8.3 / 10.0 / 100 / S
119 / Ji 2005-8 / CHN / 9.0 / 1.7 / 100 / S
120 / Ji 2005-13 / CHN / 8.3 / 5.0 / 100 / S
121 / Ji 2006-2348 / CHN / 8.3 / 3.3 / 100 / S
122 / Qing 02-11 / CHN / 9.0 / 0.0 / 96.7 / S
123 / Nonglin 20 / CHN / 7.0 / 23.3 / 95.0 / S
124 / Long jiao 92-66 / CHN / 9.0 / 0.0 / 100 / S
125 / Song 9023 / CHN / 5.7 / 55.0 / 96.7 / M
126 / Jiheijing / CHN / 1.0 / 95.0 / 100 / T
127 / Jinong da 3 / CHN / 6.3 / 30.0 / 100 / S
128 / Dong nong 91-11 / CHN / 7.7 / 15.0 / 100 / S
129 / Tong yu 139 / CHN / 7.7 / 11.7 / 95.0 / S
130 / Sasanisikix2302 / CHN / 8.3 / 5.0 / 100 / S
131 / Song 98-10 / CHN / 9.0 / 1.7 / 100 / S
132 / Yan jing 105 / CHN / 8.3 / 5.0 / 98.3 / S
133 / Te you 12 / CHN / 7.7 / 23.3 / 100 / S
134 / Fuyuan 3 / CHN / 6.3 / 18.3 / 100 / S
135 / Tezhan 2 / CHN / 6.3 / 41.7 / 100 / M
136 / Eluosidao / CHN / 5.0 / 53.3 / 100 / M
137 / Dun neidao / CHN / 7.0 / 20.0 / 100 / S
138 / Ruanxiangjing / CHN / 9.0 / 6.7 / 100 / S
139 / Long dun 97-1 / CHN / 8.3 / 10.0 / 100 / S
140 / W-14 / CHN / 1.0 / 100.0 / 100 / T
141 / W-15 / CHN / 1.0 / 100.0 / 100 / T
142 / IKSAN558 / KOR / 9.0 / 0.0 / 100 / S
143 / HeugjinjuByeo / KOR / 9.0 / 3.3 / 100 / S
144 / Nokyang / KOR / 9.0 / 1.7 / 100 / S
145 / IKSAN541 / KOR / 6.3 / 48.3 / 100 / M
146 / Suweon 546 / KOR / 6.3 / 28.3 / 100 / M
147 / HwaseongByeo / KOR / 8.3 / 11.7 / 100 / S
148 / JunganByeo / KOR / 9.0 / 5.0 / 100 / S
149 / Suweon 541 / KOR / 7.7 / 20.0 / 98.3 / S
150 / Milyang 237 / KOR / 8.3 / 3.3 / 100 / S
151 / IlpumByeo / KOR / 7.0 / 15.0 / 100 / S
152 / Josaengheugchal / KOR / 9.0 / 5.0 / 100 / S
153 / JinbuByeo / KOR / 6.3 / 30.0 / 100 / M
154 / Iksan 527 / KOR / 7.0 / 33.3 / 96.7 / M
155 / Seopyeong / KOR / 6.3 / 35.0 / 100 / M
156 / Milyang 234 / KOR / 2.3 / 85.0 / 100 / T
157 / Milyang 276 / KOR / 9.0 / 3.3 / 100 / S
158 / SobiByeo / KOR / 6.3 / 43.3 / 100 / M
159 / HeugkwangByeo / KOR / 9.0 / 1.7 / 100 / S
160 / Suweon 540 / KOR / 9.0 / 1.7 / 100 / S
161 / Suweon 525 / KOR / 9.0 / 0.0 / 100 / S
162 / HongjinjuByeo / KOR / 1.7 / 91.7 / 100 / T
163 / Joun / KOR / 9.0 / 5.0 / 100 / S
164 / Cheolweon 84 / KOR / 7.7 / 23.3 / 100 / S
165 / Dami / KOR / 2.3 / 85.0 / 100 / T
166 / DonganByeo / KOR / 7.7 / 25.0 / 100 / S
167 / Suwon 563 / KOR / 9.0 / 1.7 / 98.3 / S
168 / DaelipByeo 1 / KOR / 7.0 / 45.0 / 100 / M
169 / Milyang 260 / KOR / 9.0 / 0.0 / 100 / S
170 / DongjinByeo / KOR / 3.7 / 51.7 / 100 / M
171 / Milyang 256 / KOR / 9.0 / 1.7 / 98.3 / S
172 / Suweon 530 / KOR / 3.7 / 71.7 / 100 / T
173 / Gopum / KOR / 7.7 / 21.7 / 100 / S
174 / HwaseonChalByeo / KOR / 3.7 / 60.0 / 95.0 / T
175 / Chilsung / KOR / 3.7 / 66.7 / 100 / T
176 / Suweon 544 / KOR / 9.0 / 11.7 / 100 / S
177 / OdaeByeo / KOR / 8.3 / 6.7 / 100 / S
178 / Iksan 555 / KOR / 3.0 / 78.3 / 100 / T
179 / Suwon 555 / KOR / 5.7 / 41.7 / 100 / M
180 / Milyang 282 / KOR / 9.0 / 1.7 / 100 / S
aVR: Vigor Rating (1=strong vigor; 9 = weak vigor)
bGR: Germination Rate (%)
cLTG: low temperature germinability class: T, Tolerant; M, Moderate, S, Sensitive
Table S2. Distribution of SNP markers identified by reduced representation sequencing and used in the LTG association analysis
Chromosome / SNPs / Kb/SNP1 / 593 / 74
2 / 449 / 80
3 / 429 / 84
4 / 379 / 93
5 / 352 / 84
6 / 372 / 83
7 / 410 / 72
8 / 318 / 89
9 / 347 / 65
10 / 348 / 65
11 / 427 / 66
12 / 253 / 109
Sum / 4677
Fig.S1. Phenotypic variation of the germplasm for LTG after 14 days at 13°C.T, Tolerant; S, sensitive; M, moderate.
Fig. S2. Classification of germplasm for low temperature germinability
Fig.S3. Dot graph for comparison of the germination rate by origin. Each dot represents each accession’s germination rate. Black line is grand mean of all germplasm and green diamond is mean of germination rate. The diamond’s width represents the number of accessions. Error bar is shown in the diamond. Significant difference of germination rate by origin was observed between China-S.Korea and Japan-N.Korea (p<0.05).
Fig. S4. Distribution of qLTG3-1 alleles by country of origin. Black, Italica Livorno allele; Grey, Nipponbare allele, Dark Grey, Hayamasarialllele
Fig. S5. Average germination rate of germplasm by qLTG3-1 alleles
Fig. S6. Manhattan plot for association between marker and LTG trait. The negative log10-transformed p-values are plotted against the marker position in the rice chromosome. Dotted line: P=1.0e-03.A. GLM model without correction. B. GLM(Q) correction for population structure. C. MLM(K) correction for kinship. D. MLM(Q+K) correction for both population structure and kinship
Fig. S7. Positions of LTG markers identified by association analysis. A total of 8 markers were detected significantly at p < 0.001. Two markers in chromosome 4 were only 35kb apart from each other. Horizontal black lines represent the positions of the markers. Vertical grey boxes are QTLs reported previously.