• Using variable importance measures to identify a small set of SNPs to predict heading date in perennial ryegrass.

      Byrne, Stephen; Conaghan, Patrick; Barth, Susanne; Arojju, Sai Krishna; Casler, Michael; Michel, Thibauld; Velmurugan, Janaki; Milbourne, Dan; E.U. Marie Skłodowska-Curie Fellowship; Teagasc Walsh Fellowship Programme; et al. (Nature, 2017-06-15)
      Prior knowledge on heading date enables the selection of parents of synthetic cultivars that are well matched with respect to time of heading, which is essential to ensure plants put together will cross pollinate. Heading date of individual plants can be determined via direct phenotyping, which has a time and labour cost. It can also be inferred from family means, although the spread in days to heading within families demands roguing in first generation synthetics. Another option is to predict heading date from molecular markers. In this study we used a large training population consisting of individual plants to develop equations to predict heading date from marker genotypes. Using permutation-based variable selection measures we reduced the marker set from 217,563 to 50 without impacting the predictive ability. Opportunities exist to develop a cheap assay to sequence a small number of regions in linkage disequilibrium with heading date QTL in thousands of samples. Simultaneous use of these markers in non-linkage based marker-assisted selection approaches, such as paternity testing, should enhance the utility of such an approach.
    • Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae)

      Barth, Susanne; Jankowska, Marta J; Hodkinson, Trevor R; Vellani, Tia; Klaas, Manfred; European Union; KBBE-2011-5-289461). (Biomed Central, 22/03/2016)
      Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3 % Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.
    • 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.