Genomic Resources and Tools for Gene Function Analysis in Potato

Potato, a highly heterozygous tetraploid, is undergoing an exciting phase of genomics resource development. The potato research community has established extensive genomic resources, such as large expressed sequence tag (EST) data collections, microarrays and other expression profiling platforms, and large-insert genomic libraries. Moreover, potato will now benefit from a global potato physical mapping effort, which is serving as the underlying resource for a full potato genome sequencing project, now well underway. These tools and resources are having a major impact on potato breeding and genetics. The genome sequence will provide an invaluable comparative genomics resource for cross-referencing to the other Solanaceae, notably tomato, whose sequence is also being determined. Most importantly perhaps, a potato genome sequence will pave the way for the functional analysis of the large numbers of potato genes that await discovery. Potato, being easily transformable, is highly amenable to the investigation of gene function by biotechnological approaches. Recent advances in the development of Virus Induced Gene Silencing (VIGS) and related methods will facilitate rapid progress in the analysis of gene function in this important crop

Generation and Screening of a BAC Library from a Diploid Potato Clone to Unravel Durable Late Blight Resistance on Linkage Group IV

We describe the construction and screening of a large insert genomic library from the diploid potato clone HB171(13) that has been shown to express durable quantitative field resistance to Phytophthora infestans, the causal agent of potato late blight disease. Integrated genetic mapping of the field resistance quantitative trait locus with markers developed from populations segregating for Rpi-blb3, Rpi-abpt, R2, and R2-like resistance, all located on linkage group IV, has positioned the field resistance QTL within the proximity of this R gene cluster. The library has been successfully screened with resistance gene analogues (RGA) potentially linked to the R gene cluster. Over 30 positive BAC clones were identified and confirmed by PCR and Southern hybridisations to harbour RGA-like sequences. In addition, BAC end sequencing of positive clones has corroborated two BAC clones with a very high level of nucleotide similarity to the RGA probes utilised

Environmental and genetic factors associated with Solanesol accumulation in potato leaves

Solanesol is a high value 45-carbon, unsaturated, all-trans-nonaprenol isoprenoid. Recently solanesol has received particular attention because of its utility, both in its own right and as a precursor in the production of numerous compounds used in the treatment of disease states. Solanesol is found mainly in solanaceous crops such as potato, tomato, tobacco and pepper where it accumulates in the foliage. There is considerable potential to explore the extraction of solanesol from these sources as a valuable co-product. In this study we have characterised the genetic variation in leaf solanesol content in a biparental, segregating diploid potato population. We demonstrate that potato leaf solanesol content is genetically controlled and identify several quantitative trait loci associated with leaf solanesol content. Transient over-expression of genes from the methylerythritol 4-phosphate (MEP) and mevalonic acid (MVA) pathways, either singly or in combination, resulted in enhanced accumulation of solanesol in leaves of Nicotiana benthamiana, providing insights for genetically engineering the pathway. We also demonstrate that in potato, leaf solanesol content is enhanced by up to six-fold on exposure to moderately elevated temperature and show corresponding changes in expression patterns of MEP and MVA genes. Our combined approaches offer new insights into solanesol accumulation and strategies for developing a bio-refinery approach to potato production

Characterisation and mapping of a <i>Globodera pallida</i> resistance derived from the wild potato species <i>Solanum spegazzinii</i>

The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato

Characterisation and mapping of a <i>Globodera pallida</i> resistance derived from the wild potato species <i>Solanum spegazzinii</i>

The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato

How Bulk Sensitive is Hard X-ray Photoelectron Spectroscopy: Accounting for the Cathode-Electrolyte Interface when Addressing Oxygen Redox.

Sensitivity to the "bulk" oxygen core orbital makes hard X-ray photoelectron spectroscopy (HAXPES) an appealing technique for studying oxygen redox candidates. Various studies have reported an additional O 1s peak (530-531 eV) at high voltages, which has been considered a direct signature of the bulk oxygen redox process. Here, we find the emergence of a 530.4 eV O 1s HAXPES peak for three model cathodes-Li2MnO3, Li-rich NMC, and NMC 442-that shows no clear link to oxygen redox. Instead, the 530.4 eV peak for these three systems is attributed to transition metal reduction and electrolyte decomposition in the near-surface region. Claims of oxygen redox relying on photoelectron spectroscopy must explicitly account for the surface sensitivity of this technique and the extent of the cathode degradation layer

Natural resistance to Potato virus Y in <i>Solanum tuberosum</i> Group Phureja

This work was supported by funding from the Scottish Government’s Rural and Environmental Science and Analytical Services (RESAS) Division.A new source of genetic resistance derived from Solanum tuberosum Group Phureja against Potato virus Y (PVY) was identified and genetically characterised in three diploid biparental potato populations. Segregation data for two populations (05H1 and 08H1) suggested the presence of a single dominant gene for resistance to PVY which, following DaRT analysis of the 08H1 cross, was mapped to chromosome 9. More detailed genetic analysis of resistance utilised a well-characterised SNP-linkage map for the 06H1 population, together with newly generated marker data. In these plants, which have both S. tuberosum Group Phureja and S. tuberosum Group Tuberosum in their pedigree, the resistance was shown to map to chromosome 9 at a locus not previously associated with PVY resistance, although there is evidence for at least one other genetic factor controlling PVY infection. The resistance factor location on chromosome 9 (named as Ry(o)phu) suggests a potential role of NB-LRR genes in this resistance. Phenotypic analysis using a GUS-tagged virus revealed that a small amount of PVY replication occurred in occasional groups of epidermal cells in inoculated leaves of resistant plants, without inducing any visible hypersensitive response. However, the virus did not enter the vascular system and systemic spread was completely prevented.Publisher PDFPeer reviewe

A critical comparison of technologies for a plant genome sequencing project

BACKGROUND: A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read-only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates. RESULTS: Here, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs. CONCLUSIONS: The field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.</p

Effective management of ecological resilience – are we there yet?

1. Ecological resilience is developing into a credible paradigm for policy development and environmental management for preserving natural capital in a rapidly changing world. However, resilience emerges from complex interactions, limiting the translation of theory into practice. 2. Main limitations include the following: (i) difficulty in quantification and detection of changes in ecological resilience, (ii) a lack of empirical evidence to support preventative or proactive management and (iii) difficulties in managing processes operating across socio-ecological systems that vary in space and time. 3. We highlight recent research with the potential to address these limitations including new and/or improved indicators of resilience and tools to assess scale as a driver of resilience. 4. Synthesis and applications. Effective resilience-based management must be adaptive in nature. To support this, we propose an operational model using resilience-based iterative management actions operating across scales

TERMINAL FLOWER-1/CENTRORADIALIS inhibits tuberization via protein interaction with the tuberigen activation complex

This work was funded by the Scottish Government Rural and Environment Science and Analytical Services Division as part of the Strategic Research Programme 2016-2021, by a GCRF Foundation Awards for Global Agricultural and Food Systems Research funded by the BBSRC project BB/P022553/1 and also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement number 835704. Research in Prat’s lab was funded by the Spanish Ministerio de Economía y Competitividad BIO2015-73019-EXP, and the aligned Japan EIG CONCERT (PIA102017-1) projects.Potato tuber formation is a secondary developmental program by which cells in the subapical stolon region divide and radially expand, to further differentiate into starch accumulating parenchyma. Whilst some details of the molecular pathway that signals tuberization are known, important gaps in our knowledge persist. Here the role of a member of the TERMINAL FLOWER 1/ CENTRORADIALIS gene family (termed StCEN ) in the negative control of tuberization is demonstrated for the first time. It is shown that reduced expression of StCEN accelerates tuber formation whereas transgenic lines over‐expressing this gene display delayed tuberization and reduced tuber yield. Protein‐protein interaction studies (yeast two hybrid and bimolecular fluorescence complementation) demonstrate that StCEN binds components of the recently described tuberigen activation complex. Using transient transactivation assays we show that the StSP6A tuberization signal is an activation target of the tuberigen activation complex, and that co‐expression of StCEN blocks StFD‐Like‐1 activation of the StSP6A gene. Transcriptomic analysis of transgenic lines mis‐expressing StCEN identify early transcriptional events in tuber formation. These results demonstrate that StCEN suppresses tuberization by directly antagonizing StSP6A function in stolons, identifying StCEN as a breeding marker to improve tuber initiation and yield, through the selection of genotypes with reduced StCEN expression.Publisher PDFPeer reviewe