title: The ecology and evolution of brassicas in Western Europe, featuring feral populations and underground microbial communities
Creators: name: Mittell, Elizabeth
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: Microbial communities, population genomics, brassicas, domestication, food security.

description: One concern about climate change is its effects on maintaining stable food production (food security). To address this situation, research into how we can increase the productivity of crop plants whilst simultaneously increasing their resilience to future environmental variation is required. Furthermore, alternative strategies need to be explored that do not rely on chemical inputs, as these are an expensive and in some instances a decreasing finite resource. The overall motivation for this thesis was to use plants in the genus Brassica to investigate two promising avenues for crop improvement: using wild crop relatives as genomic resources and exploiting interactions with the microbial community in the soil to facilitate rapid adaptation to changing environmental conditions. To improve food security, one option would be to facilitate the adaptation of crop plants to different climatic scenarios, such as increases in precipitation. For this we can look to crop wild relatives and their gene pools that are already locally adapted to a range of environmental conditions. Wild populations of Brassica oleracea established along the Atlantic coasts of Western Europe are thought to be the result of crop plants establishing in the wild after escaping from domestic situations in the last thirty to a few hundred years. However, not enough is known about their origins, population structure and adaptive capacity to inform strategies for their use in crop improvement. Chapter 2 aimed to use genome-wide single nucleotide polymorphism genotyping to investigate relationships among extant populations and to investigate whether there was evidence for adaptation to local environmental conditions. I found relatively low within population genetic diversity, and a population genetic structure that was disconnected to geography, supporting a single domestication bottleneck in the Mediterranean. This means that wild B. oleracea in the Atlantic might have gone through a second bottleneck upon escape. However, these recently established wild populations still showed signals of local adaptation to climatic variation that covered a 14˚ latitudinal gradient. Therefore, the wild B. oleracea populations in the Atlantic region demonstrate that rapid adaptation to novel environments occurs within this species from cultivated plants, so could occur again in crop plants, and highlights their use as a genetic resource. From an agricultural perspective, even adaptation that is rapid on an evolutionary timescale can be considered slow. Therefore, additional factors to increase the resilience of crop plants under environmental change in the interim are also vital. Microbial communities, with their different spatial and temporal scales of life and rapid generation times, can more rapidly adapt to environmental conditions than plants. The microbial communities associated with plant roots (the rhizosphere) are important for plant growth and health, and could mitigate against environmental changes in the short-term whilst plants are adapting. A drawback of studying these microbial communities is that the vast majority of organisms in them are unknown, both in terms of their taxonomy and function. In order to overcome these unknowns, a priority is to discover and characterise `core' microbial communities associated with plant roots, which may contain key plant-microbe associations. The purpose of chapter 3 was to investigate variation in root-associated microbial communities associated with wild populations of B. oleracea occurring across a wide geographic range. In six geographically discrete wild populations of B. oleracea with different amounts of shared plant genetic ancestry, 16s rRNA amplicon sequencing was used to target the root-associated microbial communities. Environmental variation was a significant contributor to the variation seen in the microbial communities, but there was also evidence of a `core' B. oleracea root microbiome. Alongside B. oleracea, B. rapa and B. napus are important agricultural species within Western Europe. These three species vary in their life histories and mating systems, as well as ploidy; B. napus is an allotetraploid (A and C genomes, n=19) from the diploid progenitors B. rapa (A genome, n=10) and B. oleracea (C genome, n=9). The Brassica genus also contains a huge diversity of crops, including vegetables with very different morphologies (e.g., broccoli, Brussels sprouts, cabbage, pak choi, swede) for consumption, and oilseeds for consumption, biofuels and industry. However, little is known about how this phenotypic diversity in the plants affects their root-associated microbial communities. Chapter 3 used a common garden experiment involving 11 cultivars from these three species of Brassica to investigate variation in rhizosphere communities across hosts, space and time. A significant amount of the variation in the microbial communities was explained by spatial (the environment) and temporal (sampling month) factors. Nevertheless, species and cultivar also explained a significant amount of variation in the root-associated microbial communities, as well as varying in their growth and life-history traits. Therefore, results from this chapter indicated that not only is the environment an important consideration for healthy soil microbial communities in agriculture, but the morphology, life-history, domestication status and ploidy of crops may influence their requirements. The different approaches taken in this PhD thesis have made a substantial contribution to our knowledge on Brassica crops in Western Europe, both in terms of the plant population genetics and root-associated microbial communities. In addition, it has shown that sustainable resources for future agricultural improvements in this genus probably already exist on our doorstep. From here, future Brassica research would benefit from: (1) studying plant population genetics and root-associated microbial communities in `wild' populations of B. rapa and B. napus; and (2) common garden experiments that investigate the influence of environmental variation found in the wild on root-associated microbial communities, including predicted environmental changes.