Plant Cell Reports

, Volume 38, Issue 4, pp 475–485 | Cite as

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

  • Jianping Zhou
  • Xuhui Xin
  • Yao He
  • Hongqiao Chen
  • Qian Li
  • Xu Tang
  • Zhaohui Zhong
  • Kejun Deng
  • Xuelian Zheng
  • Sayed Abdul Akher
  • Guangze Cai
  • Yiping QiEmail author
  • Yong ZhangEmail author
Original Article


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.


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.


CRISPR–Cas9 Multiplex genome editing Rice QTLs 



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).

Compliance with ethical standards

Conflict of interest

The authors have no conflict of interests to declare.

Supplementary material

299_2018_2340_MOESM1_ESM.pptx (932 kb)
Supplementary material 1 (PPTX 931 KB)
299_2018_2340_MOESM2_ESM.docx (27 kb)
Supplementary material 2 (DOCX 26 KB)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biotechnology, Center for Informational Biology, School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengduPeople’s Republic of China
  2. 2.Xichang UniversityXichangChina
  3. 3.Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkUSA
  4. 4.Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleUSA

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