NIAB EMR: R. Harrison & F. Fernandez
University of Nottingham: Amanda Rasmussen
AHDB: N. Harrison
Rootstocks are an essential component for successful tree fruit production, yet the below ground root systems are little understood. This studentship will aim to identify the genetic basis of root system architecture in apple rootstocks and to associate root type with nutrient use efficiencies in this woody perennial species. This research could have significant potential impact for other high value perennial crops including cherry, pear and apricot. This studentship will provide and develop the students skills in molecular biology, woody crop physiology and horticultural practices, whilst contributing to new scientific ideas in plant science and horticulture.
Recent studies at NIAB EMR have identified several different types of root system associated with commercial rootstocks utilised in apple orchards. With new advances in molecular marker development including the availability of genome sequences for several commercially available rootstocks, it is now crucial to understand how root system architecture can be optimised for both anchorage and nutrient use efficiencies, and how these important traits can then be deployed in breeding programmes to aid rootstock selection for new, improved rootstocks.
To advance this work and further our understanding of root system architecture, we have developed three main objectives within this proposal:
- Strategic rootstock crosses and phenotypic analyses of root system architecture (RSA) in rootstock progeny
- Selection of segregating populations for genotyping for quantitative trait loci (QTL) analysis; mapping of root architecture traits.
- Assess root function in relation to Nitrogen and water use efficiencies.
- Comparative genomics of genetic factors controlling root architecture and the relationship to nutrient use efficiency in plants.
Approaches and work packages
This PhD studentship will study root architecture and root function to assess the impact of root development on water and nutrient uptake to understand water and nutrient use efficiencies in apple. The student will use existing segregating seedling mapping populations to assess seedling root architecture and root development in several populations, with the aim of developing molecular markers for important root traits. In addition, root architecture will be explored in relation to root function and soil management techniques, including nutrient use efficiency.
We have developed the following work packages to address the objectives of this studentship:
WP1. Strategic rootstock crosses and phenotypic analyses of root system architecture (RSA) in rootstock progeny
Preliminary studies assessing seedling root architecture in spring 2015 have identified rootstock populations that segregate for different root system architecture, RSA. The student will develop new rootstock populations that will provide segregating populations for phenotypic studies of RSA. These populations will be grown from seed in rhizotrons and imaged using a custom made camera set-up and imaging rig. Images of seedling root development will be taken over time and analysed using our recently developed root imaging software. This will enable the student to obtain robust trait data for the analysis of quantitative trait loci. In addition, whole plant trait data (including plant height, stem girth and internode length) will also be collected and analysed to provide insights into the association between RSA and above ground canopy traits.
WP2. Selection of segregating populations for genotyping for quantitative trait loci analysis; mapping of root architecture traits
The student will genotype at least one of the new seedling populations using either the new 20k illumina SNP chip or Genotyping-by-sequencing approaches depending upon costs and methodologies. Currently, two linkage maps comprising 2,272 SNP and 306 SSR markers and 797 additional SNP markers respectively have been developed for an existing rootstock mapping population (M.27 x M.116) using the 9K apple and pear Illumina SNP array and are also available for this study.
WP3. Assess root function in relation to Nitrogen and water use efficiencies
Using stable isotopes of Nitrogen and water, the student will measure short-term accumulation of these isotopes within root segments of intact plants. Using prior knowledge of the RSA of different genotypes of commercial apple rootstocks, the productivity of a particular genotype in relation to root type and RSA size will be compared to determine root function efficiencies for Nitrogen uptake and water use efficiency. Commercial rootstocks will be established in large rhizotrons for several months and then supplied with labelled nutrients for a short period. The root systems will then be sampled and the accumulation rate of nutrients quantified in different segments of roots.
WP4. Comparative genomics of genetic factors controlling root architecture and the relationship to nutrient use efficiency in plants
As a final part of the project, the student will assess the results of these studies with other published works to compare genes and other genetic factors such as microRNAs, previously identified for RSA and nutrient uptake, with those for apple rootstocks to determine whether RSA development and root function is conserved across land plants.
The research outlined in this application will significantly advance rootstock research and subsequently contribute to the UK capacity for research into perennial fruit crops.