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

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.

Part of the toolbox of scientists and plant breeders are the use wild relative species of crops to introduce new traits into crops to produce enhanced and more resilient varieties. In the case of cultivated sweetpotato such an approach is severely limited by a lack of knowledge of what wild plants are the immediate progenitors of the crop. This proposed research will establish the veracity of the recent discovery of the wild form of sweetpotato in Ecuador. These wild populations were presumably not subject to the constraints associated with domestication, and therefore have the potential to contribute unique resources for sweetpotato improvement. Our proposal seeks to quantify, through a combination of fieldwork and genomic studies, the genetic and phenotypic diversity existing within populations of this wild form in comparison to the cultivated crop. In addition, we aim to investigate the processes that led to cultivated sweetpotato from this presumed wild progenitor. It will achieve this through a combination of DNA sequencing and field work in Ecuador to establish the geographical limits of the wild form. By measuring and documenting the phenotypic traits of these wild plants we can establish how they differ from the cultivated form and how much phenotypic variability they might have relative to the cultivated form. We can use this information to sequence the genomes of a representative number (96 samples) of specimens throughout the range at low coverage to compare to an existing dataset of whole chloroplast genomes and 605 nuclear genes of the cultivated sweet potato and other wild relatives. We will also sequence the whole genome of this wild form at high coverage in order to establish how this genome differs from the draft cultivated sweet potato genome and two other published genomes of wild relative species.

Online resources for sweetpotato research
We aim to make the results of our research freely available to sweetpotato breeders and to the entire scientific community through different channels. One of these channels is the Ipomoea Project website, which will be published online at the beginning of 2019. This website will feature the results of four years of taxonomic and phylogenetic research on the genus Ipomoea with a particular focus on the sweetpotato and its CWR. The website, hosted at Oxford, includes a BRAHMS database with descriptions, pictures and maps of all species, as well as phylogenetic trees and all the molecular data generated during these four years. Importantly, we have developed an online tool that facilitates the quick and reliable identification of all species closely related to the sweetpotato using DNA barcodes. An online version of this tool and the code written in Python will be freely available through the website.
In addition, from the research presented in this proposal we will develop tools to visualize and interrogate the genomes produced as part of our project, as well as to download all the data generated. Similar tools are already available for the sweetpotato (e.g. the Sweetpotato GARDEN Japanese project) but do not exist for its wild relatives yet. We will build a genomic platform based on the JBrowse genome browser [37] to make the genome of the new Ecuadorian entity freely available to sweetpotato researchers and breeders worldwide .