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We have developed PotatoMASH (Potato Multi-Allele Scanning Haplotags), a novel low-cost, genome-scanning marker platform. We designed a panel of 339 multi-allelic regions placed at 1 Mb intervals throughout the euchromatic portion of the genome. These regions were assayed using a multiplex amplicon sequencing approach, which allows for genotyping hundreds of plants at a cost of 5 EUR/sample. We applied PotatoMASH to a population of over 700 potato lines. We obtained tetraploid dosage calls for 2012 short multi-allelic haplotypes in 334 loci, which ranged from 2 to 14 different haplotypes per locus. The system was able to diagnose the presence of targeted pest-resistance markers, to detect quantitative trait loci (QTLs) by genome-wide association studies (GWAS) in a tetraploid population, and to track variation in a diploid segregating population. PotatoMASH efficiently surveys genetic variation throughout the potato genome, and can be implemented as a single low-cost genotyping platform that will allow the routine and simultaneous application of marker-assisted selection (MAS) and other genotyping applications in commercial potato breeding programmes. [ABSTRACT FROM AUTHOR]

Aims: Zinc biofortification through agronomic and/or genetic approaches is one of the strategies to enrich food with this essential element to fulfil nutritional requirements in poor diets. This study aimed to unravel the physiological basis of differential tuber-Zn concentration between potato cultivars and to identify the major source(s) of Zn to the tubers. Methods: Two potato cultivars, accumulating high (Lady Rosetta) and low (Cara) tuber-Zn, were evaluated and the patterns of biomass and Zn accumulation between organs assessed over the growth period. Furthermore, Zn partition in reciprocal grafted plants and in sixteen F1 genotypes following a cross between those cultivars was assessed at harvest. Results: The cultivars differed in Zn-concentration, Zn-content and biomass partitioning between organs, although total plant-Zn content was comparable (4.7 and 5.1 mg Zn/plant for Cara and Lady Rosetta, respectively). At harvest the relative amount of Zn retained in roots, stems, leaves and tubers was 2 %,25 %,5 % and 68 % for Cara and 1 %,17 %,5 % and 77 % for Lady Rosetta. The differential tuber-Zn was associated with internal Zn distribution between shoots and tubers. Lady Rosetta translocated higher amounts of Zn to the tubers while Cara accumulated relatively more Zn in the stems associated with higher stem biomass. Remobilization of Zn from leaves and stems, and continuous root to xylem-phloem transfers during tuber bulking were the major sources of Zn supply to the tubers. Conclusions: This study suggests that the potato stem plays an important role in regulating Zn distribution and also as a site for Zn deposition. [ABSTRACT FROM AUTHOR]

Aim: Potato cultivars vary in biomass production and Cd concentration. Differences in growth can lead to differences in tuber cadmium (Cd) concentration through growth dilution and/or limited uptake of Cd from the soil. The aims of this study were to investigate the relative importance of shoot (above ground plant parts) and root in dry weight (DW) accumulation, total Cd uptake and Cd distribution between organs and how this affects tuber Cd concentration.Materials and methods: Three experiments were carried out, two with reciprocal grafting between high and low tuber Cd accumulating cultivars under two soil Cd conditions, and the other was involving the evaluation of F1 genotypes, from a cross between these high and low tuber Cd accumulating cultivars. These experiments were carried out under controlled greenhouse conditions.Results: The results showed that the root system is important for total Cd uptake but less important for growth and Cd distribution between organs. On the other hand, the shoot system is important for regulating growth of shoot and roots, and for determining Cd distribution between organs.Conclusion: The data suggest that tuber Cd concentration was mainly regulated by shoot source and to a lesser extent by total uptake of Cd. [ABSTRACT FROM AUTHOR]

Potatoes grown in soil with high Cd concentrations can accumulate high levels of Cd in the tubers. Although there is significant environmental variation involved in the trait of crop uptake of Cd, there are also distinctive cultivar differences. In order to understand this differential Cd accumulation mechanism, two potato cultivars were chosen that accumulate high and low levels of Cd in tubers. The patterns of Cd concentration, Cd content and dry weight accumulation of the two cultivars were examined at different stages of plant growth. The data suggest that differences in total Cd uptake and in Cd partitioning among organs are the mechanisms governing differential Cd-tuber accumulation in the two cultivars. The low tuber-Cd accumulator exhibited lower root-to-shoot and shoot-to-tuber translocation driven by higher root and shoot biomass that retained more Cd in roots and shoots, respectively, reducing its movement to the tubers. Higher remobilization and more efficient tuber loading was observed in the high tuber-Cd accumulator, indicating that remobilization of Cd from leaves to tubers was a major factor, not only in tuber-Cd loading, but also in the establishment of differential tuber-Cd levels. Regardless of cultivar differences, the concentration of Cd in the tuber was very low compared to that in other organs suggesting that, despite its high phloem mobility, Cd tends to be sequestered in the shoots. [ABSTRACT FROM AUTHOR]

Background: In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. Results: A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. Conclusions: S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths. [ABSTRACT FROM AUTHOR]

Globodera pallida is a major nematode pest causing severe constraints in many potato production regions worldwide. The most prevalent G. pallida pathotypes are Pa2 and Pa3, which exist in mixed populations referred to as Pa2/3. Due to heterogeneity for avirulence genes within these nematode populations, so far, breeders have failed to identify a single resistance gene source which offers complete resistance. Currently, there are two quantitative trait loci (QTL) available, $$ GpaIV_{adg}^{s} $$ and Gpa5, conferring partial levels of resistance to G. pallida pathotype Pa2/3. The objective of this research was to pyramid $$ GpaIV_{adg}^{s} $$ and Gpa5 through marker-assisted selection to investigate whether or not pyramiding provides increased resistance to G. pallida Pa2/3. We developed a population segregating for both resistance QTLs and, using diagnostic genetic markers (Contig237 and HC), we identified groups of individuals from this population containing each individual QTL, both QTLs simultaneously, and neither QTL. These individuals were assessed for their resistance levels against G. pallida Pa2/3 population Chavornay. We demonstrated that individuals carrying both QTLs showed a significant reduction in the number of cysts formed in comparison to genotypes carrying $$ GpaIV_{adg}^{s} $$ or Gpa5, indicating an additive effect. Overall these results show that MAS-based pyramiding of these QTLs is an effective strategy for breeding cultivars exhibiting very high levels of resistance to G. pallida pathotype Pa2/3. [ABSTRACT FROM AUTHOR]

Quantitative resistance to Globodera pallida pathotype Pa2/3, originally derived from Solanum tuberosum ssp. andigena Commonwealth Potato Collection (CPC) accession 2802, is present in several potato cultivars and advanced breeding lines. One genetic component of this resistance, a large effect quantitative trait locus (QTL) on linkage group IV (which we have renamed GpaIV) has previously been mapped in the tetraploid breeding line 12601ab1. In this study, we show that GpaIV is also present in a breeding line called C1992/31 via genetic mapping in an F1 population produced by crossing C1992/31 with the G. pallida susceptible cultivar Record. C1992/31 is relatively divergent from 12601ab1, confirming that GpaIV is an ideal target for marker-assisted selection in currently available germplasm. To generate markers exhibiting diagnostic potential for GpaIV , three bacterial artificial chromosome clones were isolated from the QTL region, sequenced, and used to develop 15 primer sets generating single-copy amplicons, which were examined for polymorphisms exhibiting linkage to GpaIV in C1992/31. Eight such polymorphisms were found. Subsequently, one insertion/deletion polymorphism, three single nucleotide polymorphisms and a specific allele of the microsatellite marker STM3016 were shown to exhibit diagnostic potential for the QTL in a panel of 37 potato genotypes, 12 with and 25 without accession CPC2082 in their pedigrees. STM3016 and one of the SNP polymorphisms, C237(119), were assayed in 178 potato genotypes, arising from crosses between C1992/31 and 16 G. pallida susceptible genotypes, undergoing selection in a commercial breeding programme. The results suggest that the diagnostic markers would most effectively be employed in MAS-based approaches to pyramid different resistance loci to develop cultivars exhibiting strong, durable resistance to G. pallida pathotype Pa2/3. [ABSTRACT FROM AUTHOR]

Biotechnology-based tools are now widely used to enhance and expand the traditional remit of potato in food production. By modifying its functionality, the capacity of the potato to produce, for example, therapeutic or industrial compounds is now a reality, and its ability to resist disease can also be radically improved. Two developments have been crucial to expanding the role of potato: the recent advances in the fields of structural and functional potato genomics and the ability to integrate genes of interest into the potato genome. In this review we discuss how both developments have diversified the remit of this crop. [Copyright &y& Elsevier]

Potatoes destined for crisping are normally stored above 8 degrees; below this glucose accumulates leading to very dark fry colors and potential acrylamide build up. Unfortunately, sprouting occurs above 4 degrees and impacts product quality, necessitating the use of sprout suppressant chemicals. Therefore, a goal of breeders is to develop potatoes with excellent fry color, which is maintained under storage below 8 degrees. Genomic or marker-assisted selection offers an opportunity to improve the efficiency of potato breeding and thereby assist breeders in achieving this goal. In this study, we have accumulated fry-color data on a large population of potato lines and combined this with genotypic data to carry out a GWAS and to evaluate accuracy of genomic prediction. We were able to identify a major QTL on chromosome 10 for fry color, and predict fry color with moderate accuracy using genome-wide markers. Furthermore, our results provide evidence that it is possible to identify a small subset of SNPs for processing characteristics that can give moderate predictive ability, albeit lower than that achieved with genome-wide markers. [ABSTRACT FROM AUTHOR]

An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in ‘skeleton bin maps,’ which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in ‘bins.’ A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net). [ABSTRACT FROM AUTHOR]

Segregation data were obtained for 1260 potato linkage group I-specific AFLP loci from a heterozygous diploid potato population. Analytical tools that identified potential typing errors and/or inconsistencies in the data and that assembled cosegregating markers into bins were applied. Bins contain multiple-marker data sets with an identical segregation pattern, which is defined as the bin signature. The bin signatures were used to construct a skeleton bin map that was based solely on observed recombination events. Markers that did not match any of the bin signatures exactly (and that were excluded from the calculation of the skeleton bin map) were placed on the map by maximum likelihood. The resulting maternal and paternal maps consisted of 95 and 101 bins, respectively. Markers derived from EcoRI/MseI, PstI/MseI, and SacI/ MseI primer combinations showed different genetic distributions. Approximately three-fourths of the markers placed into a bin were considered to fit well on the basis of an estimated residual "error rate" of 0-3%. However, twice as many PstI-based markers fit badly, suggesting that parental PstI-site methylation patterns had changed in the population. Recombination frequencies were highly variable across the map. Inert, presumably centromeric, regions caused extensive marker clustering while recombination hotspots (or regions identical by descent) resulted in empty bins, despite the level of marker saturation. [ABSTRACT FROM AUTHOR]