An elite haplotype of the glutamine synthetase gene <i>TaGS1.1-6A</i> is associated with increased nitrogen use- and yield-related traits in wheat

Yazhou Wang; Wan Teng; Mingyang Lei; Yanpeng Wang; Xiang Ouyang; Caixia Gao; Ruilian Jing; Junming Li; Yiping Tong

doi:10.1016/j.jgg.2025.12.008

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An elite haplotype of the glutamine synthetase gene TaGS1.1-6A is associated with increased nitrogen use- and yield-related traits in wheat

doi: 10.1016/j.jgg.2025.12.008

a. State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
b. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
c. Laboratory of Advanced Breeding Technologies, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
d. State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center (HHRRC), Changsha, Hunan 410125, China;
e. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
f. College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050024, China

Funds:

This research was supported by the National Key Research and Development Program of China (2021YFF1000404), the National Natural Sciences Foundation of China (U22A6009 and 32072660), the National Key Research and Development Program of China (2022YFD1200204), the Biological Breeding-National Science and Technology Major Project (2023ZD0402401).

Received Date: 2025-09-02
Accepted Date: 2025-12-18
Rev Recd Date: 2025-12-16

Available Online: 2025-12-25

Abstract

Abstract

Glutamine synthetase (GS) plays a crucial role in nitrogen (N) assimilation. Identifying elite alleles of GS genes can facilitate the breeding of wheat (Triticum aestivum) varieties with improved N use efficiency (NUE). Here, meta-quantitative trait loci (QTL) analysis based on five bi-parental linkage mapping populations reveals that TaGS1.1-6A co-localizes with a meta-QTL for N use- and yield-related traits. The promoter region of TaGS1.1-6A contains a variation caused by a miniature inverted-repeat transposable element (MITE) insertion. The MITE insertion induces DNA hypermethylation in the adjacent regions, thereby repressing TaGS1.1-6A transcription. The haplotype TaGS1.1-6A^HapII without the MITE insertion has been subjected to selection during wheat breeding, and is associated with increased photosynthetic N use efficiency, N utilization efficiency, spike grain number, and grain yield per plant when a BC₃F₄ population is grown under varying N supply levels. Conversely, CRISPR/Cas9-mediated mutation of TaGS1.1 shows reduction in these traits. Furthermore, we develop a breeding strategy to enhance wheat grain yield under different N supply conditions by pyramiding TaGS1.1-6A^HapII and the leaf senescence-delaying haplotype of TaNAM-A1. These findings suggest that TaGS1.1-6A contributes to N use- and yield-related traits, and TaGS1.1-6A^HapII holds significant value for breeding wheat with improved NUE and yield.
- Glutamine synthetase,
- Grain number,
- Miniature inverted-repeat transposable element (MITE),
- Nitrogen use efficiency,
- Triticum aestivum

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