PhD: IMPRINTING AND PLOIDY IN BUMBLEBEES, LEICESTERDeadline for applications: 7 January 2022Project highlights– Building on NERC funded and CENTA PhD work on bumblebees, an important pollinator.– How are imprinted diploid genes used in a haploid sex?– Are different genes imprinted at different stages?OverviewThis project asks how can imprinted genes exist in a haplodiploid organism. Genomic imprinting is when the expression of an allele is dependent on the parent it came from, Genomic imprinting is an important area of research in plant breeding and in evolutionary biology and has relevance to some human cancers and developmental syndromes.Recently, as part of a current NERC funded research grant and a CENTA 1 PhD, we have discovered imprinted genes in bumblebees (see Figure 1). This is a major finding and opens the door to multiple other questions. Bumblebees are haplodiploid, that is fertilised eggs (diploids) become females. Unfertilised eggs (haploids) become males. This leads to a paradox, genomic imprinting restricts expression of certain genes to one parental allele. As a consequence, both maternal and paternal chromosomes are required for successful development. How can males function, given that we would predict a number of genes to be imprinted and therefore non-functional.A corollary of this, through a quirk of inbreeding in bumblebees, diploid males are easy to produce. How do these animals function give that they presumably have doubled the number of alleles compared to their haploid brothers? Previous work suggests that they have similar expression levels to haploid males, but what about the imprinted genes in these diploids.A final area of interest is imprinting at different stages. Our data shows imprinting in the adult bee. When does this arise? Are different genes imprinted at different stages?MethodologyThe student will produce haploid males from ten normal colonies. Diploid males will come from ten inbred colonies. RNA from these will be extracted. Imprinted gene expression will be analysed using candidate gene RNA-seq analysis.Imprinted genes showing interesting patterns (differences between females, haploid and diploid males) will have their gene expression altered using RNAi to examine the resultant phenotype.The reciprocal cross used in the initial work (NERC funded) will be repeated and this time samples will be taken at larval and pupal stages. They will be analysed using RNA-seq and GLMs to identify stage specific imprinted genes.Training and skillsThe student will be provided with training, as required, in R, a powerful and increasing popular statistical programming language, Python, a general-purpose, high-level programming language widely used in bioinformatics, molecular biology and bee husbandry.Training will also be provided in the preparation of both transcriptomic NGS libraries. The student will also become conversant with general molecular biology techniques such as PCR, qPCR and cloning.Partners and collaborationThis is a collaborative project between the lead supervisor Mallon and co-supervisor Rosato. The supervisors have complimentary interests and expertise in gene expression and social insects and of next generation sequencing techniques to investigating these areas. Mallon will provide specific expertise in the role of epigenetics and gene expression, while Rosato provides expertise in candidate gene molecular biology. This proposal will benefit greatly from the ongoing collaboration between M and R in co-supervising a current PhD student working on bumblebees.Further detailsPlease contact Eamonn Mallon, Department of genetics and genome biology, University of Leicester, ebm3@le.ac.uk for further details. https://www2.le.ac.uk/projects/selabTo apply to this project please visit: https://le.ac.uk/study/research-degrees/funded-opportunities/centa-phd-studentships Possible timelineYear 1: Haploid males. Bee husbandry. Collecting samples. Carrying out treatments. Production and sequencing of libraries. Begin analysis.Year 2: Diploid males. Bee husbandry. Collecting samples. Carrying out treatments. Production and sequencing of libraries. Begin analysis.Year 3: Reciporcal crosses, RNA-seq and RNAi.Further readingHua Yan, Roberto Bonasio, Daniel F. Simola, Jürgen Liebig, Shelley L. Berger, and Danny Reinberg (2015)DNA Methylation in Social Insects: How Epigenetics Can Control Behavior and Longevity.. Annual Review of Entomology, Vol. 60: 435 -452M Pegoraro, H Marshall, ZN Lonsdale, EB Mallon (2017) Do social insects support Haig’s kin theory for the evolution of genomic imprinting? Epigenetics 12 (9),725-742Marshall, H. van Zweden, J.S., Van Geystelen, A., Benaets, K., Wäckers, F., Mallon, E.B. & Wenseleers, T. (2020) Genome-wide search for parent-of-origin allele specific expression in Bombus terrestris. Evolution Letters 4 (6), 479-490