Skip to main content
Log in

Multiplex QTL editing of grain-related genes improves yield in elite rice varieties

  • Original Article
  • Published:
Plant Cell Reports Aims and scope Submit manuscript

Abstract

Key message

Significant yield increase has been achieved by simultaneous introduction of three trait-related QTLs in three rice varieties with multiplex editing by CRISPR–Cas9.

Abstract

Using traditional breeding approaches to develop new elite rice varieties with high yield and superior quality is challenging. It usually requires introduction of multiple trait-related quantitative trait loci (QTLs) into an elite background through multiple rounds of crossing and selection. CRISPR–Cas9-based multiplex editing of QTLs represents a new breeding strategy that is straightforward and cost effective. To test this approach, we simultaneously targeted three yield-related QTLs for editing in three elite rice varieties, namely J809, L237 and CNXJ. The chosen yield-related QTL genes are OsGS3, OsGW2 and OsGn1a, which have been identified to negatively regulate the grain size, width and weight, and number, respectively. Our approach rapidly generated all seven combinations of single, double and triple mutants for the target genes in elite backgrounds. Detailed analysis of these mutants revealed differential contributions of QTL mutations to yield performance such as grain length, width, number and 1000-grain weight. Overall, the contributions are additive, resulting in 68 and 30% yield per panicle increase in triple mutants of J809 and L237, respectively. Our data hence demonstrates a promising genome editing approach for rapid breeding of QTLs in elite crop varieties.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokininoxidase regulates rice grain production. Science 309:741–745

    Article  CAS  PubMed  Google Scholar 

  • Cermak T, Curtin SJ, Gil-Humanes J, Cegan R, Kono TJY, Konecna E, Belanto JJ, Starker CG, Mathre JW, Greenstein RL, Voytas DF (2017) A multipurpose toolkit to enable advanced genome engineering in plants. Plant Cell 29:1196–1217

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ding D, Chen K, Chen Y, Li H, Xie K (2018) Engineering introns to express RNA guides for Cas9- and Cpf1-mediated multiplex genome editing. Mol Plant 11:542–552

    Article  CAS  PubMed  Google Scholar 

  • Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  CAS  PubMed  Google Scholar 

  • Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, Cao F, Zhu S, Zhang F, Mao Y, Zhu JK (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23(10):1229–1232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He Y, Zhang T, Yang N, Xu M, Yan L, Wang L, Wang R, Zhao Y (2017) Self-cleaving ribozymes enable the production of guide RNAs from unlimited choices of promoters for CRISPR/Cas9 mediated genome editing. J Genet Genomics 44:469–472

    Article  PubMed  PubMed Central  Google Scholar 

  • He Y, Zhu M, Wang L, Wu J, Wang Q, Wang R, Zhao Y (2018) Programmed self-elimination of the CRISPR/Cas9 construct greatly accelerates the isolation of edited and transgene-free rice plants. Mol Plant. https://doi.org/10.1016/j.molp.2018.05.005

    Article  PubMed  Google Scholar 

  • Ikeda M, Miura K, Aya K, Kitano H, Matsuoka M (2013) Genes offering the potential for designing yield-related traits in rice. Curr Opin Plant Biol 16:213–220

    Article  CAS  PubMed  Google Scholar 

  • Jiang Y, Cai Z, Xie W, Long T, Yu H, Zhang Q (2012) Rice functional genomics research: progress and implications for crop genetic improvement. Biotechnol Adv 30:1059–1070

    Article  CAS  PubMed  Google Scholar 

  • Lee CM, Park J, Kim B, Seo J, Lee G, Jang S, Koh HJ (2015) Influence of multi-gene allele combinations on grain size of rice and development of a regression equation model to predict grain parameters. Rice (NY) 8:33

    Article  Google Scholar 

  • Li Q, Zhang D, Chen M, Liang W, Wei J, Qi Y, Yuan Z (2016a) Development of japonica photo-sensitive genic male sterile rice lines by editing carbon starved anther using CRISPR/Cas9. J Genet Genom 43(6):415–419

    Article  Google Scholar 

  • Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H (2016b) Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front Plant Sci 7:377

    PubMed  PubMed Central  Google Scholar 

  • Li S, Zhang X, Wang W, Guo X, Wu Z, Du W, Zhao Y, Xia L (2018) Expanding the scope of CRISPR/Cpf1-mediated genome editing in rice. Mol Plant 11(7):995–998

    Article  CAS  PubMed  Google Scholar 

  • Lowder LG, Zhang D, Baltes NJ, Paul JW, Tang X, Zheng X, Voytas DF, Hsieh TF, Zhang Y, Qi Y (2015) A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol 169:971–985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lowder L, Malzahn A, Qi Y (2016) Rapid evolution of manifold CRISPR systems for plant genome editing. Front Plant Sci 7:1683

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma X, Chen L, Zhu Q, Chen Y, Liu YG (2015) Rapid decoding of sequence-specific nuclease-induced heterozygous and biallelic mutations by direct sequencing of PCR products. Mol Plant 8:1285–1287

    Article  CAS  PubMed  Google Scholar 

  • Ma X, Zhu Q, Chen Y, Liu YG (2016) CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Mol Plant 9:961–974

    Article  CAS  PubMed  Google Scholar 

  • Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579–19584

    Article  PubMed  PubMed Central  Google Scholar 

  • Meng X, Hu X, Liu Q, Song X, Gao C, Li J, Wang K (2018) Robust genome editing of CRISPR-Cas9 at NAG PAMs in rice. Sci China Life Sci 61(1):122–125

    Article  CAS  PubMed  Google Scholar 

  • Miao C, Xiao L, Hua K, Zou C, Zhao Y, Bressan RA, Zhu JK (2018) Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity. Proc Natl Acad Sci USA 115(23):6058–6063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ren B, Yan F, Kuang Y, Li N, Zhang D, Zhou X, Lin H, Zhou H (2018) Improved base editor for efficiently inducing genetic variations in rice with CRISPR/Cas9-guided hyperactive hAID mutant. Mol Plant 11(4):623–626

    Article  CAS  PubMed  Google Scholar 

  • Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686–688

    Article  CAS  PubMed  Google Scholar 

  • Shan Q, Wang Y, Li J, Gao C (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9:2395–2410

    Article  CAS  PubMed  Google Scholar 

  • Shen L, Hua Y, Fu Y, Li J, Liu Q, Jiao X, Xin G, Wang J, Wang X, Yan C, Wang K (2017) Rapid generation of genetic diversity by multiplex CRISPR/Cas9 genome editing in rice. Sci China Life Sci 60:506–515

    Article  CAS  PubMed  Google Scholar 

  • Shen L, Wang C, Fu Y, Wang J, Liu Q, Zhang X, Yan C, Qian Q, Wang K (2018) QTL editing confers opposing yield performance in different rice varieties. J Integr Plant Biol 60:89–93

    Article  CAS  PubMed  Google Scholar 

  • Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630

    Article  CAS  PubMed  Google Scholar 

  • Tang X, Zheng X, Qi Y, Zhang D, Cheng Y, Tang A, Voytas DF, Zhang Y (2016) A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Mol Plant 9:1088–1091

    Article  CAS  PubMed  Google Scholar 

  • Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, Zhong Z, Chen Y, Ren Q, Li Q, Kirkland ER, Zhang Y, Qi Y (2017) A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants 3:17018

    Article  CAS  PubMed  Google Scholar 

  • Tang X, Liu G, Zhou J, Ren Q, You Q, Tian L, Xin X, Zhong Z, Liu B, Zheng X, Zhang D, Malzahn A, Gong Z, Qi Y, Zhang T, Zhang Y (2018) A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol 19(1):84

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with Agrobacterium allows high-speed transformation of rice. Plant J 47:969–976

    Article  CAS  PubMed  Google Scholar 

  • Wang C, Shen L, Fu Y, Yan C, Wang K (2015) A simple CRISPR/Cas9 system for multiplex genome editing in rice. J Genet Genom 42:703–706

    Article  Google Scholar 

  • Wang Y, Geng L, Yuan M, Wei J, Jin C, Li M, Yu K, Zhang Y, Jin H, Wang E, Chai Z, Fu X, Li X (2017a) Deletion of a target gene in Indica rice via CRISPR/Cas9. Plant Cell Rep 36(8):1333–1343

    Article  CAS  PubMed  Google Scholar 

  • Wang M, Mao Y, Lu Y, Tao X, Zhu JK (2017b) Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol Plant 10(7):1011–1013

    Article  CAS  PubMed  Google Scholar 

  • Wang M, Mao Y, Lu Y, Wang Z, Tao X, Zhu JK (2018) Multiplex gene editing in rice with simplified CRISPR-Cpf1 and CRISPR-Cas9 systems. J Integr Plant Biol 60(8):626–631

    Article  CAS  PubMed  Google Scholar 

  • Xie K, Minkenberg B, Yang Y (2015) Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci USA 112:3570–3575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu R, Yang Y, Qin R, Li H, Qiu C, Li L, Wei P, Yang J (2016) Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. J Genet Genom 43(8):529–532

    Article  Google Scholar 

  • Zeng D, Tian Z, Rao Y, Dong G, Yang Y, Huang L, Leng Y, Xu J, Sun C, Zhang G, Hu J, Zhu L, Gao Z, Hu X, Guo L, Xiong G, Wang Y, Li J, Qian Q (2017) Rational design of high-yield and superior-quality rice. Nat Plants 3:17031

    Article  PubMed  Google Scholar 

  • Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F (2017) Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol 35:31–34

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK (2016) A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep 35:1519–1533

    Article  CAS  PubMed  Google Scholar 

  • Zheng X, Yang S, Zhang D, Zhong Z, Tang X, Deng K, Zhou J, Qi Y, Zhang Y (2016) Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. Plant Cell Rep 35(7):1545–1554. https://doi.org/10.1007/s00299-016-1967-1

    Article  CAS  Google Scholar 

  • Zhong Z, Zhang Y, You Q, Tang X, Ren Q, Liu S, Yang L, Wang Y, Liu X, Liu B, Zhang T, Zheng X, Le Y, Zhang Y, Qi Y (2018) Plant genome editing using FnCpf1 and LbCpf1 nucleases at redefined and altered PAM sites. Mol Plant 11(7):999–1002

    Article  CAS  PubMed  Google Scholar 

  • Zhou J, Deng K, Cheng Y, Zhong Z, Tian L, Tang X, Tang A, Zheng X, Zhang T, Qi Y, Zhang Y (2017) CRISPR-Cas9 based genome editing reveals new insights into microRNA function and regulation in rice. Front Plant Sci 8:1598

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by Program for International Science and Technology Cooperation and Exchanges of Sichuan province (2018HH0112), Sichuan Youth Science and Technology Foundation (2017JQ0005) and the National Science Foundation of China (31771486).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Yiping Qi or Yong Zhang.

Ethics declarations

Conflict of interest

The authors have no conflict of interests to declare.

Additional information

Communicated by Fabien Nogué.

This paper is for the special issue on precision genetic engineering tools.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PPTX 931 KB)

Supplementary material 2 (DOCX 26 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhou, J., Xin, X., He, Y. et al. Multiplex QTL editing of grain-related genes improves yield in elite rice varieties. Plant Cell Rep 38, 475–485 (2019). https://doi.org/10.1007/s00299-018-2340-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00299-018-2340-3

Keywords

Navigation