IDEAS home Printed from https://ideas.repec.org/a/spr/jagbes/v25y2020i4d10.1007_s13253-020-00403-5.html
   My bibliography  Save this article

The Design of Early-Stage Plant Breeding Trials Using Genetic Relatedness

Author

Listed:
  • Brian R. Cullis

    (University of Wollongong)

  • Alison B. Smith

    (University of Wollongong)

  • Nicole A. Cocks

    (University of Wollongong
    BASF)

  • David G. Butler

    (University of Wollongong)

Abstract

The use of appropriate statistical methods has a key role in improving the accuracy of selection decisions in a plant breeding program. This is particularly important in the early stages of testing in which selections are based on data from a limited number of field trials that include large numbers of breeding lines with minimal replication. The method of analysis currently recommended for early-stage trials in Australia involves a linear mixed model that includes genetic relatedness via ancestral information: non-genetic effects that reflect the experimental design and a residual model that accommodates spatial dependence. Such analyses have been widely accepted as they have been found to produce accurate predictions of both additive and total genetic effects, the latter providing the basis for selection decisions. In this paper, we present the results of a case study of 34 early-stage trials to demonstrate this type of analysis and to reinforce the importance of including information on genetic relatedness. In addition to the application of a superior method of analysis, it is also critical to ensure the use of sound experimental designs. Recently, model-based designs have become popular in Australian plant breeding programs. Within this paradigm, the design search would ideally be based on a linear mixed model that matches, as closely as possible, the model used for analysis. Therefore, in this paper, we propose the use of models for design generation that include information on genetic relatedness and also include non-genetic and residual models based on the analysis of historic data for individual breeding programs. At present, the most commonly used design generation model omits genetic relatedness information and uses non-genetic and residual models that are supplied as default models in the associated software packages. The major reasons for this are that preexisting software is unacceptably slow for designs incorporating genetic relatedness and the accuracy gains resulting from the use of genetic relatedness have not been quantified. Both of these issues are addressed in the current paper. An updating scheme for calculating the optimality criterion in the design search is presented and is shown to afford prodigious computational savings. An in silico study that compares three types of design function across a range of ancillary treatments shows the gains in accuracy for the prediction of total genetic effects (and thence selection) achieved from model-based designs using genetic relatedness and program specific non-genetic and residual models. Supplementary materials accompanying this paper appear online.

Suggested Citation

  • Brian R. Cullis & Alison B. Smith & Nicole A. Cocks & David G. Butler, 2020. "The Design of Early-Stage Plant Breeding Trials Using Genetic Relatedness," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(4), pages 553-578, December.
    • Handle: RePEc:spr:jagbes:v:25:y:2020:i:4:d:10.1007_s13253-020-00403-5
    DOI: 10.1007/s13253-020-00403-5
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s13253-020-00403-5
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1007/s13253-020-00403-5?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Fred Glover, 1989. "Tabu Search---Part I," INFORMS Journal on Computing, INFORMS, vol. 1(3), pages 190-206, August.
    2. Júlio S. de S. Bueno Filho & Steven G. Gilmour, 2003. "Planning Incomplete Block Experiments When Treatments Are Genetically Related," Biometrics, The International Biometric Society, vol. 59(2), pages 375-381, June.
    3. Alison Smith & Brian Cullis & Robin Thompson, 2001. "Analyzing Variety by Environment Data Using Multiplicative Mixed Models and Adjustments for Spatial Field Trend," Biometrics, The International Biometric Society, vol. 57(4), pages 1138-1147, December.
    4. Gilmour, Arthur & Cullis, Brian & Welham, Sue & Gogel, Beverley & Thompson, Robin, 2004. "An efficient computing strategy for prediction in mixed linear models," Computational Statistics & Data Analysis, Elsevier, vol. 44(4), pages 571-586, January.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Martin P. Boer & Hans-Peter Piepho & Emlyn R. Williams, 2020. "Linear Variance, P-splines and Neighbour Differences for Spatial Adjustment in Field Trials: How are they Related?," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(4), pages 676-698, December.
    2. Maryna Prus & Hans-Peter Piepho, 2021. "Optimizing the Allocation of Trials to Sub-regions in Multi-environment Crop Variety Testing," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(2), pages 267-288, June.
    3. Hans-Peter Piepho & Robert J. Tempelman & Emlyn R. Williams, 2020. "Guest Editors’ Introduction to the Special Issue on “Recent Advances in Design and Analysis of Experiments and Observational Studies in Agriculture”," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(4), pages 453-456, December.
    4. Linda M. Haines, 2021. "Augmented Block Designs for Unreplicated Trials," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(3), pages 409-427, September.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Nha Vo‐Thanh & Hans‐Peter Piepho, 2023. "Generating designs for comparative experiments with two blocking factors," Biometrics, The International Biometric Society, vol. 79(4), pages 3574-3585, December.
    2. Chiara Gruden & Irena Ištoka Otković & Matjaž Šraml, 2020. "Neural Networks Applied to Microsimulation: A Prediction Model for Pedestrian Crossing Time," Sustainability, MDPI, vol. 12(13), pages 1-22, July.
    3. Chou, Jui-Sheng & Truong, Dinh-Nhat, 2021. "A novel metaheuristic optimizer inspired by behavior of jellyfish in ocean," Applied Mathematics and Computation, Elsevier, vol. 389(C).
    4. Anurag Agarwal, 2009. "Theoretical insights into the augmented-neural-network approach for combinatorial optimization," Annals of Operations Research, Springer, vol. 168(1), pages 101-117, April.
    5. Mohammad Javad Feizollahi & Igor Averbakh, 2014. "The Robust (Minmax Regret) Quadratic Assignment Problem with Interval Flows," INFORMS Journal on Computing, INFORMS, vol. 26(2), pages 321-335, May.
    6. Сластников С.А., 2014. "Применение Метаэвристических Алгоритмов Для Задачи Маршрутизации Транспорта," Журнал Экономика и математические методы (ЭММ), Центральный Экономико-Математический Институт (ЦЭМИ), vol. 50(1), pages 117-126, январь.
    7. H. A. J. Crauwels & C. N. Potts & L. N. Van Wassenhove, 1998. "Local Search Heuristics for the Single Machine Total Weighted Tardiness Scheduling Problem," INFORMS Journal on Computing, INFORMS, vol. 10(3), pages 341-350, August.
    8. C N Potts & V A Strusevich, 2009. "Fifty years of scheduling: a survey of milestones," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 60(1), pages 41-68, May.
    9. Nair, D.J. & Grzybowska, H. & Fu, Y. & Dixit, V.V., 2018. "Scheduling and routing models for food rescue and delivery operations," Socio-Economic Planning Sciences, Elsevier, vol. 63(C), pages 18-32.
    10. Cazzaro, Davide & Fischetti, Martina & Fischetti, Matteo, 2020. "Heuristic algorithms for the Wind Farm Cable Routing problem," Applied Energy, Elsevier, vol. 278(C).
    11. İbrahim Muter & Ş. İlker Birbil & Güvenç Şahin, 2010. "Combination of Metaheuristic and Exact Algorithms for Solving Set Covering-Type Optimization Problems," INFORMS Journal on Computing, INFORMS, vol. 22(4), pages 603-619, November.
    12. Kadri Sylejmani & Jürgen Dorn & Nysret Musliu, 2017. "Planning the trip itinerary for tourist groups," Information Technology & Tourism, Springer, vol. 17(3), pages 275-314, September.
    13. Huang, Yeran & Yang, Lixing & Tang, Tao & Gao, Ziyou & Cao, Fang, 2017. "Joint train scheduling optimization with service quality and energy efficiency in urban rail transit networks," Energy, Elsevier, vol. 138(C), pages 1124-1147.
    14. B Dengiz & C Alabas-Uslu & O Dengiz, 2009. "Optimization of manufacturing systems using a neural network metamodel with a new training approach," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 60(9), pages 1191-1197, September.
    15. S-W Lin & K-C Ying, 2008. "A hybrid approach for single-machine tardiness problems with sequence-dependent setup times," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 59(8), pages 1109-1119, August.
    16. J-F Chen & T-H Wu, 2006. "Vehicle routing problem with simultaneous deliveries and pickups," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 57(5), pages 579-587, May.
    17. Joseph B. Mazzola & Robert H. Schantz, 1997. "Multiple‐facility loading under capacity‐based economies of scope," Naval Research Logistics (NRL), John Wiley & Sons, vol. 44(3), pages 229-256, April.
    18. Kadri Sylejmani & Jürgen Dorn & Nysret Musliu, 0. "Planning the trip itinerary for tourist groups," Information Technology & Tourism, Springer, vol. 0, pages 1-40.
    19. Abdmouleh, Zeineb & Gastli, Adel & Ben-Brahim, Lazhar & Haouari, Mohamed & Al-Emadi, Nasser Ahmed, 2017. "Review of optimization techniques applied for the integration of distributed generation from renewable energy sources," Renewable Energy, Elsevier, vol. 113(C), pages 266-280.
    20. Masoud Yaghini & Mohammad Karimi & Mohadeseh Rahbar, 2015. "A set covering approach for multi-depot train driver scheduling," Journal of Combinatorial Optimization, Springer, vol. 29(3), pages 636-654, April.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:jagbes:v:25:y:2020:i:4:d:10.1007_s13253-020-00403-5. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.