Fingerprinting of some Egyptian rice genotypes using Intron-exon Splice Junctions (ISJ) markers

DNA fingerprinting has become an important tool for diversity assessment and varietal identification in plant breeding programs. Semi- random PCR primers targeting intron-exon splice junctions (ISJ) were used to evaluate the potential of these markers in identification and classification of rice genotypes. A total of 12 ISJ primers were used for screening fourteen Egyptian rice genotypes, including six Japonica, four Indica and four Indica/Japonica rice genotypes. A total of 117 amplified fragments were generated among which 76 fragments were polymorphic revealing average polymorphic ratio of 58.9%. Number of amplified fragments per genotype across the primers ranged from 65 in Japonica rice variety Sakha101 to 85 in Indica/Japonica rice variety Giza179. Number of polymorphic amplified fragments ranged from 3 for primer ISJ-1 to 24 for primer ISJ-2. The average numbers of amplified bands per primer per genotype were 16.71 and 10.24, respectively. Polymorphic information content (PIC) values ranged from 0.289 for ISJ-9 to 0.480 for ISJ-1 with an average of 0.375. The coefficient of similarities based on semi-random data among the studied genotypes ranged from 0.53 to 0.9 with an average of 0.66. All genotypes clearly grouped into two major clusters in the dendrogram at 58% similarity based on Jaccard’s similarity index. The first cluster represents the Indica and Indica/Japonica rice genotypes, while the second cluster represents the Japonica genotypes. These results indicate that fingerprinting using semi-specific DNA markers may be an efficient tool for varietal identification and assessing genetic diversity in rice. The results highlight the existing diversity among the studied genotypes and hence their potential use in breeding programs. The simplicity and reproducibility of ISJ markers indicates the potential utilization for molecular characterization, identification and purity assessment of rice genotypes.