Changes in the Expression of the Soybean TPS Gene Family Under Salt Stress and Haplotype Selection Analysis

doi:10.11983/CBB24110

Abstract

Abstract: INTRODUCTION Trehalose-6-phosphate synthase (TPS) is a key enzyme involved in the synthesis of trehalose and has been reported to participate in regulating photosynthesis, carbohydrate metabolism, growth and development, and stress responses in various species. Currently, reports on TPS genes in soybean are scarce. RATIONALE TPS is a stable non-reducing disaccharide, whose synthesis, decomposition and regulation not only provide energy for plant, but also play an important role in plant growth and development and stress tolerance. The in-depth study of soybean TPS genes and its relationships with salt stress is of great significance in elucidating the molecular mechanism of soybean salt tolerance and improving soybean yield. RESULTS This study identified 20 soybean TPS genes and their associated 10 conserved protein motifs in the soybean genome. Molecular analysis of the promoter elements revealed that the TPS gene promoters are rich in stress-responsive elements. After salt stress treatment, the expression of 17 TPS genes changed, with 12 genes up-regulated and 5 genes down-regulated. Haplotype and selection analyses revealed two major allelic variations in TPS8, TPS13, TPS15, TPS17, and TPS18. Notably, variants carrying TPS15^H2, TPS13^H2, TPS17^H2, and TPS18^H2 were significantly enriched in improved cultivars that underwent strong artificial selection. CONCLUSION This study reveals the molecular characteristics of the soybean TPS gene family, their expression patterns under salt stress, and their evolutionary history, providing a theoretical basis and genetic material for further elucidating the functions of soybean TPS genes and breeding salt-tolerant soybean varieties. TPS genes were subjected to intense artificial selection. The natural variations of TPS8, TPS13, TPS15, TPS17, and TPS18 have been subjected to strong artificial selection during soybean domestication and improvement, with the variants carrying TPS15^H2, TPS13^H2, TPS17^H2, and TPS18^H2 being heavily enriched in improved cultivars.

Key words: soybean, trehalose-6-phosphate synthase, expression analysis, salt tolerance, artificial selection

Jie Cao, Qiulian Lu, Jianping Zhai, Baohui Liu, Chao Fang, Shichen Li, Tong Su. Changes in the Expression of the Soybean TPS Gene Family Under Salt Stress and Haplotype Selection Analysis[J]. Chinese Bulletin of Botany, 2025, 60(2): 172-185.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24110

https://www.chinbullbotany.com/EN/Y2025/V60/I2/172

Figures/Tables 6

Figure 1 Phylogenetic tree of trehalose-6-phosphate synthase (TPS) from Arabidopsis and legumes The TPS proteins from Arabidopsis and legumes are divided into two clades (clade I and clade II). The soybean TPS proteins are highlighted in red. At: Arabidopsis thaliana; Gm: Glycine max; Pv: Phaseolus vulgaris; Mt: Medicago truncatula; Lj: Lotus japonicus

Figure 2 Conserved protein motif of trehalose-6-phosphate synthase (TPS) in soybean Phylogenetic relationships among TPS members and distribution of conserved protein motifs in soybean, ten motifs were identified. The bottom scale represents the amino acid sequence length (aa).

Figure 3 Chromosomal distribution and inter-chromosomal relationships of TPS genes in soybean Red curves connecting pairs of genes indicate segmental duplications.

Figure 4 Cis-element analysis of TPS genes in soybean The cis-elements in the 2 Kb upstream promoter regions of each TPS gene are mapped, with different types of cis-elements represented by different colors, as indicated on the right. The scale bars at the bottom of the figure represent the length of the promoter sequence (bp).

Figure 5 qRT-PCR analysis of the TPS genes expression under salt stress From left to right and top to bottom in the picture, they are TPS1 to TPS20 in sequence. * P<0.05; ** P<0.01; N.S. indicate no significant difference.

Figure 6 TPS genes subjected to intense artificial selection (A), (C), (E), (G), and (I) represent the haplotypes of TPS8, TPS13, TPS15, TPS17, and TPS18, respectively. The figure shows several important TPS haplotypes. (B), (D), (F), (H), and (J) represent the proportions of different alleles in wild (W) soybeans, Landraces (L) and cultivated varieties (C), respectively. Data were obtained from 559 sequenced accessions (121 wild soybeans, 207 landraces, and 231 improved cultivars).

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