Characterization and genetic diversity of Dioscorea bacilliform viruses present in a Pacific yam germplasm collection

• Published in: Plant pathology Vol. 69; no. 3; pp. 576 - 584
• Main Authors: Sukal, Amit C., Kidanemariam, Dawit B., Dale, James L., Harding, Rob M., James, Anthony P.
• Format: Journal Article
• Language: English
• Published: Oxford Wiley Subscription Services, Inc 01.04.2020
• Subjects: badnavirus; Collection; DBALV; DBALV2; Dioscorea; Dioscorea bacilliform virus; Exploitation; Gene sequencing; Genetic diversity; Genomes; Germplasm; next generation sequencing; Ribonuclease H; RNA-directed DNA polymerase; Viruses; yam; Yams
• DOI: 10.1111/ppa.13133
• ISSN: 0032-0862

Yam is an important food staple in many Pacific Island countries, but its production is limited by several factors including virus infection. The presence of viruses also hinders the exploitation of the crop by restricting the international dissemination of yam germplasm due to quarantine concerns. In this study, a total of 224 yam accessions present in the Pacific germplasm collection at SPC‐CePaCT, Fiji, were tested for the presence of badnaviruses using a combination of rolling circle amplification (RCA) and sequencing. Of these, 35 tested positive for either Dioscorea bacilliform AL virus (DBALV) or Dioscorea bacilliform AL virus 2 (DBALV2). DBALV was only detected in samples from Vanuatu and Tonga, while DBALV2 was restricted to Papua New Guinean samples. Ten complete genome sequences of DBALV and DBALV2 were obtained and pairwise comparison of the partial reverse transcriptase/ribonuclease H (RT/RNase H)‐coding sequence revealed identities ranging from 89% to 100% and 92% to 100%, respectively. The results suggest that DBALV and DBALV2 are the prevalent badnavirus species infecting yams in the Pacific region. The Pacific yam germplasm collection was screened for badnavirus infection using RCA and sequencing, with 35 out of 224 accessions testing positive and two virus species identified, namely DBALV and DBALV2.