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Rudi Appels

An interview of Rudi Appels by Stephen Baenziger

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Rudi Appels is Honorary Professor at the University of Melbourne and Research Fellow at AgriBio (Latrobe University), both in Melbourne, Australia.

Rudi Appels is well known in the IWGSC as he has been at the heart and soul of the consortium since its inception in 2005. He was instrumental in the creation of the consortium, having initiated, along with Bikram Gill, discussions with interested colleagues on sequencing the wheat genome, at the ITMI meeting in Winnipeg in 2002, and organized, in 2003 in Washington, the first workshop designed to push forward the sequencing of the bread wheat genome.

Since the beginning of the IWGSC, Rudi has been involved in all aspects of the consortium – from establishing the overall vision to defining the steps in the roadmap that would ensure a useful sequence for breeders. He has been an IWGSC leadership team and Board member since 2005 and led the team that sequenced chromosome 7A. He is currently involved in the functional and manual annotation of the IWGSC reference sequence.

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“Rudi has been a tireless advocate for sequencing the wheat genome and an energetic leader in advancing IWGSC strategies and research projects,” said Kellye Eversole, Executive Director of the IWGSC. “I have often been asked what the secrets are to our success and one of those is having leaders who are not merely interested in advancing their own career but interested in achieving a broader vision. Rudi epitomizes this kind of leader.”

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Stephen Baenziger is Emeritus Professor and Wheat Growers Presidential Chair at the University of Nebraska Lincoln, USA. He is a world leader in wheat breeding and has released 44 wheat, seven barley and 13 triticale cultivars.

Stephen first met Rudi in 1986 at an international wheat conference. In 2009, he spent four months in Rudi’s laboratory in Perth as a visiting scholar to learn the rudiments of molecular biology in wheat so that he could help his students with their projects.

Stephen enthusiastically agreed when we asked him to interview Rudi.

“Rudi and I are very good friends, so we have had a number of discussions on how molecular biology and breeding will intersect for better crops and food security. He is also my go to person when it comes to a question about molecular biology and the current state of the research,” said Stephen Baenziger in an email in preparation for this interview.

Of the many projects you have worked on, which one or two are you the proudest of and why? Or of your research, what aspect would you most like to be remembered for.

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Kellye Eversole and Rudi Apples when he received the IWGSC Outstanding Leadership Award at the Plant and Animal Genome Conference in 2017

Each project over the past 53 years has been a “heart & soul” effort so it is hard to pick favorites.

The wheat genome sequencing project is high on the list in defining my research effort after moving from CSIRO to Murdoch University in Western Australia in 2001. The project, through the IWGSC, was basically started at the 2002 Winnipeg ITMI meeting when group discussions with Bikram Gill and myself agreed that a wheat genome sequence was long overdue. The ongoing project of almost 20 years, driven by Kellye Eversole as Executive Director of the IWGSC, included publications in Science (2014, 2018) as well as a recent (2021) update in Plant Journal.

The focus on chromosome 7A was Australia’s specific contribution to the international project (Gabriel Keeble-Gagnere, Josquin Tibbits and Matthew Hayden, AgVic, Melbourne). The project also formed the basis for a major engagement with China through the Australia-China Centre for Wheat Improvement initiative between CAAS (He Zhonghu) and Murdoch University (Wujun Ma) in 2013 which was the only Asian-century agricultural program from among a total of eight Australia-wide proposals that was funded.

Reducing-to-practice the development of molecular markers for breeding programs has been an ongoing project and I am particularly proud of the adoption of the markers for granule bound starch synthase for udon noodle quality (established with Peter Sharp’s group in University of Sydney and Ian Batey, CSIRO), imidazolinone resistance (with Dora Li, Iain Barclay, Department of Agriculture West Australia), Sr2 resistance (with Wolfgang Spielmeyer and Evan Lagudah, CSIRO) and APO1 for yield (with colleagues in AgVic, Melbourne). The repetitive sequence arrays that been particularly useful (with Lynne McIntyre, CSIRO) as markers fall into this mix.

At the risk of overshooting the “one or two” limit, the work in my CSIRO-years leading the wheat starch biosynthesis studies (with Matthew Morell) and protein quality studies (with Frank Bekes) are important since the outputs from this work continue to underpin my current interests at the University of Melbourne.

You are famous for having visiting scientists come to your laboratory to learn molecular biology, especially for wheat genetics. Why were you so open and generous to visitors who wanted to learn your technology?

During the 1980’s and 90’s colleagues from New Zealand, Canada, USA and UK, carried out experiments in CSIRO and (later) yourself, Stephen, in Murdoch University Western Australia, and it was always the “hands-on” experiences that were so satisfying.

Without exception the benefits were always in both directions and allowed a level of engagement, for me, with wheat researchers and breeders that would simply not have been possible through the standard conference-level of interactions.

One of the really memorable examples was importing Bikram Gill’s complete collection of Triticum tauschii accessions following his stay in CSIRO. The analysis of this collection combined with the accessions from G. O’Halloran subsequently attracted Evans Lagudah to do a post-doc with me and he then went on to establish his research program for uncovering rust/disease resistance genes at CSIRO.

You have published seminal papers in Drosophila melanogaster and in wheat and related species. What motivated you to move from Drosophila research to wheat research?

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Rudi Appels in 2018 at the Plant and Animal Genome Conference, a meeting he attended regularly over the years and that he considers very important for his research development

One of the unique experiences in my career was collaborating with Art Hilliker in Drosophila research and in particular learning to appreciate the power of analyzing and generating variation in the structure of chromosomes.

When the local Drosophila genetic stocks had to be kept without technical support it was clear that a move to wheat was about right, particularly since Jim Peacock was interested in analyzing the heterochromatic regions in rye instead of Drosophila.

At the time (1977), there were technical issues with C-banding providing a clear indication of the number of rye chromosomes in triticale varieties being considered for release and we developed the molecular probes as an alternative. The rye heterochromatin DNA sequences were early probes into particularly variable features of cereal genome structure (with Cedric May, NSW Dept of Agriculture).

The strong driver to move into wheat at the time (1977) was when I learnt about the existence of the 1RS.1BL translocation in commercial wheat varieties. The possibilities of studying such a unique, cloned, chromosome was an opportunity not to be missed. Just last year, in 2020, a collaboration with colleagues in CAAS, China (Jia Jizeng) completed the genome sequence for the 1RS.1BL chromosome which is now used as a template for functional studies to determine its contribution to yield attributes.

If you had one piece of advice to give to the next generation of scientists, what would it be?

The following points are related to the different aspects of appreciating the biological pipeline to defining phenotype:

  • Enjoy the discovery process and allow yourself to visualize, for example, the molecules moving on-off the DNA/chromatin complex to generate RNA molecules affecting development or for translation into protein as well as the numerous ways proteins interface with their immediate (atomic level) environments.
  • Embrace the mental visualization and capture of images that are practiced in the arts community to facilitate the discovery process.

The above points come together in advice I was given as a young CSIRO scientist by a well-known Drosophila geneticist, Mel Green, namely “look down a microscope or in the field for the future directions in your own research.”

What will be the scientific success that you would most like to see in the future?

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Rudi Appels with Kellye Eversole, Catherine Feuillet and Brikram Gill at the Plant and Animal Genome Conference in 2018

Large sections of the genome, particularly in wheat, comprise long arrays of relatively short sequences repeated many hundreds of times. From a practical application point-of-view, these sequences (found in heterochromatin or C-bands in wheat) have a valued history as molecular markers for identifying chromosome segments. From a fundamental point-of-view however these regions of the genome still need to find a place in the networks that “make wheat, wheat”.

In Drosophila studies specific heterochromatic regions can be experimentally shown to have different biological roles from genome segments housing genes. The structure/function analysis of heterochromatic regions flanking the ribosomal rRNA gene array on the X chromosome clearly indicated that heterochromatic regions modified a range of phenotypes including the relative expression (nucleolar dominance) of the rDNA on the X and Y chromosomes. Similarly, the regions flanking the rDNA in wheat have been argued to moderate nucleolar dominance between the rDNA loci on chromosomes 1B, 5D and 6B.

So, the genetics of repetitive arrays of short sequences is likely to be quite distinct from, and more complex than, that associated with structural genes. A scientific success I would like to see is an integration of the repetitive arrays in models for controlling development and contributing to generating the exquisite and reproducible phenotypes in life-forms and, of course, wheat. Examples surface in the analysis of human cancers and cell development and with the very extensive genome sequence database now available for wheat it is becoming feasible to interpret induced structural changes in a specific chromosome segment such as 1RS in the context of networks controlling development.

Of your own research, what study gave you the most surprising result and why was it surprising?

The high level of diversity at the genome level in the intergenic space contrasting with the conserved gene order continues to surprise me. It is impressive how nature seems to muddle through an apparent jumble of coding and non-coding DNA sequences to reproducibly generate organisms that have such stunning phenotypes.

Who made the greatest impact on your career and why?

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Rudi Appels with Bikram Gill, Catherine Feuillet and Jan Dvorak at the Plant and Animal Genome Conference in 2015

Where to start! … Over the decades so many good students and colleagues in our profession have been patient in their collaborations with me during my PhD (1969-1972) on avian red blood maturation in Adelaide University Biochemistry Department, my post docs in CSIRO, Canberra and Karolinske Institutet Stockholm and my subsequent appointment to CSIRO-Division of Plant Industry Canberra.

I feel I “graduated” from the Division of Plant Industry under Jim Peacock’s leadership, after 27 years, keen to contribute more directly to agriculture as leader of the WA node (in Perth, Murdoch University, WA) of the Molecular Plant Breeding Collaborative Research Centre (CRC) headquartered in Adelaide, South Australia. In this 15-year period in Perth, a major engagement with the Chinese Academy of Agricultural Sciences (CAAS) was established as well as the IWGSC wheat genome sequencing project.

In 2015/16, an Honorary Professor appointment at the University of Melbourne and fellow at AgriBio, both in Melbourne, provided, and continues to provide, a foundation for consolidating the wheat molecular biology and genome studies.

In this entire period, my loving partner, Dianne, gave me much needed stability and boundless support.

So, to pick three individuals:

  • From 1972 – 2001, Jim Peacock (CSIRO, Division of Plant Industry) applied his own style of mentoring in terms of opportunities for me to broaden my expertise and knowledge that I continue to appreciate so many years after leaving CSIRO.
  • Jan Dvorak and Art Hilliker were experts and committed to their respective research interests in wheat and Drosophila. At the time, they worked in the Canberra laboratories in CSIRO-Plant Industry, the analysis of the ribosomal DNA loci provided a common ground that allowed me to take ownership of a level of knowledge of the genome that I could otherwise have just dreamt of.

What question would you like to be asked and how would you answer that question?

“Do you think there exists a good balance between creativity and technical expertise in your area of crop genomics?”

In the area of genome studies over the past 30 years, human genome sequencing has led a high intensity, technology process for generating advances in DNA and RNA sequencing and, taken together with the necessary bioinformatics and computing requirements, has focused on technical expertise in organisms such as wheat.

So, for current wheat research, I feel the balance between creativity and technical expertise is leaning too much to the technical side and I look forward to seeing wheat genomic analyses moving toward the Arabidopsis/rice models of increased creative use of genome modification through mutations and CRISPR to delineate challenges in wheat development.