Gene expression responses to Rice tungro spherical virus in susceptible and resistant near-isogenic rice plants.

Rice cultivar Taichung Native 1 (TN1) is susceptible to Rice tungro spherical virus (RTSV). TW16 is a backcross line developed between TN1 and RTSV-resistant cultivar Utri Merah. RTSV accumulation in TW16 was significantly lower than in TN1, although both TN1 and TW16 remained asymptomatic. We compared the gene expression profiles of TN1 and TW16 infected by RTSV to identify the gene expression patterns accompanying the accumulation and suppression of RTSV. About 11% and 12% of the genes in the entire genome were found differentially expressed by RTSV in TN1 and TW16, respectively. About 30% of the differentially expressed genes (DEGs) were detected commonly in both TN1 and TW16. DEGs related to development and stress response processes were significantly overrepresented in both TN1 and TW16. Evident differences in gene expression between TN1 and TW16 instigated by RTSV included (1) suppression of more genes for development-related transcription factors in TW16; (2) activation of more genes for development-related peptide hormone RALF in TN1; (3) TN1- and TW16-specific regulation of genes for jasmonate synthesis and pathway, and genes for stress-related transcription factors such as WRKY, SNAC, and AP2-EREBP; (4) activation of more genes for glutathione S-transferase in TW16; (5) activation of more heat shock protein genes in TN1; and (6) suppression of more genes for Golden2-like transcription factors involved in plastid development in TN1. The results suggest that a significant number of defense and development-related genes are still regulated in asymptomatic plants even with a very low level of RTSV, and that the TN1- and TW16-specific gene regulations might be associated with regulation of RTSV accumulation in the plants.

Single nucleotide polymorphisms in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to Rice tungro spherical virus.

Rice tungro disease (RTD) is a serious constraint to rice production in South and Southeast Asia. RTD is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. Rice cv. Utri Merah is resistant to RTSV. To identify the gene or genes involved in RTSV resistance, the association of genotypic and phenotypic variations for RTSV resistance was examined in backcross populations derived from Utri Merah and rice germplasm with known RTSV resistance. Genetic analysis revealed that resistance to RTSV in Utri Merah was controlled by a single recessive gene (tsv1) mapped within an approximately 200-kb region between 22.05 and 22.25 Mb of chromosome 7. A gene for putative translation initiation factor 4G (eIF4G(tsv1)) was found in the tsv1 region. Comparison of eIF4G(tsv1) gene sequences among susceptible and resistant plants suggested the association of RTSV resistance with one of the single nucleotide polymorphism (SNP) sites found in exon 9 of the gene. Examination of the SNP site in the eIF4G(tsv1) gene among various rice plants resistant and susceptible to RTSV corroborated the association of SNP or deletions in codons for Val(1060-1061) of the predicted eIF4G(tsv1) with RTSV resistance in rice.

Suppression of two tungro viruses in rice by separable traits originating from cultivar Utri Merah.

Rice tungro disease (RTD) is caused by Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV) transmitted by green leafhoppers. Rice cv. Utri Merah is highly resistant to RTD. To define the RTD resistance of Utri Merah, near-isogenic lines (NIL, BC(5) or BC(6)) developed from Utri Merah and susceptible cv. Taichung Native 1 (TN1) were evaluated for reactions to RTSV and RTBV. TW16 is an NIL (BC(5)) resistant to RTD. RTBV was able to infect both TN1 and TW16 but the levels of RTBV were usually significantly lower in TW16 than in TN1. Infection of RTSV was confirmed in TN1 by a serological test but not in TW16. However, the global gene-expression pattern in an RTSV-resistant NIL (BC(6)), TW16-69, inoculated with RTSV indicated that RTSV can also infect the resistant NIL. Infection of RTSV in TW16 was later confirmed by reverse-transcription polymerase chain reaction but the level of RTSV was considerably lower in TW16 than in TN1. Examination for virus accumulation in another NIL (BC(6)), TW16-1029, indicated that all plants of TW16-1029 were resistant to RTSV, whereas the resistance to RTBV and symptom severity were segregating among the individual plants of TW16-1029. Collectively, these results suggest that RTD resistance of Utri Merah involves suppression of interacting RTSV and RTBV but the suppression trait for RTSV and for RTBV is inherited separately.

Characterization of Oryza rufipogon-Derived Resistance to Tungro Disease in Rice.

Rice tungro disease (RTD) is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus (RTBV), both of which are transmitted by green leafhoppers (GLH). In order to define the resistance against RTD in rice cv. Matatag 9 which was developed by interspecific hybridization between RTD-susceptible cv. IR64 and Oryza rufipogon, the reactions of Matatag 9 to the viruses and GLH were evaluated in comparison with RTD-susceptible and -resistant rice cultivars. The incidences of infection with RTSV and RTBV in Matatag 9 were significantly lower than those in the susceptible parent cv. IR64; however, no substantial differences in virus accumulation were observed between IR64 and Matatag 9 once infected with the viruses. Symptoms in Matatag 9 infected with RTBV and RTSV were milder than those observed in IR64. A higher level of antixenosis to GLH was observed in Matatag 9 compared with IR64. The levels of antibiosis against GLH in Matatag 9 were comparable with those in another GLH-resistant cultivar, and significantly higher than those in RTD-susceptible cultivars. Collectively, these results suggest that tolerance to tungro viruses and resistance to GLH both contribute to the apparent resistance to RTD in Matatag 9, although possible involvement of other resistance mechanisms cannot be excluded.

Sequence changes in six variants of rice tungro bacilliform virus and their phylogenetic relationships.

The DNA of three biological variants, G1, Ic and G2, which originated from the same greenhouse isolate of rice tungro bacilliform virus (RTBV) at the International Rice Research Institute (IRRI), was cloned and sequenced. Comparison of the sequences revealed small differences in genome sizes. The variants were between 95 and 99% identical at the nucleotide and amino acid levels. Alignment of the three genome sequences with those of three published RTBV sequences (Phi-1, Phi-2 and Phi-3) revealed numerous nucleotide substitutions and some insertions and deletions. The published RTBV sequences originated from the same greenhouse isolate at IRRI 20, 11 and 9 years ago. All open reading frames (ORFs) and known functional domains were conserved across the six variants. The cysteine-rich region of ORF3 showed the greatest variation. When the six DNA sequences from IRRI were compared with that of an isolate from Malaysia (Serdang), similar changes were observed in the cysteine-rich region in addition to other nucleotide substitutions and deletions across the genome. The aligned nucleotide sequences of the IRRI variants and Serdang were used to analyse phylogenetic relationships by the bootstrapped parsimony, distance and maximum-likelihood methods. The isolates clustered in three groups: Serdang alone; Ic and G1; and Phi-1, Phi-2, Phi-3 and G2. The distribution of phylogenetically informative residues in the IRRI sequences shared with the Serdang sequence and the differing tree topologies for segments of the genome suggested that recombination, as well as substitutions and insertions or deletions, has played a role in the evolution of RTBV variants. The significance and implications of these evolutionary forces are discussed in comparison with badnaviruses and caulimoviruses.