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Identification of genetic loci related to low phosphorus tolerance at the seedling stage in wheat and analysis of candidate genes

CAO Zhi-Yang1,**,GAO Li-Feng2,**,JIANG Dong-Yan1,WANG Shu-Guang1,YANG Jin-Wen1,JIA Ji-Zeng2,LI Ning1,*,SUN Dai-Zhen1,*   

  1. 1 College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi, China; 2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2025-03-27 Revised:2025-07-09 Accepted:2025-07-09 Published:2025-07-22
  • Supported by:
    This study was supported by the National Key R&D Program of China (2022YFD1200201, 2024YFD1201100) and the Breeding Engineering Program of College of Agriculture, Shanxi Agricultural University (YZ2021-0).

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Abstract:

Phosphorus (P) is an essential macronutrient for crop growth and development. However, only a small fraction of the phosphorus present in soil is effectively utilized by plants, and long-term application of P fertilizers can lead to environmental pollution. Therefore, it is of great significance to screen for varieties with strong tolerance to low-P conditions and to identify associated QTLs and candidate genes. In this study, a natural population consisting of 389 wheat varieties was used as experimental material. A three-year hydroponic experiment (2022, 2023, and 2024) was conducted under both normal-P (control) and low-P conditions at the wheat seedling stage. Nine traits were measured, including seedling height, main root length, root number, shoot dry weight, root dry weight, total root length, root surface area, root diameter, and number of root tips. For each trait, the low-P tolerance coefficient and BLUP values were calculated, and comprehensive evaluation D-values were derived based on these coefficients. Correlation analysis of BLUP values across the three environments revealed significant positive correlations among most traits, except for root diameter, under both low-P and control conditions. Cluster analysis of the comprehensive D-values identified ‘Fengdecunmai 1’ as a strongly low-P-tolerant variety across all four environments (2022, 2023, 2024, and BLUP). A genome-wide association study (GWAS) was carried out using low-P tolerance coefficients and D-values for the nine traits across the four environments, based on the 660K SNP chip. A total of 1,197 significant SNP markers were detected, forming 464 QTLs. Among these, 20 QTLs were repeatedly detected in two environments, and 7 QTLs were detected in three or four environments, with the phenotypic variance explained (R2) ranging from 4.09% to 10.58%. Based on previously published transcriptomic data and gene functional annotation, three candidate genes associated with low-P tolerance were identified within the regions of the seven QTLs. TraesCS4D02G022900 and TraesCS4D02G023300 encode F-box family proteins. Their Arabidopsis ortholog, At5g21040, encodes a protein containing both WD40 and F-box domains and functions as a negative regulator of the P starvation response. TraesCS6D02G154700 encodes a receptor-like protein kinase involved in plant growth, development, and responses to stress and disease. Further analysis of the expression patterns of these three candidate genes in both leaves and roots under low-P stress revealed differential expression consistent with previous transcriptomic results. These findings provide a solid foundation for the development of low-P-tolerant wheat cultivars and for elucidating the functions and regulatory mechanisms of genes associated with low-P stress.

Key words: wheat, low phosphorus stress, GWAS, SNP, candidate genes

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