Discovery of a naturally-occurring allele of eIF4E1.S in Nicotiana tabacum and development of a co-dominant marker
Abstract Background: The Potato Virus Y (PVY) resistance tobacco mutant VAM, which was produced by X-ray irradiation, and its derived mutant va were previously shown to contain large chromosomal deletions. Among the genes deleted in lines containing these loci is a specific eukaryotic translation initiation factor 4E (eIF4E) gene, designated eIF4E1.S, whose protein product has been shown to facilitate infection by certain potyviruses, the most important of which from an agronomic perspective is PVY. Because the extent of the deletions and the exact nature of their specific breakpoints have not been precisely established for VAM or va, it has not been possible to develop co-dominant markers for these loci. Results: Here, we identified a PVY-resistant tobacco landrace Fuquanliuye with a deletion in the 3' region of the eIF4E1.S gene. The approximate position of the 5' deletion breakpoint was defined by segmented amplification, cloning and sequencing. Using information from this analysis, a chromosome walk was initiated and the nucleotide sequence of the deletion junction was obtained. Through comparison with the tobacco reference genome, it was found that an approximately 27 kb sequence including the 3' region of the eIF4E1.S gene was deleted from the Fuquanliuye genome and nine extra nucleotides of unknown origin were inserted at the breakpoint. Based on the information above, a PCR-based co-dominant molecular marker for the identification of the eIF4E1.S mutant allele was developed. Using this co-dominant marker, we genotyped F2 plants segregating for the eIF4E1.S mutant allele and confirmed good consistency between the genotype and the phenotype to PVY virus. Conclusions: We report a novel naturally-occurring mutant allele of eIF4E1.S from the PVY-resistant tobacco landrace Fuquanliuye, designated eIF4E1.Fu, and a PCR-based co-dominant marker specific for eIF4E1.Fu. This may provide a valuable genetic resource and a basis for marker-assisted selection to improve the PVY resistance of breeding cultivars/lines.
