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Genome-wide association study of root traits in wheat seedlings and identification of a superior allele at TaSRL-3B

CAI Jin-Shan1, LI Chao-Nan2WANG Jing-Yi2, LI Ning1, LIU Yu-Ping2, JING Rui-Lian2, LI Long2,*, SUN Dai-Zhen1,*   

  1. 1 College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi, China; 2 State Key Laboratory of Crop Gene Resources and Breeding / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2025-02-24 Revised:2025-06-01 Accepted:2025-06-01 Published:2025-06-10
  • Supported by:
    This study was supported by the National Key R&D Program of China (2022YFD1200201) and the China Agriculture Research System of MOF and MARA (CARS-03-5).

Abstract:

The root system is the primary organ responsible for water and nutrient uptake in wheat, and its morphological characteristics are closely associated with yield and tolerance to abiotic stress. Therefore, identifying genetic loci and favorable alleles that control root morphology is of great importance for wheat improvement. In this study, 277 wheat accessions were evaluated using a gel-chamber-based observation method to characterize eight root morphological traits at the seedling stage, including total root length, root surface area, and root angle. Based on genotyping with the Wheat 660K SNP Array, a genome-wide association study (GWAS) was performed using three models (GLM, MLM, and FarmCPU), leading to the identification of 52 associated loci. Among them, six pleiotropic loci (Loci17, Loci20, Loci22, Loci38, Loci46, and Loci47) were located on chromosomes 3A, 3B, 3D, 5A, 6A, and 6B, respectively. Within Loci20, the candidate gene TaSRL-3B, associated with root morphology, was cloned. This gene has a full-length sequence of 1089 bp, lacks introns, and contains a conserved NAC domain between amino acids 78 and 235. A 20-bp insertion/deletion (InDel717) in the coding region of TaSRL-3B caused a frameshift mutation and showed strong linkage (R2 = 0.84) with the candidate SNP (AX-108758584) in Loci20. Accessions carrying the TaSRL-3BIn allele exhibited significantly greater maximum root length, total root length, and root surface area compared to those with the TaSRL-3BIn. A backcross introgression line population (BC3F5) was developed using Lumai 14 (LM14, carrying TaSRL-3BDel as the recurrent parent and Shanhe 6 (SH6, carrying TaSRL-3BIn as the donor. A molecular marker based on InDel717 was used to identify five near-isogenic lines (NILs) carrying TaSRL-3BIn from this population. Compared to LM14, these lines showed significant improvements in maximum root length, total root length, root surface area, and root volume, further confirming the role of TaSRL-3B in shaping seedling root morphology. Notably, the frequency of the long-root allele TaSRL-3BIn has declined in modern Chinese cultivars compared to landraces. This study provides valuable insights into the genetic regulation of wheat root traits and supports the genetic improvement of root systems for enhanced wheat performance.

Key words: wheat, seedling, root morphology, genome-wide association analysis, candidate gene

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