J Integr Plant Biol ›› 2025, Vol. 67 ›› Issue (9): 2480-2490.DOI: 10.1111/jipb.13926

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  • 收稿日期:2025-02-10 接受日期:2025-04-10 出版日期:2025-09-01 发布日期:2025-09-02

Directional improvement of agronomic traits in salt-tolerant rice by multiplex-genome-editing

Yu Hao1†, Bingqun Xu1†, Wubei Zong1,2, Shengting Li1, Duoduo Du1, Miaomiao Chen1, Dongdong Xiao1, Yingang Song1, Xiaotong Guo1, Weitao Li1, Zeqiang Wu1, Kai Zhang1, Nan Liao1, Dan Hu1, Yao‐guang Liu1* and Jingxin Guo1*   

  1. 1. Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
    2. College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China

    †These authors contributed equally to this work.
    *Correspondences: Yao‐guang Liu (ygliu@scau.edu.cn); Jingxin Guo (jingxinguo@scau.edu.cn, Dr. Guo is fully responsible for the distributions of all materials associated with this article)
  • Received:2025-02-10 Accepted:2025-04-10 Online:2025-09-01 Published:2025-09-02
  • Supported by:
    This research was funded by grants from the National Key R&D Program of China (2023ZD04073), the Major Program of Guangdong Basic and Applied Research (2019B030302006) the open competition program of top 10 critical priorities of Agricultural Science and Technology Innovation for the 14th Five‐Year Plan of Guangdong Province (2022SDZG05), Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops Major Project (FCBRCE‐202502, FCBRCE‐202504).

Abstract: Soil salinization has emerged as a major threat affecting crop yields. Global warming leads to a massive loss of terrestrial water and makes soils saltier. Cultivating salt-tolerant crops is the major strategy adopted for utilizing these salinized soils. Sea Rice 86 (SR86) is one such elite salt-tolerant rice variety derived from ancient indica rice. However, SR86 has multiple wild traits, such as tallness and strong photoperiod sensitivity (PS), which have limited its application in agricultural production. In this study, we edited 13 genes responsible for 10 traits in SR86 to develop an improved SR86M line by using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 multiplex-genome-editing technology, high-throughput sequencing, crossing, and progeny selection. Subsequent analysis of SR86M detected nine genes with expected mutations, leading to changes in seven traits, including improvements of plant architecture, plant height and PS decreased, grain number, grain length, fragrance, and nitrogen utilization efficiency increased. The improved agronomic traits in SR86M are similar to modern cultivated rice, along with elite salt tolerance like SR86, indicating suitability for potential cultivation. Our results also reveal the efficiency of multiplex-genome-editing in directional improvement of crop varieties.

Key words: CRISPR/Cas9 technology, directional improvement, multiplex‐genome‐editing, salt‐tolerant rice, Sea Rice 86

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