• Detection of Novel QTLs for Late Blight Resistance Derived from the Wild Potato Species Solanum microdontum and Solanum pampasense

      Meade, Fergus; Hutten, Ronald; Wagener, Silke; Prigge, Vanessa; Dalton, Emmet; Kirk, Hanne Grethe; Griffin, Denis; Milbourne, Dan; Department of Agriculture, Food and the Marine; IPM Potato Group; et al. (MDPI AG, 2020-06-30)
      Wild potato species continue to be a rich source of genes for resistance to late blight in potato breeding. Whilst many dominant resistance genes from such sources have been characterised and used in breeding, quantitative resistance also offers potential for breeding when the loci underlying the resistance can be identified and tagged using molecular markers. In this study, F1 populations were created from crosses between blight susceptible parents and lines exhibiting strong partial resistance to late blight derived from the South American wild species Solanum microdontum and Solanum pampasense. Both populations exhibited continuous variation for resistance to late blight over multiple field-testing seasons. High density genetic maps were created using single nucleotide polymorphism (SNP) markers, enabling mapping of quantitative trait loci (QTLs) for late blight resistance that were consistently expressed over multiple years in both populations. In the population created with the S. microdontum source, QTLs for resistance consistently expressed over three years and explaining a large portion (21–47%) of the phenotypic variation were found on chromosomes 5 and 6, and a further resistance QTL on chromosome 10, apparently related to foliar development, was discovered in 2016 only. In the population created with the S. pampasense source, QTLs for resistance were found in over two years on chromosomes 11 and 12. For all loci detected consistently across years, the QTLs span known R gene clusters and so they likely represent novel late blight resistance genes. Simple genetic models following the effect of the presence or absence of SNPs associated with consistently effective loci in both populations demonstrated that marker assisted selection (MAS) strategies to introgress and pyramid these loci have potential in resistance breeding strategies.
    • A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages

      Destefanis, M.; Nagy, Istvan; Rigney, Brian; Bryan, Glenn J; McLean, Karen; Hein, Ingo; Griffin, Denis; Milbourne, Dan; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine, Ireland; et al. (Biomed Central, 24/10/2015)
      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.
    • Distribution and incidence of viruses in Irish seed potato crops

      Hutton, Fiona; Spink, John; Griffin, Denis; Kildea, Steven; Bonner, D.; Doherty, G.; Hunter, A. (Teagasc (Agriculture and Food Development Authority), Ireland, 30/12/2015)
      Virus diseases are of key importance in potato production and in particular for the production of disease-free potato seed. However, there is little known about the frequency and distribution of potato virus diseases in Ireland. Despite a large number of samples being tested each year, the data has never been collated either within or across years. Information from all known potato virus testing carried out in the years 2006–2012 by the Department of Agriculture Food and Marine was collated to give an indication of the distribution and incidence of potato virus in Ireland. It was found that there was significant variation between regions, varieties, years and seed classes. A definition of daily weather data suitable for aphid flight was developed, which accounted for a significant proportion of the variation in virus incidence between years. This use of weather data to predict virus risk could be developed to form the basis of an integrated pest management approach for aphid control in Irish potato crops.
    • A note on the early transcriptional response in leaves and root of potato plants to cadmium exposure

      Mengist, M.F.; Byrne, Stephen; Griffin, Denis; Milbourne, Dan; Department of Agriculture, Food and the Marine; 11SF308 (Teagasc, 2021-03-26)
      Potato plants can accumulate a high amount of cadmium (Cd) in the tuber when grown in soils rich in Cd. The molecular mechanisms governing Cd accumulation in the potato plant are poorly understood. Here we performed an RNA-sequencing experiment to identify genes differentially expressed in the leaf and root of potato during early stages of Cd exposure. Results did not identify any significant transcriptional response in leaves under 1 or 5 mg kg−1 Cd after 72 h. However, in the roots we did identify 2,846 genes that were significantly differentially expressed after 72 h between plants grown in 5 mg kg−1 Cd and controls. These included genes involved in photosynthesis and autophagy being up-regulated, and genes involved in intracellular transport being down-regulated. This study is the first report on the transcriptome-wide response of potato to Cd stress, providing insight into the molecular mechanisms involved in the response.
    • Potato Breeding at Oak Park 2000-2006

      Dowley, L.J.; Griffin, Denis (Teagasc, 01/07/2009)
      The potato breeding programme at Oak Park was started in the 1960's and has consisted of a number of distinct phases. In the first phase the focus was on the evaluation of the main domestic and foreign varieties for suitability for the Irish market. This was followed by a breeding programme for the domestic market, with particular emphasis on the production of a blight resistant replacement for Kerr’s Pink. The emphasis then switched to breeding for the export market, with the focus on the UK and Mediterranean markets. Since then the breeding programme has been focused on both the domestic, processing and export markets. The process of breeding, testing and multiplying a new potato variety from the making of the initial cross until the new variety can be commercially grown takes about 15 years (see Appendix 1). This report covers the period 2001-2006 (RMIS NO 4720).
    • Potatoes in Ireland: Sixty years of potato research and development, market evolution and perspectives on future challenges

      Griffin, Denis; Bourke, L.; Mullins, Ewen; Hennessy, M.; Phelan, S.; Kildea, Steven; Milbourne, Dan (Teagasc, 2022-02-25)
      Potato is often considered synonymous with Ireland, due to the great Irish famine in 1845, and remains the most important primary food crop in Ireland. Over the last 60 yr, the area of potatoes has reduced from 86,000 ha to 9,000 ha. This trend has occurred in most developed countries but in Ireland it is due to decreasing consumption, increasing yield, decline in seed production and potatoes no longer being use for animal feed. Significant specialisation occurred in the industry during the 1990s, with improvements in agronomy, on farm investment in storage and field equipment, consolidation of packing facilities, and a significant shift in cultivar choice, with Rooster becoming the dominant cultivar. These developments led to an increase in yield from 20 t/ha in the mid-1980s to over 40 t/ha today. Potato research in Ireland has focused on breeding, pathology and agronomy, while there have been significant changes in how knowledge is communicated to growers and the industry in this period. The industry faces many challenges in the future, largely framed by climate change, the need to reduce fertiliser and plant protection products as part of the EU Farm to Fork Strategy and industry size constraints. New superior potato varieties and novel breeding techniques will have potential to help address many challenges in combination with integrated pest management principles. Multi-actor approaches will be necessary to address all challenges but particularly to aid the industry grow and exploit emerging opportunities.
    • Yield losses caused by late blight (Phytophthora infestans (Mont.) de Bary) in potato crops in Ireland

      Dowley, L.J.; Grant, Jim; Griffin, Denis (Teagasc, Oak Park, Carlow, Ireland, 2008)
      Field experiments, using foliage blight susceptible cultivars, were conducted at Oak Park, Carlow from 1983 to 2007 to determine the loss in potato production caused by crop infection with Phytophthora infestans. In each of the 25 years an untreated control was compared with protectant and with systemic fungicide programmes to determine the effect of late blight on the defoliation percentage at the end of the season, the area under the disease progress curve, marketable tuber yield, total tuber yield and yield of blighted tubers. The earliest date of first recorded late blight was 22 June and the latest was 15 September, but in 15 of the 25 years, blight was first recorded between 17 July and 13 August. Disease reached epidemic proportions in all but 4 of the years. Yields varied considerably among years. The mean loss in total yield from not using a fungicide was 10.1 t/ha. Differences in yield were significant across the 25 seasons. No overall increase in aggressiveness of the pathogen could be detected over the 25-year period.