Project title: The genetic basis of Boron efficiency in Brassica napus
Supervisor 1: Ian Bancroft – ian.bancroft@york.ac.uk
Supervisor 2: Sue Kennedy (Elsoms Seeds Ltd.)
Funding notes
The studentship is funded via a Biosciences KTN CASE Studentship awarded to the
University of York. The industry partner is Elsoms Seeds Ltd.
Project description
In addition to macronutrients, such as nitrogen and phosphorus, plants need a range of
micronutrients for growth. Boron has long been recognised as essential to plant growth
(Warrington, 1923) and is one of the most widely encountered micronutrient deficiency
encountered in the field (Gupta, 1979). It is important in many processes, including a key
role in the formation and structural integrity of the cell wall (O’Neill et al. 1996; Ishii et al.,
2001). Boron deficiency is a particular problem in crops such as swede, which is a crop type
of the species Brassica napus. A greater understanding of the genetic bases for variation in
susceptibility to Boron deficiency would enable marker-assisted breeding to maximise
micronutrient use efficiency, reducing the cost of fertilizer inputs and stabilising crop yields.
In Arabidopsis thaliana, a member of the Brassicaceae family, channel proteins for boric acid
transport have been identified (NIP5;1, NIP6;1; Takano et al., 2006; Tanaka et al., 2008), a
transcription factor has been identified as essential for root growth under Boron deficiency
(WRKY6; Kasajima et al., 2010) and an efflux-type transported for xylem loading of Boron
has been identified (BOR1; Takano et al., 2002). In Brassica napus, the expression of two
orthologues of this transporter is induced by Boron deficiency (Sun et al., 2011).
Technologies for exploiting second generation sequencing are revolutionising crop genetic
research. The research program of the supervisor’s group is at the forefront. Based on their
understanding of genome structure and evolution in Brassica species (O’Neill et al., 2000;
Town et al., 2006; The Brassica rapa Genome Sequencing Project Consortium, 2011), they
developed Illumina transcriptome sequencing-based technologies for rapid, cost effective
discovery of SNP markers (Trick et al., 2009), construction of high density (>20k) linkage
maps (Bancroft et al., 2011), analysis of gene expression (Higgins et al., 2012) and
Associative Transcriptomics; an advanced form of association genetics that relates trait
variation with the variation of both gene sequences and gene expression (Harper et al.,
2012).
The aim of the research is to understand the genetic basis of variation for Boron use
efficiency in Brassica napus, with practical application for the cultivation of swede crops.
The principal hypothesis to be tested is whether variation in genes identified previously as
being involved in transport or transcriptional control under deficiency is causative of the
heritable variation observed for Boron efficiency in B. napus (which includes several crop
types: oilseed rape, fodder and leafy vegetables, in addition to swede). If not, the important
loci will be identified.
The project will be undertaken in collaboration with Prof. Martin Broadley of the University of
Nottingham, who has extensive experience of plant nutrition research.
The supervisor of the project coordinates a BBSRC Strategic Longer and Larger Award
grant (BB/L002124/1), which runs to the end of 2018. As part of that project, a diversity
panel of ~400 accessions of B. napus will be functionally genotyped, i.e. leaf transcriptome
sequencing will be undertaken to score for genome-wide single nucleotide polymorphism
(SNP) variation and gene expression variation. Leaves of this panel will also be analysed for
quantitative elemental composition (including Boron) by the Broadley group, using ICP-MS.
The student will exploit the functional genotypes and leaf Boron data (both of which will be
available shortly after the start of the project) to undertake an Associative Transcriptomics
analysis to identify loci controlling variation for leaf concentrations of Boron. To test the
principal hypothesis, these will be compared with the positions in the genome of B. napus of
orthologues of candidate genes.
With guidance from the supervisors and collaborating academic, the student will design new
experiments to understand both the partitioning of boron within the plant and the genetic
basis of efficiency. These experiments will include boron partitioning between different
tissue types (based on ICP-MS analysis) and assessment of whether the molecular markers
identified are predictive of micronutrient responses.
The inferred causative relationships between molecular variation (sequence and/or
expression) of genes not previously implicated in Boron efficiency will be confirmed by the
analysis of knock-out mutants of the orthologues of candidate genes in Arabidopsis thaliana,
selected from the extensive T-DNA and transposon tagging collections available in that
species.
The project will involve working with the industry partner and swede growers, providing
insights into crop breeding and the practicalities of crop production.
References
Bancroft et al. Nature Biotechnology 29:762-6, 2011
Gupta, Adv. Agron. 31:273-307, 1979
Harper et al. Nature Biotechnology 30:798-802, 2012
Higgins et al. BMC Genomics 13:247, 2012
Ishii et al. Plant Physiol. 126:1698-1705, 2001
Kasajima et al. Physiol. Plantarum 139:80-92, 2010
O’Neill et al. J. Biol. Chem. 271:22923-22930, 1996
O’Neill et al. Plant Journal 23:233-243, 2000
Stangoulis et al. Plant Soil 225:243-251, 2000
Sun et al. Mol. Biol. Rep. 39:1963-1973, 2011
Takano et al. Nature 420:337-340, 2002
Takano et al. Plant Cell 18:1498-1509, 2006
Tanaka et al. Plant Cell 20:2860-2875, 2008
The Brassica rapa Genome Sequencing Project Consortium, Nature Genetics 43:10351039, 2011
Town et al. Plant Cell 18:1348-1359, 2006
Trick et al. Plant Biotechnology J. 7:334-346, 2009
Warrington, Ann. Bot. 37:457-466, 1923