Biography
I received my basic education in China, earning a BSc in Agricultural Sciences from Huazhong Agricultural University in Wuhan, and a PhD in Plant Molecular Genetics from the University of Cologne and the Max-Planck-Institute for Plant Breeding Research in Koeln, Germany. My post-doctoral research involved studying both model plants like Arabidopsis and staple crops such as barley and potato, with a focus on molecular genetics for disease resistance. In my current role as a potato pre-breeder and geneticist, I effectively utilize my extensive and diverse experience in plant breeding, molecular genetics, and mathematical data sciences. One notable achievement in this position is the development of a new type of KASP markers for disease resistance, which are highly diagnostic and transferable across breeding lines. Keeping pace with the rapid advancements in AI technology, I am now developing innovative tools for high-throughput genotyping to manage important yet complex traits through machine learning-based modelling and trait predictions.
Research
- Development of tools and strategies for quantitative trait manipulation:
The potato plant serves as an important model for studying fundamental aspects of carbohydrate metabolism, transport, starch-sugar interconversion, and repartitioning between source and sink tissues. Extensive knowledge exists regarding the biochemistry, physiology, and genetics underlying crucial potato traits, including dry matter (DM) content, starch/sugar content, and frying colour. This wealth of knowledge provides excellent opportunities to utilize the candidate gene approach for trait analysis and improvement.
Within the potato genome, more than 500 annotated genes are involved in metabolic processes, with over 120 genes directly associated with starch-sugar interconversion. To harness the potential of these genes, we have compiled a comprehensive collection of functional genes relevant to carbohydrate traits. This compilation has led to the development of a breeding-oriented targeted sequencing platform called BrenSeq (Breeding-oriented enrichment sequencing). BrenSeq enables genotyping of candidate genes across a diverse panel of breeding materials that encompass the traits of interest.
Through association analysis, we have successfully recaptured a plethora of l high-profile candidate genes as being most significant for the trait variations. The results not only provide new insights into the genetic basis of these traits for further in-depth studies but also establish a solid foundation for developing innovative tools and strategies to translate these findings into practical breeding programs. One important translational application is the development of highly transferable markers and the integration of AI technologies, particularly machine learning, into breeding programs.
In a pilot study based on BrenSeq, we have achieved impressive enhancements in prediction accuracy, with improvements of over 10% based on just a small number of high-profile candidate genes. Currently, we are refining our machine learning-based modelling and trait prediction by expanding and enriching the BrenSeq database through close collaboration with our industrial partners.
- Development of Sli-mediated pure inbred lines for accelerated mobilization of climate-resilient traits from CPC accessions:
The Commonwealth Potato Collection (CPC) is a unique and invaluable gene bank that holds approximately 1800 accessions of 82 wild and primitive cultivated potato species. These wild species possess significant value for potato breeding as they exhibit adaptations to a wide range of biotic and abiotic challenges. However, integrating desirable traits from wild species into cultivated potatoes can be challenging due to issues like linkage drag and high genetic loads. The utilization of the Sli-gene offers an opportunity to convert CPC accessions into pure inbred lines carrying homozygous Sli-genes, which can be readily used for diploid potato breeding. This ongoing work aims to develop novel germplasm resources by harnessing the potential of the Sli-gene for accelerated mobilization of climate-resilient traits.
Past research
- April 2011-present: CMS, The James Hutton Institute, UK. Potato prebreeding and genetics.
- 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).
