The contribution of plasticity to adaptive divergence: domestication as a model

可塑性对适应性分歧的贡献：驯化作为模型

• 批准号: NE/S002022/1
• 负责人: Mark Chapman
• 金额: $ 60.29万
• 依托单位: University of Southampton
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FS002022%2F1
• 关键词: contribution; plasticity; adaptive; divergence; domestication

The appearance of every plant and animal is affected by a combination of nature (inherited genes) and nurture (life experiences in a given environment). Plants growing in poor soils will usually grow slower than genetically identical plants in good quality soils, for example. In the same way, different environments will provide different cues to individuals, turning certain genes on or off depending on the processed signal. These environmentally-induced differences in morphology and gene expression are called phenotypic plasticity. The traditional nature vs nurture conflict is far too simplistic - the two interact. Identifying the precise ways in which this interplay plays out is a new frontier for evolutionary biology.A modified trait, such as leaf size or antenna length, might help a plant or animal survive, colonise and thrive in a new environment. This potentially could give rise to a new population or even a new species. However, in some cases a population in a novel environment might develop a worse phenotype and either not survive, or have to evolve to persist. While we can construct hypotheses for how plasticity aids in the exploitation of new environments and the exploration of new morphology, both of which can provoke the emergence of new species, we lack good data on how common these different pathways are when populations diverge and new species form.To do this we will compare turnips, cabbages and other domesticated Brassica crops with their closest wild relatives. In our pilot study, wild turnips look different when grown in crowded and uncrowded conditions (to mimic a wild and cultivated environment, respectively). In particular, the wild turnip develops larger roots in the uncrowded environment, i.e. the wild plant grows more like the cultivated plant when grown in a cultivated environment. Similarly, wild plant gene expression, when grown in cultivated conditions, resembles the cultivated plant more closely than when grown in wild conditions. This suggests that plasticity of the wild relative may have been important in the origin of the domesticated species, "pushing it" in the right direction for humans to select. By analysing several Brassica crops and their wild relatives we can see if the same changes happen in the different species too. This replication forms a model example for understanding how evolution works, and how important the different types of plasticity are in driving evolutionary divergence.We will further test whether plasticity played an important role in the early stages of domestication by growing multiple species that are closely related to the wild progenitor, but have never been domesticated. If we find that the never-domesticated species do not exhibit the same degree of plasticity in the traits we identify as involved in domestication, then the progenitor is unique in its plasticity, predisposing it to domestication.In addition, this will also let us know which genes are important for making a cultivated plant, significant information which can be used by crop breeders to improve the food we eat, as indicated through our discussions with Brassica breeders. Our data will also reveal whether changes in gene sequence or gene expression are involved in the differences between wild and cultivated plants. It will also reveal whether a third way in which genes can be turned on and off (specific chemical modifications called methylation) is important in the evolution of plasticity. Methylation might be especially important because these modifications can occur much faster (within minutes or hours) than DNA sequence changes.Not only will we be answering fundamental questions about how new species form, but the findings could help to develop crops that can withstand different environmental stresses. In a future facing climate change and an increasing human population we need this sort of information to plan better strategies to feed more people.

每种植物和动物的外观都受到自然（遗传基因）和养育（特定环境中的生活经历）的影响。例如，生长在贫瘠土壤中的植物通常比生长在优质土壤中的基因相同的植物生长得慢。同样，不同的环境会给个体提供不同的线索，根据处理的信号打开或关闭某些基因。这些环境诱导的形态和基因表达差异被称为表型可塑性。传统的先天与后天的冲突过于简单化了--两者相互作用。确定这种相互作用的确切方式是进化生物学的一个新前沿。一个改变的性状，如叶子的大小或触角的长度，可能有助于植物或动物在新的环境中生存，殖民和繁荣。这可能会产生一个新的种群，甚至一个新的物种。然而，在某些情况下，新环境中的种群可能会发展出更差的表型，要么无法生存，要么必须进化才能生存。虽然我们可以构建关于可塑性如何帮助开发新环境和探索新形态的假设，这两者都可以引发新物种的出现，但我们缺乏良好的数据来说明当种群分化和新物种形成时，这些不同的途径有多常见。在我们的试点研究中，野生萝卜在拥挤和不拥挤的条件下生长时看起来不同（分别模仿野生和栽培环境）。特别地，野生芜菁在不拥挤的环境中生长更大的根，即野生植物在栽培环境中生长时更像栽培植物。类似地，当在栽培条件下生长时，野生植物基因表达比在野生条件下生长时更接近栽培植物。这表明野生亲属的可塑性可能在驯化物种的起源中发挥了重要作用，将其“推向”了人类选择的正确方向。通过分析几种芸苔属作物及其野生亲缘植物，我们可以看到同样的变化是否也发生在不同的物种中。这种复制形成了一个模型例子，用于理解进化是如何工作的，以及不同类型的可塑性在驱动进化分歧中的重要性。我们将通过种植与野生祖先密切相关但从未被驯化的多个物种，进一步测试可塑性是否在驯化的早期阶段发挥了重要作用。如果我们发现从未驯化过的物种在我们确定为与驯化有关的性状上没有表现出相同程度的可塑性，那么祖先在可塑性方面是独一无二的，使其易于驯化。此外，这也将让我们知道哪些基因对培育植物很重要，这些重要信息可以被作物育种家用来改善我们所吃的食物，正如我们与芸苔属育种者讨论所表明的那样。我们的数据还将揭示基因序列或基因表达的变化是否涉及野生植物和栽培植物之间的差异。它还将揭示基因开启和关闭的第三种方式（称为甲基化的特定化学修饰）是否在可塑性的进化中很重要。甲基化可能特别重要，因为这些修饰的发生速度比DNA序列变化快得多（几分钟或几小时内）。我们不仅将回答有关新物种如何形成的基本问题，而且这些发现可能有助于开发能够承受不同环境压力的作物。在面临气候变化和人口增长的未来，我们需要这种信息来制定更好的战略来养活更多的人。

项目成果

Extensive crop-wild hybridization during Brassica evolution and selection during the domestication and diversification of Brassica crops.

• DOI: 10.1093/genetics/iyad027
• 发表时间: 2023-04-06
• 期刊: GENETICS
• 影响因子: 3.3
• 作者: Saban, Jasmine M.;Romero, Anne J.;Ezard, Thomas H. G.;Chapman, Mark A.
• 通讯作者: Chapman, Mark A.

Genome resources for underutilised legume crops: genome sizes, genome skimming and marker development

未充分利用的豆科作物的基因组资源：基因组大小、基因组撇取和标记开发

• DOI: 10.1007/s10722-023-01636-2
• 发表时间: 2023
• 期刊: Genetic Resources and Crop Evolution
• 影响因子: 2
• 作者: Diakostefani A

Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security.

除了参考基因组之外，还没有充分利用的孤儿作物的pangenomes和人群基因组学，以实现未来的食物和营养安全。

• DOI: 10.1111/nph.18021
• 发表时间: 2022-06
• 期刊: NEW PHYTOLOGIST
• 影响因子: 9.4
• 作者: Chapman, Mark A.;He, Yuqi;Zhou, Meiliang
• 通讯作者: Zhou, Meiliang

Extensive crop-wild hybridisation during Brassica evolution, and selection during the domestication and diversification of Brassica crops

芸苔属进化过程中的广泛作物-野生杂交，以及芸苔属作物驯化和多样化过程中的选择

• 发表时间: 2023
• 期刊: Genetics
• 影响因子: 3.3
• 作者: Saban, JM