University of Dundee

2019

Andrews M, Condron LM, Kemp PD, Topping JF, Lindsey K, Hodge S, Raven JA. 2019. Elevated CO2 effects on nitrogen assimilation and growth of C3 vascular plants are similar regardless of N-form assimilated. Journal of Experimental Botany. 70(2):683-690. https://doi.org/10.1093/jxb/ery371

Armstrong M, Vossen JH, Lim JT-Y, Hutten RCB, Xu J, Strachan SM, Harrower B, Champouret N, Gilroy EM, Hein I. 2019. Tracking disease resistance deployment in potato breeding by enrichment sequencing. Plant Biotechnology Journal. 17(2):540-549. https://doi.org/10.1111/pbi.12997

Bayer M, Morris JA, Booth C, Booth A, Uzrek N, Russell JR, Waugh R, Hedley PE. 2019. Exome Capture for Variant Discovery and Analysis in Barley. Harwood WA, editor. In Barley: Methods and Protocols. New York: Humana Press. pp. 283-310. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8944-7_18

Bielska E, Birch PRJ, Buck AH, Abreu-Goodger C, Innes RW, Jin H, Pfaffl MW, Robatzek S, Regev-Rudzki N, Tisserant C, Wang S, Weiberg A. 2019. Highlights of the mini-symposium on extracellular vesicles in inter-organismal communication, held in Munich, Germany, August 2018. Journal of Extracellular Vesicles. 8(1):1-8. https://doi.org/10.1080/20013078.2019.1590116

Boldrin D, Leung AK, Bengough AG, Jones HG. 2019. Potential of thermal imaging in soil bioengineering to assess plant ability for soil water removal and air cooling. Ecological Engineering. 141:1-6. https://doi.org/10.1016/j.ecoleng.2019.105599

Bustos-Korts D, Dawson IK, Russell J, Tondelli A, Guerra D, Ferrandi C, Strozzi F, Nicolazzi EL, Molnar-Lang M, Ozkan H, Megyeri M, Miko P, Çakır E, Yakışır E, Trabanco N, Delbono S, Kyriakidis S, Booth A, Cammarano D, Mascher M, Werner P, Cattivelli L, Rossini L, Stein N, Kilian B, Waugh R, van Eeuwijk FA. 2019. Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. Plant Journal. 99(6):1172-1191. https://doi.org/10.1111/tpj.14414

Calixto C, Tzioutziou N, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown J. 2019. Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. Frontiers in Plant Science. 10:1-16. https://doi.org/10.3389/fpls.2019.00235

Caradonia F, Ronga D, Catellani M, Azevedo CVG, Alegria Terrazas R, Robertson-Albertyn S, Francia E, Bulgarelli D. 2019. Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants. Phytobiomes Journal . 3(4):315-325. https://doi.org/10.1094/PBIOMES-06-19-0028-R

Colas I, Barakate A, Macaulay M, Schreiber M, Stephens J, Vivera S, Halpin C, Waugh R, Ramsay L. 2019. desynaptic5 carries a spontaneous semi-dominant mutation affecting Disrupted Meiotic cDNA 1 in barley. Journal of Experimental Botany. 70(10):2683-2698. https://doi.org/10.1093/jxb/erz080

Coulter M, Büttner B, Hofmann K, Bayer M, Ramsay L, Schweizer G, Waugh R, Looseley ME, Avrova A. 2019. Characterisation of barley resistance to rhynchosporium on chromosome 6HS. Theoretical and Applied Genetics. 132(4):1089-1107. https://doi.org/10.1007/s00122-018-3262-8

Daly P, McClellan C, Maluk M, Oakey H, Lapierre C, Waugh R, Stephens J, Marshall D, Barakate A, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. 2019. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. Plant Biotechnology Journal. 17(3):594-607. https://doi.org/10.1111/pbi.13001

Dantas LLB, Calixto CPG, Dourado MM, Carneiro MS, Brown JWS, Hotta CT. 2019. Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. Frontiers in Plant Science. 10:1-15. https://doi.org/10.3389/fpls.2019.01614

Darrier B, Russell J, Milner SG, Hedley PE, Shaw PD, Macaulay M, Ramsay L, Halpin C, Mascher M, Fleury DL, Langridge P, Stein N, Waugh R. 2019. A comparison of mainstream genotyping platforms for the evaluation and use of barley genetic resources. Frontiers in Plant Science. 10:1-14. https://doi.org/10.3389/fpls.2019.00544

Duan Y, Duan S, Armstrong M, Xu J, Zheng J, Hu J, Chen X, Hein I, Li G, Jin L. 2019. Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans. G3: Genes, Genomes, Genetics. 10(2):623-634. https://doi.org/10.1534/g3.119.400818

Escudero-Martinez C, Bulgarelli D. 2019. Tracing the evolutionary routes of plant-microbiota interactions. Current Opinion in Microbiology. 49:34-40. https://doi.org/10.1016/j.mib.2019.09.013

Froussios K, Schurch N, Mackinnon K, Gierlinski M, Duc C, Simpson G, Barton G. 2019. How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in A. thaliana. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz089

Froussios K, Mourao K, Simpson G, Barton G, Schurch N. 2019. Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq [version 1; referees: 1 approved, 2 approved with reservations]. F1000 Research. 8:1-20. https://doi.org/10.12688/f1000research.17916.1

Garcia-Gimenez G, Russell J, Aubert MK, Fincher GB, Burton RA, Waugh R, Tucker MR, Houston K. 2019. Barley grain (1,3;1,4)-β-glucan content: effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes. Scientific Reports. 9:1-11. https://doi.org/10.1038/s41598-019-53798-8

Gleason FH, Larkum AWD, Raven JA, Manohar CS, Lilje O. 2019. Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments. Fungal Ecology. 39:380-387. https://doi.org/10.1016/j.funeco.2018.12.011

Godoy Herz MA, Kubaczka MG, Brzyżek G, Servi L, Krzyszton M, Simpson C, Brown J, Swiezewski S, Petrillo E, Kornblihtt AR. 2019. Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation. Molecular Cell. 73(5):1066-1074.e3. https://doi.org/10.1016/j.molcel.2018.12.005

Gómez-Consarnau L, Raven JA, Levine NM, Cutter LS, Wang D, Seegers B, Arístegui J, Fuhrman JA, Gasol JM, Sañudo-Wilhelmy SA. 2019. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Science Advances. 5(8):1-8. https://doi.org/10.1126/sciadv.aaw8855

Halpin C. 2019. Lignin engineering to improve saccharification and digestibility in grasses. Current Opinion in Biotechnology. 56:223-229. https://doi.org/10.1016/j.copbio.2019.02.013

Hurd CL, Beardall J, Comeau S, Cornwall CE, Havenhand JN, Munday PL, Parker LM, Raven JA, McGraw CM. 2019. Ocean acidification as a multiple driver: How interactions between changing seawater carbonate parameters affect marine life. Marine and Freshwater Research. https://doi.org/10.1071/MF19267

Hurst CH, Turnbull D, Hemsley PA. 2019. Determination of Protein S-Acylation State by Enhanced Acyl-Switch Methods. Linder ME, editor. In Protein Lipidation: Methods and Protocols. New York: Springer . pp. 3-11. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9532-5_1

Hurst C, Wright KM, Turnbull D, Leslie K, Jones S, Hemsley P. 2019. Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function. Scientific Reports. 9:1-9. https://doi.org/10.1038/s41598-019-49302-x

Jones HG, Hutchinson PA, May T, Jamali H, Deery DM. 2019. Corrigendum to “A practical method using a network of fixed infrared sensors for estimating crop canopy conductance and evaporation rate” [Biosystems Engineering 165 (2018) 59–69]. Biosystems Engineering. 179:155-156. https://doi.org/10.1016/j.biosystemseng.2018.12.008

Jouet A, Saunders DGO, McMullan M, Ward B, Furzer O, Jupe F, Cevik V, Hein I, Thilliez GJA, Holub E, Oosterhout CV, Jones JDG. 2019. Albugo candida race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field. New Phytologist. 221(3):1529-1543. https://doi.org/10.1111/nph.15417

Kim M, Pernice M, Watson-Lazowski A, Guagliardo P, Kilburn MR, Larkum AWD, Raven JA, Ralph PJ. 2019. Effect of reduced irradiance on 13C uptake, gene expression and protein activity of the seagrass Zostera muelleri. Marine Environmental Research. 149:80-89. https://doi.org/10.1016/j.marenvres.2019.06.004

Langridge P, Waugh R. 2019. Harnessing the potential of germplasm collections. Nature Genetics. 51(2):200-201. https://doi.org/10.1038/s41588-018-0340-4

Leles SG, Mitra A, Flynn KJ, Tillmann U, Stoecker D, Jeong HJ, Burkholder JA, Hansen PJ, Caron DA, Glibert PM, Hallegraeff G, Raven JA, Sanders RW, Zubkov M. 2019. Sampling bias misrepresents the biogeographical significance of constitutive mixotrophs across global oceans. Global Ecology and Biogeography. 28(4):418-428. https://doi.org/10.1111/geb.12853

Lewandowska D, Zhang R, Colas I, Uzrek N, Waugh R. 2019. Application of a Sensitive and Reproducible Label-Free Proteomic Approach to Explore the Proteome of Individual Meiotic-Phase Barley Anthers. Frontiers in Plant Science. 10:1-15. https://doi.org/10.3389/fpls.2019.00393

Leybourne DJ, Valentine TA, Robertson JAH, Pérez-Fernández E, Main AM, Karley AJ, Bos J. 2019. Defence gene expression and phloem quality contribute to mesophyll and phloem resistance to aphids in wild barley. Journal of Experimental Botany. 70(15):4011-4026. https://doi.org/10.1093/jxb/erz163

Macreadie PI, Anton A, Raven JA, Beaumont N, Connolly RM, Friess DA, Kelleway JJ, Kennedy H, Kuwae T, Lavery PS, Lovelock CE, Smale DA, Apostolaki ET, Atwood TB, Baldock J, Bianchi TS, Chmura GL, Eyre BD, Fourqurean JW, Hall-Spencer JM, Huxham M, Hendriks IE, Krause-Jensen D, Laffoley D, Luisetti T, Marbà N, Masque P, McGlathery KJ, Megonigal JP, Murdiyarso D, Russell BD, Santos R, Serrano O, Silliman BR, Watanabe K, Duarte CM. 2019. The future of Blue Carbon science. Nature Communications. 10(1):1-13. https://doi.org/10.1038/s41467-019-11693-w

McKim S. 2019. How Plants Grow Up. Journal of Integrative Plant Biology . 61(3):257-277. https://doi.org/10.1111/jipb.12786

Melandri G, Prashar A, Mccouch SR, Van Der Linden G, Jones HG, Kadam N, Jagadish K, Bouwmeester H, Ruyter-Spira C. 2019. Association mapping and genetic dissection of drought-induced canopy temperature differences in rice. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erz527

Mittmann S, Arrieta M, Ramsay L, Waugh R, Colas I. 2019. Preparation of Barley Pollen Mother Cells for Confocal and Super Resolution Microscopy. Harwood WA, editor. In Barley: Methods and Protocols. New York: Humana Press. pp. 167-179. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8944-7_11

Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. 2019. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biology. 20(1):1-18. https://doi.org/10.1186/s13059-019-1899-5

Morera-Margarit P, Bulgarelli D, Pope T, Graham R, Mitchell C, Karley AJ. 2019. The bacterial community associated with adult vine weevil (Otiorhynchus sulcatus) in UK populations growing on strawberry is dominated by Candidatus Nardonella. Entomologia Experimentalis et Applicata. 167(3):186-196. https://doi.org/10.1111/eea.12757

Mourão K, Schurch NJ, Lukoszek R, Froussios K, Mackinnon K, Duc C, Simpson G, Barton G. 2019. Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA. F1000 Research. 8:1-7. https://doi.org/10.1101/425900, https://doi.org/10.12688/f1000research.18952.1

Paajanen P, Kettleborough G, Lopez-Girona E, Giolai M, Heavens D, Baker D, Lister A, Wilde G, Hein I, Macaulay I, Bryan GJ, Clark MD. 2019. A critical comparison of technologies for a plant genome sequencing project. Giga Science. 8(3):1-12. https://doi.org/10.1093/gigascience/giy163

Patil V, McDermott HI, Mcallister T, Cummins M, Clara Silva J, Mollison E, Meikle R, Morris JA, Hedley PE, Waugh R, Dockter C, Hansson M, McKim S. 2019. APETALA2 control of barley internode elongation. Development. 146(11):1-16. https://doi.org/10.1242/dev.170373

Rapazote-Flores P, Bayer M, Milne L, Mayer C-D, Fuller J, Guo W, Hedley PE, Morris J, Halpin C, Kam J, McKim SM, Zwirek M, Casao MC, Barakate A, Schreiber M, Stephen G, Zhang R, Brown JWS, Waugh R, Simpson CG. 2019. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics. 20(1). https://doi.org/10.1186/s12864-019-6243-7

Raven JA, Gobler CS, Hansen PJ. 2019. Dynamic CO 2 and pH levels in coastal, estuarine, and inland waters: Theoretical and observed effects on harmful algal blooms. Harmful Algae. https://doi.org/10.1016/j.hal.2019.03.012

Ren Y, Armstrong M, Qi Y, McLellan H, Zhong C, Du B, Birch PRJ, Tian Z. 2019. Phytophthora infestans RXLR effectors target parallel steps in an immune signal transduction pathway. Plant Physiology. 180(4):2227-2239. https://doi.org/10.1104/pp.18.00625

Schreiber M, Barakate A, Uzrek N, Macaulay M, Sourdille A, Morris J, Hedley PE, Ramsay L, Waugh R. 2019. A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing. Plant Methods. 15:1-14. https://doi.org/10.1186/s13007-019-0486-9

Simpson CG, Fuller J, Rapazote-Flores P, Mayer CD, Calixto CPG, Milne L, Hedley PE, Booth C, Waugh R, Brown JWS. 2019. High-Resolution RT-PCR Analysis of Alternative Barley Transcripts. Harwood WA, editor. In Barley: Methods and Protocols. New York: Humana Press. pp. 269-281. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-8944-7_17

Strachan SM, Armstrong MR, Kaur A, Wright KM, Lim TY, Jones J, Bryan GJ, Blok V, Hein I. 2019. Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato. Theoretical and Applied Genetics. 132(4):1283-1294. https://doi.org/10.1007/s00122-019-03278-4

Thilliez GJA, Armstrong M, Lim JT-Y, Baker K, Jouet A, Ward B, Oosterhout CV, Jones JDG, Huitema E, Birch P, Hein I. 2019. Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. New Phytologist. 221(3):1634-1648. https://doi.org/10.1111/nph.15441

Thorpe P, Escudero‐Martinez CM, Eves-van den Akker S, Bos JIB. 2019. Transcriptional changes in the aphid species Myzus cerasi under different host and environmental conditions. Insect Molecular Biology. https://doi.org/10.1111/imb.12631

Turnbull D, Wang H, Breen S, Malec M, Naqvi S, Yang L, Welsh L, Hemsley P, Tian Z, Brunner F, Gilroy EM, Birch P. 2019. Effector PiAVR2 targets BSL family members which act as susceptibility factors to suppress immunity. Plant Physiology.

Turnbull D, Wang H, Breen S, Malec M, Naqvi S, Yang L, Welsh L, Hemsley PA, Zhendong T, Brunner F, Gilroy EM, Birch PRJ. 2019. AVR2 targets BSL family members, which act as susceptibility factors to suppress host immunity. Plant Physiology. 180(1):571-581. https://doi.org/10.1104/pp.18.01143

Volk H, Marton K, Flajsman M, Radisek S, Tian H, Hein I, Podlipnik Č, Thomma BPHJ, Kosmelj K, Javornik B, Berne S. 2019. Chitin-Binding Protein of Verticillium nonalfalfae Disguises Fungus from Plant Chitinases and Suppresses Chitin-Triggered Host Immunity. Molecular Plant-Microbe Interactions. 32(10):1378-1390. https://doi.org/10.1094/MPMI-03-19-0079-R

Wang S, McLellan H, Bukharova T, He Q, Murphy F, Shi J, Sun S, van Weymers P, Ren Y, Thilliez G, Wang H, Chen X, Engelhardt S, Vleeshouwers V, Gilroy EM, Whisson SC, Hein I, Wang X, Tian Z, Birch PRJ, Boevink PC. 2019. Phytophthora infestans RXLR effectors act in concert at diverse subcellular locations to enhance host colonization. Journal of Experimental Botany. 70(1):343-356. https://doi.org/10.1093/jxb/ery360

Wang H, He H, Qi Y, McLellan H, Tian Z, Birch PRJ, Tian Z. 2019. The oomycete microbe-associated molecular pattern Pep-13 triggers SERK3/BAK1-independent plant immunity. Plant Cell Reports. 38(2):173-182. https://doi.org/10.1007/s00299-018-2359-5

Zwirek M, Waugh R, McKim SM. 2019. Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytologist. 221(4):1950-1965. https://doi.org/10.1111/nph.15548

Wheat and Barley Legacy for Breeding Improvement (WHEALBI) consortium, Pont C, Leroy T, Seidel M, Tondelli A, Duchemin W, Armisen D, Lang D, Bustos-Korts D, Goué N, Balfourier F, Molnár-Láng M, Lage J, Kilian B, Özkan H, Waite D, Dyer S, Letellier T, Alaux M, Russell J, Keller B, van Eeuwijk F, Spannagl M, Mayer KFX, Waugh R, Stein N, Cattivelli L, Haberer G, Charmet G, Salse J. 2019. Tracing the ancestry of modern bread wheats. Nature Genetics. 51(5):905-911. https://doi.org/10.1038/s41588-019-0393-z