Genetic identification and inference on genetic relationships of important Citrus rootstocks with microsatellite markers

Introduction - Rootstocks are the vital component of citrus production but a well-defined system for their characterization is lacking. Morphological markers to characterize and distinguish the citrus germplasm are scanty. Further, such markers prove inadequate to differentiate the rootstocks at seedling stage and become redundant soon after budding/grafting of a scion variety. This study aims to demonstrate how the use of molecular markers like microsatellites (SSR) can provide an accurate system for rootstock fingerprinting and diverse germplasm identification for citrus improvement program. Materials and methods - Forty-one citrus rootstock accessions were characterized with 49 SSR markers. The unweighted neighbor joining (NJ) tree and factorial analysis were used to decipher the genetic relatedness among the 41 citrus accessions. Results and discussion - The 49 SSR markers amplified a total of 260 alleles with range from 2 to 11 alleles per marker. A subset of 8 SSR markers was selected for their unique PCR amplification pattern, which were able to distinguish 35 of the 41 accessions. Among these, the SSR marker CS41 could differentiate trifoliate orange and its hybrids from other citrus accessions while SSR marker DY287851 produced a similar amplification profile for rough lemons, 'Volkamer' lemon, 'Nasnaran' and 'Ada jamir'. The combined use of NJ tree and factorial relationship helped in deciphering the genetic relatedness of the accessions. The NJ tree classified individuals in three different clusters. The acidic mandarins namely 'Cleopatra' mandarin, 'Pectinifera' and 'Shekwasha' accessions formed a separate group but showed closeness with phylogenetically related individuals in factorial analysis. Contrarily, sour orange and its relatives grouped with trifoliate hybrids in NJ tree but were well resolved in factorial analysis. Conclusion - The SSR based DNA fingerprinting has potential in proper identification of citrus rootstocks and the information generated about their genetic proximities will prove useful in breeding programs.