Molecular Detection and Genetic Parameters of Sugarcane Mosaic Virus Isolates from Iran

Sugarcane mosaic virus (SCMV) is recognized as an economically important virus in global sugarcane cultivation. Herein, real-time polymerase chain reaction (RT-PCR) was applied for the detection of SCMV isolates in samples collected from sugarcane fields in Khuzestan province (southwest Iran). For this purpose, a primer pair was designed and validated through gradient PCR. Moreover, the sensitivity and efficiency of the primers were assayed using RT-PCR. A total number of 25 Iran-originated SCMV coat protein (CP) nucleotide sequences were subjected to phylogenetic and polymorphism analysis. Non-synonymous (dN) and synonymous (dS) substitution rates and dN/dS ratio were calculated. The SCMV isolates were placed in different clusters of the phylogenetic tree. Haplotype and nucleotide diversity were calculated as 1.000 and 0.02190, respectively. The mean nucleotide differences were 19.447. Insertion–deletion polymorphism was not observed. The rates of dN and dS were calculated as − 2.57559 (p < 0.001) and  − 0.59514 (p > 0.10), respectively. The dN/dS ratio was 4.32769 and at least 11 recombination events were observed. The codon usage bias (CUB) indices were determined and the results showed a significant positive correlation (p < 0.005) between G + C and G + C3S. Also, the possible effects of mutation pressure in shaping CUB were determined. The mean ENC ranged from 50.316 to 54.970 indicating less orientation in codon usage. The maximum RSCU was 2.82 for the CCA codon (proline) with a high preference for that codon compared to other synonymous codons of that amino acid. The results demonstrate that SCMV CP from Iran-originated isolates exhibit genetic variation and are under selection pressure.