Genetic mapping has also led to knowledge of locations of many potato genes, notably those conferring resistance to many of the pests and pathogens that present a threat to potato [ 5 ] and genes influencing tuber traits [ 6 ]. Despite these advances, the lack of described mutational variation for potato is a disadvantage of its outbreeding mating habit, and renders genetic complementation problematic for the majority of genes.
However, potato is relatively easy to transform, and so technologies such as overexpression and antisense technology are options for investigating gene function. Results of such experiments are not always so easy to interpret, and improved methods for functional analysis are critical to the future of potato breeding and genetics.
This article provides an overview of genomics resources currently available for potato, and the likely future developments in this area, paying particular emphasis to tools being developed for investigating gene function. The potato genome is very similar in size to its close relative tomato, and genetic maps of the two species show high levels of macrocolinearity [ 9 ]. Information on how well the two genomes are conserved at the microsyntenic level should start to become available as outputs from the respective genome projects accumulate.
The tomato genome mainly comprises low-copy-number sequences, which diverged rapidly in evolutionary time [ 10 ]. Schweizer et al. It is also known that the majority of tomato heterochromatin is found in centromeric regions with almost all of the euchromatic DNA located distally in long uninterrupted tracts, a structural feature likely to be true of potato [ 12 ].
Gene isolation and recent BAC-end sequencing efforts are providing the first detailed glimpses of the genome structure in potato. The generation of large expressed sequence tag EST collections is a primary route for large-scale gene discovery. There have been several efforts to generate EST resources for potato [ 14 — 16 ]. For instance, EST data from a number of different genotypes are also a rich source for the discovery of single nucleotide polymorphism SNP and simple sequence repeat SSR markers.
For example, Tang et al. Bacterial artificial chromosome BAC libraries have become the main vehicle for performing map-based gene cloning and physical mapping in potato. Several BAC libraries have been constructed from cultivated potato [ 18 ] and some of its wild relatives, for example, the diploids Solanum bulbocastanum [ 19 ] , Solanum pinnatisectum [ 20 ], and the Mexican hexaploid Solanum demissum [ 21 ]. These libraries represent a potentially useful resource for the study of comparative genome organisation and evolution in potato and the wider Solanaceae.
A BAC library has been constructed from the male parent RH of the cross used to make the ultra-high-density UHD genetic map of potato with 10 loci [ 2 ], and is being used for construction of a genome-wide potato physical map. Other significant developments arising from the use of these BAC libraries include the use of BAC clones and fluorescence in situ hybridization FISH to develop chromosome-specific cytogenetic DNA markers for chromosome identification in potato [ 22 ]. Mapping efforts in potato have also led to the generation of knowledge concerning the genetic architecture of a number of characters, including pest and disease resistance, tuber quality traits, dormancy, tuber shape, and colour.
Also, several potato genes have been isolated using a map-based approach [ 18 , 23 , 24 ], with most of these aimed at isolation of major genes for resistance to the more serious pests and pathogens of potato, the late blight pathogen Phytophthora infestans Mont. These activities have necessitated the development of dense genetic maps around the target resistance loci, as well as concomitant generation of genomic resources, such as BAC libraries. These gene cloning efforts have afforded early glimpses into the structure of the potato genome, through the sequencing of a considerable number of large-insert clones.
The R3 locus, which maps to a cluster of genes for resistance against P. The R3 locus was found to be syntenic with the I2 locus of tomato, and a comparative approach was used to isolate R3a , which is constitutively expressed along with some of its paralogous genes [ 26 ]. It is highly likely that the same approach will allow the future isolation of other P. A notable example is the recent work on potato chromosome IV, whereby several resistance genes against P. These are but a few of several successful map-based gene isolation efforts, but these illustrate how comparative genomics, either between different potato genotypes or between different Solanaceous plant species, can be used as a tool for accelerating the normally laborious task of gene isolation, and they bode well for the future of Solanaceae genomic research.
As knowledge of the genome structure of potato and tomato increases, the isolation of such genes should become more facile. A candidate gene approach has also been used for isolating plant genes that underlie specific traits [ 30 ]. The marker was used to isolate 15 members of a closely related gene family from genomic libraries. By taking into account all available information inheritance patterns in resistant and susceptible germplasm, mapping data, DNA sequence information , it was possible to reduce the number of candidates to three genes, which were subsequently tested for complementation of a susceptible phenotype by stable transformation.
The potato gene cosegregated with purple tuber colour in a diploid population and was found to be expressed in tuber skin only in the presence of the anthocyanin regulatory locus I. The study focused on tetraploid potato cultivars, which were assessed for chip quality and tuber starch content. Two closely correlated invertase alleles, invGE-f and invGF-d , were associated with better chip quality in three breeding populations, and one allele invGF-b was associated with lower tuber starch content.
The potato invGE gene was also found to be orthologous to the tomato invertase gene Lin5 , causal for a fruit-sugar-yield QTL. These results suggested that natural variation for sugar yield in tomato fruits and that for sugar content in potato tubers are controlled by functional variants of orthologous invertase genes. These few examples clearly demonstrate the potential of using the candidate gene approach in potato.
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It is also clear that the extensive knowledge of tuber biochemistry and the large number of potato gene sequences should enable its further application for tuber quality traits. The ultra-high-density UHD genetic map of potato [ 2 ] forms the underlying framework for construction of a genome-wide physical map of the potato genome. Physical map construction is being carried out in two phases. The second phase entails anchoring of the contigs and single BACs to the UHD map using a BAC pooling method, which should also reduce the number of contigs and increase the average contig size.
Subsequent contiging will use a reduced stringency alignment approach which will reduce the number of contigs still further. The integrated genetic and physical map will be the main platform, which will be used for obtaining the DNA sequence of the potato genome. It is expected that approximately contigs will be anchored to the genetical map, and these scaffolds will be the starting point for genome sequencing. A BAC-end sequence resource, comprising more than reads, has also been generated for the project [ 13 ].
The ongoing tomato and potato sequencing projects will have huge implications for those working in the Solanaceae, and will further sharpen the requirement for functional genomics tools. A wide range of gene expression technologies have been used by potato researchers. The cDNA-AFLP technique has been used to study gene expression from stolon formation to sprouting in a range of different tissues during the potato tuber life cycle [ 34 , 35 ].
The sequence similarities of these TDFs to known genes give insights into the kinds of processes occurring during tuberisation, dormancy, and sprouting. This technique is extremely sensitive and can detect differences among gene family members indistinguishable by Northern blotting. A useful advance has been the realization that a large proportion of cDNA-AFLP fragments show genetic polymorphism in segregating populations and can be mapped as transcriptome-derived genetic markers [ 36 ]. Importantly, these markers show less centromeric clustering than AFLP markers derived directly from genomic DNA and appear to be targeted specifically to transcriptionally active regions of the genome.
This method has been used to perform a large scale survey of genes differentially expressed during the tuber life cycle, and the isolation of some of their promoter regions [ 37 ]. Many genes expressed in the tuber life cycle are involved in defence, stress, storage, and signal transduction pathways. Twelve cis-acting elements were identified, and are known to be responsive to environmental stimuli known to play an important role during the tuber life cycle light, sugars, hormones, etc. One of the disadvantages of cDNA-AFLP is that it does not provide gene sequence information and requires laborious isolation of gene fragments from polyacrylamide gels for sequence characterization.
Serial analysis of gene expression SAGE , which generates short cDNA sequence tags [ 39 , 40 ] using a concatemerization-based method, has been used to examine global gene expression in potato tubers, generating 58 sequence tags of length 19 nucleotides of which 22 were unique [ 41 ]. There were no transcripts found which were involved in photosynthesis. Of the 50 most abundant transcripts from the mature tuber, protease inhibitors were the dominant class, which is in good agreement with previous EST projects [ 14 , 15 ].
The methodologies described briefly in this section are alternatives to the microarrays, which may ultimately be replaced by NGS methods. For example, Emrich et al. The authors used a laser capture microdissection method to isolate rare transcripts from shoot apical meristems and then sequenced the corresponding cDNAs using technology. This type of approach could be used in potato to identify transcripts not present in current EST databases or to extend the range of potato germplasm represented, currently limited to a few cultivars. This issue will be addressed in a subsequent section of this article.
The available potato EST resources comprise an unknown but significant fraction of the gene complement of potato, and are derived from several genotypes, tissues, and environmental influences. Moreover, the same organisation offered a transcription profiling service to allow the evaluation of these arrays by a wide range of users working on different Solanaceous plant species asking different biological questions. However, this platform had the disadvantage of containing a very small proportion of the potato gene repertoire.
Rensink et al. In another detailed study, expression of genes during tuber development was examined, where transient changes in gene expression were found to be relatively uncommon and several new genes were found to be differentially expressed during tuber development [ 44 ]. These studies, while informative, highlight the dilemma faced by plant molecular biologists in prioritizing genes for further study from a large number of candidate genes in the absence of genetic information and mutations in target trait genes. Long oligonucleotide arrays that have been manufactured by various technology providers have also been found useful in potato since the use of short oligonucleotide arrays may lead to misinterpretations due to high degree of allelic heterozygosity in this crop.
This system is very flexible and allows for redesign of the array as more gene sequence information becomes available. Kloosterman et al. Potato geneticists and breeders have generated a great deal of information about the location of genes and QTLs coding for important potato traits, including pest and disease resistance and tuber traits. The volume of gene sequence information, notably from cDNA sequencing and the genome project, will increase rapidly in the coming years. Developments in genetics and structural genomics are beginning to be matched by concomitant development of functional genomics tools.
Relatively high-throughput methods are also needed for testing and assessing gene function. The availability of mutant populations of potato will also be of tremendous value in this regard [ 46 ]. The nonavailability of mutants may largely be overcome by recourse to use of diploid self-compatible potato clones for the development of mutant populations or by mining of variant alleles in heterozygous germplasm. Functional studies currently rely on the use of transformation-based techniques or use of viral vector-mediated gene delivery systems for the establishment of information regarding gene function.
Of course gene expression profiling or microarray studies have a role to play in the identification of a pool of candidate genes potentially involved in any given biological process. These methods, in combination with other functional genomics tools such as RNA interference RNAi , virus-induced gene silencing VIGS , and activation tagged lines, have the potential to facilitate the identification of the role of thousands of potato genes over the next several years. Furthermore, combining structural genetics approaches such as QTL and candidate gene mapping with functional genomics information such as microarray-derived gene expression data for candidate genes has great potential for the dissection of many complex, polygenic potato traits.
Virus-induced gene silencing VIGS is a powerful tool for plant functional genomics. This phenomenon has been exploited for gene silencing through the use of virus vectors carrying host target genes that are directed against the corresponding plant mRNAs [ 48 ]. VIGS is increasingly used to generate transient loss-of-function assays, and is a powerful reverse-genetics tool in functional genomic programs as an alternative to stable transformation.
Faivre-Rampant et al. In this study, silencing was maintained throughout the foliar tissues and tubers and could also be triggered and sustained in in vitro micropropagated tetraploid potato for several cycles and on in vitro generated microtubers. In the same study, silencing of known resistance genes e. TRV-based silencing of genes such as PDS, a 20S proteasome subunit PB7 or Mg-protoporphyrin chelatase Chl H by agrodrench has been shown to be efficient for different members of the Solanaceae including Nicotiana benthamiana , tomato, pepper, tobacco, potato, and petunia.
Indeed, many silencing studies have been conducted in N. Recently, for example, Gilroy et al. Silencing of cathepsin B in N. The ease of silencing in N. Naturally occurring PVX resistance in S. Silencing of either gene resulted in loss of organ identity. These studies show the potential for use of N. In addition to their role in VIGS, virus vectors can be used for overexpressing genes in plants. For example, overexpression of P.
Information emerging from effectoromic studies will be useful to identify the cognate host R genes as sources of durable disease resistance and to develop novel control strategies that are intrinsically difficult for the pathogen to overcome. The discovery of a conserved motif, RxLR, within many avirulence genes [ 61 , 62 ] that is required for translocation of the effectors from pathogen haustoria into the plant cell [ 63 ] has had a tremendous impact on the prediction of pathogen effectors. Overexpression via pGR in N. Similarly, the recognition of the P.
Coinfiltration of N. Using the P. Two similar studies have been reported that utilize the two Avr3a alleles described above to identify potentially novel resistance mechanisms within wild potato accessions [ 66 , 67 ]. One study [ 66 ] utilized PVX to express the different Avr3a alleles in wild Solanum species, whereas the other [ 67 ] utilized Agrobacterium-only-based expression of the Avr3a alleles to circumvent the relative high level of resistance against PVX within the wild species tested Figure 1.
Potato has entered an exciting new era, whereby the development of extensive genetic and genomic resources have opened up many new possibilities for studying important potato traits relevant to potato agronomy. Development of biotechnological tools for assaying potato gene function is likely to progress rapidly in the coming years. National Center for Biotechnology Information , U.
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