Salt stress is a major abiotic factor that limits wheat production worldwide. However, this threat is increasing significantly because soil salinity affects approximately 20% of the irrigated agricultural land globally, leading to significant yield losses by impairing plant growth and photosynthetic efficiency. This study aimed to identify single-nucleotide polymorphisms (SNPs) associated with salt tolerance in wheat core collections during the heading stage under saline stress conditions. Chlorophyll content, a physiological indicator of salt tolerance at heading, and soil electrical conductivity (EC) were measured in 609 accessions and a Salt Tolerance Index (STI) was subsequently constructed. Genome-wide association studies (GWAS) were performed using a 35 K SNP chip to identify significant marker-trait associations. Three models (MLM, FarmCPU, and BLINK) were employed for the GWAS, with FarmCPU and BLINK demonstrating superior power over the MLM in controlling false positives. GWAS results revealed four significant SNPs (AX-94929101, AX- 94615611, AX-94510535, and AX-94411611) located on chromosomes 3D, 5D, and 7D. AX-94510535 exhibited significant phenotypic differences based on SNP genotype, suggesting its potential as a marker for STI. Furthermore, the identified candidate genes, TraesCS3D02G218100, TraesCS5D02G059500, and TraesCS5D02G175000, were implicated in biological processes such as DNA replication, cell death, and photosynthesis.

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• Integrated Genomic and Transcriptomic Analyses Reveal a Two-Tier Adaptive Strategy for Wheat Root Salt Tolerance: Constitutive Auxin Biosynthetic Capacity and Stress-Responsive Transcriptional Repression
  Kyung-Hee Kim, Ji Yu Jeong, Taekyeom Kim, Sang Yong Park, Byung-Moo Lee, Jae Yoon Kim
  Biology.2026; 15(12): 965.     CrossRef

Sybeans have been grown by plant breeding for decades. As soybeans have very limited genetic variation, it is difficult for soybean breeders to find new genetic resources for abiotic stressors. Recently, soybeans have been exposed to flooding stress from intensive summer rainfall owing to climate change. Glycine soja, a wild soybean, is known to have greater genetic variation and greater resistance to a variety of biotic and abiotic stresses than ordinary soybeans. In this study, high-throughput transcriptome analysis was performed using flood-treated Glycine soja. Differentially expressed genes (DEGs) were analyzed using reads mapped to reference sequences, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using selected DEGs. In addition, RT-qPCR analysis was performed to further analyze the expression of specific candidate genes. Several novel genes that could explain various mechanisms related to water stress were identified as related transcripts and adaptation mechanisms through cell wall expansion, alcoholic fermentation under anaerobic conditions, and structural changes. In addition, most of the isoflavonoid daidzein pathway genes exhibited upregulated expression under flooding stress. Interestingly, expression of the DIR (dirigent protein 1-like) gene, which is known to decrease in response to flooding stress in soybeans (Glycine max), was upregulated in Glycine soja. The expression of DIR revealed that DIR may play a key role in conferring flooding stress resistance in Glycine soja. This study provides useful information regarding the genes and comprehensive adaptation mechanisms related to flooding stress tolerance that can be utilized for cultivated soybeans through the Korean wild soybean.

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• De Novo Transcriptome Sequencing and Gene Expression Profiling of Vicia hirsuta (L.) Gray in Response to Flooding Stress
  Sang Yong Park, Heeyoun Hwang, Jae Yoon Kim
  Plant Molecular Biology Reporter.2026;[Epub]     CrossRef
• Understanding the molecular mechanisms of drought tolerance in wild soybean (Glycine soja) through multi-omics-based alternative splicing predictions
  Taekyeom Kim, Heeyoun Hwang, Geul Bang, Jungmin Ha, Yong-Jin Park, Jae Yoon Kim
  Environmental and Experimental Botany.2024; 225: 105872.     CrossRef

Globally, wheat (Triticum aestivum) is a major food crop for humans with no regional restrictions. However, it is still difficult for Korea to achieve self-sufficiency owing to production limitations. Moreover, food security is unstable owing to the unpredictable climate and unstable international economy. Pre-harvest sprouting (PHS) is among the factors that occurs frequently due to irregular climates, and damages the value of wheat. In this study, RNA-seq was conducted on PHS-treated samples (for Korean representative cultivar ‘keumgang’) and PHS-resistant mutation line ‘Jeonju 377ho’. Gene functional annotation and DEGs analysis were performed using 234,131,980 mapped reads. Associated transcripts were analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and were mainly used to search for genes associated with ATP synthesis and starch and sucrose metabolism related to seed germination and seed dormancy. Candidate DEGs were compressed through cluster set analysis, and gene expression was conducted to search for genes related to seed germination and dormancy to explain them in greater detail based on biological and chemical mechanisms.

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• Transcriptome Analysis for Flooding Stress-related Gene Identification inGlycine soja
  Tae Kyeom Kim, Sang Yong Park, Jae Yoon Kim
  Korean Journal of Breeding Science.2022; 54(4): 315.     CrossRef
• Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat (Triticum aestivum)
  Sang Yong Park, Woo Joo Jung, Geul Bang, Heeyoun Hwang, Jae Yoon Kim
  Plants.2022; 11(21): 2807.     CrossRef