Plants fight viruses through two resistance mechanisms, including passive and active resistance regulation. In previous studies, some silenced genes or resistance genes (R genes) could mediate certain dominant active resistance mechanisms. Some R genes have characteristic special domains, such as (CC)-NBS-LRR or NBS-LRR (Li et al., 2018). Generally, potyviruses need to infect host plants, as they depend on host plant factors to encode proteins for replication and translation (Carrington et al., 1996; Wang and Krishnaswamy, 2012). In recent years, a variety of resistance (R) genes have been identified and used to improve brassicaceous crop resistance against turnip mosaic virus (TuMV), which not only to ensure vegetable production, but also to provide approaches for the control of other viruses, such as cucumber mosaic virus (CMV) and tobacco mosaic virus (TMV). Many genes that demonstrate resistance to TuMV have been mapped in brassica crops, such as TuRB01, TuRB02, TuRB03, TuRB04, TuRB05, and ConTR01. Dominant resistance genes control resistance to a narrower spectrum of TuMV isolates than the recessive genes (Li et al., 2016). In other plants, the eukaryotic initiation factor (eIF) genes were also found to be resistant to viruses. There are many types of eIF genes, including eIF4E, eIF4G, eIF(iso)4E, and eIF(iso)4G, which play an important role in recessive resistance genes with broad-spectrum resistance to viral infection (Dinkova et al., 2016).

To date, most mutations of the eIF4E or eIFiso4E genes have been mapped to natural recessive resistance to potyvirus, and the long co-existence of plants and potyviruses has promoted the emergence of virulent isolates that have adapted to the recessive resistance in plants (Sanfaçon, 2015). Many resistance genes have been cloned, especially after the genomes of brassica crops were assembled (BRAD, http://brassicadb.org/brad/). Some genes have been shown to be eIF family genes, and there are various eIF4E family members in brassica crops, such as ConTR01 [eIF(iso)4E.c], retr01/retr02 [eIF(iso)4E.a], and retr03 (eIF2Bβ). The reported susceptibility/resistance associated with eIF4E or eIF(iso)4E is mostly based on the interaction between these proteins and the genome-linked viral protein (VPg) covalently attached at the 5′ end of the viral-positive RNA strand (Michon et al., 2006). However, the phenomenon of eIF4E-VPg interaction does not provide sufficient evidence to explain the observed results in TMV-eIF4E (Roudet-Tavert et al., 2007). Therefore, additional hosts and virus determinants may be required to determine the interaction between TuMV VPg and eIF genes, as well as their functions during TuMV infection. Several functions have been summarized for the interaction of eIFs-TuMV VPgs during viral infection. First, TuMV VPg imitates the 5′ cap of cellular mRNAs, which may be important for viral RNA translation and might accelerate protein translation through the interaction with eIF genes (Contreras-Paredes et al., 2013). Second, the interactions between eIF4E and virus VPgs might promote viral replication and facilitate virus movement to other tissues to result in the infection of the entire plant (Wang and Krishnaswamy, 2012). Third, during the viral infection cycle, the interactions of virus VPgs and eIFs might boost viral RNA translation through restraining entire or specific cellular translation (Léonard et al., 2000).

In Brassica rapa, three genes, namely, retr01, retr02, and trs, are associated with eIF(iso)4E genes for recessive resistance (Kim et al., 2014; Qian et al., 2013; Rusholme et al., 2007). Sequencing with a sequence-based genetic map of B. rapa confirmed that retr02 is retr01 rather than a different allele. Nellist et al. (2014) reported retr01/retr02 broad-spectrum resistance to TuMV due to a natural mechanism based on the mis-splicing of the eIF(iso)4E allele in B. rapa. Kim et al. (2014) proved that there were some key variations in the B. rapa eIF(iso)4E protein for the interactions of TuMV VPg and eIF(iso)4E using a yeast two-hybrid (Y2H) system. In addition, the TuMVC4/CDN1/UK1 VPg could not interact with eIF4E, but only with the eIF(iso)4E of B. rapa based on Y2H and bimolecular fluorescence complementation (BiFC) assays (Li et al., 2018). Additionally, some single nucleotide polymorphisms (SNPs) were identified that may influence the interaction between eIF(iso)4E and VPg, such as the SNP T₁₀₆C in BraA.eIF(iso)4E.c and the SNP A₁₅₄C in VPg (Li et al., 2017, 2018). In addition to the recessive genes retr01 and retr02, the other recessive gene retr03 was mapped and cloned in Brassica juncea and encodes the eukaryotic translation initiation factor 2B-beta (eIF2Bβ), representing a new class of virus resistance genes conferring resistance to pathogens (Shopan et al., 2017).

Some amino acids have a significant influence on the interactions between TuMV VPg and eIF(iso)4E in B. rapa. A Y2H assay and co-immunoprecipitation analysis demonstrated that the W₉₅L, K₁₅₀L, and W₉₅L/K₁₅₀E amino acid mutations in B. rapa eIF(iso)4E proteins interrupted their interactions with TuMV VPg (Kim et al., 2014). Meanwhile, TuMV VPg could interact with eIF(iso)4E, but not with eIF4E, in B. rapa, and some SNPs were identified that may affect the interactions between eIF(iso)4E and VPg, such as the SNP T₁₀₆C in BraA.eIF(iso)4E.c and the SNP A₁₅₄C in VPg (Li et al., 2018). Based on the findings of a previous study, the interactions between TuMV-CHN2/CHN3 isolates and eIF4E/eIF(iso)4E were identified in this study, and some key amino acids were observed. In addition, an interaction model was constructed to infer the key amino acids influencing the structure of protein complexes. This study may be helpful for mapping new eIF(iso)4E resistance loci and further revealing the resistance mechanisms of TuMV to eIF(iso)4E in B. rapa.

The Potyviridae family, which includes many economically important pathogens of cultivated crops especially members of the genus Potyvirus, is one of the largest families of plant viruses in the world (Gibbs and Ohshima, 2010). Crop species have co-evolved with potyviruses, resulting in the development of recessive resistance. To date, mutations in the eIF4E or eIFiso4E genes have been mapped for natural recessive resistance to potyviruses (Sanfaçon, 2015). Sixteen genes resistant to potyviruses have been detected based on eIF4Es, such as pvr1/pvr1² in Capsicum spp. (Arroyo et al., 1996; Kang et al., 2005); mo1 in Lactuca sativa (German-Retana et al., 2008; Nicaise et al., 2003); sbm1/wlv/cyv2 in Pisum sativum (Gao et al., 2004); bc-3 in Phaseolus vulgaris (Naderpour et al., 2010); pot-1 in Solanum habrochaites (Ruffel et al., 2005); rym4/rym5 in Hordeum vulgare (Kanyuka et al., 2005); SNP-mapping in Citrullus lanatus (Ling et al., 2009); several quantitative trait loci in Prunus armeniaca (Marandel et al., 2009); cum1-1 in A. thaliana (Sato et al., 2005); eIF4E RNAi in Cucumis melo (Rodríguez-Hernández et al., 2012); Sle-IF4E1-G1485A (Piron et al., 2010), eIF4E-1 and eIF4E-2 (Mazier et al., 2011) in Solanum lycopersicum; and pvr1² (Cavatorta et al., 2011), eIF4E (Cavatorta et al., 2011), and Eva1 (Duan et al., 2012) in Solanum tuberosum. In addition, seven resistance genes to potyviruses were detected based on eIF(iso)4Es, such as retr01 (Rusholme et al., 2007), retr02 (Qian et al., 2013), and trs (Kim et al., 2013), overexpression mutagenesis (Kim et al., 2014) in B. rapa; EMS mutagenesis (Lellis et al., 2002), Spm (Jenner et al., 2010) in A. thaliana, and RNAi mutagenesis in Prunus domestica (Wang et al., 2013).

TuMV VPg, and eIF4E/eIF(iso)4E have co-evolved in plants. The eIF4E and eIF(iso)4E proteins shared 50% amino acid sequence identity, and interestingly, eIF(iso)4E and eIF4E were functionally redundant following knockout of the eIF(iso)4E gene, which was compensated for by the increased expression of eIF4E (Sanfaçon, 2015). There are several copies of eIF4E and eIF(iso)4E in plants, and so if eIF4E or eIF(iso)4E mutate, the other copies can compensate their function to interact with TuMV. Additionally, there are at least 124 isolates of TuMVs (Jenner and Walsh, 1996) that could threaten all Cruciferae vegetables, including horticultural brassica crops (calabrese, cauliflower, broccoli, brussels sprout, cabbage, swede, kale, kohlrabi, and Chinese cabbage), arable brassica crops (oilseed rape, B. napus, and B. rapa), edible horticultural non-brassica crops (peas, watercress, radish, rhubarb, chicory, spinach, chrysanthemum, tobacco, and lettuce), ornamentals (Abutilon, stocks, and wallflowers), and 14 weed plants from various families (Jenner and Walsh, 1996; Provvidenti, 1982; Shattuck, 1992). If one TuMV isolate mutates, the other isolates substitute it to infect plants.

Some amino acid positions that are relevant for potyvirus resistance have been analyzed. The G₁₀₇R mutation in the eIF(iso)4E protein 3D ribbon, which could affect both VPg and cap binding, is associated with virus resistance in pea, tomato, and pepper, while L₇₉R, which is located in an external loop, could affect VPg but not cap binding (Kang et al., 2005; Nicaise et al., 2003; Ruffel et al., 2005). Some amino acid changes in eIF genes located in the central domain could be associated with eIF4E-mediated resistance (Ruffel et al., 2005, 2007). Twenty-two eIF4E sequences have been obtained from monocot and dicot plant species, which suggests that there are four SNP positions for natural and positive selection (Sanfaçon, 2015). Furthermore, the eIF4E/eIF(iso)4E protein 3D ribbon was constructed based on the wheat eIF4E protein structure (Li et al., 2018). Therefore, the assessment of eIF family gene resistance spectra and genetic backgrounds would be helpful for eIF4E-mediated resistance mechanism analysis (Dinkova et al., 2016; Li et al., 2019).

In our previous study, we used TuMV-C4 VPg as a template and found that the amino acid change I₅₂L was important for the interaction between TuMV VPg and eIF(iso)4E (Li et al., 2018). However, in this study, the TuMV-UK1 VPg was used as a template, and the amino acid substitution I₅₂L was non-essential for the interaction between TuMV-CHN2/CHN3 VPgs and eIF(iso)4E, which indicated that it may not be just one amino acid that could influence the interaction between TuMV VPg and eIF(iso)4E, but may rather be several loci working together, with one or two sites playing a key role. Of course, we obtained sitedirected mutagenesis using different isolates as the templates (TuMV-UK1/C4 VPg), which have great differences in genetic background.

Natural recessive virus resistance has provided new insights into the interactions between translation factors and plant viruses (Sanfaçon, 2015). In addition, the systematic identification of the interactions between translation factors and viral RNAs or proteins has established new potential targets for antiviral resistance. With the development of plant genome sequencing, our understanding of eIF family gene evolution, as well as other translation factors in plants, has expanded. However, it is unclear whether viruses possess special functions in regulating the interactions between plants and viruses (Dinkova et al., 2016). For instance, when the eIF family genes knocked-out or subjected to other abiotic stresses such as drought, salinity, and so forth, how do plants survive? Genetics, biotechnology, bioinformatics, and biochemistry approaches should be combined to address these challenges in agriculturally relevant species.