It is estimated that approximately 40-50% of the world's arable lands had become acidic by the year 2015, with nearly 60% of these acidic lands concentrated in tropical and subtropical regions, which are the primary grain-producing areas [
1]. Recent societal developments have exacerbated soil acidification due to anthropogenic factors such as the indiscriminate application of synthetic fertilizers, accumulation of organic matter, and disruptions in the natural nutrient cycling within the soil [
2]. Aluminum (Al), the third most abundant element in the Earth's crust, assumes a paramount role in this effect as it represents the most crucial and widespread factor limiting crop yields in acidic soils. In such acidic environments, aluminum dissolves into a toxic ionic form, notably Al
3+, originating from less harmful alumino-silicates or aluminum oxides [
3].
Numerous studies have indicated that primary symptoms of Al toxicity in plants include inhibited root growth and biomass, resulting in altered root morphology [
4,
5]. The root apical transition zone (TZ), located between the meristem and elongation zone, is particularly sensitive to Al exposure [5-9]. Another significant consequence of Al toxicity in plants is the rapid production and accumulation of reactive oxygen species (ROS), such as hydrogen peroxide (H
2O
2), superoxide (O
2·−), and hydroxyl (OH
·−) radicals. This ROS buildup leads to membrane lipid peroxidation, intensifying damage to the membrane system, protein degradation, and ultimately programmed cell death [5,10-12]. To counteract the excessive ROS accumulation induced by Al, plants activate an enzyme-mediated antioxidant defense system, which includes superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidases (POD) [
13,
14]. SOD plays a pivotal role in the oxidative stress response by catalyzing the dismutation of O2
·− into oxygen and H
2O
2, marking the initial step in this process, after which H
2O
2 is further converted into water through the catalytic actions of APX, CAT and POD [
15]. Furthermore, non-enzymatic antioxidants, including proline, ascorbate and glutathione, have been documented to effectively detoxify ROS and enhance Al tolerance [
16,
17], whose production and activation are integral components of the internal tolerance mechanism that plants employ to combat Al toxicity. In addition to this internal mechanism, plants also combat Al toxicity through intracellular Al chelation and the compartmentalization of Al-organic acid complexes within vacuoles [
5,
18,
19]. Beyond intracellular Alisolation, the Al exclusion mechanisms have received substantial attention in research. This mechanism involves the secretion of organic acids (OAs) as a well-characterized and extensively studied response to Al stress, including citrate, malate and oxalic acids, which serve to chelate Al and form non-toxic complexes [
1,
5]. Citrate and malate are the main types of OA secreted in many plant species. For example, crops such as rice [
20], maize [
21] and pea [
22] have been shown to release citrate in response to Al stress. Malate secretion has been identified in plants like rape [
23] and sorghum [
24]. Additionally, some species, including
Arabidopsis [
25], soybean [
26] and barley [
27], can secrete both citrate and malate when confronted with Al stress. In contrast, oxalic acid secretion has been detected in buckwheat and taro, with no known transporters identified for its secretion in response to Al toxicity. Numerous experiments have pinpointed the involvement of gene families such as
multidrug and toxic compound extrusion (
MATE), responsible for encoding citrate transporters on the plasma membrane, and Al-activated malate transporter (ALMT), an anion channel activated by Al
3+ on the plasma membrane, in facilitating the release of the respective OAs from plant root cells into the rhizosphere under Al stress [20-27]. However, transporters for oxalic acid secretion in response to Al toxicity remain unidentified. In certain Al-tolerant species like
Melastoma malabathricum and
Melaleuca cajuputi, besides exuding OAs for Al chelation, they also produce phenolic compounds in their roots that can chelate Al [
17]. Hence, the extent of Al tolerance varies among different plant species. Alfalfa (
Medicago sativa L.), a widely cultivated forage crop renowned for its nutritional value and high yield capacity, is highly sensitive to Al stress and has been associated with severely curtailing alfalfa productivity in acidic soils [
28]. Therefore, it is important to investigate alfalfa's response to Al stress and adopt appropriate strategies to enhance alfalfa yield.
Melatonin (N-acetyl-5-methoxytryptamine) is an indole derivative that was initially discovered in vascular plants in 1995 [
29]. It has been identified as a key regulator in various physiological processes, including the regulation of circadian rhythms [
30], promotion of seed germination, root development, enhancements in photosynthesis [
31], and the postponement of leaf and flower senescence [
32]. One of the most extensively characterized and studied roles of melatonin is its ability to enhance plant tolerance to various abiotic stresses. For instance, exogenous melatonin has been shown to improve salt tolerance in sunflower [
33] and rice [
34], play a crucial role in mitigating the toxicity of heavy metals, and alleviate cadmium toxicity in Chinese cabbage seedlings [
35], chromium toxicity in maize [
36], and copper toxicity in cucumber [
37]. Researchers have also explored the potential alleviating effects of melatonin on Al toxicity. Its application has been found to enhance resistance to Al toxicity by increasing the antioxidant defense system and promoting the exudation of Al-induced malate and citrate in soybean [
38] and wheat [
39]. Ren et al. [
40] demonstrated that melatonin mitigates Al-induced growth inhibition in maize [
41] by modulating carbon and nitrogen metabolism and regulating redox homeostasis. However, it remains poorly understood whether melatonin can alleviate the inhibitory effects of Al treatment on alfalfa, and the molecular mechanisms underlying how melatonin mitigates Al-induced growth inhibition in alfalfa have not been adequately elucidated.
In recent years, RNA sequencing (RNA-seq) has emerged as an indispensable tool for transcriptome analysis because it can generate a vast number of reads, providing a comprehensive overview of the transcriptomic landscape. Consequently, RNA sequencing has been applied to investigate Al response mechanisms in various plant species, including
Pinus massoniana [
42], sugarcane [
43], aspen [
44], peanut [
45] and alfalfa [
46], uncovering numerous physiological and metabolic processes involved in Al stress such as oxidative stress, organic acid exudation, defense against cell wall toxicity, and hormone signal transduction. Despite extensive information on Al stress responses, the specific mechanisms via which melatonin regulates Al toxicity in alfalfa remain unexplored. In our study, we integrate physiological and transcriptomic analyses to investigate the regulatory mechanisms through which melatonin might mitigate Al toxicity in alfalfa and provide valuable insights into a theoretical foundation for enhancing alfalfa yield in acidic soil conditions.