Bayesian optimisation for yield in high-dimensional trait-space identifies crop ideotypes in Oil Seed Rape
Bayesian optimisation for yield in high-dimensional trait-space identifies crop ideotypes in Oil Seed Rape
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DOI：
10.1101/2021.07.19.452946
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发表时间：
2021-07
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影响因子：
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通讯作者：
A. Calderwood;L. Siles;P. Eastmond;S. Kurup;R. Morris
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作者：
A. Calderwood;L. Siles;P. Eastmond;S. Kurup;R. Morris
作物产量的提高长期以来一直是主要的育种目标，并且日益成为许多植物研究领域的目标。产量已被证明是一个复杂的性状，取决于多个基因，植物结构和植物-环境相互作用。这种复杂性通常通过关注产量的贡献因素（产量性状）来降低。然而，产量性状之间的相互作用的定量理解，以及这些关系对产量的影响在很大程度上是未开发的。因此，作物品种在给定环境中实现其最佳形态的程度以及这对种子产量的影响是未知的。在这里，我们使用因果推理模型的层次结构的影响，27宏观和微观产量性状在植物发育过程中，在春季和冬季油菜种子产量。我们对建模的产量潜力进行贝叶斯优化，确定理想型植物的形态，预计这些植物的产量将高于研究小组中的现有品种。我们发现，现有的春季品种占据了最佳区域的性状空间，但潜在的高产策略是未开发的现有的冬季品种。除了对油菜品种改良的具体建议外，这项工作还为作物育种作为优化问题的研究提供了一个新颖的、通用的方法框架。
The improvement of crop yield has long been a major breeding target and is increasingly becoming a goal in many areas of plant research. Yield has been shown to be a complex trait, depending on multiple genes, plant architecture and plant-environment interactions. This complexity is frequently reduced by focussing on contributing factors to yield (yield traits). However, a quantitative understanding of the interplay between yield traits, and the effect of these relationships on yield is largely unexplored. Consequently, the extent to which crop varieties achieve their optimal morphology in a given environment and how this impacts on seed yield is unknown. Here we use causal inference to model the hierarchically structured effects of 27 macro and micro yield traits on each other over the course of plant development, and on seed yield in Spring and Winter oilseed rape plants. We perform Bayesian optimisation on the modelled yield potential, identifying the morphology of ideotype plants which are expected to be higher yielding than the existing varieties in the studied panels. We find that existing Spring varieties occupy the optimal regions of trait-space, but that potentially high yielding strategies are unexplored in extant Winter varieties. In addition to concrete recommendations for varietal improvement in oilseed rape, this work provides a novel, general methodological framework for the study of crop breeding as an optimisation problem.