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Stephen Byrne

Research Officer

Research Interests

My research is focussed on plant genetics and genomics, and in particular on using genomics in the breeding of plant varieties that will add value to Irish agriculture. I am interested in genome assembly and annotation, using sequencing to directly characterise genetic variation across populations, genome wide association studies, and genomic prediction.

Current Projects

H2020-MSCA-IF-2014 – 658031 – GenSPI: Genomic Selection for Potato Improvement

  • Byrne S, Nagy I, Pfeifer M, Armstead I, Swain S, Studer B, Mayer K, Campbell JD, Czaban A, Hentrup S, Panitz F, Bendixen C, Hedegaard J, Caccamo M, Asp T, 2015. A synteny-based draft genome sequence of the forage grass Lolium perenne. The Plant Journal (DOI: 10.1111/tpj.13037).
  • Ashraf B, Byrne S, Fè D, Czaban S, Asp T, Greve Pedersen M, Lenk I, Roulund N,Didion T,  Jensen CS,  Jensen J, Janss L, 2015. Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing. Theoretical and Applied Genetics (DOI: 10.1007/s00122-015-2607-9).
  • Yu X, Pijut PM, Byrne S, Asp T, Bai G, Jiang Y, 2015. Candidate gene association mapping for winter survival and spring regrowth in perennial ryegrass. Plant Science 235, 37-45.
  • Abeynayake SW, Etzerodt TP, Jonavi-ìien-ù K, Byrne S, Asp T, Boelt B, 2015. Fructan metabolism and changes in fructan composition during cold acclimation in perennial ryegrass. Frontiers in Plant Science, 6: 329.
  • Parijs FRD, Ruttink T, Boerjan W, Haesaert G, Byrne SL, Asp T, Roldán‐Ruiz I, Muylle H, 2015. Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne. Plant Biology, 17(4):877-92.
  • Czaban A, Sharma S, Byrne SL, Spannagl M, Mayer KFX, Asp T, 2015. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation. BMC Genomics 16 (1), 249.
  • Phelan S, Fitzgerald T, Grant J, Byrne S, Meade C, Mullins E, 2015. Propensity for seed-mediated gene flow from potato crops and potential consequences for the coexistence of GM and non-GM potato systems. European Journal of Agronomy 67, 52-60.
  • Foito A, Hackett CA, Byrne SL, Stewart D, Barth S (2015) Quantitative trait loci analysis to study the genetic regulation of non-polar metabolites in perennial ryegrass. Metabolomics 11:412-424.
  • Farrell JD, Byrne S, Paina C, Asp T (2014) De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy. PLoS ONE 9(8): e103567.
  • Paina C, Byrne SL, Domnisoru C, Asp T (2014) Vernalization mediated changes in the Lolium perenne transcriptome. PLoS ONE 9(9): e107365.
  • Pfeiffer M, Martis M, Asp T, Mayer KFX, Lübberstedt T, Byrne S, Frei U, Studer, B. 2013. The perennial ryegrass GenomeZIpper – Targeted use of Genome Resources for Comparative Grass Genomics. Plant Physiology, 161: 571-582
  • Shofiqul I, Studer B, Byrne S, Farrell JD, Panitz F, Bendixen C, Møller IM, Asp T. 2013. The genome and transcriptome of perennial ryegrass mitochondria. BMC Genomics, 14:202
  • Byrne S, Czaban A, Studer B, Panitz F, Bendixen C, Asp T. 2013. Genome Wide Allele Frequency Fingerprints (GWAFFs) of populations via genotyping by sequencing. PLOS ONE, 8(3): e57438
  • Studer, B, Byrne, S, Nielsen, R, Panitz, F, Bendixen, C, Islam, MS, Pfeiffer, M, Lübberstedt, T & Asp, T,   2012. A transcriptome map of perennial ryegrass (Lolium perenne L.)', BMC Genomics, 13:140.
  • Foito A, Byrne SL, Hackett CA,  Stewart D and Barth S 2012 Short-term response in leaf metabolism of perennial ryegrass (Lolium perenne) to alterations in nitrogen supply. Metabolomics.  9(1):145-156.
  • Tomaszewski C, Byrne S, Foito A,  Kildea  S, Kopecký D, Doležel J, Heslop-Harrison PJS, Stewart D, Barth S 2011 Genetic linkage mapping in an F2 perennial ryegrass population using DArT markers. Plant Breeding, 131 (2),  345-349.
  •   Asp TByrne SGundlach HBruggmann RMayer KFAndersen JR, Xu M, Greve MLenk ILübberstedt T 2011 Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice.Molecular Genetics and Genomics. 286:433-447.
  • Byrne SL*,  Foito A*, Hedley PE, Morris JA, Stewart D and Barth S 2010 Early response mechanisms of perennial ryegrass (Lolium perenne) to phosphorus deficiency. Annals of Botany, 107(2): 243–254.
  • Byrne SL, Durandeau K, Nagy I and Barth S 2010 Identification of ABC transporters from Lolium perenne L. that are regulated by toxic levels of selenium. Planta 231, 901-911.
  • Foito A*, Byrne SL*, Shepherd T, Stewart D and Barth S 2009 Transcriptional and metabolic profiles of Lolium perenne L. genotypes in response to a PEG-induced water stress. Plant Biotechnology Journal 7, 719-732.
  • Byrne S, Guiney E, Barth S, Donnison I, Mur LAJ and Milbourne D 2009 Identification of coincident QTL for days to heading, spike length and spikelets per spike in Lolium perenne L. Euphytica 166, 61-70.
  • Byrne SL, Guiney E, Donnison I S, Mur LAJ , Milbourne D and Barth S 2009 Identification of genes involved in the floral transition at the shoot apical meristem of Lolium perenne L. by use of suppression subtractive hybridisation. Plant Growth Regulation 59, 215-225.
  • Anhalt U C M, Heslop-Harrison J S, Piepho H P, Byrne S and Barth S 2009 Quantitative trait loci mapping for biomass yield traits in a Lolium inbred line derived F-2 population. Euphytica 170, 99-107.
  • Anhalt U C M, Heslop-Harrison P, Byrne S, Guillard A and Barth S 2008 Segregation distortion in Lolium: evidence for genetic effects. Theoretical and Applied Genetics 117, 297-306.