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Pigeon pea (Cajanus cajan L.) is one of the important legume crop that contributes significantly to the nutritional stability and economy of billions of people in most developing nations (Sharma et al., 2020). Like other legumes, pigeon pea often offers more balanced and nutrient-dense calories and proteins (20%–22%) than cereals, making them essential in terms of food security. It is the sixth most significant legume food crop in the world, with a cultivation area of about 5 million hectares (ha) (Varshney et al., 2012). However, environmental stressors pose a persistent threat to the pigeon pea crop’s production, yield, and quality. Among them waterlogging is one of the most harmful stress in pigeon pea which results in huge yield and economic losses around the world (Sultana et al., 2013; Tyagi et al., 2017; Tyagi et al., 2022). Overall, waterlogging has been observed to cause an annual loss of about .28–1.1 million tons per hectare which reduces production by 25%–30% in pigeon pea (Sultana, 2010; ICRISAT, 2011; Bansal and Srivastava, 2012). Waterlogging affects pigeon pea at all growth stages, but is more severe during the seedling and vegetative phases, thereby showing wilting, senescence and chlorosis (Bansal and Srivastava, 2012). Additionally, waterlogging also makes pigeon pea plants more susceptible to fungal diseases like Fusarium wilt and Phytophthora blight which results in significant yield losses (Yohan et al., 2017). Generally, pigeon pea is grown in lowinput, risk-prone marginal environments and low-lying places that are more susceptible to waterlogging (Varshney et al., 2012; Duhan and Sheokand 2020). During waterlogging, the inhibition of aerobic respiration hinders growth and a variety of developmental processes, including seed germination, vegetative growth, and subsequent reproductive growth (Pan et al., 2021). Additionally, in waterlogged soils, ethylene and carbon dioxide levels increase dramatically in the root area which in turn alters the functions of soil microbiome that leads to an intense de-nitrification and accumulation of ammonium and polyphenolic compounds (Arduini et al., 2019). Also, it restricts the availability of nutrients like nitrogen (N) and sulphur (S) or changes them into a form that plants cannot absorb. It also changes ion homeostasis zinc (Zn), phosphorous (P), manganese (Mn), and iron (Fe), which can reach lethal levels to plants (Arduini et al., 2019). The most common effect of waterlogging stress is oxygen deficiency (hypoxia) and ethylene accumulation in plants, which can restrict root growth and root permeability, both of which lead to cell death (Sasidharan et al., 2018; Pan et al., 2021). However, plants use their multifaceted defense system in response to waterlogging stress by regulating their morphological, biochemical and molecular traits. For example, the formation of aerenchyma in roots is one of the main traits in plants that confer waterlogging tolerance (Luan et al., 2018). At the physiological and biochemical levels, OPEN ACCESS