Genomic variation in self-pollinated clove (Syzygium aromaticum (L.) Merr. & Perry) accessions from the Western Ghats

Clove, the dried, unopened flower buds of Syzygium aromaticum (L.) Merr. & Perry, is the mainstay of income for farmers in India, Indonesia, Tanzania and Sri Lanka and is a self-pollinated crop. A study conducted in the Southern Western Ghats of India identified phenotypic variations in the clustering of clove flower buds. Four clove accessions (Acc.1, Acc.3, Acc.5 and Acc.7) that showed superior yield and variation in floral characteristics were selected and DNA was isolated from the floral tissue using the CTAB method. Random Amplified Polymorphic DNA (RAPD) analysis using Operon primers (OPB 01 to OPB 10) detected polymorphism among the accessions, with OPB-01 showing the highest Polymorphic Information Content (PIC), followed by OPB-04 and OPB-06. Similarity coefficients were calculated based on the presence or absence of polymorphic bands, with coefficients ranging from 0.47 to 0.72. The resulting phylogenetic tree classified the accessions into two main groups based on their bud clustering habit (branching): branching (Acc. 1 and Acc. 5) and non branching (Acc. 3 and Acc. 7). Acc. 3 showed distinct separation from the other genotypes at a coefficient of 0.47, while Acc. 7 separated from Acc. 1 and Acc. 5 at a coefficient of 0.60. Acc. 5 appeared genetically distinct, as it showed separation from the other accessions based on RAPD analysis. The distinctiveness of Acc.5 was further confirmed through 18S rRNA sequencing, suggesting potential intra-species genomic variations among the four clove phenotypes and hinting at the possibility of cross pollination.