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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (11): 2706-2714.doi: 10.3724/SP.J.1006.2022.14220

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Construction and application of soybean CRISPR/Cas9 multiplex editing vector

CHEN Xiang-Qian(), JIANG Qi-Yan(), SUN Xian-Jun, NIU Feng-Juan, ZHANG Hui-Yuan, HU Zheng*(), ZHANG Hui*()   

  1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2021-11-26 Accepted:2022-02-25 Online:2022-11-12 Published:2022-03-08
  • Contact: HU Zheng,ZHANG Hui E-mail:chen810702351@gmail.com;jiangqiyan@caas.cn;huzheng@caas.cn;zhanghui06@caas.cn
  • Supported by:
    The Key Research and Development Program of Hainan Province(ZDYF2022XDNY135);The Agricultural Science and Technology Program for Innovation Program(CAAS-ZDRW202201);The National Key Research and Development Program of China(2021YFD1201603-2);The National Natural Science Foundation of China(31601302)

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Abstract:

Most members of one gene family have similar function in soybean. Construction of soybean multiplex editing vector to edit multiple genes or gene families have important application value in soybean gene editing and gene functions, especially for the soybean with low transformation efficiency. Here, we reported a CRISPR/Cas9 multiplex editing vector, pCambia3301- Cas9-GmU6n-gDNAn, that enabled the editing of multiple genes in soybean. In this vector, different sgRNAs were driven by different soybean U6 promoters, and multiple sgRNA expression cassettes were assembled into pCambia3301-Cas9 vector by isocaudamers. The result showed that this system could simultaneously produce multiple mutations in soybean hairy roots by targeting multiple GRF genes via single transformation events. This vector can improve the efficiency of gene editing in soybean, and provide a simple toolbox for studying functions of multiple genes and gene families in soybean for basic research and genetic improvement.

Key words: soybean, GmU6 promoter, CRISPR/Cas9 multiplex editing vector, hairy root

Table 1

Primers used in this study"

引物名称
Primer name		 引物序列
Primer sequence (5°-3°)
载体构建引物Primers used in construction of vectors
PDS-HF GAAATGTGCCACCACATGGATTggtgaccGCGCACAACCCTTTCCAGTTTCT
PDS-HR AACTTGCTATTTCTAGCTCTAAAAcctaggCATCATAGTTACTAACCTCACT
GmU6-2-HF TGTAAAACGACGGCCAGAGAATTCGAGCTCGAGTCCAATATGCCC
GmU6-2-HR AACTGGAAAGGGTTGTGCGCGGTCACCAACATCTTGAATGTTGTATGTC
GmU6-8-HF TGTAAAACGACGGCCAGAGAATTCGAGCTCGAGATTCGAGCTCGA
GmU6-8-HR AACTGGAAAGGGTTGTGCGCGGTCACCAATCCATATGTTTTCCTGGGACT
GmU6-11-HF TGTAAAACGACGGCCAGAGAATTCGAGCTCGAGATGGTCTATGAG
GmU6-11-HR AACTGGAAAGGGTTGTGCGCGGTCACCAACCAGTTTGTTCCATCTCTG
串联sgRNA构建引物Primers used in assembling of multiple sgRNA expression cassettes
U2-GRF TGACATACAACATTCAAGATGTTGAAACCGTTCAAGAAAGCCTGGTTTTAGAGCTAGAAATAGCAAGT
U8-GRF TAGTCCCAGGAAAACATATGGATTGCCACAGGCTTTCTTGAACGAGTTTTAGAGCTAGAAATAGCAAGT
U10-GRF GAAATGTGCCACCACATGGATTGGTTCCACAGGCTTTCTTGAAGTTTTAGAGCTAGAAATAGCAAGT
U11-GRF CAGAGATGGAACAAACTGGTTGGAATCGTTCAAGAAAGCCTGGTTTTAGAGCTAGAAATAGCAAGT
GRF突变检测PCR引物Primers used in the detection of GRF mutations
GRF5-F/R GAGCCAGGGAGGTGTAGGAG/AATGTGATGAATGGAATAAACGA
GRF6-F/R ATGGAAAGAAATGGCGATGC/ACCAACCACAAACGAGGAAA
GRF7-F/R ATGGGATGAGGATGATGATGT/GAGGAATGAGGAGGAATAGGG
GRF8-F/R GAGCCAGGCAGGTGTAGGAG/ACGAATGAGGTGGAAGAGGG
GRF9-F/R CACATCCTCTTCTCGCTCTTC/GAAACTCACCTGGGTTCCTTAT
GRF10-F/R GTTCACAGTGGATGGTGGTTT/CAAGGTATGGCTGAGTGGTAGTA
GRF13-F/R GCAGGAGGACTGATGGAAAA/TACTTGGAATCGCATAGGGA
GRF14-F/R CCATTTTGTCTTTATTGCTGC/TGGGAAGGTTTTGGAAGTTTA
GRF15-F/R TGTTGATTGGTTATTTGGTGC/TGTGATAGTGGGTTTGGTCTGA
GRF16-F/R ATATTAGTGATAAAGTAGAGGTGGGA/AACTCAATAACAAGCAGACGC
GRF17-F/R ATGAGCGTTCCTCCGCCGTCT/CCCTTGCGCCATTGATGTGC
GRF18-F/R TGACCTCCTTCTCCCCATTC/CAGTTGCAGTTCCAGAAACATTA
GRF19-F/R AATCAGGGTATTGGGGTAGAG/AGGGTGGTGAACAAATGGAA
GRF20-F/R AGGGTATTGGGGTAGAGGAGC/CGAAGAAGATCAAATGGGGAT
GRF21-F/R TCAGGGTACTACTGGCGAAGA/TGACCGAGGTGAAGGAGATT

Fig. 1

Vector construction of sgRNA3.0 with different sgRNAs driven by different soybean U6 promoters A and B: construction of pGmU6-sgRNA3.0 vector, M: DL2000; A1: PCR clone of PDS gene; A2: pGmU6-10-sgRNA2.0 digested with Bsa I; A3: pGmU6-10-sgRNA3.0 digested with BstE II and Avr II; B1: pGmU6-2-sgRNA3.0 digested with BstE II and Xho I; B2: GmU6-2, B3: GmU6-8, B4: GmU6-11. C: structure of pGmU6-sgRNA3.0 vector."

Fig. 2

Vector construction of pCambia3301-Cas9-GmU6n-gDNAn A: pGmU6-sgRNA3.0 digested with BstE II and Avr II. M: DL2000; 1-4: pGmU6-2/8/10/11-sgRNA3.0 digested with BstE II and Avr II. B: pGmU6-gDNA digested with appropriate restriction enzymes. M: DL2000; 1: pGmU6-10-gDNA digested with BamH I and Sal I; 2-4: pGmU6-2-gDNA, pGmU6-8-gDNA, pGmU6-11-gDNA digested with BamH I and Xho I separately. C: vector construction of pCambia3301-Cas9-GmU6n-gDNAn. M: 1 kb ladder; 1: pCambia3301-Cas9 digested with EcoR I and Hind III; 2: pGmU6n-gDNAn digested with EcoR I and Hind III; 3: pCambia3301-Cas9-GmU6n-gDNAnv vector; 4: pCambia3301-Cas9-GmU6n-gDNAn digested with EcoR I and Hind III."

Fig. 3

Diagram of binary CRISPR/Cas9 multiplex editing vectors Cas9 fused with a single nuclear localization signal (NLS) is expressed with a Cauliflower mosaic virus 35S (CaMV 35S) promoter. Synthetic guide RNA (sgRNA) is derived using different soybean U6 promoters. The synthetic skeleton of multiplex editing vector consists of tandemly arrayed GmU6-gDNA-sgRNA units, containing one soybean U6 promoter (GmU6-2/8/10/11), a target-specific spacer (gDNA1/2/3/4) and conserved sgRNA scaffold in each unit. LB: left border; RB: right border."

Fig. 4

Detection of GRF mutation with PCR-T7 Endonuclease I Lanes 1-12 indicates digested products with T7 Endonuclease I of GRF gene cloned in different single hairy root of soybean, and the single band means no mutation in GRF, multiple bands mean mutation in GRF gene (indicated with arrows). M: DL2000 marker."

Fig. 5

Mutation detection by sequencing of GRF gene cloned in the same transgenic hairy root in soybean Wild-type sequences of the target genes are the PAM sequence highlighted in red and gDNA sequence highlighted in blue. GRFn indicates the mutant sequence of GRF gene, and the change in the number of nucleotides is the right of each sequence. -: deletion."

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