Supplementary Table 2 Evaluation criteria of reaction to RSV at seedling stage in rice

Damage score / Damage symptoms
A / Severely retarded growth; part or all leaf tissue withered.
B / Retarded growth without leaf withering. The lesion is continuous and streaky light yellow symptoms appear on lower leaves, and discolored yellow green symptoms appear on the upper leaves.
Bt / Same as type B, but growth is less retarded.
Cr / Retarded growth and slightly rolled leaves. Lesions are light yellow with scattered spots or striping. Clear borders between the healthy and diseased tissues are clear.
C / Retarded growth with scattered spot type lesions that are light yellow and distinct from the healthy parts.
D / Near normal with minor symptom development on seedlings.

Supplementary Table 3 Phenotypic performance of backcross inbred lines (BILs) and their parents in four tests of RSV response

Check (DRI)a / Parent (RDRI)b / BILs (RDRI)b
Method / IR36 / WYJ3 / Sasanishiki / Habataki / Mean / Range
FT / 0 / 78.06±3.42 / 66.89±1.47A / 0A / 42.62±2.18A / 0-(104.13±2.51)
MIT / 1.13±0.27 / 74.67±2.87 / 60.87±2.10A / 2.51±0.26B / 54.65±1.83B / (8.46±1.47)-(114.16±2.87)
ST / 6.25±0.35 / 65.71±1.74 / 76.08±2.02B / 32.41±3.79C / 60.02±3.17BC / (13.89±0.63)-(126.03±3.70)
12D-MIT / 4.00±0.22 / 83.33±3.26 / 108.92±4.53C / 9.60±1.12B / 71.54±2.81C / 0-(128.89±1.96)

aResistant and susceptible controls were IR36 and Wuyujing 3 (WYJ3), respectively. Disease rating index (DRI) was used to evaluate the RSV response of the controls

bRelative disease rating index (RDRI) was used to represent the RSV responses of the mapping population and two parents

Numbers on the same line with the same superscript letter do not differ significantly from one another at p0.05 in the same material with different inoculation methods

Supplementary Table 4 Polymorphic markers were used in this study

Primer Id / Motif type / Left sequence / Right sequence / Product size (bp) in Nipponbare
R15 / InDel / 5'GGGCTTTCAACTCGTACTCTG3' / 5'ATGAACTGCGGGTCCAATAA3' / 338
R21 / InDel / 5'CAACGTGGTTGATTGTTC3' / 5'TTGCCAGGTTAGTTGTAC3' / 104
R22 / InDel / 5'CACAAATCAGCGAAGAAA3' / 5'GAGGCAAGCCAATGTCGT3' / 133
R25 / InDel / 5'GTTAATAAAGCAATTGTTAGAC3' / 5'TTTACTCTACGCCCTAAA3' / 162
R48 / InDel / 5'GCCTTCATCCGTAAATCCATAAGC3' / 5'GAGTACCACATGGCATTATGAGAGC3' / 166
R69 / InDel / 5'TTGGTAAGGTTTATTTTAGC3' / 5'AGATAACTGAAGTAGCAACG3' / 125
R72 / InDel / 5'GCTTGGAAGACGAGGCTGA 3' / 5'CCACATGGAACACCACGAA3' / 168
R73 / InDel / 5'TTAGTTCACTTTGGACTCTTT3' / 5'GTGGCATTGAAATCTCACT3' / 210
RM21 / SSR / 5'ACAGTATTCCGTAGGCACGG3' / 5'GCTCCATGAGGGTGGTAGAG3' / 132
RM187 / SSR / 5'CCAAGGGAAAGATGCGACAATTG3' / 5'GTGGACGCTTTATATTATGGG3' / 136
RM209 / SSR / 5'ATATGAGTTGCTGTCGTGCGTGCG3' / 5'CAACTTGCATCCTCCCCTCC 3' / 125
RM457 / SSR / 5'CTCCAGCATGGCCTTTCTAC3' / 5'ACCTGATGGTCAAAGATGGG3' / 228
RM5961 / SSR / 5' GTATGCTCCTCCTCACCTGC 3' / 5' ACATGCGACGTGATGTGAAC 3' / 129

Supplementary Fig. 1 Genetic materials used in evaluations of RSV response.

5

Supplementary Fig. 2 Typical samples for each grade of damage score.

5

8

Supplementary Fig. 3 Validation of QTLs conferring resistance to RSV using chromosome segmental substitution lines (CSSLs). A: Relative disease rating indices (RDRI) of CSSLs and parents in the field test (FT). For each line, bars denote the mean value with standard deviation (n=4). Black bars represent susceptible (RDRI 40 to 69) and highly susceptible (RDRI 70.0) lines; hatched bars indicate the single highly resistant line (RDRI 29.0); white bars are the parents. B: Phenotypic details of lines SL409 (carrying qSTV3), SL436 (corresponding to qSTV11HAB-1), SL437 (harboring qSTV11HAB-1 and qSTV11HAB-2) and SL438 (carrying no QTL). White and black bars represent genetic materials of Sasanishiki and Habataki, respectively. The t-test was conducted to compare target CSSLs with Sasanishiki. * and ** indicate significance at P=0.05 and 0.01, respectively aInoculation method: FT, field test; MIT, mass inoculation test; ST, seedling test; 12d-MIT, 12 day mass inoculation test; RDRIs were taken as phenotypic values of RSV response. bIn testing for SBPH response, antixenosi and antibiosis was represented by number of insects per plant, and insect survival percentage, respectively

Supplementary Fig. 4 Frequency distribution of F2:3 lines (n = 145, derived from Aichi 97/Habataki with relative disease rating index (RDRI) as the phenotype. Means of the parents are indicated by arrows. The broken line denotes the boundary of resistant (RDRI<40) and susceptible (RDRI≥40) lines

8