• Evaluation of Lolium perenne L. cv. AberDart and AberDove for silage production

      Conaghan, Patrick; O'Kiely, Padraig; Howard, H.; O'Mara, Frank P.; Halling, M.A.; European Union; Teagasc Walsh Fellowship Programme; QLK5-CT-2001-0498 (Teagasc, Oak Park, Carlow, Ireland, 2008)
      The objective of this study was to assess the value, for silage production, of intermediateheading Lolium perenne L. cultivars, AberDart and AberDove (diploid), bred for increased water-soluble carbohydrate (WSC) concentrations, relative to four control cultivars (Fennema, AberElan and Spelga (diploid), and Greengold (tetraploid)). Cultivars were evaluated for forage dry matter (DM) yield, ground cover and indirect laboratory measures of nutritional value and ensilability over 3 harvest years within intensive silage-production systems. AberDove was the most desirable diploid for silage production producing on average 316 kg/ha higher (2%) DM yield per annum, having a 10 g/kg higher (1%) dry matter digestibility (DMD) and, based primarily on a 6 g/L higher (19%) concentration of WSC expressed in the aqueous extract (WSCAE), offered the greatest potential to produce well preserved silage. Ensiling AberDart compared to the diploid controls offered a slightly greater probability of producing well preserved silage based on a modest increase of 2 g/L (6%) in WSCAE concentration. The dilemma for silage production is that AberDart, on average produced 558 kg/ha less (4%) DM yield per annum but had a greater (1%) DMD of 6 g/kg than the diploid controls. The tetraploid control had, on average, 13 and 8 g/kg higher (2% and 1%, respectively) DMD than AberDart and AberDove, but at a cost of lower ensilability with lower (6% and 21%, respectively) WSCAE values of 2 and 6 g/L. In its favour, the tetraploid control outyielded AberDart by, on average, 917 kg/ha DM per annum (7%) and produced comparable yields to AberDove. Final ground cover ratings were high (≥ 95%) for all cultivars. Evaluation of nutritional value and ensilability offers further grounds to differentiate and select cultivars for animal production potential.
    • Genomic prediction of crown rust resistance in Lolium perenne

      Arojju, Sai Krishna; Conaghan, Patrick; Barth, Susanne; Milbourne, Dan; Casler, M.D.; Hodkinson, Trevor R; Michel, Thibauld; Byrne, Stephen L.; Department of Agriculture, Food and the Marine, Ireland; Marie Sklodowska-Curie; et al. (Biomed Central, 29/05/2018)
      Background Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. Results Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. Conclusion Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
    • Grazing and ensiling of energy-rich grasses with elevated sugar contents for the sustainable production of ruminant livestock (Acronym: SweetGrass)

      O'Kiely, Padraig; Conaghan, Patrick; Howard, H.; Moloney, Aidan P; Black, Alistair D; European Union; QLK5-CT-2001-0498 (Teagasc, 2005-09-01)
      Permanent grassland dominates the Irish landscape and for many decades perennial ryegrasses have been the main constituent in seed mixtures for grassland.
    • Influence of testing procedure on evaluation of white clover (Trifolium repens L.)

      Gilliland, T. J.; McGilloway, D.; Conaghan, Patrick (Teagasc, Oak Park, Carlow, Ireland, 2009)
      This study examined data sets derived from the white clover cultivar evaluation programmes of AFBI (N. Ireland), and DAFF (Republic of Ireland) to determine whether elite performing genotypes are identifiable, independent of test procedure and leaf size factors. Genetic variation in yield and persistency, independent of the leaf size continuum effect, was observed. Identification of elite cultivars by breeders or testers therefore required readjustment of assessment standards to account for the mostly curvilinear relationships between performance and leaf size. The different testing procedures, involving cutting or grazing at different heights, frequencies and nitrogen rates changed the relative performances between the cultivars, making it difficult to predict performance potential beyond specific test conditions. The underlying causes for these changes in rankings was considered, including sensitivity to season and location, the antagonistic affects of defoliation pressure and companion grass competition, the independence of different seasonal profiles and the probable role of other morphological characteristics. In is concluded that testing authorities must calculate the management by leaf size relationships to adjust pass/fail standards if elite performing cultivars are to be correctly indentified.
    • Irish Grassland Research — main achievements and advancements in the past 60 yrs and where to progress to next

      O’Donovan, Michael; Dillon, P.; Conaghan, Patrick; Hennessy, Deirdre (Teagasc, 2022-02-09)
      In the last 60 yr Irish grassland production has increased substantially in no small part due to high-quality fundamental grassland research. Increased production from grassland has arisen from improved understanding (research and practice) of soil and plant nutrition, plant physiology and variety improvement, while improved understanding of feed evaluation, ruminant nutrition, grazing management and silage technology has contributed to increased utilisation of grassland. Annual grass DM production varies from 12.7 to 15.0 t DM/ha based on Department of Agriculture, Food and the Marine grass variety trials. More recent data from PastureBase Ireland indicate that average annual grass production (2020) on efficient dairy and dry stock farms is 13.5 and 10.0 t DM/ha, respectively. Ireland is now one of the world leaders in grassland research, particularly in the area of grazing utilisation, the development and use of grassland databases, decision support systems and grass selection indices for grass varieties. Future pasture-based systems must extend beyond food production to deliver additional benefits to farmers, to consumers and the wider society. Future systems will require more robust grazing animals with healthier functional traits, more diverse swards supporting improved animal performance and require fewer fertiliser and chemical inputs, and will support more biodiversity and enhanced carbon storage.
    • Markers associated with heading and aftermath heading in perennial ryegrass full-sib families

      Arojju, Sai Krishna; Barth, Susanne; Milbourne, Dan; Conaghan, Patrick; Velmurugan, Janaki; Hodkinson, Trevor R; Byrne, Stephen L.; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; EU Marie-Sklodowska-Curie Fellowship; et al. (Biomed Central, 16/07/2016)
      Background Heading and aftermath heading are important traits in perennial ryegrass because they impact forage quality. So far, genome-wide association analyses in this major forage species have only identified a small number of genetic variants associated with heading date that overall explained little of the variation. Some possible reasons include rare alleles with large phenotypic affects, allelic heterogeneity, or insufficient marker density. We established a genome-wide association panel with multiple genotypes from multiple full-sib families. This ensured alleles were present at the frequency needed to have sufficient statistical power to identify associations. We genotyped the panel via partial genome sequencing and performed genome-wide association analyses with multi-year phenotype data collected for heading date, and aftermath heading. Results Genome wide association using a mixed linear model failed to identify any variants significantly associated with heading date or aftermath heading. Our failure to identify associations for these traits is likely due to the extremely low linkage disequilibrium we observed in this population. However, using single marker analysis within each full-sib family we could identify markers and genomic regions associated with heading and aftermath heading. Using the ryegrass genome we identified putative orthologs of key heading genes, some of which were located in regions of marker-trait associations. Conclusion Given the very low levels of LD, genome wide association studies in perennial ryegrass populations are going to require very high SNP densities. Single marker analysis within full-sibs enabled us to identify significant marker-trait associations. One of these markers anchored proximal to a putative ortholog of TFL1, homologues of which have been shown to play a key role in continuous heading of some members of the rose family, Rosaceae.
    • A theoretical and practical analysis of the optimum breeding system for perennial ryegrass

      Conaghan, Patrick; Casler, M.D. (Teagasc (Agriculture and Food Development Authority), Ireland, 2011)
      The goal of plant breeding is to effectively and efficiently select for the best phenotypes leading to the development of improved cultivars. The objectives for this review are to describe and critically evaluate breeding methods appropriate to the improvement of perennial ryegrass (Lolium perenne L.) in a long-term breeding programme. The optimum breeding system is dependent on the traits for improvement, and the available physical and human resources. Forage dry matter yield, persistency, disease resistance, nutritional value and seed yield are considered among the most important traits for improvement. Careful consideration should be given to the expression of the trait under the management regime imposed in the breeding programme and under real-world sward conditions in the target sowing region. Recurrent selection programmes for intrapopulation improvement are most appropriate for breeding perennial ryegrass. Three distinct types of recurrent selection may be implemented: (i) phenotypic recurrent selection, (ii) genotypic recurrent selection and (iii) marker-assisted selection. Genotypic recurrent selection will be a necessary part of the breeding system if forage yield is a trait for improvement. Genotypic recurrent selection may be practiced using full-sib or half-sib families, each with their own advantages and disadvantages. Phenotypic recurrent selection in tandem (i.e., within-family selection) or in succession with genotypic recurrent selection should be used to improve traits that have a high-correlation between performance from spaced plants and from sward plots. Genome-wide selection represents the most interesting and exciting potential application of marker-assisted selection, although it remains to be seen how beneficial it will be in practice.
    • 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.