The aim of Joanna’s research is the genomic and molecular characterisation of Restorer-of-Fertility-like (RFL) genes in plants and their application to hybrid breeding in crops. Joanna’s genome-wide analyses of the RFL clade in cereals (rice, barley, wheat, and rye) have revealed the evolutionary plasticity of RFL genes in plants and proposed mechanisms that drive the creation of new gene variants capable of suppressing the expression of novel mitochondrial genes that cause cytoplasmic male sterility (CMS).

Hybrid varieties are favoured for their attractive agronomic traits and higher and more stable yields. However, for many staple crops like wheat or barley, hybrid seed production on a commercial scale remains difficult. The major limiting factor is the absence of an efficient way to control self-pollination. Most promising approach uses CMS induced by a gene encoded in the mitochondrial genome, and nuclear RFL genes able to overcome this sterility in the hybrids. RFL proteins block expression of CMS genes by inducing cleavage of their transcripts.

In addition to this agricultural application, the suppression of CMS by nuclear restorer genes represents an intriguing example of mitochondrial-nuclear genome interactions that are integral to the process of speciation by natural selection and are therefore of great interest to a broader research community.

After completing her Master’s thesis at the August Cieszkowski Agricultural University in Poznan, Poland, Joanna pursued a PhD position in the Plant Cell Biology group led by Professor Karin Krupinska and relocated to Kiel, Germany. Her PhD studies focused on characterizing DNA-protein complexes present in chloroplasts. She obtained her PhD degree in 2011.

In 2012, Joanna relocated to sunny Perth, Western Australia to start postdoctoral work at The University of Western Australia in the Australian Research Council Centre of Excellence in Plant Energy Biology under the guidance of Professor Ian Small. Since 2014, her research has shifted its focus to plant mitochondria, specifically to a group of proteins known as Restorer of Fertility (Rf) proteins. Rf proteins play a crucial role in the development of hybrid cultivars in cereals, making them of significant agronomic importance.

In 2022, Joanna was awarded the ARC Future Fellowship and accepted an offer for a Senior Lecturer and Group Leader Position in the Division of Plant Sciences at the Research School of Biology at the Australian National University. She relocated to Canberra in October 2023. Her research group employs molecular biology and computational methods to investigate the interactions between mitochondrial and nuclear genomes in plants, with the goal of applying this knowledge to breed high-yielding and stress-resistant hybrid crops. Of particular interest to her is the family of mitochondrial transcription termination factors known as mTERFs and their role in fertility restoration in cereals, including wheat, rye, barley, and sorghum.

Joanna collaborates with Groupe Limagrain, the world's fourth-largest seed-producing company, on the identification and characterization of restorer genes in wheat. Additionally, through collaboration with Professor Nils Stein from The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany, she has contributed to the characterization and annotation of the PPR/RFL family in the reference genome of bread wheat and became a member of the International Wheat Genome Sequencing Consortium. Joanna also collaborates with Professor David Jordan and Dr Emma Mace from the University of Queensland, as well as Professor Adam Lukaszewski from the University of California, Riverside (to name a few).

Project 1. Characterisation of a new clade within the mitochondrial transcription termination factor (mTERF) family implicated in fertility restoration in plants.

Most restorer genes in crops encode RNA-binding pentatricopeptide repeat (PPR) proteins. Plants have hundreds of PPR proteins but only a few act as Restorers-of-fertility and these define a clade referred to as ‘Restorer-of-fertility-like’ PPRs (RFL-PPRs). Our research concerns the molecular characterisation of plant RFL genes and their application to hybrid crop breeding.

Recently, several candidates for restorer genes have been found to encode members of the mitochondrial transcription termination factor (mTERF) family in rye and barley. No sequence similarity between mTERF and PPR proteins exists, however, like PPRs, mTERFs function in RNA-associated processes and can directly bind to RNA. However, mTERFs remain a largely understudied group of organellar sequence-specific RNA-binding proteins in plants.

Our studies have shown that a group of mTERF genes share several genomic features with the RFL-PPR clade. We demonstrated that, as for RFL-PPRs, one clade of mTERF genes is highly expanded in plants, especially cereals and that they are organised into clusters adjacent to or intermixed with RFL-PPR clusters in the genome. Our analyses revealed that the location of RFL-mTERF clusters overlaps with mapped Rf loci in wheat and rye. Based on these discoveries we named this clade RFL-mTERFs.

Our identification of clustered mTERF sequences that share genome locations and patterns of evolution with RFL-PPRs together with the demonstrated binding of mTERF proteins to organellar RNA are strong indicators mTERFs play a major and hitherto unappreciated role in fertility restoration. The goal of this project is to characterise the newly discovered RFL-mTERF clade and understand its contribution to fertility restoration in plants.

The specific aims of the project are to:

Aim 1: Understand how RFL-mTERF proteins contribute to fertility restoration in plants (molecular biology approaches)

Aim 2: Identify new Rf genes in plant genomes and cereal collections (genomic analyses)

Aim 3: Develop designer RFL-mTERF proteins for hybrid breeding and beyond (synbio approaches).

This project is funded by the ARC Future Fellowship (Australian Research Council) and the Thomas Davis Research Grant for Marine, Soil and Plant Biology (Australian Academy of Sciences)

The Melonek lab has several opportunities for Honours, Masters, and PhD projects.

The projects encompass bioinformatics (genome-wide sequence analyses) as well as molecular biology approaches, and a project can be tailored to align with students' preferences.

Please get in touch with Dr Melonek for more details.

As I have only recently relocated to ANU, I continue to co-supervise two highly-talented PhD students,Thien and Gilang, at the University of Western Australia.

Thien is currently investigating the expression and processing of orf279 in Triticum timopheevii – the cytoplasm donor for hybrid wheat breeding. Meanwhile, Gilang's research focuses on improving binding of Rf1 and Rf3 proteins to their RNA targets.

For more details about their work, please visit their profiles on the UWA website:

Thien Tran https://research-repository.uwa.edu.au/en/persons/dao-anh-thien-tran

Gilang Fajar Suhono https://research-repository.uwa.edu.au/en/persons/gilang-bintang-fajar-suhono