Rice Science ›› 2021, Vol. 28 ›› Issue (5): 427-430.DOI: 10.1016/j.rsci.2021.07.003
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Binte Monsur Mahmuda1,#, Ni Cao1,#, Xiangjin Wei1, Lihong Xie1, Guiai Jiao1, Shaoqing Tang1, Sreenivasulu Nese2, Gaoneng Shao1(
), Peisong Hu1()
Received:2020-10-11
Accepted:2021-03-04
Online:2021-09-28
Published:2021-09-28
About author:#These authors contributed equally to this work
Binte Monsur Mahmuda, Ni Cao, Xiangjin Wei, Lihong Xie, Guiai Jiao, Shaoqing Tang, Sreenivasulu Nese, Gaoneng Shao, Peisong Hu. Improved Eating and Cooking Quality of indica Rice Cultivar YK17 via Adenine Base Editing of Wxa Allele of Granule-Bound Starch Synthase I (GBSS I)[J]. Rice Science, 2021, 28(5): 427-430.
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Fig. S1. Waxy genotype of YK17. Hap 1, Hap 2 and Hap 3 are three genotypes as described in Zhang et al (2019). GC2, Q11 and Nip are three rice accessions with different Waxy genotypes.
Fig. 1. Desirable amylose content of indica rice cultivar YK17 via adenine base editing of Wx gene. A, Structure of Wxa and the mutations in edited T1 lines. Protospacer-adjacent motifs (PAMs) include three bases (NGG) with a red underline. The red letters indicate altered bases. Q, Glutamine; R, Arginine; N, Asparagine; D, Aspartate. B-E, Gross morphologies of the wild type YK17 and its mutants MT1, MT2 and MT3. Scale bars are 10 cm. F-I, Appearance and transverse sections of brown rice of YK17 and mutants. Scale bars are 1 mm. J, Amylose content. K, Gel consistency. L, Alkali spreading values of the wild type and mutants. Data are Mean ± SD (n = 3) in J-L. Samples with different lowercase letters show a significant difference at P < 0.05 according to the Duncan’s test. M, Pasting properties of endosperm starch of YK17 and mutants. N, Western blotting of GBSS I in YK17 and mutant rice grains at 10 d after flowering. Actin was used as an internal control. NIP, Nipponbare; YK17, Zhongjiazao 17.
| Primer | Sequence (5' to 3') | For use |
|---|---|---|
| Waxy-target site 1-F | GGCGAAGAACAACTACCAGCCCAA | Vector construction |
| Waxy-target site 1-R | AAACTTGGGCTGGTAGTTGTTCTT | Vector construction |
| Waxy-target site 2-F | GGCGAAGATCAACTGGATGAAGGC | Vector construction |
| Waxy-target site 2-R | AAACGCCTTCATCCAGTTGATCTT | Vector construction |
| Waxy-target site 3-F | GGCGCGACCAGTACAAGGACGCTT | Vector construction |
| Waxy-target site 3-R | AAACAAGCGTCCTTGTACTGGTCG | Vector construction |
| Waxy-target site 1-seq-F | GGATGTTGTGTTCGTCTGCA | Target site sequencing |
| Waxy-target site 1-seq-R | AGGAGATGTTGTGGATGCAGA | Target site sequencing |
| Waxy-target site 2-seq-F | ACCCTGCACTACTGTCCATC | Target site sequencing |
| Waxy-target site 2-seq-R | CTAGGATCCCACTCGCTGAC | Target site sequencing |
| Waxy-target site 3-seq-F | TTGTGTTCTTTGCAGGCGAA | Target site sequencing |
| Waxy-target site 3-seq-R | TCGTACCTGTCTGCAACCTT | Target site sequencing |
| Target site 1-Chr1-seq-F | CGTTGCCCTACCATTGAAGA | Off-target sequencing |
| Target site 1-Chr1-seq-R | ACATTGGCTGCTGCTACTAC | Off-target sequencing |
| Target site 1-Chr5-seq-F | TGCGACAAGCTGTGGTATTT | Off-target sequencing |
| Target site 1-Chr5-seq-R | GCCTGTATGTAGCTCTGTTGA | Off-target sequencing |
| Target site 1-Chr11-seq-F | GTCATGAAGTGCCTGGAGAG | Off-target sequencing |
| Target site 1-Chr11-seq-R | TCGAAGAACATGAAGCGAGG | Off-target sequencing |
| Target site 1- Chr6-seq-F | GTAGCACCCAAAAGGAGCTT | Off-target sequencing |
| Target site 1- Chr6-seq-R | GTTTCTCCCCTTCTGCACTT | Off-target sequencing |
| Target site 1- Chr12-seq-F | TACTGGTGGTGAGGTTGTGA | Off-target sequencing |
| Target site 1- Chr12-seq-R | GGTAATATATGCATAGCAAACCTG | Off-target sequencing |
| Target site 2-Chr6-seq-F | CGCAAGTTACAGTTACAGGCT | Off-target sequencing |
| Target site 2-Chr6-seq-R | CTCCTTTCACCGGAAGATCC | Off-target sequencing |
| Target site 2-Chr5-seq-F | CCGATTAGGCGATTCTCCAG | Off-target sequencing |
| Target site 2-Chr5-seq-R | GCCAGGAAAACAGAAACAGC | Off-target sequencing |
| Target site 2-Chr3-seq-F | TGTCCAGCTAGATCCAACGA | Off-target sequencing |
| Target site 2-Chr3-seq-R | CGCCCTGATGTTGGTGTT | Off-target sequencing |
| Target site 2-Chr7-seq-F | TCAAGCACACACACAATCCA | Off-target sequencing |
| Target site 2-Chr7-seq-R | TCCAAATTTCAGCCACCGAA | Off-target sequencing |
| Target site 2-Chr9-seq-F | ACCATAAAGGTCACACCAGC | Off-target sequencing |
| Target site 2-Chr9-seq-R | CTCGGTTTAAACGTACTTACTGC | Off-target sequencing |
| Target site 3-Chr10-seq-F | CTCATCTTTCCTCCCCGTTG | Off-target sequencing |
| Target site 3-Chr10-seq-R | CTACTCCATCGCCTTATCAGC | Off-target sequencing |
| Target site 3-Chr2-seq-F | GCAATTGTGTGAACCATCGG | Off-target sequencing |
| Target site 3-Chr2-seq-R | ACCAGAAATTACTGCGCGAT | Off-target sequencing |
| Target site 3-Chr1-seq-F | GTCATCATCATGTACGGCGA | Off-target sequencing |
| Target site 3-Chr1-seq-R | TGCCGTTTATACTTGCGTGT | Off-target sequencing |
| Target site 3-Chr6-seq-F | TTTTACGTGCCCTTGAACCA | Off-target sequencing |
| Target site 3-Chr6-seq-R | ATCCATTAGAGGCAAGCGAG | Off-target sequencing |
| Target site 3-Chr9-seq-F | TGTCCTCTAGTTCTGGCGAA | Off-target sequencing |
| Target site 3-Chr9-seq-R | ATTTCTTGCCCCCACACAAT | Off-target sequencing |
Table S1 Primers used in this study.
| Primer | Sequence (5' to 3') | For use |
|---|---|---|
| Waxy-target site 1-F | GGCGAAGAACAACTACCAGCCCAA | Vector construction |
| Waxy-target site 1-R | AAACTTGGGCTGGTAGTTGTTCTT | Vector construction |
| Waxy-target site 2-F | GGCGAAGATCAACTGGATGAAGGC | Vector construction |
| Waxy-target site 2-R | AAACGCCTTCATCCAGTTGATCTT | Vector construction |
| Waxy-target site 3-F | GGCGCGACCAGTACAAGGACGCTT | Vector construction |
| Waxy-target site 3-R | AAACAAGCGTCCTTGTACTGGTCG | Vector construction |
| Waxy-target site 1-seq-F | GGATGTTGTGTTCGTCTGCA | Target site sequencing |
| Waxy-target site 1-seq-R | AGGAGATGTTGTGGATGCAGA | Target site sequencing |
| Waxy-target site 2-seq-F | ACCCTGCACTACTGTCCATC | Target site sequencing |
| Waxy-target site 2-seq-R | CTAGGATCCCACTCGCTGAC | Target site sequencing |
| Waxy-target site 3-seq-F | TTGTGTTCTTTGCAGGCGAA | Target site sequencing |
| Waxy-target site 3-seq-R | TCGTACCTGTCTGCAACCTT | Target site sequencing |
| Target site 1-Chr1-seq-F | CGTTGCCCTACCATTGAAGA | Off-target sequencing |
| Target site 1-Chr1-seq-R | ACATTGGCTGCTGCTACTAC | Off-target sequencing |
| Target site 1-Chr5-seq-F | TGCGACAAGCTGTGGTATTT | Off-target sequencing |
| Target site 1-Chr5-seq-R | GCCTGTATGTAGCTCTGTTGA | Off-target sequencing |
| Target site 1-Chr11-seq-F | GTCATGAAGTGCCTGGAGAG | Off-target sequencing |
| Target site 1-Chr11-seq-R | TCGAAGAACATGAAGCGAGG | Off-target sequencing |
| Target site 1- Chr6-seq-F | GTAGCACCCAAAAGGAGCTT | Off-target sequencing |
| Target site 1- Chr6-seq-R | GTTTCTCCCCTTCTGCACTT | Off-target sequencing |
| Target site 1- Chr12-seq-F | TACTGGTGGTGAGGTTGTGA | Off-target sequencing |
| Target site 1- Chr12-seq-R | GGTAATATATGCATAGCAAACCTG | Off-target sequencing |
| Target site 2-Chr6-seq-F | CGCAAGTTACAGTTACAGGCT | Off-target sequencing |
| Target site 2-Chr6-seq-R | CTCCTTTCACCGGAAGATCC | Off-target sequencing |
| Target site 2-Chr5-seq-F | CCGATTAGGCGATTCTCCAG | Off-target sequencing |
| Target site 2-Chr5-seq-R | GCCAGGAAAACAGAAACAGC | Off-target sequencing |
| Target site 2-Chr3-seq-F | TGTCCAGCTAGATCCAACGA | Off-target sequencing |
| Target site 2-Chr3-seq-R | CGCCCTGATGTTGGTGTT | Off-target sequencing |
| Target site 2-Chr7-seq-F | TCAAGCACACACACAATCCA | Off-target sequencing |
| Target site 2-Chr7-seq-R | TCCAAATTTCAGCCACCGAA | Off-target sequencing |
| Target site 2-Chr9-seq-F | ACCATAAAGGTCACACCAGC | Off-target sequencing |
| Target site 2-Chr9-seq-R | CTCGGTTTAAACGTACTTACTGC | Off-target sequencing |
| Target site 3-Chr10-seq-F | CTCATCTTTCCTCCCCGTTG | Off-target sequencing |
| Target site 3-Chr10-seq-R | CTACTCCATCGCCTTATCAGC | Off-target sequencing |
| Target site 3-Chr2-seq-F | GCAATTGTGTGAACCATCGG | Off-target sequencing |
| Target site 3-Chr2-seq-R | ACCAGAAATTACTGCGCGAT | Off-target sequencing |
| Target site 3-Chr1-seq-F | GTCATCATCATGTACGGCGA | Off-target sequencing |
| Target site 3-Chr1-seq-R | TGCCGTTTATACTTGCGTGT | Off-target sequencing |
| Target site 3-Chr6-seq-F | TTTTACGTGCCCTTGAACCA | Off-target sequencing |
| Target site 3-Chr6-seq-R | ATCCATTAGAGGCAAGCGAG | Off-target sequencing |
| Target site 3-Chr9-seq-F | TGTCCTCTAGTTCTGGCGAA | Off-target sequencing |
| Target site 3-Chr9-seq-R | ATTTCTTGCCCCCACACAAT | Off-target sequencing |
| Target | Homozygous | Heterozygous | Wild type | Total plants | Mutation efficiency (%) |
|---|---|---|---|---|---|
| Target site 1 (MT1) | 2 | 16 | 8 | 26 | 69.23 |
| Target site 2 (MT2) | 1 | 8 | 15 | 24 | 37.50 |
| Target site 3 (MT3) | 3 | 10 | 16 | 29 | 44.83 |
Table S2 Mutation efficiency in T0 generation.
| Target | Homozygous | Heterozygous | Wild type | Total plants | Mutation efficiency (%) |
|---|---|---|---|---|---|
| Target site 1 (MT1) | 2 | 16 | 8 | 26 | 69.23 |
| Target site 2 (MT2) | 1 | 8 | 15 | 24 | 37.50 |
| Target site 3 (MT3) | 3 | 10 | 16 | 29 | 44.83 |
Fig. S2. Sequencing results of target loci of YK17 and three mutants (MT1, MT2 and MT3).PAM, Protospacer adjacent motif.
Fig. S3. Selection of hygromycin-resistant transgenic plants. (+), Hygromycin containing; (-), Hygromycin free.
Fig. S4. Alignment of amino acids of Wxa mutants MT1, MT2 and MT3 conserved in different plant species.MT1 to MT3, Three mutants; WH, Wheat; MZ, Maize; SR, Sorghum; AR, Arabidopsis thaliana; SB, Soybean.
| Target | Putative off-target locus | Off-target sequence | Mutation |
|---|---|---|---|
| Target site 1 | Chr1: Os01g0607900 (intron) | TACAAAAACTACCAGGCCAATGG | 0 |
| Chr5: Os05g05370 (intron) | AAGAATAACTACCAACCAAAAGA | 0 | |
| Chr6: Os06g0230000 (exon) | AAGAACACATACCAGCCTTATGT | 0 | |
| Chr11: 18470801(intergenic) | AAGAAGAACTACCACACCAAAAG | 0 | |
| Chr12: Os12g0586600 (exon) | AAGAACAAATACCACTGCAAGGG | 0 | |
| Target site 2 | Chr3: Os03g0403501 (exon) | AAGCTCGACAGGATGAAGGCCGC | 0 |
| Chr5: Os05g0124600 (intron) | AGGATCAACTGGAAGAAGCCAGG | 0 | |
| Chr6: 5669112 (intergenic) | AAGATCAATTGGGTAAAGACAGG | 0 | |
| Chr7: Os07g0119300 (exon) | AAGAGCAACTGGATGAGCACCGC | 0 | |
| Chr9: Os09g0134500 (exon) | AAGATCACCTGGATCAAGACCTT | 0 | |
| Target site 3 | Chr1: Os01g0830700 (exon) | CGACCTGTCCAAGGGCGAGTGGG | 0 |
| Chr2: Os02g0590800 (exon) | CGTCGAGTACAAGGACGGTTGGG | 0 | |
| Chr6: Os06g0611500 (exon) | CGGCCGGTACAAGGACGAGCGGG | 0 | |
| Chr9: 4319579 (intergenic) | CGAGCAGTACAGGGAGGATTGGG | 0 | |
| Chr10: 9307021 (intergenic) | CGATCAAAATAAGGACGCTTGGG | 0 |
Table S3 Identification of off-target effects.
| Target | Putative off-target locus | Off-target sequence | Mutation |
|---|---|---|---|
| Target site 1 | Chr1: Os01g0607900 (intron) | TACAAAAACTACCAGGCCAATGG | 0 |
| Chr5: Os05g05370 (intron) | AAGAATAACTACCAACCAAAAGA | 0 | |
| Chr6: Os06g0230000 (exon) | AAGAACACATACCAGCCTTATGT | 0 | |
| Chr11: 18470801(intergenic) | AAGAAGAACTACCACACCAAAAG | 0 | |
| Chr12: Os12g0586600 (exon) | AAGAACAAATACCACTGCAAGGG | 0 | |
| Target site 2 | Chr3: Os03g0403501 (exon) | AAGCTCGACAGGATGAAGGCCGC | 0 |
| Chr5: Os05g0124600 (intron) | AGGATCAACTGGAAGAAGCCAGG | 0 | |
| Chr6: 5669112 (intergenic) | AAGATCAATTGGGTAAAGACAGG | 0 | |
| Chr7: Os07g0119300 (exon) | AAGAGCAACTGGATGAGCACCGC | 0 | |
| Chr9: Os09g0134500 (exon) | AAGATCACCTGGATCAAGACCTT | 0 | |
| Target site 3 | Chr1: Os01g0830700 (exon) | CGACCTGTCCAAGGGCGAGTGGG | 0 |
| Chr2: Os02g0590800 (exon) | CGTCGAGTACAAGGACGGTTGGG | 0 | |
| Chr6: Os06g0611500 (exon) | CGGCCGGTACAAGGACGAGCGGG | 0 | |
| Chr9: 4319579 (intergenic) | CGAGCAGTACAGGGAGGATTGGG | 0 | |
| Chr10: 9307021 (intergenic) | CGATCAAAATAAGGACGCTTGGG | 0 |
| Variety | Grain length (mm) | Grain width (mm) | Grain thickness (mm) | 1000-grain weight (g) |
|---|---|---|---|---|
| YK17 | 7.29 ± 0.10 | 2.62 ± 0.05 | 2.10 ± 0.06 | 16.28 ± 1.16 |
| MT1 | 7.46 ± 0.05* | 2.82 ± 0.04* | 2.27 ± 0.07* | 18.20 ± 0.18* |
| MT2 | 7.52 ± 0.14* | 2.76 ± 0.06* | 2.19 ± 0.09* | 15.97 ± 0.60 |
| MT3 | 7.52 ± 0.02* | 2.79 ± 0.04* | 2.12 ± 0.07 | 15.10 ± 1.31 |
Table S4 Agronomic traits of YK17 and mutants (MT1, MT2 and MT3).
| Variety | Grain length (mm) | Grain width (mm) | Grain thickness (mm) | 1000-grain weight (g) |
|---|---|---|---|---|
| YK17 | 7.29 ± 0.10 | 2.62 ± 0.05 | 2.10 ± 0.06 | 16.28 ± 1.16 |
| MT1 | 7.46 ± 0.05* | 2.82 ± 0.04* | 2.27 ± 0.07* | 18.20 ± 0.18* |
| MT2 | 7.52 ± 0.14* | 2.76 ± 0.06* | 2.19 ± 0.09* | 15.97 ± 0.60 |
| MT3 | 7.52 ± 0.02* | 2.79 ± 0.04* | 2.12 ± 0.07 | 15.10 ± 1.31 |
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