Sequence diversity within the three agents of groundnut rosette disease

ABSTRACT Sequence diversity was examined in the coat protein (CP) gene of Groundnut rosette assistor virus (GRAV), the overlapping open reading frames (ORFs) 3 and 4 of Groundnut rosette virus (GRV), and the satellite RNA (sat-RNA) of GRV obtained from field isolates from Malawi and Nigeria. These three agents cause groundnut rosette disease, a major disease of groundnut in sub-Saharan Africa (SSA). Sequence analysis showed that the GRAV CP gene was highly conserved (97 to 99%) independent of its geographic source. The nucleotide sequence of the overlapping ORFs 3 and 4 of GRV was highly conserved (98 to 100%) from isolates within a geographic region but less conserved (88 to 89%) between isolates from the two distinct geographic regions. Phylogenetic analysis of the overlapping ORFs 3 and 4 show that the GRV isolates cluster according to the geographic region from which they were isolated, indicating that Malawian GRV isolates are distinct from Nigerian GRV isolates. Similarity within the sat-RNA sequences analyzed ranged from 88 to 99%. Phylogenetic analysis also showed clustering within the sat-RNA isolates according to country of origin, as well as within isolates from two distinct regions of Malawi. Because the GRAV CP sequence is highly conserved, independent of the geographic source of the GRAV isolates, the GRAV CP sequence represents the most likely candidate to use for pathogen-derived resistance in groundnut and may provide effective protection against groundnut rosette disease throughout SSA.