The viruses

Potato virus Y (PVY), Potato virus A (PVA) and Potato virus V (PVV) are species in the genus Potyvirus, and Potato virus X (PVX) is a species in the genus Potexvirus. Symptoms caused by these viruses are described in Jeffries (1998), or for a fuller description of the viruses, see Adams et al. (1998). The importance of these and other potato viruses, and the need for resistance, are discussed in Solomon-Blackburn & Barker (2001).

The main strains of PVY are PVYO (common strain), PVYN and PVYC. PVYN causes necrosis in tobacco (Nicotiana tabacum) (De Bokx & Huttinga, 1981). More recently, the strain PVYNTN has been described (Beczner et al., 1984; Le Romancer et al., 1994); it causes necrotic ring blemishes on tubers. The main strain groups of PVX are groups 1–4, defined by Cockerham (1955) in terms of resistance genes in potato, and the resistance-breaking strain PVXHB (Moreira et al., 1980). Group 2 is commonly called B. Group 3 is the ‘common strain’.

The host and its genetics

The cultivated potato Solanum tuberosum ssp. tuberosum (or Tuberosum) is a self-compatible outbreeding tetraploid, derived from another tetraploid subspecies, S. tuberosum ssp. andigena (or Andigena), which probably evolved from diploid species (Bradshaw & Mackay, 1994). S. tuberosum is generally considered to be more or less an autotetraploid whose genes are inherited tetrasomically (Cadman, 1942; Howard, 1970). However, it may be a segmental allotetraploid rather than a true autotetraploid, with consequent occasional deviations from the expected tetrasomic segregation ratios (Bradshaw, 1994). Genes have been introduced into Tuberosum (by crossing) from various wild Solanum species (Davidson, 1980; Ross, 1986; Bradshaw & Mackay, 1994), of which most are diploids or allopolyploids in which inheritance is disomic (Cockerham, 1970; Ross, 1986).

In potato breeding programmes, initial hybridization with these wild species has been followed by several generations of backcrossing to establish euploidy and climatic adaptation, and to eliminate unwanted wild characteristics; Ross (1986) considered that this can be achieved within four to six generations. Cockerham (1970) reported that progeny of a sixth backcross generation from hybrids with the allotetraploid S. acaule behaved as autotetraploids with tetrasomic inheritance, with very occasional double reduction (and hence random chromatid association) indicated by unexpected homozygous recessive seedlings. S. stoloniferum (4x), S. demissum (6x) and S. hougasii (6x) showed disomic inheritance (Cockerham, 1970), but in Tuberosum breeding lines descended from hybrids with S. stoloniferum or S. hougasii, segregation ratios indicative of tetrasomic inheritance have been seen (Solomon-Blackburn & Mackay, unpubl. obs.). Ross (1958) found that hybrids between S. stoloniferum and Tuberosum up to the first Tuberosum backcross generation appeared to segregate disomically.

Disomic and tetrasomic segregation ratios

When a parent with dominant major-gene resistance at a single locus is crossed with a susceptible (homozygous recessive) parent, disomic inheritance would result in a segregation ratio of 1:1 (if the parent is simplex) or ∞:0 (duplex) resistant:susceptible seedlings (as in a diploid). Tetrasomic inheritance will result in a ratio of 1:1 (if the parent is simplex), 5:1 (duplex) or ∞:0 (triplex or quadruplex) if the gene is close to the centromere so that there is random chromosome association. Otherwise, chromatid segregation or double reduction (Bradshaw, 1994) causes an excess of recessive segregants, giving ratios down to 0.86:1 (simplex), 3.67:1 (duplex) and 27:1 (triplex) (Ross, 1986; Bradshaw & Mackay, 1994; Mendoza et al., 1996).

Resistance

Natural virus resistance in potato was reviewed by Valkonen (1994), and in Ross (1986). A comprehensive list of host genes identified for resistance to the potyviruses and PVX in potato is given in Table 1. The nomenclature of the genes is explained below. The relative utility of these genes for breeding purposes is discussed by Solomon-Blackburn & Barker (2001). Further lists of resistances to these viruses in or from various wild Solanum species, without genes identified, were published by Webb & Schultz (1961), Horváth, (1968), Bagnall (1972), Tozzini et al. (1991) and Valkonen (1997). For examples of potato cultivars with specified virus resistance genes, see Cockerham (1943b), Ross (1986) and Jones (1990). The nomenclature for types of host response to viruses in plants was reviewed by Cooper & Jones (1983) and, for virus resistance in potato, by Valkonen (1994) and Valkonen et al. (1996).

Table 1 Host genes for virus resistance in potato
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Plants with extreme resistance (ER) to a virus show no symptoms, or limited necrosis (e.g. pinpoint lesions, flecks, or localized stem necrosis), when inoculated with virus. Only extremely low amounts of virus, if any, can be detected by sensitive techniques. ER can be comprehensive, conferring resistance to several strains (e.g. Rx genes) or even two or three viruses, e.g. Rysto confers resistance to PVY, PVA and PVV (Table 1, unless this represents two or three genes in a very tight linkage group (Barker, 1996). Recently, however, ER genes specific to PVA have also been discovered, e.g. Rasto, Raadg (Barker, 1996; Hämäläinen et al., 1998).

Plants with hypersensitive resistance (HR) show either local necrotic lesions, which prevent the infection from spreading further, or systemic necrosis. Virus can almost always be detected in affected leaves. HR is often strain-specific. It can also be affected by environmental conditions or by the physiology of the host plant (e.g. maturity). ER and HR to PVX and potyviruses can be determined by sap-inoculation or graft-inoculation (De Bokx, 1972), observing the response (Cockerham, 1970), and testing for infection.

A connection between ER and HR has been suggested, because necrosis can sometimes occur in plants with ER genes (Ross, 1958; Cockerham, 1970; Delhey, 1974). Hinrichs et al. (1998) reported that PVY replicated in initially infected leaf cells of inoculated plants of cultivars with the ER gene Rysto, and was transported into neighbouring cells, prior to a limited necrotic reaction after which the infection ceased. The ER gene Rxadg in cv. Cara has now been found to control separate virus resistance and cell death responses (Bendahmane et al., 1999); cell death does not normally occur when plants carrying Rxadg are inoculated with PVX because the ER is epistatic over the HR. When studying S. stoloniferum genes conferring resistance to PVY & PVA, Cockerham (1970) found genes for ER to be dominant or epistatic over genes for HR. Valkonen et al. (1994) also found the ER gene Ryadg to be epistatic to the HR gene Nyadg in an Andigena-derived genotype.

Resistance to virus movement occurs where some kind of movement of virus through the plant is impeded, for example where a lower percentage of the tuber progeny plants of an infected plant are infected. HR could be regarded as a kind of resistance to virus movement, because movement is arrested or impeded by cell death. Other types of resistance are described in Solomon-Blackburn & Barker (2001) but do not apply to known major genes for resistance to these four viruses.

Nomenclature of major resistance genes

This paper follows selected proposals of Valkonen et al. (1996). The initial letter, a capital to denote a dominant resistance gene, indicates the type of resistance (usually N for HR and R for extreme or other resistance). A second, lower case letter, indicates the virus or strain resisted, and then the species in which the resistance is found or originated is indicated in lower case subscript. In a few cases, the virus letter is followed by the virus strain in upper case subscript: hence RxHBscr is a gene in S. sucrense conferring ER to the HB strain of PVX. In Table 2, we adhere to the nomenclature of Cockerham (1970) to avoid confusion in comparisons with literature cited. [Ryston1, Ryston2 and Rxacln might be renamed Nysto1, Nysto2 and Nxacl otherwise.] All gene names are italicized.

Table 2 Host gene relationships deduced from phenotypic data
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Inheritance

Where the inheritance of ER or HR to these viruses has been investigated in potato, it is monogenic, with dominance for resistance, a situation which might be expected to evolve in the wild for genes conferring fitness. Earlier models for the inheritance of ER to PVX in USDA 41956, for two dominant complementary genes (Stevenson et al., 1939) and for a recessive allele to a gene for HR (Hutton & Wark, 1952), were tested by Mills (1965) and Cockerham (1970), whose data did not fit these models; both concluded that a single dominant gene was responsible (Rxtbr in Table 1).

Gene relationships deduced from phenotypic segregation data (as opposed to molecular mapping) are listed in Table 2. Some of this research was performed on diploids (e.g. S. chacoense, S. sparsipilum and dihaploids of S. tuberosum) or allopolyploid species (e.g. S. stoloniferum, S. demissum and S. hougasii) with disomic inheritance. In other cases (e.g. autotetraploids S. tuberosum ssp. tuberosum and ssp. andigena, some with genes introgressed from S. acaule) inheritance was tetrasomic, involving segregation ratios as explained above (Cockerham, 1970).

Molecular mapping

The chromosomal locations of resistance genes can be mapped by examining segregations in relation to linked molecular markers. Virus-resistance genes mapped so far in potato are summarized in Table 3. Advances in molecular marker technology, and an expanding map of markers, have improved the prospects for mapping and cloning genes in potato, as well as for marker-assisted selection (Milbourne et al., 1997, 1998; summarized in Solomon-Blackburn & Barker 2001). In the longer term, large-scale sequencing may lead to the development of a complete gene map in potato (W de Jong, pers. comm., discussed in Solomon-Blackburn & Barker, 2001).

Table 3 Virus resistance genes mapped in potato by molecular methods
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Further to the linked virus-resistance gene loci in Tables 2 and 3, disease resistance gene clusters (covering a diverse range of pathogens) have been found in many plant species, including potato (Leister et al., 1996; De Jong et al., 1997; Hämäläinen et al., 1998; Van Der Voort et al., 1999), sometimes at the same chromosomal positions in different plant genera. These linkage groups would facilitate efficient selection for several disease resistances at once, in nature as well as in plant breeding, and would therefore be at a selective advantage over independent genes.

Once mapped, a gene can be cloned, by transposon mutagenesis or by positional cloning. The genes Rxadg (from cv. Cara) and Rx2 have been cloned (Bendahmane et al., 1999; Bendahmane & Baulcombe, pers. comm.). Attempts are also being made to clone Nbtbr (De Jong et al., 1997) and Rysto (Brigneti et al., 1997). Gene cloning has applications in research on resistance mechanisms and evolutionary studies (Gebhardt, 1997). Several common sequence motifs have been found in genes for resistance to a diverse range of pathogens in a diverse range of plant species. Gebhardt (1997) reported that six or seven classes of resistance genes (with different common sequence motifs) had been isolated, and that there were probably more to be discovered. Possible functions and cellular locations for the proteins encoded have been inferred from these common motifs. For example, a leucine-rich repeat (LRR) of approximately 25 amino acids is frequently found in (predicted proteins encoded by) genes for resistance to viruses, bacteria, fungi or nematodes. Proteins with LRR domains tend to be involved in protein–protein interactions, so a role as receptors was suggested (Gebhardt, 1997). Analysis of resistance and susceptibility alleles of genes isolated from different plant species may help to identify structural features that determine pathogen specificity, which could be manipulated to produce resistance genes tailored for specific crop needs (Leister et al., 1996).

The Rxadg gene in cv. Cara has been found to be very similar to the tightly linked gene Gpa2 for resistance to potato cyst nematode (PCN) (Bendahmane et al., 1999; van der Voort et al., 1999; Van Der Vossen et al., 2000). Clusters of genes resembling resistance genes in sequence motif have also been found around known resistance gene loci. Hämäläinen et al. (1998) found three of these resistance-gene-like (RGL) sequences (of the LRR type), two of which were closely linked to (or possibly part of) Ryadg on chromosome XI, in Andigena; Leister et al. (1996) had found three RGL sequences homologous to those three, in the same region of chromosome XI in Tuberosum (using the same PCR primers designed from sequence motifs common to resistance genes in Nicotiana tabacum and Arabidopsis thaliana). This region of chromosome XI carries several disease resistance genes in solanaceous species (Leister et al., 1996; Brigneti et al., 1997; Hämäläinen et al., 1997, 1998), including the gene N for HR to Tobacco mosaic virus in N. tabacum which contains sequences homologous with these RGL sequences in potato (Leister et al., 1996). Common sequence motifs may facilitate the discovery and isolation of unknown resistance genes (Leister et al., 1996). These could include genes for ‘nonhost’ resistance (i.e. from plant species not infected by the pathogen) which could be used to transform plants of other species (Leister et al., 1996; Gebhardt, 1997).

Concluding remarks

From the 1930s to the present, much work has been carried out on characterizing host resistance genes and phenotypes (Table 1), providing a sound basis for further research and applications to potato breeding. It is inevitable that there are more of these genes yet to be discovered, in view of recently discovered genes and evidence on gene clusters.

Molecular mapping provides more precise information on gene locations than phenotypic linkage studies, although the information from phenotypic linkage studies is also useful in relation to mapping data. Once a gene is mapped, its locus relative to those of other mapped genes is revealed and leads to a more useful map, particularly as shared marker libraries develop.

Cloned genes are used for research on resistance mechanisms and provide insight into the evolutionary processes involved in disease resistance (discussed above). Gene clusters also raise the question of the conceptual difference between a comprehensive resistance gene and two or more adjacent specific resistance genes, as does the dual ER/cell death mechanism found in Rxadg (Bendahmane et al., 1999), and genes such as Rystona, which confers ER to PVY and HR to PVA (Cockerham, 1970). It is possible that the comprehensive Ry genes could, in fact, be tightly linked groups of specific resistance genes (Barker, 1996).

At one time, genes of identical phenotype from different sources that segregated as alleles were considered identical, because there was no evidence to suggest otherwise, e.g. Rxadg from accession CPC 1673 and Rxtbr from USDA 41956 (Cockerham, 1970). However, in the light of recent findings on resistance gene clusters, this may not have been correct. Also, Rysto and Ryadg have been mapped to the same, or very similar, position as each other (Table 3; Brigneti et al., 1997; Hämäläinen et al., 1997); these two genes confer the same phenotype with respect to PVY but not PVA. Cockerham (1970) also reported two loci with two or three different PVY resistance alleles in S. stoloniferum (Table 2). Allelism or repulsion linkage of dominant major genes for resistance to the same pathogen would confer a selective advantage in nature, in a similar way to multiplex-resistant parents in potato breeding (Wastie et al., 1992; Bradshaw & Mackay, 1994): more of the progeny are resistant when an autotetraploid resistant parent is duplex or triplex than when it is simplex at two or three independent loci (Solomon-Blackburn & Mackay, 1993). In an allopolyploid such as S. stoloniferum, all the progeny (except recombinants) will be resistant if a resistant parent is effectively homozygous in one genome (through allelism or repulsion linkage), whereas, if it is heterozygous at two independent loci, one quarter of the progeny will be susceptible in a cross with a susceptible parent. On the other hand, coupling linkage of genes for resistance to different pathogens would be advantageous, as discussed above.

The following paper (Solomon-Blackburn & Barker, 2001) discusses the use of host genes and these technologies in potato breeding for virus resistance, in relation to other emerging technologies and conventional methods. The applications of cloned genes, mapped locations and linked markers in potato breeding, the use of host gene-mediated resistance by conventional breeding methods, and the use and potential of pathogen-derived and other transgenic resistance are also examined.