Molecular diversity of Benin populations of Scutellonema bradys based on ITS1 rDNA and COI mtDNA genes

Despite the importance of yam in the diet in Benin, its farming is still facing several constraints because of yield and quality reduction by the yam nematode Scutellonema bradys . Implementation of efficient management techniques requires better understanding of this pest. The current study aimed at identifying the Scutellonema spp. associated with yam and investigating the phylogenetic relationships between Benin’s Scutellonema populations. Nematodes of the genus Scutellonema were obtained from tubers exhibiting external dry rot symptoms. The 138 populations were collected in 49 fields from 29 villages. DNA could be extracted from 53 populations and the ITS1 and COI regions were amplified via PCR, sequenced and compared with available sequences in the NCBI database. All populations were identified as belonging to S. bradys . Maximum likelihood was used to construct a 60% consensus phylogenetic trees based on 53 sequences. This phylogenetic analysis did not reveal any genetic separation by cultivar, village, diversity nor by agroecological zones. Neither could any subgroups within Scutellonema bradys be separated, indicating that all nematodes examined have the same genetic origin and no subspecies were present. A species-specific primer (Humpreys-Pereira et al ., 2013) was verified with the DNA of the 53 sequences. The PCR assay using this species-specific primer set, turned out to be a reliable and fast method for S. bradys identification. The assay can therefore be used for high throughput analysis of samples from yam and yam fields to detect S. bradys .