Comparative Transcriptomic Analysis in Roots of a Domestic Wheat Cultivar (Triticum aestivum L. cv. Keumkang) Seedlings Under Waterlogging Stress

Waterlogging stress is the most frequent abiotic factor affecting the agricultural productivity of major crop species. Profiling of the waterlogging response-related transcriptome of Keumkang, a domestic wheat cultivar cultivated mainly in South Korea, has not yet been conducted, despite advancing research in this field. Based on RNA sequencing (RNA-seq), we performed a comparative transcriptome analysis of cv. Keumkang seedlings subjected to waterlogging stress for up to 24 h. Comparative analysis revealed that waterlogging treatment increased the expression levels of most representative transcripts, including those of ethylene biosynthesis or activated signaling pathways, Ca²⁺ signaling pathways, and lignin biosynthetic pathways, suggesting that increased transcription of these genes under waterlogging conditions leads to the formation of aerenchyma and a radial oxygen loss barrier in wheat roots. Genes involved in anaerobic respiration and nitrate assimilation or reduction showed upregulated expression under waterlogging conditions compared to those under normal conditions, suggesting that waterlogging stress affects carbohydrate and nitrogen metabolism in wheat roots. The expression of randomly selected genes was evaluated using real-time quantitative PCR to validate the reliability of our RNA-seq results. The potential waterlogging stress-related transcripts identified herein are candidate genes for molecular studies of the adaptability of cv. Keumkang waterlogged stress.