Research
Leaf rust caused by Puccinia hordei is an important fungal disease on barley. Resistance of barley to leaf rust (Poccinia hordei) is genetically controlled by both single genes (R-genes) and multiple quantitative loci (QTL). Due to the short-term effectiveness of R-gene-mediated resistance, exploration and use of the durable partial resistance have become a more favorable strategy to control the disease. However, identification of the underlying genes through map-based approach is a process both cumbersome and time consuming.
The current project adapts a novel alternative approach termed as genetical genomics to investigate the genetic architecture of gene expression in barley after challenge with P. hordei through QTL analysis by treating the transcript abundance as a quantitative trait. The strategy is based on the assumption that if the phenotypic trait variation were caused by the genetic variation (QTL) through its effects on gene expression, the genetic determinants for the phenotype QTL would serve as cis expression QTL (eQTL) responsible for the expression variation of the gene itself. Thus, co-localisation of eQTL with resistance QTL can help directly point to the molecular basis and speed up the identification of causal genes underlying the partial resistance.
We have conducted an experiment using the two-channel Agilent microarray system in combination with the ‘distant-pair’ design for eQTL analysis. We recorded RNA transcript abundance corresponding to each probe on a 15K Agilent custom barley microarray in seedlings from Steptoe and Morex and their doubled haploid population. Analyses combining eQTL and pQTL mapping and conserved synteny with rice allowed us to prioritise six genes as candidates for Rphq11, the pQTL of largest effect, and highlight one, a phospholipid hydroperoxide glutathione peroxidase (HvPHGPx) for detailed analysis. We are currently underway of validation through transformation by over- and down-expressing the candidate gene in Golden Promise.
Collaborator – Rients Niks, Laboratory of Plant Breeding Wageningen University, the Netherlands.
Past research
- April 2011-present: Genetics Programme, The James Hutton Institute, UK. Transcript genetics of barley.
- 2006-April 2011: Genetics Programme, SCRI, UK. Transcript genetics of barley.
- 2003-2006: Disease and Stress Biology Department, John Innes Centre, UK. Development and characterisation of Arabidopsis-F. graminearum patho-system.
- 2001-2002: Institute of Cell and Molecular Biology (ICMB), University of Edinburgh. Identification and characterisation of Arabidopsis mutants involved in defense responses against biotrophic pathogens.
- 1997-2000: PhD, Max-Planck-Institute for Plant Breeding Research, Koeln, Germany. Mapping functional genes involved in carbohydrate metabolism and transport in potato.
Publications
Journals
- Gartner, U.; Hein, I.; Brown, L.H.; Chen, X.; Mantelin, S.; Sharma, S.K.; Dandurand, L.-M.; Kuhl, J.C.; Jones, J.T.; Bryan, G.J.; Blok, V.C. (2021) Resisting potato cyst nematodes with resistance, Frontiers in Plant Science, 12, Art. 661194
- Zheng, J.Y.; Duan, S.G.; Armstrong, M.R.; Duan, Y.F.; Xu, J.F.; Chen, X.W.; Hein, I.; Jin, L.P.; li, G.C. (2020) New findings on the resistance mechanism of an elite diploid wild potato species JAM1-4 in response to a super race strain of Phytophthora infestans., Phytopathology, 110, 1375-1387.
- Duan, Y.F.; Duan, S.G.; Armstrong, M.R.; Xu, J.F.; Zheng, J.Y. Hu, J.; Chen, X.W.; Hein, I.; Li, G.C.; Jin, L.P. (2020) Comparative transcriptome profiling reveals compatible and incompatible patterns of potato toward phytophthora infestans., G3- Genes Genomes Genetics, 10, 623-634.
- 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, E.M.; Whisson, S.W.; Hein, I.; Wang, X.; Tian, Z.; Birch, P.R.J.; Boevink, P.C. (2019) Phytophthora infestans RXLR effectors act in concert at diverse subcellular localisations to enhance host colonisation., Journal of Experimental Botany, 70, 343-356.
- Chen, X.; Lewandowska, D.; Armstrong, M.R.; Baker, K.; Lim, T.Y.; Bayer, M.; Harrower, B.; McLean, K.; Jupe, F.; Witek, K.; Lees, A.K.; Jones, J.D.; Bryan, G.J.; Hein, I. (2018) Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies, Theoretical and Applied Genetics, 131(6), 1287-1297
- Van Weymers, P.S.M.; Baker, K.; Chen, X.W.; Harrower, B.; Cooke, D.E.L.; Gilroy, E.M.; Birch, P.R.J.; Thilliez, G.J.A.; Lees, A.K.; Lynott, J.S.; Armstrong, M.R.; McKenzie, G.; Bryan, G.J.; Hein, I. (2016) Utilizing ‘Omic’ technologies to identify and prioritize novel sources of resistance to the oomycete pathogen Phytophthora infestans in potato germplasm collections., Frontiers in Plant Science, 7, Article No. 762.
- Chapman, S.; Stevens, L.J.; Boevink, P.C.; Engelhardt, S.; Alexander, C.J.; Harrower, B.; Champouret, N.; McGeachy, K.; Van Weymers, P.S.M.; Chen, X.; Birch, P.R.J.; Hein, I. (2014) Detection of the virulent form of AVR3a from phytophthora infestans following artificial evolution of potato resistance gene R3a., PLoS ONE, 9, Article No. e110158.
- Chen, X.W.; Hedley, P.E.; Morris, J.; Liu, H.; Niks, R.E.; Waugh, R. (2011) Combining genetical genomics and bulked segregant analysis-based differential expression: an approach to gene localization., Theoretical and Applied Genetics, 122, 1375-1383.
- Chen, X.W.; Niks, R.E.; Hedley, P.E.; Morris, J.; Druka, A.; Marcel, T.C.; Vels, A.; Waugh, R. (2010) Differential gene expression in nearly isogenic lines with QTL for partial resistance to Puccinia hordei in barley., BMC Genomics, 11(629).
- Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Booth, C.; Druka, A.; Marcel, T.C.; Vels, A.; Bayer, M.M.; Milne, I.; Morris, J.; Ramsay, L.; Marshall, D.F.; Cardle, L.; Waugh, R. (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley., PLoS ONE, 5, 1-15.
- Druka, A.; Potokina, E.; Luo, Z.W.; Jiang, N.; Chen, X.W.; Kearsey, M.J.; Waugh, R. (2010) Expression quantitative trait loci analysis in plants., Plant Biotechnology Journal, 8, 10-27.
- Tani, H.; Chen, X.W.; Nurmberg, P.; Grant, J.J.; SantaMaria, M.; Chini, A.; Gilroy, E.M.; Birch, P.R.J.; Loake, G.J. (2004) Activation tagging in plants: a tool for gene discovery., Functional and Integrative Genomics, 4, 258-266.
Books
- Jupe, F.; Chen, X.; Verweij, W.; Witek, K.; Jones, J.D.G.; Hein I. (2014) Genomic DNA library preparation for resistance gene enrichment and sequencing (RenSeq) in plants., In: Birch, P.R.J., Jones, J.T. & Bos, J.I.B. (eds.). Plant-Pathogen Interactions: Methods in Molecular Biology. Volume 1127, Humana Press, New York, 2nd ed, Chapter 22, pp291-303.
Conference papers
- Chen, X.; Bayer, M.; Harrower, B.; Stevens, L.; Chapman, S.; Gilroy, E.; van Weymers, P.; Jupe, F.; Witek, K.; Jones, J.; Birch, P.; Bryan, G.; Hein, I. (2014) Using the potato genome to map and clone durable resistance genes more rapidly., Crop Protection in Northern Britain, Environmental Management and Crop Protection, West Park Conference Centre, Dundee, 25-26 February 2014.
- Stevens, L.; Chapman, S.; Boevink, P.; Engelhardt, S.; Chen, X.; Birch, P.; Hein, I. (2014) Shuffling resistance genes to protect solanaceous plants., British Society for Plant Pathology Presidential Meeting, University of St Andrews, 1-2 September 2014.
- Griffiths, B.S.; Chen, X.; Daniell, T.J.; Neilson, R.; O’Flaherty, V. (2011) Long-term effects of P fertiliser on nematode community structure assessed by molecular and morphological methods., 50th Annual Meeting of the Society of Nematologists, Corvallis, Oregon, USA, 17-20 July 2011 (Talk).
- Waugh, R.; Marshall, D.F.; Druka, A.; Comadran, J.; Russell, J.R.; Chen, X.W.; Thomas, W.T.B.; Close, T.J.; Stein, N.; Ramsay, L. (2008) Genomic dissection of phenotypic variation in barley., BSPP Cereal Pathosystems Conference 2008, Queen Mary, University of London, 16-17 December 2008, p63.
Conference posters
- Stevens, L,; Chapman, S.; Chen, X.; Engelhardt, S.; Birch, P.; Hein, I. (2012) The molecular characterisation of two gain-of-function R3a* variants., British Society for Plant Pathology Presidential Meeting, Norwich, 16-18 December 2012. (Poster)
- Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Druka, A.; Marcel, T.C.; Waugh, R. (2010) eQTL analysis of partial resistance to Puccinia hordei Otth in barley., Plant & Animal Genome XVIII. San Diego, California, USA, 9-13 January 2010 (Abstract).
