Abstract
BackgroundRice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima).ResultsHere we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV.ConclusionThis study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.
Highlights
Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa
Comparison with O. sativa we looked for polymorphisms at RYMV1, constitutive expression of pathogenesis related protein-5 (CPR5)–1 and NLRRYMV3 in O. sativa based on the SNPSeek database [25], which pools genotyping data from the 3000 Rice Genomes Project [26]
256 F2 plants from populations developed with the resistant Tog7291 accession were resistant (Table 3), while a single one was susceptible. These results demonstrated that the different truncated forms of CPR5–1 were resistance alleles of the RYMV2 recessive resistance gene
Summary
Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. An independent rice domestication process occurred in Africa, which gave rise to the cultivated species Oryza glaberrima [1, 2]. Breeding initiatives over the last 60 years have essentially concerned O. sativa varieties and have further widened the gap in yield potential between varieties of the two species. O. glaberrima has specific traits of interest and adaptation to local stresses, such as drought, iron toxicity, infertile soils and weed competition [3, 4]. This rich source of gene diversity is of substantial breeding interest to increase rice yield in a setting of global warming and reduced inputs. O. glaberrima was introduced in breeding programs [5, 6] leading for instance to the New Rice for Africa (NERICA) varieties, that resulted from O. sativa x O. glaberrima interspecific crosses and were successfully disseminated in the 2000s [7, 8]
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