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Article

GWAS-Based Prediction of Genes Regulating Trehalose and Sucrose in Potato Tubers

by
Ke Deng
1,†,
Yuting Bao
1,†,
Minghao Xu
1,
Chunna Lv
1,
Long Zhao
1,
Jian Wang
1,2,* and
Fang Wang
1,2,*
1
Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China
2
Key Laboratory of Qinghai-Tibet Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Horticulturae 2025, 11(9), 1033; https://doi.org/10.3390/horticulturae11091033
Submission received: 9 July 2025 / Revised: 25 August 2025 / Accepted: 30 August 2025 / Published: 1 September 2025
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
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Abstract

As the fourth-largest global food crop, the quality and functional characteristics of processed potato products are closely linked to endogenous sugar metabolism in tubers, with the trehalose–sucrose metabolism playing a key role in processing adaptability. This study analyzed 333 accessions from a tetraploid potato natural population. The trehalose and sucrose content of potato tubers at harvest was quantified using the high-performance liquid chromatography (HPLC) method. Combined with whole-genome resequencing, a genome-wide association study (GWAS) was conducted to map regulatory loci and identify candidate genes. The results showed that relative trehalose content in tubers was 20.38–24.78, while relative sucrose content was 10.32–19.50. Frequency histograms for both sugars exhibited normal distributions characteristic of quantitative traits, and a positive correlation was observed between them. GWAS for trehalose identified 111 significant SNP loci, mainly on chromosomes 10 and 12, leading to the identification of 88 candidate genes. Kyoto encyclopedia of genes and genomes analysis (KEGG) revealed that trehalose-related genes were primarily involved in pathways such as ABC transporters, tricarboxylic acid (TCA) cycle, and cysteine and methionine metabolism. Candidate genes potentially regulating tuber trehalose content included GH10, GH28, GH127, UXS, UGT, PMEI, and MYB108. For sucrose, GWAS identified 279 significant SNP loci, mainly on chromosomes 5, 6, and 12, resulting in 111 candidate genes. KEGG enrichment analysis showed that sucrose-related genes were enriched in pathways including starch and sucrose metabolism, cyanoamino acid metabolism, and phenylpropanoid biosynthesis. Candidate genes potentially regulating tuber sucrose content included GH17, GH31,GH47, GH9A4, SPP1, BGLU12, GSA1, TPS8, cwINV4, HXK, UST, MYB5, MYB14, and WRKY11. Therefore, this study provides marker loci for trehalose and sucrose metabolism research, aiming to clarify their regulatory mechanisms and support potato variety improvement and superior germplasm development.

1. Introduction

Potato (Solanum tuberosum L.), a globally important food crop and industrial raw material, has garnered significant attention due to the nutrient-rich and functionally diverse nature of its processed products [1,2]. According to the FAOSTAT, global potato production in 2023 reached 383 million metric tons. During the same year, global imports and exports of frozen potatoes totaled 9.41 million metric tons and 9.60 million metric tons, respectively (http://www.fao.org/faostat/es/#data (accessed on 1 August 2025)). Traditional products like potato chips and French fries continue to dominate the market [3]. Their quality largely depends on the tubers’ biochemical properties, with the metabolic dynamics of sucrose and trehalose being particularly critical. Sucrose is the primary form of photosynthetic product transportation in potatoes, supplying energy and carbon skeletons for tuber bulking [4,5]. Its accumulation influences tuber formation and starch synthesis [4,5]. During high-temperature frying, sucrose participates in the Maillard reaction, producing harmful substances like acrylamide, which affects the color and flavor of chips and fries [6,7]. Elevated sucrose levels intensify this issue [8]. Trehalose, a non-reducing disaccharide, helps potatoes withstand stresses such as drought and cold by stabilizing cell membranes and protein structures [9,10]. Furthermore, its moisture retention and thermal stability properties can inhibit browning in processed potato products and extend shelf life [11,12]. Post-harvest storage at low temperatures (4–8 °C) significantly increases sucrose and trehalose accumulation due to stress-induced metabolism, complicating processing [4,13].
Trehalose consists of two glucose molecules linked by an α,α-1,1-glycosidic bond and has 45% of the sweetness of sucrose [14]. In plants, it mainly functions as an osmoprotectant and signaling molecule involved in stress responses and the regulation of growth and development. Exogenous application of trehalose has been shown to mitigate various abiotic stresses, including drought, heat, heavy metals, and salinity [15,16,17]. Trehalose has been detected at low concentrations in many angiosperms, such as rice and tobacco [18,19]. However, these low levels are not solely due to its functional role but result from tight regulation of trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) gene expression and enzyme activity [20]. Overexpression of OsTPS1 in rice increases trehalose and proline accumulation, induces stress-related genes, and enhances tolerance to low temperature, salinity, and drought [21]. The OsTPP1 gene is transiently upregulated under salt, osmotic, and abscisic acid (ABA) treatments, and more gradually under cold stress. Its overexpression confers salt and cold stress tolerance in rice [22]. Silencing tomato genes SlTPS3, SlTPS4, SlTPS5, SlTPS7, and SlTPP2 alters trehalose levels in plants infected or uninfected with Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000, indicating trehalose’s key role in pathogen defense [23]. Trehalose metabolism is also modulated by various transcription factors. For example, overexpression of peach PpSnRK1α enhances bZIP11 activity and modulates trehalose metabolism to protect plants from trehalose-induced damage [24]. Rice OsNAC23 increases Tre6P levels by repressing TPP1 and forms a feed-forward loop with SnRK1a, synergistically regulating carbon allocation to sink organs and boosting yield by 13–17% in elite rice varieties [25].
Despite these advances in other plants, the regulatory network of trehalose metabolism in potato remains poorly understood. Sucrose metabolism is regulated through multiple molecular mechanisms acting synergistically. At the transcriptional level, transcription factors such as MYB, bZIP, WRKY, NAC, and Dof regulate sucrose synthesis, degradation, and allocation by activating or repressing key genes like SPS (sucrose phosphate synthase), SUS (sucrose synthase), and INV (invertase) [26]. Additionally, several enzymes—such as sucrose transporters (SUTs), hexokinase (HXK), and TPP—also participate directly or indirectly in this regulation. In pear (Pyrus ussuriensis), PuMYB12 promotes sucrose accumulation by enhancing PuSUT4-like expression, while the bHLH family member PuPRE6 inhibits it [27]. The bZIP transcription factor plays dual roles in stress resistance and development: its C-/S1-bZIP-SnRK1 complex regulates carbohydrate and amino acid metabolism, mediating salt stress responses independently of ABA [28]. It also regulates key physiological processes like seed maturation, root development, and flowering [29]. Research found that tomato (Solanum lycopersicum) SlbZIP1 increases fruit sugar content through sucrose-induced translational repression (SIRT) without stunting growth [30]. Maize ZmbZIP22 reportedly affects the endosperm’s physiology in maize and rice seeds, altering starch biosynthesis gene expression [31]. Watermelon ClNAC68 enhances sucrose accumulation during fruit ripening by binding to the invertase (CINV) promoter and suppressing its expression [32]. In cotton, GhDOFD45 activates GhSWEET10, promoting sucrose accumulation in seeds [33]. In pitaya (dragon fruit), HpWRKY3 boosts sugar accumulation during ripening by activating sucrose metabolism genes (HpINV2 and HpSuSy1) [34]. In potato, the R2R3-MYB transcription factor StAN1 regulates flavonol biosynthesis and sucrose metabolism by targeting promoters of sucrose degradation genes like SUSY1 and INV1 [35]. Although transcriptional regulation plays a vital role in sucrose metabolism, the regulatory mechanisms governing sucrose synthesis and degradation in potato tubers are still not fully understood.
This study measures trehalose and sucrose content in tubers from a natural population of 333 tetraploid potato accessions. Using genome-wide association analysis (GWAS), we aim to identify genetic variants associated with trehalose and sucrose levels in potato tubers and pinpoint candidate genes involved in their metabolism. Therefore, this study provides a reference for breeding programs targeting trehalose and sucrose contents in potato tubers and provides genetic resources for exploring their underlying regulatory mechanisms.

2. Materials and Methods

2.1. Planting Accessions and Field Experiment Design

The tetraploid potato natural population materials used in this study were obtained from the Qinghai Academy of Agricultural and Forestry Sciences, China. A total of 333 accessions were arranged in a completely randomized block design with three replicates under standard field management. In 2023, tubers were planted at the Highland Potato Experimental Station (36°68′ N, 101°26′ E) in Huangyuan County, Qinghai Province, China. This site features a cold climate suitable for potato growth and characteristic maintenance. At physiological maturity, one uniformly sized, mature, and disease-free tuber was selected from each of three different plants per replicate. Tubers were thoroughly scrubbed under running tap water to remove soil and debris. After cleaning, the surfaces were dried with clean absorbent paper and placed in a well-ventilated area until completely dry. Tubers were peeled, cut into chunks, and thoroughly mixed. A 50–100 g subsample of the homogenate was immediately flash-frozen in liquid nitrogen. Frozen samples were lyophilized in a freeze dryer (Christ Delta 1-24/2-24 LSCplus, Osterode am Harz, Germany) at −40 °C for 7 days (pressure: 0.100 mbar) and subsequently ground to a dry powder.

2.2. Determination of Trehalose and Sucrose Content in Potato Tubers

Freeze-dried samples from 333 tuber samples were ground into powder, and 0.05–0.1 g of sample powder was suspended with 70% methanol water solution in a ratio of 1:10,000. Untargeted metabolomic profiling was performed using a high-performance liquid chromatography (HPLC)-based method coupled with triple quadrupole mass spectrometry (LC-ESI-QQQ-MS/MS; LCMS-8060, Shimadzu, Kyoto, Japan) operating in scheduled multiple reaction monitoring (MRM) mode [36,37,38]. The HPLC conditions were as follows: column: Shim-pack GIS C18 (1.9 µm, 2.1 × 100 mm); mobile phase: A: water containing 0.04% acetic acid; B: acetonitrile containing 0.04% acetic acid; flow rate: 0.4 mL/min; column temperature: 40 °C; injection volume: 2 µL. The electrospray ionization (ESI) source parameters were as follows: nebulizing gas flow: 3 L/min; heating gas flow: 10 L/min; interface temperature: 500 °C; desolvation line (DL) temperature: 250 °C; heat block temperature: 400 °C; drying gas flow: 10 L/min. Data acquisition and processing were conducted using LabSolutions software (version 5.91) to quantify the relative contents of trehalose and sucrose (Table S1), an approach that has been applied for GWAS analysis in crops such as rice and cassava [39,40,41].

2.3. GWAS of Potato Tuber Trehalose and Sucrose

In a previous study, we performed whole-genome resequencing of 769 accessions of tetraploid potato with an average sequencing depth of ~10×. Following filtering, we obtained 19,170,130 high-quality SNPs [42]. Detailed information on the population structure of this tetraploid potato panel is provided in our earlier publication [43]. In this study, genome-wide association studies (GWASs) for tuber trehalose and sucrose content were conducted using this previously published resequencing data [42]. For single-locus association analysis, we applied the compressed mixed linear model (CMLM) incorporating principal components and a kinship matrix (PCA + K) using the R/GAPIT software package (version 3.1.0). Genotype data were extracted from genomic regions spanning 60 kb upstream and downstream of significant SNP loci for haplotype analysis. Allelic effect analysis was subsequently performed by integrating phenotypic and genotypic data. Manhattan plots were generated using the R package CMplot, and significant SNP loci were identified using a significance threshold of p < 10−5.

2.4. Candidate Gene Mining and Enrichment Analysis

Significant SNP loci were used to define candidate intervals based on the population LD value (60 kb) [43], with intervals extending to flanking linkage regions. Based on the Q9 reference genome [44], genes were considered candidates if their entire genomic region, or more than 90% of it, overlapped with a candidate interval. Through prior functional annotations, further screening and verification were conducted to determine the final candidate genes. KOBAS 3.0 (http://bioinfo.org/kobas/ (accessed on 17 July 2025)) was used to perform KEGG enrichment analysis (using the Hypergeometric test and Fisher’s exact test) on candidate genes to identify relevant metabolic pathways. Transcription factors (TFs) among the candidate genes were identified using the PlantTFDB v5.0 database website (http://planttfdb.gao-lab.org/ (accessed on 17 July 2025)). This analysis helped elucidate the genetic regulation of trehalose and sucrose accumulation in potato tubers and identify superior candidate genes.

3. Results

3.1. Phenotypic Analysis of Trehalose and Sucrose

The trehalose and sucrose contents in potato tubers are influenced by variety, developmental stage, harvest maturity, storage duration, and environmental conditions [45,46]. To investigate the genetic basis of trehalose and sucrose accumulation, we measured their levels in tubers from 333 tetraploid potato accessions at harvest using high-performance liquid chromatography (HPLC). The relative tuber trehalose content ranged from 20.38 to 24.78, while the sucrose content ranged from 10.32 to 19.50 (Table S1). Frequency histograms of both traits followed a normal distribution, consistent with quantitative trait characteristics and suitable for further analysis (Figure 1A,B). A positive correlation was observed between tuber trehalose and sucrose content (Figure 1C), suggesting that trehalose levels increase with sucrose levels.

3.2. Genome-Wide Association Analysis of Trehalose and Sucrose

Using a Perl script, we converted the high-quality filtered genotype file to Hapmap format. We then performed a GWAS for tuber trehalose content using the GAPIT software with a mixed linear model (Figure 2A) and visualized the results with CMplot-generated Manhattan plots. A total of 111 significant SNP markers were identified (Table S2), with 99 (89.19%) located in haplotypes A2, A3, and A4 on chromosome 12 (Figure 2B).
A separate GWAS for tuber sucrose content (Figure 2C) identified 279 significant SNP markers (Table S3), of which 153 (54.85%) were located in the A3 haplotype on chromosome 5, the A3 haplotype on chromosome 6, and the A4 haplotype on chromosome 12 (Figure 2D).

3.3. Analysis of Haplotypes and Allelic Variation Effects of Trehalose

To identify key molecular markers associated with trehalose content, four significant SNPs were detected in haplotypes A2, A3, and A4 on chromosome 12. We analyzed LD in the associated region using LD heatmaps and performed SNP genotyping. The four SNPs identified were Chr12A2:35849480, Chr12A3:55777825, Chr12A4:46535012, and Chr12A4:46568448 (Figure 3A–C). Joint genotype–phenotype analysis, visualized with box plots, revealed the following: (1) At Chr12A2:35849480, the AA genotype had significantly higher trehalose content than GG/GA (Figure 3D). (2) At Chr12A3:55777825, the GG genotype showed higher trehalose content than TT/TG (Figure 3E). (3) At Chr12A4:46535012, the GG genotype exceeded AA/AG in trehalose content (Figure 3F). (4) At Chr12A4:46568448, the AA genotype surpassed TT/TA in trehalose content (Figure 3G).

3.4. Analysis of Haplotypes and Allelic Variation Effects of Sucrose

To further identify molecular markers significantly associated with sucrose content, four key SNP loci were detected on haplotype A3 of chromosome 5, haplotype A3 of chromosome 6, and haplotype A4 of chromosome 12. To evaluate LD within these associated regions, LD heatmaps were generated, and SNP genotyping of the significant loci was performed. The four SNPs identified were as follows: Chr05A3:41816911, Chr05A3:41820224, Chr06A3:24891477, and Chr12A4:44643246. Joint genotype–phenotype analysis using box plots revealed the following: (1) At Chr05A3:41816911, the GG/GA genotypes showed significantly higher sucrose content than the AA genotype (Figure 4D). (2) At Chr05A3:41820224, the AA/AT genotypes showed significantly higher sucrose content than the TT genotype (Figure 4E). (3) At Chr06A3:24891477, the AA/GA genotypes showed significantly higher sucrose content than the GG genotype (Figure 4F). (4) At Chr12A4:44643246, the GG/GA genotypes had significantly higher sucrose levels than AA (Figure 4G).

3.5. Candidate Gene Analysis of Trehalose and Sucrose

Candidate intervals were determined based on population LD and the LD structure of associated regions. Genes were defined as candidate genes if their entire region, or over 90% of it, was located within a candidate interval. A total of 88 candidate genes for trehalose were identified, including enzymes related to stress response and growth regulation (e.g., PP2C, glutathione S-transferase, NB-LRR, metal tolerance protein) and transcription factors (e.g., MYB108, ABC transporter). Among these, seven genes were highlighted as potentially regulating tuber trehalose content: Glycosyl hydrolase 10 (GH10), Glycosyl hydrolases 28 (GH28), Glycosyl hydrolases 127 (GH 127), UDP-glucuronic acid decarboxylase (UXS), UDP-glycosyltransferase (UGT), plant invertase/pectin methylesterase inhibitor (PMEI), and MYB108 (Table S4). KEGG enrichment analysis of trehalose-related genes revealed significant involvement in pathways such as ABC transporters, the tricarboxylic acid (TCA) cycle, and cysteine and methionine metabolism (Figure 5A).
Similarly, 111 candidate genes were identified through sucrose association analysis. These include potential regulators of tuber sucrose content such as O-glycosyl hydrolases family 17 protein (GH17), glycosyl hydrolases family 31 protein (GH31), glycosyl hydrolase 47 (GH47), glycosyl hydrolase 9A4 (GH9A4), sucrose-phosphatase 1 (SPP1), beta-glucosidase 12 (BGLU12), UDP-glucosyltransferase (GSA1), Trehalose-6-phosphate synthase 8 (TPS8), Cell Wall INvertase 4 (cwINV4), hexokinase (HXK), UDP-sugar transporter (UST), MYB5, MYB14, and WRKY11 (Table S5). KEGG enrichment analysis of sucrose-related genes showed significant enrichment in pathways including starch and sucrose metabolism, cyanoamino acid metabolism, and phenylpropanoid biosynthesis (Figure 5B).

4. Discussion

The quality and functional properties of processed potato products are closely linked to endogenous sugar metabolism in tubers. Among these, the dynamic balance of the sucrose–trehalose metabolic network plays a key role in potato growth, development, and industrial processing by regulating mechanisms such as carbon allocation and stress-induced browning inhibition [47,48,49,50]. The relative trehalose and sucrose contents in potato tubers displayed normal distributions, consistent with polygenic quantitative traits governed by multiple genetic and environmental factors [46,51]. Notably, a significant positive correlation was observed between trehalose and sucrose levels, indicating that elevated sucrose concentrations are associated with increased trehalose accumulation. This relationship aligns with the established role of trehalose-6-phosphate (T6P) as a sucrose-signaling metabolite. Synthesized from UDP-glucose and glucose-6-phosphate, T6P functions both as a biosynthetic intermediate and a regulator of sucrose utilization [47]. Consequently, sucrose accumulation may drive trehalose pathway flux to modulate carbon partitioning—a feedback mechanism critical for maintaining osmotic homeostasis during tuber development and stress responses [52].
GWAS analysis identified seven candidate genes potentially regulating tuber trehalose content: GH10, GH28, GH127, UXS, UGT, PMEI, and MYB108. These genes are involved in sugar metabolism and plant stress responses during various developmental stages. These candidate genes are involved not only in carbohydrate metabolism, but also in plant growth, development, and defense mechanisms. GHs hydrolyze glycosidic bonds in sugar-containing compounds to generate mono- and oligosaccharides. GH10 exhibits endo-β-1,4-xylanase activity and catalyzes hemicellulose breakdown, while GH28 specifically hydrolyzes pectin [53,54,55,56]. UDP-glucose (UDP-Glc), catalyzed by UDP-glucose dehydrogenase (UGD), is converted into UDP-galacturonate (UDP-GalA) via galactoate acid transferase (GATL). UDP-GalA can be polymerized into pectin by α-1,4-Galactodate acid transferase (GAUT) and pectin acetylesterase (PAE), or decarboxylated by UXS to produce UDP-xylose (UDP-Xyl) and UDP-apiose (UDP-Api) [57,58,59]. Glycosylated volatiles represent hidden aroma precursors that influence fruit flavor profiles and participate in plant defense responses [60,61,62]. These compounds are catalyzed by uridine diphosphate (UDP)-glycosyltransferases (UGTs), which transfer sugar moieties to volatile aglycones. In grapes, UGT85A26 and UGT85A27 expression serves as the primary regulator of glycosylated volatile content [63]. PMEI affects the pectin structure and cell wall integrity of plants, participates in the growth process of pollen tubes, and enhances the mechanical resistance of seeds [64]. GhMYB212 in cotton regulates sucrose influx into fibers by activating the sugar transporter gene GhSWEET12 [65], while apple MdMYB39L responds to exogenous sorbitol by promoting hexose uptake [66]. However, further studies are needed to identify upstream regulators of these sugar-related genes and clarify their specific roles in potato tuber development to enhance our understanding of sugar metabolism regulation.
In the association analysis of sucrose, numerous candidate genes potentially regulating tuber sucrose content were identified, including GH17, GH31, GH47, GH9A4, SPP1, BGLU12, GSA1, TPS8, cwINV4, HXK, UST, MYB5, MYB14, and WRKY11. These candidate genes are primarily involved in glucose metabolism and transport (e.g., GH17, GH31, GH9A4, SPP, cwINV4, HXK), antioxidant activity and stress response (e.g., BGLU12, GSA1, TPS), and the transcriptional regulation of glucose metabolism and secondary metabolite synthesis (e.g., MYB, WRKY transcription factors). Through diverse mechanisms, they participate in plant growth and development, stress resistance, and metabolic regulation. Four GH family members were identified in particular. GH17 functions as a β-1,3-endoglucanase that targets the extracellular polysaccharide matrix of plant fungi [67]. GH31 modifies glycosidic bonds in N-glycans; its dysfunction impairs the elongation factor EF-Tu receptor (EFR), which recognizes bacteria, thereby blocking innate immune signaling and weakening plant defense [68,69]. Sucrose-phosphate phosphatase (SPP) is the final enzyme in the sucrose biosynthesis pathway, producing sucrose through the irreversible hydrolysis of sucrose phosphate [70]. Crocus sativus CsBGlu12 hydrolyzes flavonol β-glucosides and β-glycosidic bonds in cello-oligosaccharides, promoting antioxidant flavonol accumulation. Its transient overexpression in Nicotiana benthamiana enhances tolerance to abiotic stress by reducing reactive oxygen species (ROS) accumulation [71]. GSA1 encodes a UDP-glucosyltransferase with glucosyltransferase activity toward flavonoids and monolignols; its overexpression increases flavonoid and anthocyanin levels under stress, enhancing stress resistance in rice [72]. TPS, a key enzyme in trehalose biosynthesis, plays a crucial role in diverse biological processes such as stress responses and metabolic regulation [73,74]. In cassava, MeCWINV3 is expressed in vascular bundles and regulated by circadian rhythms; its overexpression reduces sugar transport from leaves to storage roots, delaying storage root development [75]. HXK regulates sucrose metabolism by catalyzing the phosphorylation of glucose to glucose-6-phosphate. In Arabidopsis, the ethylene-responsive transcription factor AtEIN3 directly binds the sucrose transporter gene AtSUC2 promoter, repressing its expression. AtHXK1 alleviates this repression by destabilizing AtEIN3, forming the AtHXK1–AtEIN3–AtSUC2 module that controls sucrose loading from leaves to sink organs such as roots [76,77]. The sucrose synthesis gene FaSPS3 is co-activated by FaMYB10 and FabHLH3 to promote sucrose accumulation, whereas jasmonic acid reduces sucrose levels by inducing FaMYB44.2, which suppresses FaSPS3 [78]. In apple, MdMYB39L is induced by sorbitol to regulate hexose metabolism [66], whereas MdMYB305 promotes sugar accumulation by binding promoters of sugar transport/metabolism genes (MdCWI1, MdVGT3, MdTMT2) and competes with MdMYB10 for MdbHLH33 binding to balance sugar and anthocyanin synthesis [79]. In papaya, WRKY3 enhances sugar accumulation by activating HpINV2 and HpSuSy1 [34]. In a bud sport variety of Nanguo pear, PuWRKY31 activates PuSWEET15 via its hyperacetylated promoter, significantly increasing its expression [80]. The sucrose regulatory pathway is critical for potato responses to abiotic stress and tuber development, highlighting its importance for cultivar breeding and storage optimization.

5. Conclusions

This study quantified relative trehalose and sucrose contents in tubers from 333 tetraploid potato germplasm accessions. GWAS of tuber trehalose identified 111 significant SNP markers, with 99 localized to chromosome 12. KEGG enrichment analysis revealed that candidate sucrose-related genes are primarily associated with starch and sucrose metabolic pathways. Within these pathways, SPP, HXK, and SPS collectively form a complex regulatory network governing sucrose biosynthesis and metabolism, facilitating plant adaptation to diverse growth conditions and stress environments. These findings provide valuable genetic resources for elucidating tuber sugar accumulation mechanisms and advancing trait improvement in potato breeding. Future work should include functional validation of candidate genes through multi-omics integration and investigation of potential gene–gene interactions influencing sugar accumulation regulation.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/horticulturae11091033/s1, Table S1: Statistics on the relative sucrose and trehalose content in 333 potato tubers; Table S2: Significant SNP loci identified in the genome-wide association analysis of trehalose content; Table S3: Significant SNP loci identified in the genome-wide association analysis of sucrose content; Table S4: Candidate genes identified in the trehalose content association analysis; Table S5: Candidate genes identified in the sucrose content association analysis.

Author Contributions

Conceptualization, F.W.; methodology, K.D.; software, K.D. and Y.B.; validation, M.X. and C.L.; formal analysis, K.D.; investigation, Y.B.; data curation, K.D. and L.Z.; visualization, K.D., Y.B. and M.X.; project administration, F.W.; supervision, F.W. and J.W.; resources, F.W. and J.W.; writing—original draft preparation, K.D. and Y.B.; writing—review and editing, F.W. and J.W.; funding acquisition, F.W. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the General Program of Science and Technology Department of Qinghai Province (2023-ZJ-909M) and the Kunlun Talent High end the Innovation and Entrepreneurship Talent Leading Talent Project of Qinghai Province.

Data Availability Statement

The original contributions presented in this study are included in this article/Supplementary Materials and further inquiries can be directed to the corresponding authors.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Frequency distribution and correlation analysis of trehalose and sucrose content in potato tubers. (A) Frequency distribution of the relative trehalose content in potato tubers. (B) Frequency distribution of the relative sucrose content in potato tubers. (C) Correlation between the relative contents of trehalose and sucrose in potato tubers. The red lines represent the linear fit line, and the gray shading represents the 95% confidence and prediction bands.
Figure 1. Frequency distribution and correlation analysis of trehalose and sucrose content in potato tubers. (A) Frequency distribution of the relative trehalose content in potato tubers. (B) Frequency distribution of the relative sucrose content in potato tubers. (C) Correlation between the relative contents of trehalose and sucrose in potato tubers. The red lines represent the linear fit line, and the gray shading represents the 95% confidence and prediction bands.
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Figure 2. Manhattan plots of trehalose and sucrose content in potato tubers. (A) Manhattan plot showing SNP associations with the relative trehalose content across the potato genome. (B) Chromosomal locations of significant SNP loci identified in the trehalose association analysis. (C) Manhattan plot showing SNP associations with the relative sucrose content across the potato genome. (D) Chromosomal locations of significant SNP loci identified in the sucrose association analysis.
Figure 2. Manhattan plots of trehalose and sucrose content in potato tubers. (A) Manhattan plot showing SNP associations with the relative trehalose content across the potato genome. (B) Chromosomal locations of significant SNP loci identified in the trehalose association analysis. (C) Manhattan plot showing SNP associations with the relative sucrose content across the potato genome. (D) Chromosomal locations of significant SNP loci identified in the sucrose association analysis.
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Figure 3. LD heatmap of significant SNP loci for trehalose and analysis of allelic variation effects. (A–C) LD heatmaps of significant SNP loci for trehalose. The triangular boxes indicate LD blocks exceeding the defined threshold. (D–G) Box plots showing the allelic effects of trehalose-associated SNPs. * p < 0.05; ** p < 0.01; *** p < 0.001; NS, not significant.
Figure 3. LD heatmap of significant SNP loci for trehalose and analysis of allelic variation effects. (A–C) LD heatmaps of significant SNP loci for trehalose. The triangular boxes indicate LD blocks exceeding the defined threshold. (D–G) Box plots showing the allelic effects of trehalose-associated SNPs. * p < 0.05; ** p < 0.01; *** p < 0.001; NS, not significant.
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Figure 4. LD heatmap of significant SNP loci for sucrose and analysis of allelic variation effects. (A–C) LD heatmaps of significant SNP loci for sucrose. The triangular boxes indicate LD blocks exceeding the defined threshold. (D–G) Box plots showing the allelic effects of sucrose-associated SNPs. ** p < 0.01; *** p < 0.001; NS, not significant.
Figure 4. LD heatmap of significant SNP loci for sucrose and analysis of allelic variation effects. (A–C) LD heatmaps of significant SNP loci for sucrose. The triangular boxes indicate LD blocks exceeding the defined threshold. (D–G) Box plots showing the allelic effects of sucrose-associated SNPs. ** p < 0.01; *** p < 0.001; NS, not significant.
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Figure 5. KEGG enrichment analysis of the candidate genes controlling potato tuber trehalose (A) and sucrose (B) content.
Figure 5. KEGG enrichment analysis of the candidate genes controlling potato tuber trehalose (A) and sucrose (B) content.
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Deng, K.; Bao, Y.; Xu, M.; Lv, C.; Zhao, L.; Wang, J.; Wang, F. GWAS-Based Prediction of Genes Regulating Trehalose and Sucrose in Potato Tubers. Horticulturae 2025, 11, 1033. https://doi.org/10.3390/horticulturae11091033

AMA Style

Deng K, Bao Y, Xu M, Lv C, Zhao L, Wang J, Wang F. GWAS-Based Prediction of Genes Regulating Trehalose and Sucrose in Potato Tubers. Horticulturae. 2025; 11(9):1033. https://doi.org/10.3390/horticulturae11091033

Chicago/Turabian Style

Deng, Ke, Yuting Bao, Minghao Xu, Chunna Lv, Long Zhao, Jian Wang, and Fang Wang. 2025. "GWAS-Based Prediction of Genes Regulating Trehalose and Sucrose in Potato Tubers" Horticulturae 11, no. 9: 1033. https://doi.org/10.3390/horticulturae11091033

APA Style

Deng, K., Bao, Y., Xu, M., Lv, C., Zhao, L., Wang, J., & Wang, F. (2025). GWAS-Based Prediction of Genes Regulating Trehalose and Sucrose in Potato Tubers. Horticulturae, 11(9), 1033. https://doi.org/10.3390/horticulturae11091033

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