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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Breeding
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1488814

Stochastic simulation to optimize rice breeding at IRRI

Provisionally accepted
  • 1 International Rice Research Institute (IRRI), Los Baños, Philippines
  • 2 University of Thies, Thiès, Thies, Senegal
  • 3 UMR AGAP Institut, CIRAD, Montpellier, France
  • 4 International Center for Tropical Agriculture (CIAT), Cali, Cauca, Colombia

The final, formatted version of the article will be published soon.

    Genetic improvement in rice increased yield potential and improved varieties for farmers over the last decades. However, the demand for rice is growing while its cultivation faces challenges posed by climate change. To address these challenges, rice breeding programs need to adopt efficient breeding strategies to provide a steady increase in the rate of genetic gain for major traits. The International Rice Research Institute (IRRI) breeding program has evolved over time to implement faster and more efficient breeding techniques such as rapid generation advance (RGA) and genomic selection (GS). Simulation experiments support data-driven optimization of the breeding program toward the desired rate of genetic gain for key traits. This study used stochastic simulations to compare breeding schemes with different cycle times. The objective was to assess the impact of different genomic selection strategies on medium-and long-term genetic gain. Four genomic selection schemes were simulated, representing the past approaches (5 years recycling), current schemes (3 years recycling), and two options for the future schemes (both with 2 years recycling). The 2-Year within-cohort prediction scheme showed a significant increase in genetic gain in the medium-term horizon. Specifically, it resulted in a 22%, 24%, and 27% increase over the current scheme in the zero, intermediate, and high genotype-byenvironment interaction (GEI) contexts, respectively. On the other hand, the 2-Year scheme based on between-cohort prediction was more efficient in the long term, but only in the absence of GEI. Consistent with our expectations, the shortest breeding schemes showed an increase in genetic gain and faster depletion of genetic variance compared to the current scheme. These results suggest that higher rates of genetic gain are achievable in the breeding program by further reducing the cycle time and adjusting the target population of environments. However, more attention is needed regarding the crossing strategy to use genetic variance optimally.

    Keywords: rice, Genetic gain, stochastic simulations, genomic selection, Breeding strategy

    Received: 30 Aug 2024; Accepted: 16 Oct 2024.

    Copyright: © 2024 Seck, Prakash, Covarrubias-Pazaran, Gueye, DIEDHIOU, Bhosale, Kadaru and Bartholomé. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Parthiban T. Prakash, International Rice Research Institute (IRRI), Los Baños, 4031, Philippines
    Jérôme Bartholomé, UMR AGAP Institut, CIRAD, Montpellier, France

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.