Transcriptome analysis reveals candidate genes for different root types of alfalfa (Medicago sativa) after water stress induced by PEG-6000

We aimed to gain insight into the response mechanism of alfalfa (Medicago sativa) to drought stress by recognizing and analyzing drought-responsive genes in the roots of different root types of alfalfa. The rhizomatous-rooted M. sativa cv.‘Qingshui’ (QS), tap-rooted M. sativa cv.‘Longdong’ (LD), and creeping-rooted M. varia cv. ‘Gongnong No. 4’ (GN) were used to analyze the transcriptome information and physiological characteristics of the root systems of the cultivars under simulated drought stress using PEG-6000. It was found that aridity caused a significant increase in the content of osmotic stress substances and antioxidant enzyme activity. The content of malondialdehyde (MDA) in QS was lower than that in LD and GN under moisture stress, indicating a stronger accumulation capacity of osmotic regulatory substances. Based on sequencing results, 14,475, 9336, and 9243 upregulated DEGs from QS, LD, and GN were annotated into 26, 29, and 28 transcription factor families, respectively. QS showed more DEGs than LD and GN. KEGG enrichment analysis identified that DEGs were significantly enriched in metabolic pathways such as amino acid biosynthesis, phenylpropanoid biosynthesis, plant hormone signaling transduction, and MAPK pathways. This suggests a strong correlation between these pathways and drought stress. The results also show that genes associated with ABA hormone signaling (MS. gene93372, MS. gene072046, and MS. gene012975) are crucial for plant’s adaptation to drought stress. These genes, such as serine/threonine protein kinases and abscisic acid receptors, play a crucial role in plant hormone signaling and MAPK pathways. They could serve as potential candidate genes for drought resistance research in alfalfa, providing a molecular foundation for studying drought resistance.