Supplemental Table S1. Rice genes targeted using theCRISPR/Cas9 system.
Target Gene
Gene Identifier
Gene Product
Expected Phenotype when Function Knocked Out References
OsPDS
OsPMS3
LOC_Os03g08570
LOC_Os12g36030
Phytoene desaturase
Non-coding RNA
albino
photo-period sensitive male sterile
[1]
[2]
OsEPSPS
OsDERF1
OsMSH1
OsMYB5
OsMYB1
OsROC5
OsSPP
LOC_Os06g04280
LOC_Os08g35240
LOC_Os04g42784
LOC_Os05g41166
LOC_Os1g12700
LOC_Os02g45250
LOC_Os06g41990
EPSP synthase
AP2 domain containing protein
DNA mismatch repair protein
MYB family transcription factor
MYB family transcription factor
Leucine zipper class IV protein
Rice stromal processing peptidase
lethal
drought-resistant
pleiotrophic phenotype
unclear
unclear
abaxial leaf rolling
early seedling leaf chlorosis
[3]
[4]
[5]
[6]
None
[7]
[8]
OsYSA
LOC_Os03g40020
Pentatricopeptide repeat domain
containing protein
albino young seedling
[9]
Supplemental Table S2. Summary of the target sequence %GC contents and
mutation rates in T0 plants. *:sgRNAs targeting the non-transcribed strand.
Target genes
Target sequence (PAM in gray)
GC content
Mutation
rate
OsMYB1
GGCGCGCGTCGAGGCGTTGGCGG
80%
66.7%
OsYSA
GCGCGCCACCTCGGCCGAAGCGG*
80%
66.7%
OsROC5
GCGGAGAACGACAGCCGGTCGGG
70%
65.1%
OsYSA
CCGCGACGAGCACCTTCATGAGG*
65%
51.4%
OsDERF1
GGAATTAGCGGCGGCGGCGAGGG
70%
50.9%
OsPDS
GGAAGGATGAAGATGGAGATTGG
45%
41.9%
OsMSH1
GGAGGTCCTGGTCTAAACCAAGG
55%
37.0%
OsMYB5
GTAGCCCTGCTGTTGAAGAAAGG
50%
31.9%
OsSPP
GGCGATTGGGAGCCTCGGCGAGG
75%
28.9%
OsPMS3
CACCTACATATAGGAGTGGGAGG
50%
26.3%
OsEPSPS
GGATGTTCACTACATGCTTGAGG
45%
21.1%
Supplemental Table S3.
Sequencing results of T0 and T1 plants.
In the T0 generation, DNA was extracted from a leaf for most plants and also from mixed tissues for some plants. The DNA was PCR amplified
and sequenced. When the sequence was one type, the genotype was assumed to be homozygous mutants or WT. For the PCR products that
contained mixed sequences, the DNA was cloned and each clone sequenced. In M/N, N is the number clones sequenced, and M is the number of
clones showing a particular sequence. In the T1 generation, DNA was extracted and PCR amplified, and then sequenced without cloning.
In
M/N, N is the number of T1 plants examined, and M is the number of plants showing that particular genotype. WT, wild-type sequence with no
mutation detected; d#, # of bp deleted from target site; d#a, same number of deletion at one site; d#b, same number of deletion at other sites;
i#, # of bp inserted at target site; i#a, same number of insertion at one site; i#b, same number of insertion of different nucleotide at the same
site; c#, combined mutation; s#, substitution; Non-homozygous mutation, more than one sequence detected in the sample and the sequencing
chromatograms showed overlapped peaks. k: Lines in Kasalath background. The name of transgenic lines is in bold font. The mutations are
marked using yellow color. The PAM motif (NGG) is marked by a grey box.
OsMYB5, sgRNA, T0-line 10
T0-leaf:
Distribution of sequenced clones
WT
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAA-GAAAGGTCCATGGACATCTTGGG
0/15
i1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAAAGAAAGGTCCATGGACATCTTGGG
8/15
d1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGA--GAAAGGTCCATGGACATCTTGGG
7/15
T0-mix tissues:
Distribution of sequenced clones
WT
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAA-GAAAGGTCCATGGACATCTTGGG
0/19
i1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAAAGAAAGGTCCATGGACATCTTGGG
9/19
d1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGA--GAAAGGTCCATGGACATCTTGGG
10/19
T1:
Distribution of plants of different genotypes
WT
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAA-GAAAGGTCCATGGACATCTTGGG
0/29
i1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAAAGAAAGGTCCATGGACATCTTGGG
8/29
d1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGA--GAAAGGTCCATGGACATCTTGGG
6/29
i1d1
15/15
OsMYB5, sgRNA, T0-line 1
T0-leaf:
Distribution of sequenced clones
WT
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAA-GAAAGGTCCATGGACATCTTGGG
9/15
i1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAAAGAAAGGTCCATGGACATCTTGGG
6/15
T0-mix tissues:
Distribution of sequenced clones
WT
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAA-GAAAGGTCCATGGACATCTTGGG
7/16
i1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAAAGAAAGGTCCATGGACATCTTGGG
8/16
d2
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTG---GAAAGGTCCATGGACATCTTGGG
1/16
T1:
Distribution of plants of different genotypes
WT
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAA-GAAAGGTCCATGGACATCTTGGG
4/17
i1
AAGATTGCAGAAGGAGCACCGTAGCCCTGCTGTTGAAAGAAAGGTCCATGGACATCTTGGG
4/17
Non-homozygous mutation
9/17
OsPMS3, sgRNA, T0-line 7
T0-leaf:
Distribution of sequenced clones
WT
TTTACAAGACTATTTCATAGCACCTACATATAGGAGT-GGGAGGCATGGTGAAGCAAAGAA
12/14
i1
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTTGGGAGGCATGGTGAAGCAAAGAA
2/14
T1:
Distribution of plants of different genotypes
WT
TTTACAAGACTATTTCATAGCACCTACATATAGGAGT-GGGAGGCATGGTGAAGCAAAGAA
7/18
i1
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTTGGGAGGCATGGTGAAGCAAAGAA
5/18
Non-homozygous mutation
6/18
OsPMS3, sgRNA, T0-line 31
T0-leaf:
Distribution of sequenced clones
WT
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTGGGAGGCATGGTGAAGCAAAGAA
14/15
d77
-----------------……------------------GGGAGGCATGGTGAAGCAAAGAA
1/15
T1:
WT
Distribution of plants of different genotypes
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTGGGAGGCATGGTGAAGCAAAGAA
Non-homozygous mutation
13/22
9/22
OsPMS3, sgRNA, T0-line 32
T0-leaf:
Distribution of sequenced clones
WT
TTTACAAGACTATTTCATAGCACCTACATATAGGAGT-GGGAGGCATGGTGAAGCAAAGAA
12/15
i1
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTTGGGAGGCATGGTGAAGCAAAGAA
2/15
d3
TTTACAAGACTATTTCATAGCACCTACATATAG---T-GGGAGGCATGGTGAAGCAAAGAA
1/15
T0-mix tissues:
Distribution of sequenced clones
WT
TTTACAAGACTATTTCATAGCACCTACATATAGGAGT-GGGAGGCATGGTGAAGCAAAGAA
14/17
i1
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTTGGGAGGCATGGTGAAGCAAAGAA
2/17
d3
TTTACAAGACTATTTCATAGCACCTACATATAG---T-GGGAGGCATGGTGAAGCAAAGAA
1/17
T1:
WT
Distribution of plants of different genotypes
TTTACAAGACTATTTCATAGCACCTACATATAGGAGTGGGAGGCATGGTGAAGCAAAGAA
Non-homogeneous mutation
21/27
6/27
OsEPSPS, sgRNA, T0-line 16
T0-leaf:
Distribution of sequenced clones
WT
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGC-TTGAGGCCCTGAAAGCCCTCGGG
7/15
i1
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGCCTTGAGGCCCTGAAAGCCCTCGGG
6/15
i1
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGCTTTGAGGCCCTGAAAGCCCTCGGG
1/15
s1
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGC-TTAAGGCCCTGAAAGCCCTCGGG
1/15
T1:
WT
Distribution of plants of different genotypes
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGC-TTGAGGCCCTGAAAGCCCTCGGG
Non-homogeneous mutation
11/18
7/18
OsEPSPS, sgRNA, T0-line 23
T0-leaf:
Distribution of sequenced clones
WT
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGC-TTGAGGCCCTGAAAGCCCTCGGG
8/15
i1
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGCTTTGAGGCCCTGAAAGCCCTCGGG
4/15
i1
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGCCTTGAGGCCCTGAAAGCCCTCGGG
2/15
s1
GACAACTTGCTGAACAGTGAGGATGTTCAATACATGC-TTGAGGCCCTGAAAGCCCTCGGG
1/15
T1:
WT
Distribution of plants of different genotypes
GACAACTTGCTGAACAGTGAGGATGTTCACTACATGCTTGAGGCCCTGAAAGCCCTCGGG
Non-homogeneous mutation
18/26
8/26
OsDERF1, sgRNA, tiller 1, T0-line 2
T0-leaf:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
4/12
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
8/12
T1:
Distribution of plants of different genotypes
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
4/20
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
4/20
Non-homozygous mutation
12/20
OsDERF1, sgRNA, tiller 2, T0-line 2
T0-leaf:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
4/11
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
7/11
T0-mix tissues:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
11/20
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
8/20
c2
AGCTAGCCATGGATCATATTGGAATTAGCGGGGGCGGACGAGGGCGGGGTGGGGTCTCCGG
1/11
T1:
Distribution of plants of different genotypes
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
1/16
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
4/16
Non-homozygous mutation
11/16
OsDERF1, sgRNA, T0-line 7
T0-leaf:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
9/17
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
8/17
T0-mix tissues:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
4/12
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
8/12
T1:
Distribution of plants of different genotypes
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
4/20
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGACGAGGGCGGGGTGGTGTCTCCGG
4/20
Non-homogeneous mutation
12/20
OsDERF1, sgRNA, T0-line 11
T0-leaf:
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
T0-mix tissues:
i1
T1:
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
Distribution of plants of different genotypes
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG 8/8
OsDERF1, sgRNA, T0-line 29
T0-leaf:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
13/20
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
7/20
T0-mix tissues:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
3/10
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
7/10
T1:
Distribution of plants of different genotypes
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGG-CGAGGGCGGGGTGGTGTCTCCGG
3/27
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
4/27
Non-homozygous mutation
20/27
OsDERF1, sgRNA, T0-line 30, tiller 1
T0-leaf:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGCGAGGGCGGGGTGGTGTCTCCGG
3/12
d4
AGCTAGCCATGGATCATATTGGAATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
9/12
T0-mix tissues:
Distribution of sequenced clones
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGCGAGGGCGGGGTGGTGTCTCCGG
3/19
d4
AGCTAGCCATGGATCATATTGGAATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
13/19
C5
AGCTAGCCATGGATCATATTGGGATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
1/19
C5
AGCTAGCCATGGATCATATCGGAATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
1/19
d9
AGCTAGCCATGGATCATATTGGAATTAGCGGCG---------GCGGGGTGGTGTCTCCGG
1/19
T1:
Distribution of plants of different genotypes
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGCGAGGGCGGGGTGGTGTCTCCGG
1/27
d4
AGCTAGCCATGGATCATATTGGAATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
4/19
d9
AGCTAGCCATGGATCATATTGGAATTAGCGGCG---------GCGGGGTGGTGTCTCCGG
1/19
Non-homozygous mutation
7/27
OsDERF1, sgRNA, tiller 2, T0-line 30
T0-leaf：
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGCGAGGGCGGGGTGGTGTCTCCGG
5/11
d4
AGCTAGCCATGGATCATATTGGAATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
6/11
T1:
Distribution of plants of different genotypes
WT
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGCGAGGGCGGGGTGGTGTCTCCGG
2/13
d4
AGCTAGCCATGGATCATATTGGAATTAGCGGCG----CGAGGGCGGGGTGGTGTCTCCGG
3/13
d9
AGCTAGCCATGGATCATATTGGAATTAGCGGCG---------GCGGGGTGGTGTCTCCGG
1/13
Non-homozygous mutation
7/23
OsDERF1, sgRNA, T0-line 32
T0-leaf:
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
T0-mix tissues:
i1
T1:
i1
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
Distribution of plants of different genotypes
AGCTAGCCATGGATCATATTGGAATTAGCGGCGGCGGTCGAGGGCGGGGTGGTGTCTCCGG
21/21
OsMYB1, sgRNA, T0-line 8
T0-leaf:
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTTTGGCGGCATGCGCGGTCATCGCT
T0-mix tissues:
i1
T1:
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTTTGGCGGCATGCGCGGTCATCGCT
Distribution of plants of different genotypes
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTTTGGCGGCATGCGCGGTCATCGCT 20/20
OsMYB1, sgRNA, T0-line 10
T0-leaf:
Distribution of sequenced clones
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT 10/19
d1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCG--TGGCGGCATGCGCGGTCATCGCT
T0-mix tissues:
0/19
9/19
Distribution of sequenced clones
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
0/18
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT
10/18
d1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCG--TGGCGGCATGCGCGGTCATCGCT
8/18
T1:
Distribution of plants of different genotypes
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT
7/27
d1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCG--TGGCGGCATGCGCGGTCATCGCT
8/27
i1d1
0/27
12/27
OsMYB1, sgRNA, T0-line 20, tiller 1
T0-leaf:
Distribution of sequenced clones
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
0/11
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT
6/11
d5
CGATCTCTGCGACGGGCGACGGCGCGCGTCGA------TGGCGGCATGCGCGGTCATCGCT
5/11
T0-mix tissues:
Distribution of sequenced clones
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT 10/18
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTTTGGCGGCATGCGCGGTCATCGCT
4/18
d5
CGATCTCTGCGACGGGCGACGGCGCGCGTCGA------TGGCGGCATGCGCGGTCATCGCT
1/18
d7
CGATCTCTGCGACGGGCGACGGCGCGCGTC--------TGGCGGCATGCGCGGTCATCGCT
3/18
T1:
Distribution of plants of different genotypes
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
0/20
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTTTGGCGGCATGCGCGGTCATCGCT
1/20
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT
3/20
d5
CGATCTCTGCGACGGGCGACGGCGCGCGTCGA------TGGCGGCATGCGCGGTCATCGCT
2/20
Non-homozygous mutation
14/20
OsMYB1, sgRNA, T0-line 20, tiller 2
T0-leaf:
Distribution of sequenced clones
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
0/11
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT
5/11
d5
CGATCTCTGCGACGGGCGACGGCGCGCGTCGA------TGGCGGCATGCGCGGTCATCGCT
6/11
T1:
Distribution of plants of different genotypes
WT
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGT-TGGCGGCATGCGCGGTCATCGCT
2/11
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTTTGGCGGCATGCGCGGTCATCGCT
2/11
i1
CGATCTCTGCGACGGGCGACGGCGCGCGTCGAGGCGTATGGCGGCATGCGCGGTCATCGCT
1/11
Non-homozygous mutation
6/11
OsMSH1, sgRNA, T0-line 6
T0-leaf:
Distribution of sequenced clones
WT
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAAACCAAGGAAAGTCTCACGAAGCAT
0/18
d1
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAA-CCAAGGAAAGTCTCACGAAGCAT
11/18
d4
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTC----CCAAGGAAAGTCTCACGAAGCAT
7/18
T0-mix tissues:
Distribution of sequenced clones
WT
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAAACCAAGGAAAGTCTCACGAAGCAT
0/20
d1
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAA-CCAAGGAAAGTCTCACGAAGCAT
14/20
d4
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTC----CCAAGGAAAGTCTCACGAAGCAT
6/20
T1:
Distribution of plants of different genotypes
WT
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAAACCAAGGAAAGTCTCACGAAGCAT
0/21
d1
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAA-CCAAGGAAAGTCTCACGAAGCAT
7/21
d4
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTC----CCAAGGAAAGTCTCACGAAGCAT
5/21
d1d4
9/21
OsMSH1, sgRNA, T0-line 26
T0-leaf:
Distribution of sequenced clones
WT
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAAACCAAGGAAAGTCTCACGAAGCAT
3/10
d2
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTA--CCAAGGAAAGTCTCACGAAGCAT
3/10
d15
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTC---------------CTCACGAAGCAT
4/10
T1:
WT
Distribution of plants of different genotypes
ACACTTCAGGCTATTTAACAGGAGGTCCTGGTCTAAACCAAGGAAAGTCTCACGAAGCAT
Non-homozygous mutation
2/19
17/19
OsPDS, sgRNA, tiller 1,T0-line 2
T0-leaf:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
4/13
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
8/13
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAGGATTGGTATGAAACTGGGCTTCA
1/13
T1:
i1
Distribution of plants of different genotypes
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
Non-homogeneous mutation
3/14
11/14
OsPDS, sgRNA, tiller 2,T0-line 2
T0-leaf:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
8/15
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
7/15
T1:
i1
Distribution of plants of different genotypes
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
Non-homogeneous mutation
5/15
10/15
OsPDS, sgRNA, tiller 3, T0-line 2
T0-leaf:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
6/12
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
5/12
d4
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGA-----GATTGGTATGAAACTGGGCTTCA
1/12
T1:
Distribution of plants of different genotypes
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
1/14
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
6/14
Non-homogeneous mutation
7/14
OsPDS, sgRNA, tiller 4, T0-line 2
T0-leaf:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
3/15
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
11/15
d6
CCTTGAACAGATAGCTGCTTGGAAGGATGAA-------GATTGGTATGAAACTGGGCTTCA
1/15
T0-mix tissues:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
7/19
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
12/19
T1:
Distribution of plants of different genotypes
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
2/11
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
3/11
Non-homogeneous mutation
6/11
OsPDS, sgRNA, T0-line 4
T0-leaf:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
11/14
d2
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATG---GATTGGTATGAAACTGGGCTTCA
2/14
d33
CCTTGAACAGATAG----------------------------------AAACTGGGCTTCA
1/14
T0-mix tissues:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
13/19
i1
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGAAGATTGGTATGAAACTGGGCTTCA
5/19
d2
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATG---GATTGGTATGAAACTGGGCTTCA
1/19
T1:
Distribution of plants of different genotypes
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
16/34
d2
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGG---ATTGGTATGAAACTGGGCTTCA
1/34
Non-homogeneous mutation
15/34
OsPDS, sgRNA, T0-line 11
T0-leaf:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
3/11
d2
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATG---GATTGGTATGAAACTGGGCTTCA
7/11
d6
CCTTGAACAGATAGCTGCTTGGAAGGATGAA-------GATTGGTATGAAACTGGGCTTCA
1/11
T0-mix tissues:
Distribution of sequenced clones
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
7/19
d2
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATG---GATTGGTATGAAACTGGGCTTCA
11/19
d4
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGA-----GATTGGTATGAAACTGGGCTTCA
1/19
T1:
Distribution of plants of different genotypes
WT
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATGGA-GATTGGTATGAAACTGGGCTTCA
2/34
d2
CCTTGAACAGATAGCTGCTTGGAAGGATGAAGATG---GATTGGTATGAAACTGGGCTTCA
11/34
Non-homogeneous mutation
21/34
OsYSA, sgRNA1,T0-line 20
T0-leaf:
Distribution of sequenced clones
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
10/12
s1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACTTGGC
1/12
d1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
1/12
T1:
WT
Distribution of plants of different genotypes
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
Non-homogeneous mutation
20/22
2/22
OsYSA, sgRNA1,T0-line 25
T0-leaf:
Distribution of sequenced clones
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
0/12
d1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
12/12
T1:
Distribution of plants of different genotypes
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
0/24
d1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
22/24
Non-homogeneous mutation
2/24
OsYSA, sgRNA1,T0-line 31
T0-leaf:
Distribution of sequenced clones
WT
CGTGCCGGGAGGCGCGCCACCTCGGCCG-AAGCGGCCCTACTCCGACATGGCACGGGCACGGCGG
d3
CGTGCCGGGAGGCGCGCCACCTCGGCCG-AAGCGGCCCTACTCCGACATGGCACGGGCAC---GG 1/11
d1
CGTGCCGGGAGGCGCGCCACCTCGGCC--AAGCGGCCCTACTCCGACATGGCACGGGCACGGCGG
5/11
i1
CGTGCCGGGAGGCGCGCCACCTCGGCCGTAAGCGGCCCTACTCCGACATGGCACGGGCACGGCGG
1/11
T1:
WT
4/11
Distribution of plants of different genotypes
CGTGCCGGGAGGCGCGCCACCTCGGCCG-AAGCGGCCCTACTCCGACATGGCACGGGCACGGCGG 12/24
Non-homogeneous mutation
12/24
OsYSA, sgRNA1,T0-line 35
T0-leaf:
Distribution of sequenced clones
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
0/13
d1a
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
8/13
d1b
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCG-AGCGGCCCTACTCCGACATGGC
5/13
T1:
WT
Distribution of plants of different genotypes
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
0/17
d1a GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
12/17
d1b GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCG-AGCGGCCCTACTCCGACATGGC
5/17
OsYSA, sgRNA1, T0-line 38
T0-leaf:
Distribution of sequenced clones
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
3/13
d1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
10/13
T1:
Distribution of plants of different genotypes
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
6/22
d1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
2/22
Non-homogeneous mutation
14/22
OsYSA, sgRNA2, T0-line 9
T0-leaf:
Distribution of sequenced clones
WT
CTCCCGCCGCATCTCCGCGACGAGCACCTTC-ATGAGGTCGAGGGCCCCGACCGCGCCGAGCTTGC 7/15
i1
CTCCCGCCGCATCTCCGCGACGAGCACCTTCTATGAGGTCGAGGGCCCCGACCGCGCCGAGCTTGC 7/15
s1
CTCCCGCCGCATCTCCGCGACGAGCACCTTC-ATGAGGTCGAGGGCCCCGACCGCGCCGAGCTCGC
T1:
1/15
Distribution of plants of different genotypes
WT
CTCCCGCCGCATCTCCGCGACGAGCACCTTC-ATGAGGTCGAGGGCCCCGACCGCGCCGAGCTTGC
5/22
i1
CTCCCGCCGCATCTCCGCGACGAGCACCTTCTATGAGGTCGAGGGCCCCGACCGCGCCGAGCTTGC
1/22
d3
CTCCCGCCGCATCTCCGCGACGAGCACC----ATGAGGTCGAGGGCCCCGACCGCGCCGAGCTTGC
5/22
d4
CTCCCGCCGCATCTCCGCGACGAGCACC-----TGAGGTCGAGGGCCCCGACCGCGCCGAGCTTGC
1/22
Non-homogeneous mutation
10/22
OsYSA, sgRNA2, T0-line 29
T0-leaf:
Distribution of sequenced clones
WT
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
9/12
d3
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCAC---CATGAGGTCGAGGGCCCCGACCGC
1/12
d4
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCA----CATGAGGTCGAGGGCCCCGACCGC
1/12
s1
GTGCCCCTCCCGCCGCATCTCCGCGTCGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
1/12
T1:
WT
Distribution of plants of different genotypes
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
Non-homogeneous mutation
17/30
13/30
OsYSA, sgRNA2, T0-line 31
T0-leaf:
Distribution of sequenced clones
WT
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
0/14
d4
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCAC----ATGAGGTCGAGGGCCCCGACCGC
12/14
d3
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACC---ATGAGGTCGAGGGCCCCGACCGC
1/14
d1
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTT-ATGAGGTCGAGGGCCCCGACCGC
1/14
T1:
Distribution of plants of different genotypes
WT
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGCGC
0/22
d4
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCAC----ATGAGGTCGAG GGCCCCGACCGCG
16/22
d3
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACC---ATGAGGTCGAGGGCCCCGACCGCGC
1/22
d1
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTT-ATGAGGTCGAGGGCCCCGACCGCGC
2/22
Non-homogeneous mutation
3/22
OsYSA, sgRNA2, T0-line 35
T0-leaf:
Distribution of sequenced clones
WT
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTC-ATGAGGTCGAGGGCCCCGACCGC
0/13
d4
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCAC-----ATGAGGTCGAGGGCCCCGACCGC
5/13
d6
GTGCCCCTCCCGCCGCATCTCCGCGACGAGC-------ATGAGGTCGAGGGCCCCGACCGC
6/13
i1
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCTATGAGGTCGAGGGCCCCGACCGC
2/13
T1:
Distribution of plants of different genotypes
WT
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTC-ATGAGGTCGAGGGCCCCGACCGC
0/16
d6
GTGCCCCTCCCGCCGCATCTCCGCGACGAGC-------ATGAGGTCGAGGGCCCCGACCGC
4/16
Non-homogeneous mutation
12/16
OsYSA, sgRNA2, T0-line 47
T0-leaf:
Distribution of sequenced clones
WT
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
9/11
d4
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCAC----ATGAGGTCGAGGGCCCCGACCGC
1/11
s1
GTGCCCCTCCCGCCGCACCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
1/11
T1:
WT
Distribution of plants of different genotypes
GTGCCCCTCCCGCCGCATCTCCGCGACGAGCACCTTCATGAGGTCGAGGGCCCCGACCGC
Non-homogeneous mutation
14/18
4/18
OsROC5, sgRNA, T0-line 8
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
0/13
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGCGTCGGGAAGCGACCATCTCGACG
5/13
d262 -------------------------------------------------------------
8/13
T1:
Distribution of plants of different genotypes
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
3/10
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGCGTCGGGAAGCGACCATCTCGACG
3/10
d262 -------------------------------------------------------------
1/10
Non-homogeneous mutation
3/10
OsROC5, sgRNA, T0-line 13
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
0/10
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
10/10
T1:
Distribution of plants of different genotypes
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
10/21
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
9/21
Non-homogeneous mutation
2/21
OsROC5, sgRNA, T0-line 28
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
0/12
i1a
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
6/12
i1b
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
5/12
i1c
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGCGTCGGGAAGCGACCATCTCGACG
1/12
T1:
Distribution of plants of different genotypes
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
0/24
i1a
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
20/24
i1b
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
3/24
Non-homogeneous mutation
1/24
OsROC5, sgRNA, T0-line 30
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
6/11
d1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCC--GTCGGGAAGCGACCATCTCGACG
1/11
i1a
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
1/11
i1b
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
1/11
s1a
CGATGACGAAGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
1/11
s1b
CGATGACGAGGGACACTGAGGCGGAGAGCGACAGCCG-GTCGGGAAGCGACCATCTCGACG
1/11
T1:
WT
Distribution of plants of different genotypes
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
24/24
OsROC5, sgRNA, T0-line 43
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
2/11
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
7/11
s1
CGATGACGAGGGACACGGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
2/11
T1:
Distribution of plants of different genotypes
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
4/13
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
3/13
Non-homogeneous mutation
6/13
OsROC5, sgRNA, T0-line 44
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACGCCA
7/15
d7
CGATGACGAGGGACACTGAGGCGGAGAACGACA--------GGGAAGCGACCATCTCGACGCCA
1/15
i1a
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACGCCA
5/15
i1b
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACGCCA
1/15
s1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACGTCA
1/15
T1:
Distribution of plants of different genotypes
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACGCCA
18/23
i1
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCC--GTCGGGAAGCGACCATCTCGACGCCA
1/23
Non-homogeneous mutation
4/23
OsSPP, sgRNA,T0-line 5
T0-leaf:
Distribution of sequenced clones
WT
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCG-GCGAGGAGAGGGAAGGGTGCCTC
9/13
d4
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAG----G-GCGAGGAGAGGGAAGGGTGCCTC
1/13
d3
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCC----GCGAGGAGAGGGAAGGGTGCCTC
2/13
i1
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCGGGCGAGGAGAGGGAAGGGTGCCTC
1/13
T1:
WT
Distribution of plants of different genotypes
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCG-GCGAGGAGAGGGAAGGGTGCCTC
24/24
OsSPP, sgRNA, T0-line 12
T0-leaf:
Distribution of sequenced clones
WT
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCG-GCGAGGAGAGGGAAGGGTGCCTC
9/12
i1a
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCGTGCGAGGAGAGGGAAGGGTGCCTC
2/12
i1b
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCGAGCGAGGAGAGGGAAGGGTGCCTC
1/12
T1:
WT
Distribution of plants of different genotypes
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCG-GCGAGGAGAGGGAAGGGTGCCTC
24/24
OsSPP, sgRNA, T0-line 17
T0-leaf:
Distribution of sequenced clones
WT
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCG-GCGAGGAGAGGGAAGGGTGCCTC
9/14
i1
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCGAGCGAGGAGAGGGAAGGGTGCCTC
5/14
T1:
WT
Distribution of plants of different genotypes
GCTGTCGGCGCGGCCTCGGCGGCGATTGGGAGCCTCG-GCGAGGAGAGGGAAGGGTGCCTC
Non-homogeneous mutation
13/14
1/14
OsYSA, sgRNA1,T0-line 20*
T0-leaf:
Distribution of sequenced clones
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCG-AAGCGGCCCTACTCCGACATGGC
0/11
i1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAAGCGGCCCTACTCCGACATGGC
5/11
d1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC--AAGCGGCCCTACTCCGACATGGC
6/11
T1:
Distribution of plants of different genotypes
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCG-AAGCGGCCCTACTCCGACATGGC
0/4
i1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAAGCGGCCCTACTCCGACATGGC
3/4
Non-homogeneous mutation
1/4
OsYSA, sgRNA1,T0-line 23*
T0-leaf:
i1
T1:
i1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGGAAGCGGCCCTACTCCGACATGGC
Distribution of plants of different genotypes
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGGAAGCGGCCCTACTCCGACATGGC
6/6
OsYSA, sgRNA1,T0-line 35*
T0-leaf:
Distribution of sequenced clones
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
5/11
i1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
6/11
T1:
Distribution of plants of different genotypes
WT
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCCGAAGCGGCCCTACTCCGACATGGC
2/13
i1
GGAGAGGGCCGTGCCGGGAGGCGCGCCACCTCGGCC-AAGCGGCCCTACTCCGACATGGC
3/13
Non-homogeneous mutation
8/13
OsROC5, sgRNA, T0-line 14*
T0-leaf:
Distribution of sequenced clones
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
0/9
i1a
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
4/9
i1b
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
5/9
T1:
Distribution of plants of different genotypes
WT
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCG-GTCGGGAAGCGACCATCTCGACG
0/9
i1a
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGAGTCGGGAAGCGACCATCTCGACG
1/9
i1b
CGATGACGAGGGACACTGAGGCGGAGAACGACAGCCGTGTCGGGAAGCGACCATCTCGACG
3/9
Non-homogeneous mutation
5/9
Supplemental Table S4. Summary of the re-sequencing quality of different transgenic rice lines. Nip: rice variety Nipponbare; Kas: rice variety
Kasalath.
Background
sgRNA
OsYSA sgRNA1
OsYSA sgRNA2
OsROC5 sgRNA
Nip
OsSPP sgRNA
OsDERF1 sgRNA
OsMYB1 sgRNA
OsYSA sgRNA1
Kas
OsROC5 sgRNA
OsSPP sgRNA
Plant ID
T0-3
T0-13
T0-2
T0-31
T0-1
T0-13
T0-2
T0-12
T1-2-20
T1-30-8
T1-20-1
T1-20-8
Nip
T0-20
T0-23
T0-35
T0-6
T0-14
T0-15
Kas
Total # of reads
197320186
164466814
249342904
251267372
291779654
261437494
231170044
207539804
106083390
93342910
103692488
96116030
255914476
101120214
103135478
108417820
122356580
115972122
116239476
61701016
# of mapped reads
193936071
162029464
244154234
247336146
282032982
256367930
226057496
201786898
104223029
91183157
102471062
94191409
249641011
93243345
94959222
99873819
112801834
106836136
107203430
56745204
Mapping ratio
98.28%
98.52%
97.92%
98.44%
96.66%
98.06%
97.79%
97.23%
98.25%
97.69%
98.82%
98.00%
97.55%
92.21%
92.07%
92.12%
92.19%
92.12%
92.23%
91.97%
Average depth
48.48
40.51
61.04
61.83
70.51
64.09
56.51
50.45
26.06
22.80
25.62
23.55
62.41
18.65
18.99
19.97
22.56
21.37
21.44
11.35
Supplemental Table S5. Summary of the analysis of the whole genome re-sequencing of rice transgenic lines and WT controls.
Background
sgRNA
Plant ID
# of SNPs
# of insertions
# of deletions
Total # of mutations
T0-3
23816
3128
5035
31979
T0-13
23292
2978
4768
31038
T0-2
23704
3216
5034
31954
T0-31
24088
3354
5138
32580
T0-1
T0-13
T0-2
24251
23546
22852
3381
3261
3244
5648
5153
5174
33280
31960
31270
T-12
22860
3167
4825
30852
T1-2-20
22128
2927
4808
29893
T1-30-8
21852
2842
4458
28902
T1-20-1
22073
2942
4827
29822
T1-20-8
22068
2850
4621
29231
23262
3182
5904
32348
T0-20
2672617
195815
198398
3066830
T0-23
2689785
197994
199877
3087656
T0-35
2705658
199140
200897
3105695
T0-15
2713033
202494
203606
3119133
T0-6
2731829
205105
205550
3142484
T0-14
2716776
202920
203755
3123451
OsYSA sgRNA1
OsYSA sgRNA2
OsROC5 sgRNA
Nip
OsSPP sgRNA
OsDERF1 sgRNA
OsMYB1 sgRNA
Nip
OsYSA sgRNA1
Kas
(Before filtering)
OsSPP sgRNA
OsROC5sgRNA
Kas
Kas
(after filtering)
OsYSA sgRNA1
2511050
175128
179403
2865581
T0-20
269221
36104
30826
336151
T0-23
281159
37884
32015
351058
T0-35
290343
38618
32833
361794
OsSPP sgRNA
OsROC5 sgRNA
T0-15
293595
41277
34824
369696
T0-6
310031
43537
36325
389893
T0-14
302743
41646
35136
379525
Supplemental Table S6. Summary of putative off-target examination. *: putative off
target candidates were searched by Blastn using the last 12 bp of the target sequence
allowing ≤2 mismatches and using the whole 20 bp target sequence with E value ≤10.
**
: SNP and indels from the whole genome sequence of transgenic lines. ***: The
number of putative off-targets with SNP or indel. a: off-target candidate with no PAM
motif (NGG) or the overlap is target itself; b: the overlap is target itself; when the
overlap number is greater than 1, more than 1 SNP or indel were found within the
target region. Nip: rice variety Nipponbare. Kas: rice variety Kasalath.
Background
Target
Plant
ID
Seed
length*
# of
# of SNP
putative
and
targets
Indels**
Nipponbare
sgRNA1
off-targetsdete
cted
31979
3a
0
31038
1b
0
31979
1b
0
31038
1b
0
31954
1b
0
32580
3a
0
31954
1b
0
32580
3a
0
33280
1b
0
31960
1b
0
33280
1b
0
31960
1b
0
31270
1b
0
30852
1b
0
31270
1b
0
30852
1b
0
29,893
6a
0
28,902
7a
0
29,893
2a
0
28,902
1b
0
29,822
2a
0
29,231
2a
0
29,822
1b
0
T1-20-8
29,231
2a
0
T0-20
336151
13a
0
351058
12a
0
12bp
338
T0-13
T0-3
20bp
156
T0-13
T0-2
12bp
OsYSA
T0-31
sgRNA2
T0-2
20bp
298
41
T0-31
T0-1
12bp
Nip
overlap***
# of
32348
T0-3
OsYSA
# of
OsROC5
T0-13
sgRNA
T0-1
20bp
126
9
T0-13
T0-2
12bp
OsSPP
T0-12
sgRNA
T0-2
20bp
244
6
T0-12
T1-2-20
12bp
OsDERF1
T1-30-8
sgRNA
T1-2-20
20bp
65,536
931
T1-30-8
T1-20-1
12bp
OsMYB1
T1-20-8
sgRNA
T1-20-1
20bp
T0-23
12bp
212
142
338
OsYSA
T0-35
361794
15a
0
sgRNA1
T0-20
336151
10a
0
351058
10a
0
361794
12a
0
389893
15a
0
379525
12a
0
389893
1b
0
Kas
T0-23
20bp
156
T0-35
T0-6
OsROC5
sgRNA
12bp
126
T0-14
T0-6
20bp
9
T0-14
379525
1b
0
OsSPP
T0-15
12bp
181
369696
1b
0
sgRNA
T0-15
20bp
6
369696
1b
0
Supplemental Table S7.
Target sequences of the six rice genes and oligos used to construct the sgRNA expression vectors. The PAM motif
(NGG) is marked by a grey box. Other sgRNAs can be found in Mao et al (2013) [10] and Feng et al (2013) [11].
Target gene
Target site (PAM in grey)
Oligo 1 (5’-3’)
Ologo 2 (5’-3’)
OsMYB5
GTAGCCCTGCTGTTGAAGAAAGG
TGGCGTAGCCCTGCTGTTGAAGAA
AAACTTCTTCAACAGCAGGGCTAC
OsPMS3
CACCTACATATAGGAGTGGGAGG
TGGCGCACCTACATATAGGAGTGGG
AAACCCCACTCCTATATGTAGGTGC
OsEPSPS
GGATGTTCACTACATGCTTGAGG
TGGCGGATGTTCACTACATGCTTG
AAACCAAGCATGTAGTGAACATCC
OsDERF1
GGAATTAGCGGCGGCGGCGAGGG
TGGCGGAATTAGCGGCGGCGGCGA
AAACTCGCCGCCGCCGCTAATTCC
OsMSH1
GGAGGTCCTGGTCTAAACCAAGG
TGGCGGAGGTCCTGGTCTAAACCA
AAACTGGTTTAGACCAGGACCTCC
OsPDS
GGAAGGATGAAGATGGAGATTGG
TGGCGGAAGGATGAAGATGGAGAT
AAACATCTCCATCTTCATCCTTCC
Supplemental Table S8. List of PCR primers and their applications.
Primer name
Primer sequence (5’-3’)
Experiment
OsDERF1-F
AACACGTCTTCCGTGCACTAT
Genotyping, sequencing
OsDERF1-R
TACGAGCCCAGCCATATCCTC
Genotyping
OsEPSPS-F
GGAGGTTTCGCACTGTACCA
Genotyping, sequencing
OsEPSPS-R
ACAGGAAACTTGCCACCACA
Genotyping
OsPMS3-F
CAGGATGCACATACTGAATCTCTC
Genotyping
OsPMS3-R
GTACCTCGTCAAGCGACACA
Genotyping, sequencing
OsMSH1-F
GTGGCATGCTTGGCTTGATT
Genotyping
OsMSH1-R
ACAACGTCATGCTAGCCTTCT
Genotyping, sequencing
OsPDS-F
ACTTCCCGCATGGCATTTCT
Genotyping, sequencing
OsPDS-R
CGTGATTGCTGGAGCAGGTA
Genotyping
OsMYB1-F
TGATCCGTGATACAGTATGTGAGT
Genotyping
OsMYB1-R
TGCTATTTATTTATGAATCCGCACC
Genotyping, sequencing
OsMYB5-F
ATTTGTTAATCTCTGCTAG
Genotyping, sequencing
OsMYB5-R
CAAGGTAAACTTACATCA
Genotyping
CAS9-F1
AAAGACCGAGGTGCAGACAG
Genotyping
CAS9-R1
ACCAGCACAGAATAGGCCAC
Genotyping
H1-F
GGAGCCCTATAAAAGAACTC
Genotyping, sequencing
H1-R
GAGGTAATAGGCGCCATTCCTG
Genotyping
H2-F
GTTCTCATCTTGCAGTCGCC
Genotyping, sequencing
H2-R
GAAGGAGACCAAGACAGAAGCA
Genotyping
H3-F
GCACGAGATCGAAGCACCTCG
Genotyping, sequencing
H3-R
CAGCGACGGCCGCTCTCCTTCC
Genotyping
H4-F
CATCTCACACAATCACACC
Genotyping, sequencing
H4-R
GGGACCCACTCGTTAGTCT
Genotyping
H5-F
CCATCTGCGCGGGCGCGATTC
Genotyping, sequencing
H5-R
CAAGCTAAGCGCAAGCAGTACAG
Genotyping
H6-F
CTGCGAGGACGAGGAGGGAAG
Genotyping, sequencing
H6-R
CTCGCTGCCCTTGCCGTCATC
Genotyping
H7-F
CACCTACGTCGTCGAAATGAG
Genotyping, sequencing
H7-R
GCATCTCTCTCTGATGTCTC
Genotyping
H8-F
CTGCCTCGCCGCCGCCCAAGC
Genotyping, sequencing
H8-R
AGTAGCCTGCGCCGCTGTCGC
Genotyping
H9-F
ACGCCTCTGCTAGACATTTCC
Genotyping, sequencing
H9-R
CCGTGCCATGTCAGAGTAGG
Genotyping
H10-F
AACGGAAATATTAGGGAAGGACCT
Genotyping, sequencing
H10-R
ATACTTGCTCTTAGTGTTGGTGATC
Genotyping
H11-F
AGAGAGTAGTCTGAATGTGTGAGTT
Genotyping, sequencing
H11-R
CGCACGCTTACAGCAACAAT
Genotyping
H12-F
GCATCAGCAGCAGCATAGC
Genotyping, sequencing
H12-R
TGGAAGTGTGGAACCAAACAAA
Genotyping
H13-F
GGGTGTTCGTGATCTCTGCTAA
Genotyping, sequencing
H13-R
CCATTCAATTTACACCGTCAGGAG
Genotyping
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4.
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