Corresponding author: Mohamed A. Abdein, E-mail: abdeingene@yahoo.com, Tel. +201091448116 (Received 10/08/2022, accepted 20/09/2022) DOI: 10.21608/EJOH.2022.155513.1206 ©2022 National Information and Documentation Centre (NIDOC) T HE experiments were performed using (Nour, Fedela, Spinosa clementines, Kishu seedless, Balady, and Seedless mandarins) to determine the compatibility or incompatibility as related to the number of seeds per fruit and the genetic relation between them. For two consecutive seasons (2020 and 2021), the growth of the pollen tube in the styles following self-pollination has been analyzed using a fuorescence microscope to detect incompatibility properties. According to Nour and Fedela clementine cultivars are highly incompatible, while the other four cultivars are incompatible. After receiving pollen, Nour and Fedela clementines had very low pollen tubes that reached style. On the other hand, the highest rate was in the other four cultivars. The DNA of the six cultivars of mandarin and clementine investigated in this study was very similar. Balady mandarin and seedless mandarin appear to have very high similarities, while Fedela clementine and seedless mandarin appear to be very low. RAPD-PCR showed a specifc molecule related to incompatibility such as (A-18) RAPD primer, at MW 361 bp. linked to the incompatibility of Nour and Fedela clementine c.vs. Keywords: Self- incompatibility, Pollen tube growth, Fruit set, RAPD marker, Mandarins. RAPD Markers are Associated with Self-incompatibility Characteristics as Related to the Number of Seeds per Fruit of Some Mandarin and Clementine Cultivars Aly M. Ibrahim 1 , Mohamed A. Abdein 2* , Sayed. Y. Mohamed 1 , Maha M. Abdel-Salam 3 , EL-Sayed M. Qaoud 4 , Sahar A. M. Shamseldin 5 , Samah O. Osman 1 , Mahmoud F. Maklad 6 1 Horticulture Research Institute, ARC, Giza 12619, Egypt. 2 Biology Department, Faculty of Arts and Science, Northern Border University, Rafha 91911, Saudi Arabia. 3 Pomology Department, Faculty of Agriculture, Assiut University, Assiut, Egypt. 4 Horticultural Department, Faculty of Agriculture, Suez Canal University, 41522, Egypt. 4 Botany Department, Women’s College for Arts, Science and Education, Ain Shams University, Cairo 11566, Egypt. 5 Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt. Egypt. J. Hort. Vol. 49, No. 2 pp. 215-230 (2022) Egyptian Journal of Horticulture https://ejoh.journals.ekb.eg/ 17 Introduction Citrus self-incompatibility is important to fruit production trait because it results in seedless fruit (Mesejo, et al., 2014, Li, 1980, Yamamoto et al., 1995 and Yamamoto et al., 2006). Many factors can lead to seedless orange fruit, such as parthenocarpy (Talon et al., 1992 and Montalt., et al., 2021), male fertility (Hu et al., 2005, 2007, Zhang et al., 2012, Xiao et al., 2007, Yu et al., 2011), inconsistencies (Yamamoto et al., 2006, Distefano et al., 2009, Wang & Lü, 2009, Wang et al., 2009, Yamasaki, et al., 2009, Ngo et al., 2010) and maturity of pollen during fruit development (Wen & Cai, 2000). Seedless is de- sirable economic features in citrus fruit markets but as seedless seeds eliminate seed shortages, it makes use and processing faster and easier. Citrus growers around the world are committed to the development of seedless fruit varieties. If not, the incompatibility itself causes pollen resistance and inhibits seed growth. It is known