CONTACT INFORMATION

Chin Jian (CJ) Yang
cjyang-work.github.io

SUMMARY STATEMENT

Detailed-oriented quantitative geneticist with 12 years of experience in genetics, breeding, domestication, statistics and simulation. Strong track records in delivering results, leading projects, writing grants and publications, teaching courses, mentoring students and engaging with diverse stakeholders. Excellent data analyst, problem solver, team player and communicator. Seeking opportunity to take on interdisciplinary challenges in a collaborative role.

EDUCATION

PhD Genetics, University of Wisconsin-Madison, WI, USA (2012-2018)
BS Biotechnology and Mathematics, Indiana University Bloomington, IN, USA (2009-2012)

RESEARCH & WORK EXPERIENCE

Quantitative geneticist at Xelect, St Andrews, UK (2024 - present)

Postdoctoral research associate at Scotland’s Rural College, Edinburgh, UK (2019 - 2024)
Advisors: Dr Ian Mackay ♦ Theme: genetic analysis, method development and strategy optimization for modern plant breeding ♦ Project 1: develop a new genomic selection model to partition favorable parental contributions for better introgression of exotic alleles into elite germplasm ♦ Project 2: evaluate the Plant Variety Rights (PVR) system and propose an evidence-based improvement with molecular markers ♦ Project 3: analyze crossing schemes in multi-parental populations, build an R package and a Shiny app for simulating and testing population designs ♦ Project 4: develop a trait-free approach for mapping genomic loci under selection in modern plant varieties ♦ Other projects: establish a breeding program for vertically farmed purslane, analyze current and improved statistical models in crop variety trials, integrate genomic selection with mutation breeding, develop novel approach for mapping epistatic and environmental interactions as variance controlling QTLs (vQTLs), test prototypes for indoor cultivation of dulse (Palmaria palmata), and analyze the digestibility effects of modern and synthetic wheat straws as chicken feed.

Postdoctoral research associate at Technical University of Munich, Freising, DE (2018 - 2019)
Advisor: Dr Chris Carolin-Schoen ♦ Theme: maize quantitative genetics ♦ Project: evaluate REML and Bayesian methods in partitioning genetic correlations of early development traits in maize.

Graduate research assistant at University of Wisconsin-Madison (2012 - 2018)
Advisor: Dr John F Doebley ♦ Theme: dissection of the genetic architecture of domestication traits in maize and its ancestor teosinte ♦ Project 1: characterize three key domestication genes responsible for shaping maize ear architecture using QTL fine-mapping and molecular tools ♦ Project 2: contribute to the development of the teosinte nested association mapping (TeoNAM) population and the use of it in QTL linkage mapping pipeline for undergraduate research training ♦ Project 3: apply quantitative genetics modelling of selection strengths and constraints during maize domestication by using large proxy populations of ancient maize and teosinte.

Undergraduate research assistant at Indiana University Bloomington (2010 - 2012)
Advisor: Dr Jeffrey D Palmer ♦ Theme: Lobeliaceae phylogenetics ♦ Project: sequence mitochondrial genes (atp8, cox1) across hundreds of species in Lobeliaceae for the use in phylogenetic analysis.

SKILLS

  • Genetics: selection, breeding, genetic gain, heritabilities, variances/covariances, epistasis, phylogenetics.
  • Statistics: linear regression, mixed model, REML, Bayesian, genomic selection, GWAS, QTL mapping.
  • Computational Tools: LINUX, UNIX, Git, Windows, Mac, Microsoft Office, TASSEL.
  • Programming: R, Shiny, Markdown, HTML, Python, SAS, ASReml, Julia.
  • Big Data: Genotype-by-Sequencing (GBS), genomic array.
  • Molecular Genetics: DNA/RNA isolation, marker development, cloning, PCR, qRT-PCR, gene expression.
  • Field Work: field trials, greenhouse trials, phenotyping, travel for work.
  • Others: teaching, menotirng, writing grants and publications, developing collaboration.

FUNDED GRANTS

  • Named staff, ROSCOE: Recommendations over Scottish Environments, to improve the statistical models for varietal recommendation system, Scottish Society for Crop Research (SSCR), 2022-2023, £5k.
  • Co-investigator, MAGS: Mutation Breeding for Quantitative Traits with Genomic Selection, to integrate genomic selection with mutation breeding, International Atomic Energy Agency (IAEA), 2022-2027, £43k.
  • Named staff, BARGAIN: Mobilising untapped genetic diversity, JHI-B1-2, to develop multi-parental barley breeding population, Rural and Environmental Science and Analytical Services (RESAS), 2022-2027, £573k.
  • Named staff, The impact of novel crops and farming practices on the Scottish agricultural landscape, JHI-B1-3, to develop multi-parental ryegrass breeding population, RESAS, 2022-2027, £713k.
  • Principal investigator, Nutrislane: nutritious purslane for the market, to develop a market for vertically farmed purslane, University Innovation Fund, 2023-2024, £15k.

STUDENTS

  • Undergraduate mentor for Jordan Michels (University of Wisconsin-Madison) on “Fine-mapping of etb1.2, a QTL regulating ear internode length in maize and teosinte”, 2013.
  • Undergraduate co-mentor for Qi Cheng (University of Wisconsin-Madison) on “Mapping prolificacy QTL in maize and teosinte”, 2015 - 2016.
  • Undergraduate co-mentor for Aria Peterson, Bailey Spiegelberg, Brandon Kim, Craig DeValk, Isaac Barber, Jack Schnell, Joe Perry, Kyle Krueger, Laura Bergstrom, Lora Daskalska, Michael Neumeyer and Sam Lawton (University of Wisconsin-Madison) on “QTL mapping of domestication traits in the teosinte nested association mapping population”, 2015 - 2018.
  • Undergraduate mentor for Amanda Alves de Melo (University of Wisconsin-Madison) on “Genetics of sexual determination in maize/teosinte terminal lateral inflorescence”, 2016.
  • Internal PhD examiner for Jon Bancic (University of Edinburgh) on “Breeding strategies for integrating new and orphan crops in production systems”, 22 November 2021.
  • Undergraduate co-supervisor for Leontien Helderman (HAS Green Academy) on “Perennial ryegrass under speed vernalization and speed breeding conditions”, 2023 - 2024.
  • PhD co-supervisor for Emma Irving (University of Edinburgh) on “Rapid domestication of purslane in a vertical farm environment”, 2023 - 2027.

TEACHING EXPERIENCE

  • Teaching assistant for General Genetics (code 466) at University of Wisconsin-Madison, Fall 2013.
  • Guest lecture on “IBD, IBS, Genetic Distance, Population Structure” for the XXIII International Master in Plant Genetics, Genomics and Breeding by CIHEAM Zaragoza, Online, 15 - 19 February 2021.
  • Guest lecture on “Conventional and Advanced Breeding Methods” and “Plant Variety Rights” for Genetics Improvement of Crops at University of Edinburgh, Fall 2022.
  • Module co-lead on “Horticultural Biotechnology” for BSc in Horticulture at SRUC, 2023 - 2024.
  • Module co-lead on “Plant Biotechnology” for MSc in Applied Plant Science at SRUC, 2023 - 2024.
  • Guest lecture on “IBD, IBS, Genetic Distance, Population Structure” for the XXIV International Master in Plant Genetics, Genomics and Breeding by CIHEAM Zaragoza, 8 - 9 February 2024.

BREEDING EXPERIENCE

  • Purslane breeding, 2022 - present. I am establishing a breeding program for purslane (novel crop) to be grown under controlled environments like vertical farms. I have identified target traits, trialed under controlled conditions, surveyed phenotypic variation, and engaged with stakeholders. I am currently attempting to register new varieties, create segregating population, and select favorable traits.

EXTENSION EXPERIENCE

  • SeedPod showcase, Aberdeen, UK, 18 November 2022. This workshop was held to foster academic collaboration with the local food and drink industry. I presented a poster on purslane breeding, engaged with the industry, and identified a commercial vertical farming partner.
  • Royal Highland Show, Edinburgh, UK, 22 - 25 June 2023. This event was state fair-like with a focus on agricultural exhibits. I presented a talk on purslane breeding, showed purslane in a demonstration cube, provided fresh purslane for taste tests, distributed flyers on purslane, and engaged with the public.

TALK

  • Accepted talk, “New ways into plant breeding using eigen/env-GWAS and origin specific genomic selection” at the UK Plant Science Presents Webinar, UK, 27 October 2020.
  • Invited talk, “MAGIC population design” at the Rank Symposium on Meiosis: Controlling the Recombination Landscape, Grasmere, UK, 4 - 7 April 2022.
  • Accepted talk, “Defining the causes and consequences of phantom epistasis in heterotic hybrids” at the 18th Eucarpia Biometrics in Plant Breeding Conference, Paris, France, 21 - 23 September 2022.
  • Invited talk, “Defining the causes and consequences of phantom epistasis in heterotic hybrids” at the Computational Genetics Discussion Group, Edinburgh, UK, 22 November 2022.
  • Invited talk, “Navigating modern plant breeding with quantitative genetics” at the Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, US, 25 July 2023.
  • Invited talk, “Breeding for tomorrow: insights from analyses of historical plant variety datasets” at the Professor Ian Mackay Memorial Seminar, Cambridge, UK, 1 February 2024.
  • Invited talk, “Plant breeding through the lens of quantitative genetics” at the Department of Plant Science, University of Dundee, Dundee, UK, 22 February 2024.

CONFERENCES AND WORKSHOPS

  • 18th Eucarpia Biometrics in Plant Breeding Conference, Paris, France, 21 - 23 September 2022.
  • Maize Genetics Conference, various locations, 2013, 2015 - 2017, 2020 - 2022.
  • Barley Away Days, Dunkeld, UK, 2020, 2024.
  • A Century of Genetics, Edinburgh, UK, 13 - 15 November 2019.
  • Forestry Workshop on Genomic Selection, Edinburgh, UK, 17 September 2019.
  • MAGIC Workshop, Cambridge, UK, 23 - 24 July 2019.
  • UW-Madison PSGSC Annual Plant Science Symposium, Madison, WI, 2012 - 2017.
  • 5th International Conference on Quantitative Genetics, Madison, WI, 12 - 17 June 2016.

FELLOWSHIPS AND AWARDS

  • 2017: Schlimgen Award; Department of Genetics, University of Wisconsin-Madison.
  • 2016 - 2017: Stone Travel Award; Department of Genetics, University of Wisconsin-Madison.
  • 2007 - 2012: National Scholarship; Public Service Department of Malaysia.

LANGUAGES

  • English: native/bilingual proficiency.
  • Malay: limited working proficiency.
  • Mandarin: limited working proficiency.

PEER REVIEWS

  • Theoretical and Applied Genetics (3)
  • Nature Plants (1)
  • Genetics (1)
  • G3: Genes, Genomes, Genetics (1)
  • Journal of Experimental Botany (1)
  • Plant Ecology & Diversity (1)
  • Genes (2)
  • Agronomy (2)
  • International Journal of Molecular Sciences (1)

PUBLICATIONS

  1. Yang CJ, Ladejobi O, Mott R, Powell W & Mackay I (2022) Analysis of historical selection in winter wheat. Theor Appl Genet 135: 3005-3023.
  2. Samayoa LF, Olukolu BA, Yang CJ, Chen Q, Stetter MG, York AM, Sanchez-Gonzalez JJ, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Yang J, Ross-Ibarra J, Buckler ES, Doebley JF, Holland JB (2021) Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte. PLoS Genet 17: e1009797.
  3. Yang CJ, Edmondson RN, Piepho H-P, Powell W & Mackay I (2021) Crafting for a better MAGIC: systematic design and test for Multiparental Advanced Generation Inter-Cross population. G3 11: jkab295.
  4. Chen Q, Samayoa LF, Yang CJ, Olukolu BA, York AM, Sanchez-Gonzalez JJ, Xue W, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Buckler ES, Holland JB & Doebely JF (2021) A conserved genetic architecture among populations of the maize progenitor, teosinte, was radically altered by domestication. Proc Natl Acad Sci USA 118: e2112970118.
  5. Yang CJ, Russell J, Ramsay L, Thomas W, Powell W & Mackay I (2021) Overcoming barriers to the registration of new plant varieties under the DUS system. Commun Biol 4: 302.
  6. Yang CJ, Sharma R, Gorjanc G, Hearne S, Powell W & Mackay I (2020) Origin specific genomic selection: a simple process to optimize the favorable contribution of parents to progeny. G3 10: 2445-2455.
  7. Chen Q, Samayoa LF, Yang CJ, Bradbury PJ, Olukolu BA, Neumeyer MA, Romay MC, Sun Q, Lorant A, Buckler ES, Ross-Ibarra J, Holland JB & Doebley JF (2020) The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication. PLoS Genet 16: e1008791.
  8. Chen Q, Yang CJ, York AM, Xue W, Daskalska LL, DeValk CA, Krueger KW, Lawton SB, Spiegelberg BG, Schnell JM, Neumeyer MA, Perry JS, Peterson AC, Kim B, Bergstrom L, Yang L, Barber IC, Tian F & Doebley JF (2019) TeoNAM: A nested assocation mapping population for domestication and agronomic trait analysis in maize. Genetics 213: 1065-1078.
  9. Yang CJ, Samayoa LF, Bradbury PJ, Olukolu BA, Xue W, York AM, Tuholski MR, Wang W, Daskalska LL, Neumeyer MA, Sanchez-Gonzalez JJ, Romay MC, Glaubitz JC, Sun Q, Buckler ES, Holland JB & Doebley JF (2019) The genetic architecture of teosinte catalyzed and constrained maize domestication. Proc Natl Acad Sci USA 116: 5643-5652.
  10. Guo L, Wang X, Zhao M, Huang C, Li C, Li D, Yang CJ, York AM, Xue W, Xu G, Liang Y, Chen Q, Doebley JF & Tian F (2018) Stepwise cis-regulatory changes in ZCN8 contribute to maize flowering-time adaptation. Curr Biol 28: 3005-2015.
  11. Yang CJ, Kursel LE, Studer AJ, Bartlett ME, Whipple CJ & Doebley JF (2016) A gene for genetic background in Zea mays: fine-mapping enhancer of teosinte branched1.2 to a YABBY class transcription factor. Genetics 204: 1573-1585.
  12. Yang L, Yang CJ, Cheng Q, Xue W & Doebley JF (2016) Mapping prolificacy QTL in maize and teosinte. J Hered 107: 674-678.