Genetic diversity of Citrullus colocynthis populations using phytochemical analysis and SCoT marker variations

Genet Resour Crop Evol https://doi.org/10.1007/s10722-023-01783-6 RESEARCH ARTICLE Genetic diversity of Citrullus colocynthis populations using phytochemical analysis and SCoT marker variations Abdelfattah Badr · Hoida Zaki Received: 4 August 2023 / Accepted: 16 October 2023 © The Author(s) 2023 Abstract Citrullus colocynthis L. Schard (bitter melon) is a drought-resistant medicinal plant growing in Egypt and many other countries in the arid environments of the World. In Egypt, it is abundant in several locations in Egypt’s Eastern Desert, extending from the Nile River eastward to the Red Sea, particularly in the Kosseir region on the Red Sea coast. It has a wide range of applications in traditional medicine due to its anti-inflammatory, antibacterial, antioxidant, and anesthetic features. In this study, the genetic diversity was explored using chemical analysis of the secondary metabolites in seed extract in 15 populations from different sites in the Eastern Desert of Egypt to correlate the chemical variation with genetic differences among populations as revealed by DNA fingerprinting using the Start Codon Targeted (SCoT) markers. A total of 81 chemical compounds were identified from the 15 populations. Retention time, peak area percentage, molecular weight, and Supplementary Information The online version contains supplementary material available at https://doi. org/10.1007/s10722-023-01783-6. A. Badr Botany and Microbiology Department, Faculty of Science, Helwan University, Cairo 11790, Egypt e-mail: H. Zaki (*) Botany and Microbiology Department, Faculty of Science, South Valley University, Qena 83523, Egypt e-mail: chemical formula were determined for each compound. Ten SCoT primers produced 137 bands in the 15 populations of these; 85 bands were polymorphic, 50 were monomorphic, and two bands were unique to a single population. Populations located in the southern part of the Eastern Desert have similar levels of phytochemical and genetic diversity and are differentiated from populations in the northern part. On the other hand, populations in the middle part show a small resemblance to other populations in the north and south, indicating an impact of the ecology on the genetic differentiation and the chemical composition of the secondary metabolites in C. colocynthis. Keywords Citrullus colocynthis · Genetic diversity · SCoT marker · GC–MS analysis Introduction Colocynth, bitter apple, bitter gourd, and bitter melon are all names given to the fruit of the Citrullus colocynthis (L.) Schrader, a wild perennial, plant of the family Cucurbitaceae. It is a perennial (rarely annual) prostrate plant that has a bitter taste and potential for poisoning (Heuzé et al. 2021). Citrullus colocynthis is predominantly a drought-resistant vine that has spread widely across the Sahara-Arabian Peninsula of Africa and the Mediterranean Basin (Dane et al. 2007; Li et al. 2022). It is abundant in Egypt, particularly in the Kosseir region on the Red Sea coast Vol.: (0123456789) 13 Genet Resour Crop Evol (Boulos 2002), but it is also plentiful in several locations in Egypt’s Eastern Desert (Sheded et al. 2006; Badr et al. 2018). The fruit of C. colocynthis has a wide range of applications in traditional medicine across several nations (Heydari et al. 2016; Torkey et al. 2009) due to its anti-inflammatory, antibacterial, antioxidant, and anesthetic qualities (Kumar et al. 2008; Rizvi et al. 2018; Hameed et al. 2020). In Egypt, notable variations exist in the morphological quantitative characteristics of C. colocynthis populations in the Eastern Desert of Egypt. These variants include a tall vine length (up to 195 cm), the presence of compound hairs, and a high hair density. The investigation of fruit rind color variation, including rind color pattern, as well as the examination of seed color and size, has garnered significant attention in the study conducted by Badr et al. (2018). However, little variations in qualitative characteristics between populations, specifically in terms of leaf hair density, leaf hair type, rind color pattern, main rind color, and rind stripe color, were observed. The observed variations in fruit and seed features among populations of C. colocynthis highlight the significance of these qualities in contributing to the diversity of this species (Badr et al. 2018). The phytochemical analysis of the C. colocynthis root, leaf, flower, and fruit independently revealed the presence of alkaloids, carbohydrates, and flavonoids and the absence of tannins, gums, and mucilage. The seeds contain large levels of various fatty acids, they include myristic, palmitic, stearic, oleic, linoleic, and linolenic (Uma and Sekar 2014). Gurudeeban et al. (2010) provided a review of the chemical makeup and the therapeutic possibilities of C. colocynthis. More detailed results were published by Kamalakar et al. (2015) and Bourhia et al. (2020, 2021) that the seed oil of C. colocynthis is edible and has a similar composition to soybean oil and the seeds have a high proportion of unsaturated fatty acids (79.80%), primarily linoleic acid and oleic acid, a low percentage of saturated fatty acids (20.20%), and a very low n-3 poly-unsaturated fatty acids level (0.5%). The seed oil potential as a biodiesel feedstock was investigated by Giwa et al. (2010), and physicochemical characterization of the seed oil showed that seed fat is made up of 10.4% palmitic acid, 6.5% stearic acid, 1.70% arachidic acid, 11.7% oleic acid, 58.5% linoleic acid, and 1.6% linolenic acid (Giwa et al. 2010; Riaz et al. Vol:. (1234567890) 13 2015). Fereshtian et al. (2017) studied phytochemical traits to evaluate the genetic diversity of some C. colocynthis accessions from Iran. Genetic diversity in plant species provides vital information on their capacity to cope with different environmental stresses (Badr 2008) because domestication and the evolution of crops reduce the diversity of crop species (Begna 2021). Increased genetic variation improves the chances of effective plant selection, making it an essential component in utilization by evaluating its scope and range (Begna 2021; Kardos et al. 2021). Different approaches have been used to determine genetic polymorphism in many plant species. Recently, estimating genetic diversity and deciphering genetic composition have both benefited greatly from the use of molecular markers, identifying the genes implicated in critical growth mechanisms and conserving genetic variation (Badr and El-Shazly 2012; El-Shazly et al. 2020). To better estimate genetic diversity, molecular techniques have been used in tandem with morphological variations. In medicinal and aromatic plants, the chemical composition assessment of secondary metabolites provide an additional source of important information (Badr et al. 2021; Talebi et al. 2021). Both the distribution of genes between populations and the range of possible variations within a species in addition life history criteri (...truncated)