Pete Hedley
Current research interests
Genome Technology group leader
- Overseeing development of sequencing and genotyping services at the James Hutton Institute.
-
Coordinating high-throughput parallel gene expression technologies, including:
- processing and design of custom Agilent microarrays
- implementation of analysis software and liaison with BioSS (experimental design and statistical analysis).
-
Developing and applying Second Generation Sequencing (2GS) technologies for:
- SNP marker discovery and application in barley and soft fruit
- candidate gene identification.
-
Collaborative projects:
- microarrays have been successfully applied to both plant pathogen (Pectobacterium) and crop (potato, barley, raspberry and blackcurrant) species. Studies include determination of pathogenicity factors, analysis of host-pathogen interactions, dissection of food quality traits, expression QTL (eQTL) isolation, characterisation of bud dormancy, and cross-species expression analysis.
Research areas
- High-throughput anchoring of physical & genetic maps in cereal species (TriticeaeGenome).
- Designing and utilising new Agilent 60k barley, potato and soft fruit microarrays.
- Developing multiplex 2GS-based genotyping assays.
Employment History
- April 2011-present: Genome Technology group, James Hutton Institute. Implementation of High-Throughput Genomics Technologies.
- 2001-2011: Sequencing & Microarray Facility, Programme of Genetics, SCRI. Development of High-Throughput Genomics Technologies.
- 2000-2001: Unit of Genome Dynamics, SCRI. Generation of Barley Genomics Resources.
- 1999-2000: Mylnefield Research Services, SCRI. Molecular Characterisation of Biotic Interactions in Barley.
- 1997-1999: Cell and Molecular Genetics, SCRI. Comparative Genome Analysis and Mapping in Conifers.
- 1995: Cell and Molecular Genetics, SCRI. Characterisation of Genes Encoding Invertase Enzymes from Potato (PhD).
- 1989-1997: Cell and Molecular Genetics, SCRI. Molecular Analysis of Low Temperature Sweetening in Potato Tubers.
- 1988-1989: Karolinska Institute, Stockholm, Sweden. Investigation of Growth Factor Genes in Porcine Development.
Bibliography
- Riddell, C.E.; Frederickson-Matika, D.; Armstrong, A.C.; Elliot, M.; Forster, J.; Hedley, P.E.; Morris, J.; Thorpe, P.; Cooke, D.E.L.; Pritchard, L.; Sharp, P.M.; Green, S. (2019) Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain., PeerJ, 7, Article No. e6931.
- Schmidt, S.D.; George, T.S.; Brown, L.K.; Booth, A.; Wishart, J.; Hedley, P.E.; Martin, P.; Russell, J.; Husted, S. (2019) Ancient barley landraces adapted to marginal soils demonstrate exceptional tolerance to manganese limitation., Annals of Botany, 123, 831-843.
- Bayer, M.; Morris, J.; Booth, C.; Booth, A.; Uzrek, N.; Russell, J.R.; Waugh, R.; Hedley, P.E. (2019) Exome capture for variant discovery and analysis in barley., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 18, pp283-310.
- Simpson, C.G.; Fuller, J.; Flores, J.; Mayer, C-D.; Calixto, C.P.G.; Milne, L.; Hedley, P.E.; Booth, C.; Waugh, R.; Brown, J.W.S. (2019) High resolution RT-PCR analysis of alternative barley transcripts., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 17, pp269-281.
- Morris, J.A.; Hedley, P.E. (2019) Microarrays for high-throughput gene expression analysis of barley., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 12, pp181-194.
- Jarret, D.A.; Morris, J.; Cullen, D.W.; Gordon, S.L.; Verrall, S.R.; Milne, L.; Hedley, P.E.; Allwood, J.W.; Brennan, R.M.; Hancock, R.D. (2018) A transcript and metabolite atlas of blackcurrant fruit development highlights hormonal regulation and reveals the role of key transcription factors., Frontiers in Plant Science, 9, Article No. 1235.
- Karpinska, B.; Zhang, K.M.; Rasool, B.; Pastok, D.; Morris, J.; Verrall, S.R.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2018) The redox state of the apoplast influences the acclimation of photosynthesis and leaf metabolism to changing irradiance., Plant Cell and Environment, 41, 1083-1097.
- Hackett, C.; Milne, L.; Smith, K.; Hedley, P.; Morris, J.; Simpson, C.; Preedy, K.; Graham, J. (2018) Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening., BMC Genetics, 19, Article No. 59.
- Trapero-Mozos, A.; Ducreux, L.J.M.; Bita, C.E.; Morris, W.; Wiese, C.; Morris, J.A.; Paterson, C.; Hedley, P.E.; Hancock, R.D.; Taylor, M.A. (2018) Correction to: A reversible light and genotype dependent acquired thermotolerance response protects the potato plant from excessive temperature., Planta, 247, 1377-1393.
- Simpson, C.G.; Barrero, R.A.; Bayer, M.; Flavell, A.; Rapazote-Flores, P.; Bellgard, M.I.; Hedley, P.E.; Zhang, R.; Waugh, R. (2018) The expressed portion of the barley genome., In: Stein, N. & Muehlbauer, G. (eds.). The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, Chapter 7, 789-107.
- Twardziok, S.; Gundlach, H.; Hedley, P.E.; Bayer, M.; Platzer, M.; Groth, M.; Waugh, R.; Spannagl, M. (2018) Gene prediction in the barley genome., In: Stein, N. & Muehlbauer, G. (eds.). The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, Chapter 6, 73-88.
- Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S.O.; Wicker, T.; Radchuk, V.; Dockter, C.; Hedley, P.E.; Russell, J.; Bayer, M.; Ramsay, L.; Liu, H.; Haberer, G.; Zhang, X.; Zhang, Q.; Barrero, R.A.; Li, L.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Bolser, D.; Colmsee, C.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Chailyan, A.; Sampath, D.; Heavens, D.; Clissold, L.; Cao, S.; Chapman, B.; Dai, F.; Han, Y.; Li, H.; Li, X.; Lin, C.; McCooke, J.K.; Tan, C.; Wang, P.; Wang, S.; Yin, S.; Zhou, G.; Poland, J.A.; Bellgard, M.I.; Borisjuk, L.; Houben, A.; Dolezel, J.; Ayling, S.; Lonardi, S.; Kersey, P.; Langridge, P.; Muehlbauer, G.J.; Clark, M.D.; Caccamo, M.; Schulman, U.; Mayer, K.F.X.; Platzer, M.; Close, T.J.; Scholz, U.; Hansson, M.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh. R.; Stein, N. (2017) A chromosome conformation capture ordered sequence of the barley genome , Nature, 544, 427-433.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- Looseley, M.E.; Bayer, M.; Bull, H.; Ramsay, L.; Thomas, W.; Booth, A.; De La Fuente Canto, C.; Morris, J.; Hedley, P.E.; Russell, J. (2017) Association mapping of diastatic power in UK winter and spring barley by exome sequencing of phenotypically contrasting variety sets., Frontiers in Plant Science, 8, Article No. 1566.
- Rasool, B.; McGowan, J.; Pastok, D.; Marcus, S.E.; Morris, J.A.; Verrall, S.R.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2017) Redox control of aphid resistance through altered cell wall composition and nutritional quality., Plant Physiology, 175, 259-271.
- Turnbull, D.; Yang, L.N.; Naqvi, S.; Breen, S.; Welsh, L.; Stephens, J.; Morris, J.; Boevink, P.C.; Hedley, P.E.; Zhan, J.; Birch, P.R.; Gilroy, E.M. (2017) RXLR effector AVR2 up-regulates a brassinosteroid responsive bHLH transcription factor to suppress immunity., Plant Physiology, 174, 356-369.
- Robertson-Albertyn, S.; Terrazas, R.A.; Balbirnie, K.; Blank, M.; Janiak, A.; Szarejko, I.; Chmielewska, B.; Karcz, J.; Morris, J.; Hedley, P.E.; George, T.S.; Bulgarelli, D. (2017) Root hair mutations displace the barley rhizosphere microbiota., Frontiers in Plant Science, 8, Article No. 1094.
- Liller, C.B.; Walla, A.; Boer, M.P.; Hedley, P.; Macaulay, M.; Effgen, S.; von Korff, M.; van Esse, G.W.; Koornneef, M. (2017) Fine mapping of a major QTL for awn length in barley using a multiparent mapping population., Theoretical and Applied Genetics, 130, 269-281.
- Delventhal, R.; Rajaraman, J.; Stefanato, F.L.; Rehman, S.; Aghnoum, R.; McGrann, G.R.D.; Bolger, M.; Usadel, B.; Hedley, P.E.; Boyd, L.; Niks, R.E.; Schweizer, P.; Schaffrath, U. (2017) A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley., BMC Plant Biology, 17, Article No. 232.
- Escudero-Martinez, C.M.; Morris, J.A.; Hedley, P.E.; Bos, J.I.B. (2017) Barley transcriptome analyses upon interaction with different aphid species identify thionins contributing to resistance., Plant Cell and Environment, 40, 2628-2643.
- Crozier, L.; Hedley, P.E.; Morris, J.; Wagstaff, C.; Andrews, S.C.; Toth, I.; Jackson, R.W.; Holden, N. (2016) Corrigendum: whole-transcriptome analysis of verocytotoxigenic Escherichia coli O157:H7 (Sakai) suggests plant-species-specific metabolic responses on exposure to spinach and lettuce extracts., Frontiers in Microbiology, 7, Article No. 1506.
- Crozier, L.; Hedley, P.E.; Morris, J.; Wagstaff, C.; Andrews, S.C.; Toth, I.; Jackson, R.W.; Holden, N. (2016) Whole-transcriptome analysis of verocytotoxigenic Escherichia coli O157:H7 (Sakai) suggests plant-species-specific metabolic responses on exposure to spinach and lettuce extracts., Frontiers in Microbiology, 7, Article No. 1088.
- Zhang, R.X.; Tucker, M.R.; Burton, R.A.; Shirley, N.J.; Little, A.; Morris, J.; Milne, L.; Houston, K.; Hedley, P.E.; Waugh, R.; Fincher, G.B. (2016) The dynamics of transcript abundance during cellularization of developing barley endosperm., Plant Physiology, 170, 1549-1565.
- Palomares-Rius, J.E.; Hedley, P.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Blok, V.C. (2016) Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate., PeerJ, 4, Article No. e1654.
- Katsarou, K.; Wu, Y.; Zhang, R.X.; Bonar, N.; Morris, J.; Hedley, P.E.; Bryan, G.J.; Kalantidis, K.; Hornyik, C. (2016) Insight on genes affecting tuber development in potato upon Potato spindle tuber viroid (PSTVd) infection., PLoS ONE, 11, Article No. e0150711.
- Travis, A.J.; Norton, G.J.; Datta, S.; Sarma, R.; Dasgupta, T.; Savio, F.L.; Macaulay, M.; Hedley, P.E.; McNally, K.L.; Sumon, M.H.; Islam, M.R.; Price, A.H. (2015) Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal., Rice, 8, Article No. 35.
- Shepherd, L.V.T.; Alexander, C.J.; Hackett, C.A.; McRae, D.; Sungurtas, J.A.; Verrall, S.R.; Morris, J.A.; Hedley, P.E.; Rockhold, D.; Belknap, W.; Davies, H.V. (2015) Impacts on the metabolome of down-regulating polyphenol oxidase in potato tubers., Transgenic Research, 24, 447-461.
- Wiesel, L.; Davis, J.L.; Milne, L.; Fernandez, V.R.; Herold, M.B.; Williams, J.M.; Morris, J.; Hedley, P.E.; Harrower, B.; Newton, A.C.; Birch, P.R.J.; Gilroy, E.M.; Hein, I. (2015) A transcriptional reference map of defence hormone responses in potato., Scientific Reports, 5, Article No. 15229.
- Cerekovic, N.; Jarret, D.; Pagter, M.; Cullen, D.W.; Morris, J.M.; Hedley, P.E.; Brennan, R.; Petersen, K.K. (2015) The effects of drought stress on leaf gene expression during flowering in blackcurrant (Ribes nigrum L.)., European Journal of Horticultural Science, 80, 39-46.
- Amar, D.; Frades, I.; Diels, T.; Zaltzman, D.; Ghatan, N.; Hedley, P.E.; Alexandersson, E.; Tzfadia, O.; Shamir, R. (2015) The MORPH-R web server and software tool for predicting missing genes in biological pathways., Physiologia Plantarum, 155, 12-20.
- Campbell, R.; Morris, W.L.; Misawa, N.; Ducreux, L.J.M.; Morris, J.A.; Hedley, P.E.; Fraser, P.D.; Taylor, M.A. (2015) Optimising ketocarotenoid production in potato tubers: effect of genetic background, transgene combinations and environment., Plant Science, 234, 27-37.
- Graham, J.; Smith, K.; McCallum, S.; Hedley, P.E.; Cullen, D.W.; Dolan, A.; Milne, L.; McNicol, J.W.; Hackett, C.A. (2015) Towards an understanding of the control of 'crumbly' fruit in red raspberry., SpringerPlus, 4, Article No. 223.
- Jaouannet, M.; Morris, J.A.; Hedley, P.E.; Bos, J.B. (2015) Characterization of Arabidopsis transcriptional responses to different aphid species reveals genes that contribute to host susceptibility and non-host resistance., PLoS Pathogens, 11, Article No. e1004918.
- Comadira, G.; Rasool, B.; Karpinska, B.; Morris, J.; Verrall, S.R.; Hedley, P.E.; Foyer, C.H.; Hancock, R.D. (2015) Nitrogen deficiency in barley (Hordeum vulgare) seedlings induces molecular and metabolic adjustments that trigger aphid resistance., Journal of Experimental Botany, 66, 3639-3655.
- Comadira, G.; Rasool, B.; Kaprinska, B.; Garcia, B.M.; Morris, J.; Verrall, S.R.; Bayer, M.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2015) WHIRLY1 functions in the control of responses to nitrogen deficiency but not aphid infestation in barley., Plant Physiology, 168, 1140-1151.
- Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
- Ashfaq, A.; Alexandersson, E.; Sandin, M.; Resjo, S.; Burra, D.D.; Lenman, M.; Hedley, P.E.; Levander, F.; Andreasson, E. (2014) Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions., BMC Genomics, 15, Article No. 497.
- Gotame, T.P.; Cullen, D.W.; Graham, J.; Hedley, P.; Smith, K.; Morris, J.; Andersen, L.; Petersen, K.K. (2014) Effect of short-term exposure to high-temperature on total gene expression in the leaves of four raspberry (Rubus idaeus L.) cultivars., Journal of Horticultural Science and Biotechnology, 89, 532-541.
- Liu, H.; Bayer, M.; Druka, A.; Russell, J.; Hackett, C.; Poland, J.; Ramsay, L.; Hedley, P.; Waugh, R. (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley., BMC Genomics, 15, Article No.104.
- Russell, J.; Hackett, C.; Hedley, P.; Lui, H.; Milne, L.; Bayer, M.; Marshall, D.; Jorgensen, L.; Gordon, S.; Brennan, R. (2014) The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences., Molecular Breeding, 33, 835-849.
- Riddell, C.E.; Frederickson-Matika, D.; Armstrong, A.C.; Elliot, M.; Forster, J.; Hedley, P.E.; Morris, J.; Thorpe, P.; Cooke, D.E.L.; Pritchard, L.; Sharp, P.M.; Green, S. (2019) Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain., PeerJ, 7, Article No. e6931.
- Schmidt, S.D.; George, T.S.; Brown, L.K.; Booth, A.; Wishart, J.; Hedley, P.E.; Martin, P.; Russell, J.; Husted, S. (2019) Ancient barley landraces adapted to marginal soils demonstrate exceptional tolerance to manganese limitation., Annals of Botany, 123, 831-843.
- Jarret, D.A.; Morris, J.; Cullen, D.W.; Gordon, S.L.; Verrall, S.R.; Milne, L.; Hedley, P.E.; Allwood, J.W.; Brennan, R.M.; Hancock, R.D. (2018) A transcript and metabolite atlas of blackcurrant fruit development highlights hormonal regulation and reveals the role of key transcription factors., Frontiers in Plant Science, 9, Article No. 1235.
- Karpinska, B.; Zhang, K.M.; Rasool, B.; Pastok, D.; Morris, J.; Verrall, S.R.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2018) The redox state of the apoplast influences the acclimation of photosynthesis and leaf metabolism to changing irradiance., Plant Cell and Environment, 41, 1083-1097.
- Hackett, C.; Milne, L.; Smith, K.; Hedley, P.; Morris, J.; Simpson, C.; Preedy, K.; Graham, J. (2018) Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening., BMC Genetics, 19, Article No. 59.
- Trapero-Mozos, A.; Ducreux, L.J.M.; Bita, C.E.; Morris, W.; Wiese, C.; Morris, J.A.; Paterson, C.; Hedley, P.E.; Hancock, R.D.; Taylor, M.A. (2018) Correction to: A reversible light and genotype dependent acquired thermotolerance response protects the potato plant from excessive temperature., Planta, 247, 1377-1393.
- Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S.O.; Wicker, T.; Radchuk, V.; Dockter, C.; Hedley, P.E.; Russell, J.; Bayer, M.; Ramsay, L.; Liu, H.; Haberer, G.; Zhang, X.; Zhang, Q.; Barrero, R.A.; Li, L.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Bolser, D.; Colmsee, C.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Chailyan, A.; Sampath, D.; Heavens, D.; Clissold, L.; Cao, S.; Chapman, B.; Dai, F.; Han, Y.; Li, H.; Li, X.; Lin, C.; McCooke, J.K.; Tan, C.; Wang, P.; Wang, S.; Yin, S.; Zhou, G.; Poland, J.A.; Bellgard, M.I.; Borisjuk, L.; Houben, A.; Dolezel, J.; Ayling, S.; Lonardi, S.; Kersey, P.; Langridge, P.; Muehlbauer, G.J.; Clark, M.D.; Caccamo, M.; Schulman, U.; Mayer, K.F.X.; Platzer, M.; Close, T.J.; Scholz, U.; Hansson, M.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh. R.; Stein, N. (2017) A chromosome conformation capture ordered sequence of the barley genome , Nature, 544, 427-433.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- Looseley, M.E.; Bayer, M.; Bull, H.; Ramsay, L.; Thomas, W.; Booth, A.; De La Fuente Canto, C.; Morris, J.; Hedley, P.E.; Russell, J. (2017) Association mapping of diastatic power in UK winter and spring barley by exome sequencing of phenotypically contrasting variety sets., Frontiers in Plant Science, 8, Article No. 1566.
- Rasool, B.; McGowan, J.; Pastok, D.; Marcus, S.E.; Morris, J.A.; Verrall, S.R.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2017) Redox control of aphid resistance through altered cell wall composition and nutritional quality., Plant Physiology, 175, 259-271.
- Turnbull, D.; Yang, L.N.; Naqvi, S.; Breen, S.; Welsh, L.; Stephens, J.; Morris, J.; Boevink, P.C.; Hedley, P.E.; Zhan, J.; Birch, P.R.; Gilroy, E.M. (2017) RXLR effector AVR2 up-regulates a brassinosteroid responsive bHLH transcription factor to suppress immunity., Plant Physiology, 174, 356-369.
- Robertson-Albertyn, S.; Terrazas, R.A.; Balbirnie, K.; Blank, M.; Janiak, A.; Szarejko, I.; Chmielewska, B.; Karcz, J.; Morris, J.; Hedley, P.E.; George, T.S.; Bulgarelli, D. (2017) Root hair mutations displace the barley rhizosphere microbiota., Frontiers in Plant Science, 8, Article No. 1094.
- Liller, C.B.; Walla, A.; Boer, M.P.; Hedley, P.; Macaulay, M.; Effgen, S.; von Korff, M.; van Esse, G.W.; Koornneef, M. (2017) Fine mapping of a major QTL for awn length in barley using a multiparent mapping population., Theoretical and Applied Genetics, 130, 269-281.
- Delventhal, R.; Rajaraman, J.; Stefanato, F.L.; Rehman, S.; Aghnoum, R.; McGrann, G.R.D.; Bolger, M.; Usadel, B.; Hedley, P.E.; Boyd, L.; Niks, R.E.; Schweizer, P.; Schaffrath, U. (2017) A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley., BMC Plant Biology, 17, Article No. 232.
- Escudero-Martinez, C.M.; Morris, J.A.; Hedley, P.E.; Bos, J.I.B. (2017) Barley transcriptome analyses upon interaction with different aphid species identify thionins contributing to resistance., Plant Cell and Environment, 40, 2628-2643.
- Crozier, L.; Hedley, P.E.; Morris, J.; Wagstaff, C.; Andrews, S.C.; Toth, I.; Jackson, R.W.; Holden, N. (2016) Corrigendum: whole-transcriptome analysis of verocytotoxigenic Escherichia coli O157:H7 (Sakai) suggests plant-species-specific metabolic responses on exposure to spinach and lettuce extracts., Frontiers in Microbiology, 7, Article No. 1506.
- Crozier, L.; Hedley, P.E.; Morris, J.; Wagstaff, C.; Andrews, S.C.; Toth, I.; Jackson, R.W.; Holden, N. (2016) Whole-transcriptome analysis of verocytotoxigenic Escherichia coli O157:H7 (Sakai) suggests plant-species-specific metabolic responses on exposure to spinach and lettuce extracts., Frontiers in Microbiology, 7, Article No. 1088.
- Zhang, R.X.; Tucker, M.R.; Burton, R.A.; Shirley, N.J.; Little, A.; Morris, J.; Milne, L.; Houston, K.; Hedley, P.E.; Waugh, R.; Fincher, G.B. (2016) The dynamics of transcript abundance during cellularization of developing barley endosperm., Plant Physiology, 170, 1549-1565.
- Palomares-Rius, J.E.; Hedley, P.; Cock, P.J.A.; Morris, J.A.; Jones, J.T.; Blok, V.C. (2016) Gene expression changes in diapause or quiescent potato cyst nematode, Globodera pallida, eggs after hydration or exposure to tomato root diffusate., PeerJ, 4, Article No. e1654.
- Katsarou, K.; Wu, Y.; Zhang, R.X.; Bonar, N.; Morris, J.; Hedley, P.E.; Bryan, G.J.; Kalantidis, K.; Hornyik, C. (2016) Insight on genes affecting tuber development in potato upon Potato spindle tuber viroid (PSTVd) infection., PLoS ONE, 11, Article No. e0150711.
- Travis, A.J.; Norton, G.J.; Datta, S.; Sarma, R.; Dasgupta, T.; Savio, F.L.; Macaulay, M.; Hedley, P.E.; McNally, K.L.; Sumon, M.H.; Islam, M.R.; Price, A.H. (2015) Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal., Rice, 8, Article No. 35.
- Shepherd, L.V.T.; Alexander, C.J.; Hackett, C.A.; McRae, D.; Sungurtas, J.A.; Verrall, S.R.; Morris, J.A.; Hedley, P.E.; Rockhold, D.; Belknap, W.; Davies, H.V. (2015) Impacts on the metabolome of down-regulating polyphenol oxidase in potato tubers., Transgenic Research, 24, 447-461.
- Wiesel, L.; Davis, J.L.; Milne, L.; Fernandez, V.R.; Herold, M.B.; Williams, J.M.; Morris, J.; Hedley, P.E.; Harrower, B.; Newton, A.C.; Birch, P.R.J.; Gilroy, E.M.; Hein, I. (2015) A transcriptional reference map of defence hormone responses in potato., Scientific Reports, 5, Article No. 15229.
- Cerekovic, N.; Jarret, D.; Pagter, M.; Cullen, D.W.; Morris, J.M.; Hedley, P.E.; Brennan, R.; Petersen, K.K. (2015) The effects of drought stress on leaf gene expression during flowering in blackcurrant (Ribes nigrum L.)., European Journal of Horticultural Science, 80, 39-46.
- Amar, D.; Frades, I.; Diels, T.; Zaltzman, D.; Ghatan, N.; Hedley, P.E.; Alexandersson, E.; Tzfadia, O.; Shamir, R. (2015) The MORPH-R web server and software tool for predicting missing genes in biological pathways., Physiologia Plantarum, 155, 12-20.
- Campbell, R.; Morris, W.L.; Misawa, N.; Ducreux, L.J.M.; Morris, J.A.; Hedley, P.E.; Fraser, P.D.; Taylor, M.A. (2015) Optimising ketocarotenoid production in potato tubers: effect of genetic background, transgene combinations and environment., Plant Science, 234, 27-37.
- Graham, J.; Smith, K.; McCallum, S.; Hedley, P.E.; Cullen, D.W.; Dolan, A.; Milne, L.; McNicol, J.W.; Hackett, C.A. (2015) Towards an understanding of the control of 'crumbly' fruit in red raspberry., SpringerPlus, 4, Article No. 223.
- Jaouannet, M.; Morris, J.A.; Hedley, P.E.; Bos, J.B. (2015) Characterization of Arabidopsis transcriptional responses to different aphid species reveals genes that contribute to host susceptibility and non-host resistance., PLoS Pathogens, 11, Article No. e1004918.
- Comadira, G.; Rasool, B.; Karpinska, B.; Morris, J.; Verrall, S.R.; Hedley, P.E.; Foyer, C.H.; Hancock, R.D. (2015) Nitrogen deficiency in barley (Hordeum vulgare) seedlings induces molecular and metabolic adjustments that trigger aphid resistance., Journal of Experimental Botany, 66, 3639-3655.
- Comadira, G.; Rasool, B.; Kaprinska, B.; Garcia, B.M.; Morris, J.; Verrall, S.R.; Bayer, M.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2015) WHIRLY1 functions in the control of responses to nitrogen deficiency but not aphid infestation in barley., Plant Physiology, 168, 1140-1151.
- Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
- Campbell, R.; Pont, S.D.A.; Morris, J.A.; McKenzie, G.; Sharma, S.K.; Hedley, P.E.; Ramsay, G.; Bryan, G.J.; Taylor, M.A. (2014) Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.)., Theoretical and Applied Genetics, 127, 1917-1933.
- Amar, D.; Frades, I.; Danek, A.; Goldberg, T.; Sharma, S.K.; Hedley, P.; Proux-Wera, E.; Andreasson, E.; Shamir, R.; Tzfadia, O.; Alexandersson, E. (2014) Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case., BMC Plant Biology, 14, 329.
- Russell, J.R.; Hedley, P.E.; Cardle, L.; Dancey, S.; Morris, J.; Booth, A.; Odee, D.; Mwaura, L.; Omondi, W.; Angaine, P.; Machua, J.; Muchugi, A.; Milne, I.; Kindt, R.; Jamnadass, R.; Dawson, I.K. (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species., PLoS ONE, 9, Article No. e102502.
- Ashfaq, A.; Alexandersson, E.; Sandin, M.; Resjo, S.; Burra, D.D.; Lenman, M.; Hedley, P.E.; Levander, F.; Andreasson, E. (2014) Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions., BMC Genomics, 15, Article No. 497.
- Bengtsson, T.; Weighill, D.; Proux-Wera, E.; Levander, F.; Resjo, S.; Burra, D.D.; Moushib, L.I.; Hedley, P.E.; Liljeroth, E.; Jacobson, D.; Alexandersson, E.; Andreasson, E. (2014) Proteomics and transcriptomics of BABA-induced resistance response in potato using a novel functional annotation approach., BMC Genomics, 15, Article No. UNSP315.
- Gotame, T.P.; Cullen, D.W.; Graham, J.; Hedley, P.; Smith, K.; Morris, J.; Andersen, L.; Petersen, K.K. (2014) Effect of short-term exposure to high-temperature on total gene expression in the leaves of four raspberry (Rubus idaeus L.) cultivars., Journal of Horticultural Science and Biotechnology, 89, 532-541.
- Liu, H.; Bayer, M.; Druka, A.; Russell, J.; Hackett, C.; Poland, J.; Ramsay, L.; Hedley, P.; Waugh, R. (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley., BMC Genomics, 15, Article No.104.
- Russell, J.; Hackett, C.; Hedley, P.; Lui, H.; Milne, L.; Bayer, M.; Marshall, D.; Jorgensen, L.; Gordon, S.; Brennan, R. (2014) The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences., Molecular Breeding, 33, 835-849.
- Schreiber, M.; Wright, F.; MacKenzie, K.; Hedley, P.E.; Schwerdt, J.G.; Little, A.; Burton, R.A.; Fincher, G.B.; Marshall, D.; Waugh, R.; Halpin, C. (2014) The barley genome sequence assembly reveals three additional members of the CsIF (1,3;1,4) - beta-glucan synthase gene family., PLoS ONE, 9, Article No. e90888.
- Bayer, M.; Morris, J.; Booth, C.; Booth, A.; Uzrek, N.; Russell, J.R.; Waugh, R.; Hedley, P.E. (2019) Exome capture for variant discovery and analysis in barley., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 18, pp283-310.
- Simpson, C.G.; Fuller, J.; Flores, J.; Mayer, C-D.; Calixto, C.P.G.; Milne, L.; Hedley, P.E.; Booth, C.; Waugh, R.; Brown, J.W.S. (2019) High resolution RT-PCR analysis of alternative barley transcripts., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 17, pp269-281.
- Morris, J.A.; Hedley, P.E. (2019) Microarrays for high-throughput gene expression analysis of barley., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 12, pp181-194.
- Simpson, C.G.; Barrero, R.A.; Bayer, M.; Flavell, A.; Rapazote-Flores, P.; Bellgard, M.I.; Hedley, P.E.; Zhang, R.; Waugh, R. (2018) The expressed portion of the barley genome., In: Stein, N. & Muehlbauer, G. (eds.). The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, Chapter 7, 789-107.
- Twardziok, S.; Gundlach, H.; Hedley, P.E.; Bayer, M.; Platzer, M.; Groth, M.; Waugh, R.; Spannagl, M. (2018) Gene prediction in the barley genome., In: Stein, N. & Muehlbauer, G. (eds.). The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, Chapter 6, 73-88.
- Druka, A.; Waugh, R.; Hedley, P.E. (2008) Gene expression profiling., In: Rapley, R. & Walker, J.R. (eds.). Molecular Biomethods Handbook. 2nd edition. Humana Press, Chapter 14, 194-212.
- Kerchev, P.I.; Saraswat, V.; Hedley, P.E.; Morris, J.; Fenton, B.; Foyer, C.H.; Hancock, R.D. (2011) Understanding local and systemic responses to aphid infestation as a tool towards breeding aphid resistant crops., Annual Report of the Scottish Crop Research Institute for 2010, pp40-42.
- Ross, H.A.; Morris, W.L.; Ducreux, L.J.M.; Hancock, R.D.; Verrall, S.R.; Morris, J.A.; Stewart, D.; Hedley, P.E.; McDougall, G.J.; Taylor, M.A. (2011) The role of pectin methyl esterase in determining potato tuber textural quality., Annual Report of the Scottish Crop Research Institute for 2010, pp32-33.
- Campbell, R.; Ducreux, L.J.M.; Morris, W.L.; Hedley, P.E.; Bryan, G.J.; Ramsay, G.; Taylor, M.A. (2010) The role of carotenoid cleavage products in heat responses of potato., Annual Report of the Scottish Crop Research Institute for 2009, pp11-13.
- Brennan, R.M.; Jones, H.G.; Russell, J.R.; Hedley, P.E.; Jorgensen, L.; Hackett, C.A.; Gordon, S. (2010) Dormancy in blackcurrant and the potential effects of future climatic conditions., Annual Report of the Scottish Crop Research Institute for 2009, pp10-11.
- Prashar, A.; George, T.S.; Ramsay, G.; Hallett, P.D.; Jones, H.G.; Hedley, P.E.; McNicol, J.W.; Dale, M.F.B.; White, P.J.; Bryan, G.J. (2010) Water use efficiency in potato., Annual Report of the Scottish Crop Research Institute for 2009, pp42-44.
- Sharma, S.K.; Millam, S.; Hedley, P.E.; Hein, I.; McNicol, J.W.; Bryan, G.J. (2008) Somatic embryogenesis in potato., Annual Report of the Scottish Crop Research Institute for 2007, pp18-19.
- Mazzitelli, L.; Hancock, R.D.; Haupt, S.; McNicol, J.W.; Viola, R.; Brennan, R.M.; Hedley, P.E.; Taylor, M.A. (2006) Understanding dormancy release in raspberry buds., Annual Report of the Scottish Crop Research Institute for 2006, pp32-33.
- Taylor, M.A.; Ducreux, L.J.M.; Morris, W.L.; Hedley, P.E.; Millam, S. (2004) Isoprenoid metabolic networks in potato tubers., Annual Report of the Scottish Crop Research Institute for 2003/2004, pp140-141.
- Caldwell, D.; McCallum, N.; Mudie, S.; Hedley, P.E.; Ramsay, L.; Liu, H.; Marshall, D.F.; Waugh, R. (2002) A physical/chemical mutation grid for barley functional genomics., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp157-158.
- Ramsay, L.; Hedley, P.E.; Liu, H.; McCallum, N.; Mudie, S.; Cardle, L.; Harrower, B.E.; Machray, G.C.; Marshall, D.F.; Waugh, R. (2002) Barley transcriptome resources., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp151-152.
- Forster, B.P.; Bengough, A.G.; Ellis, R.P.; Thomas, W.T.B.; Clark, S.; Gordon, D.C.; El-Meniae, R.; Keith, R.; Waugh, R.; Hedley, P.E.; Daniell, T.J. (2002) Genomics of the root-soil interface., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp153-154.
- Machray, G.C.; Zhang, C.J.; Wilson, T.M.A.; Davidson, D.; Harrower, B.E.; Hedley, P.E.; Powell, W. (2000) Cereal gene mining and manipulating., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp114-116.
- Machray, G.C.; Hedley, P.E.; Davidson, D.; Ibrahim, A.F.M.; Watters, J.A.; Brown, J.W.S. (1999) Promoting plant promoters., Annual Report of the Scottish Crop Research Institute for 1998/99, pp82-85.
- Simpson, C.G.; Hedley, P.E.; McQuade, C.M.; Lyon, J.M.; Clark, G.P.; Machray, G.C.; Brown, J.W.S. (1998) Splicing regulation of a potato invertase mini-exon., Annual Report of the Scottish Crop Research Institute for 1997/98, pp71-73.
- Maddison, A.; Meyer, R.C.; Hedley, P.E.; Waugh, R.; Davies, H.V.; Machray, G.C. (1996) The organisation and expression from plant multigene families., Annual Report of the Scottish Crop Research Institute for 1993, p92.
- Machray, G.C.; Hedley, P.E.; Simpson, C.G.; Waugh, R.; Brown, J.W.S. (1994) PCR methods for the analysis of expression from plant multigene families., Annual Report of the Scottish Crop Research Institute fro 1993, p116.
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