Capacity Building for Crop Improvement in Sweetpotato: Insights from Wild Populations

在一个经历重大环境剧变和人口增长的世界上，人们普遍预测，在可预见的未来，粮食安全将是一个令人关切的主要领域。提高作物的抗灾能力是一个活跃的研究领域，因为科学家的目标是用更少的资源、更少的土地来增加粮食产量。科学家和植物育种家的工具箱的一部分是利用作物的野生近缘种向作物引入新特性，以生产增强和更具弹性的品种。这种方法在香蕉、大麦、豆类、木薯、鹰嘴豆、玉米、生菜、燕麦、土豆、大米、甘蔗、向日葵、西红柿和小麦等作物上取得了成功。一种重要的全球粮食作物，由于对其野生近缘种的了解不足，无法使用这种方法，那就是甘薯（Ipomoea batatas）。然而，最近发表的研究在了解甘薯与其最密切相关的物种之间的系统发育关系方面取得了重大进展。目标1：描述甘薯的野生形态，并定义一套形态描述符，使甘薯育种者能够将其与栽培的甘薯和其他他们感兴趣的材料区分开来。目的2：构建高质量的野生甘薯基因组。这将使我们能够与已有的其他Ipomoea物种的基因组进行比较基因组研究。这些比较研究对于了解作物物种的进化以及多倍体化如何影响其基因组至关重要。此外，它将为六倍体品种基因组的组装提供高质量的参考。目的3：记录野生甘薯种群内部和种群之间在其整个分布中的表型变异。这将为了解野生形式、作物和所有其他野生近缘种之间的性状分布提供一个全面的比较框架。目的4：确定野生甘薯的遗传变异。我们将对来自厄瓜多尔不同野生甘薯种群的96个样本进行全基因组测序，并考虑到目标3中确定的地理和表型差异。这一分析将使我们不仅能够量化野生甘薯与栽培甘薯的遗传变异，而且还可以评估甘薯驯化的遗传过程，并研究“驯化基因”的适应性进化。目的5：鉴定甘薯在适应栽培过程中的正选择基因。植物驯化通常与选择适合栽培的野生植物的特定性状有关。我们将通过比较野生形式和几个甘薯品种来寻找这一选择的标志。这种类型的姐妹谱系比较将使我们能够识别同义和非同义替换的差异，并确定多态性是由于正选择还是中性漂移。此外，这些信息将使我们能够详细了解在作物进化过程中与野生形式相比重要的适应性突变。目的6：阐明甘薯多倍体的起源、途径和驯化，以及驯化在甘薯可食用贮藏根的起源和进化中所起的作用。

In a world experiencing major environmental upheaval and population growth it is widely predicted that food security will be a major area of concern for the foreseable future. Increasing the resilience of crops is an area of active research, as scientists aim to increase food production on less land using fewer resources. Part of the toolbox of scientists and plant breeders are the use wild relative species of the crop to introduce new traits into crops to produce enhanced and more resilient varieties. Such approaches have worked successfully in some crops such as banana, barley, beans, cassava, chickpeas, maize, lettuce, oats, potato, rice, sugarcane, sunflowers, tomatoes and wheat. One important global food crop for which there has been insufficient understanding of wild relatives for the use of this approach, is the sweetpotato (Ipomoea batatas). However, recent published research has made significant progress in understanding the phylogenetic relationships between sweetpotato and the species most closely related to it. Objective 1: Describe the wild form of the sweetpotato and define a set of morphological descriptors that allow sweetpotato breeders to distinguish it from cultivated Ipomoea batatas and from other materials of interest to them.Objective 2: Assemble a high-quality genome of wild sweetpotato. This will allow us to conduct comparative genomic studies with the already available genomes of other species of Ipomoea. These comparative studies are essential to understand the evolution of the crop species and how polyploidization affected its genome. In addition, it will constitute a high-quality reference for assembling the genome of the hexaploid cultivar.Objective 3: Document phenotypic variation within and between wild sweetpotato populations, across its entire distribution. This will provide a comprehensive comparative framework for understanding the distribution of traits between the wild form, the crop and all other wild relatives.Objective 4: Determine genetic variation in wild sweetpotato. We will conduct whole genome sequencing of 96 samples from different populations of wild sweetpotato across Ecuador, taking into account geographical and phenotypic variation as identified in Objective 3. This analysis will allow us to not only quantify genetic variation in the wild form of the sweetpotato compared to the cultivated form, but also to assess the genetic processes underlying sweetpotato domestication and to investigate adaptive evolution of 'domestication genes'.Objective 5: Identify genes under positive selection during the adaptation of sweetpotato to cultivation. Plant domestication is often associated with selection of specific traits in the wild plants that make them suitable for cultivation. We will look for a signature of this selection by comparison between the wild form and several sweetpotato cultivars. This type of sister-lineage comparison will allow us to identify differences in synonymous and non-synonymous substitutions and to determine whether polymorphism is due to positive selection or neutral drift. Further, this information will allow us to understand in detail the adaptive mutations that were important during the evolution of the crop compared to its wild form.Objective 6: Clarify the origin, route to polyploidy and domestication of the sweetpotato and what role domestication had in the origin and evolution of the edible storage root.