Discovery of a naturally-occurring allele of eIF4E1.S in Nicotiana tabacum and development of a co-dominant marker

Shifeng Lin,Zili Wang,Rengang Wang,Mingjin Long,Jishun Zhang,Xueliang Ren,Jie Zhang,Shizhou Yu,Ralph E Dewey,Jing Yu

doi:10.1007/s10681-021-02876-y

Abstract

Potato virus Y (PVY) is one of the most problematic pathogens affecting tobacco production. Genetic resistance to PVY in cultivated tobacco is mediated by recessive mutations, including the locus designated VAM, and its derived mutant va, both of which were previously shown to contain large chromosomal deletions. Among the genes deleted in lines containing VAM or va is eIF4E1.S, a gene whose protein product has been shown to facilitate infection by certain potyviruses, including 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 to facilitate their transfer to elite varieties using molecular breeding technologies. Here, we report the discovery of a novel naturally-occurring allele of eIF4E1.S from the Chinese tobacco landrace Fuquanliuye, designated eIF4E1.Fu, which lacks a genomic region of approximately 27 kb, including the 3'-end of eIF4E1.S. Characterization of the deletion junction enabled the development of a co-dominant PCR-based marker specific for eIF4E1.Fu, which can distinguish eIF4E1.S/eIF4E1.Fu heterozygotes from both homozygous classes. Using this co-dominant marker, we genotyped F2 plants segregating for the mutant eIF4E1.Fu allele and confirmed the correlation between genotype and phenotype. This study describes a novel source of resistance and an ideal co-dominant marker that can be applied in breeding for resistance to PVY and other potyviruses.

Highlights

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
The sequencing results showed that the thermal asymmetric interlaced PCR (PCR) products amplified from K326 with all primer sets were identical to the corresponding regions of eIF4E1.S, and the PCR products amplified from Fuquanliuye with the primer sets A, B and C were identical to the corresponding regions of eIF4E1.S
All PCR products amplified from Fuquanliuye with the primer sets covering regions D, E and F were completely different from the corresponding regions of eIF4E1.S (Fig. 1), and appeared to be products of nonspecific amplification

Summary

Introduction

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. The va locus is of particular importance as it has been widely used in breeding for the development of PVY resistant in tobacco varieties. Since the genetic distances between these markers and the va locus are long, their utility in practical breeding applications is limited

Methods

Results

Discussion

Conclusion