Current Role: Research Scientist, Agriculture Victoria

PhD title:  Simulating the Theoretical Evolution of Polyploid Crops with an Application to Modern Breeding Programs

Context:

Ryegrass is currently the major forage crop used in Australia. With the current climate changes, there will be a need for more heat and drought tolerant pastures, and tall fescue is one of the best candidate grasses to replace ryegrass. Tall fescue is a polyploid pasture, which evolved through a spontaneous hybridization of three different ancestral grasses. Thus, its genome size is equivalent to the size of these three ancestral genomes combined. Breeding for a new tall fescue cultivar is a time-consuming process that usually requires at least a decade to be completed. The current traditional practices depend on visual assessment of plants in the field which increases labour cost and limits the experiment size. Improving these conventional practices requires the adaptation of new technologies such as genomic selection, selecting best grasses depending on their genetic makeup, and speed breeding, a new breeding strategy to shorten the generation duration by growing plants under long light stress.

However, the optimal utilization of these strategies requires lots of empirical testing which is very time and resource consuming. Alternatively, large number of breeding programs and schemes can be computationally simulated in short time and almost no cost compared to empirical testing. The main idea of simulation is to create a pseudo tall fescue population that closely mimic real-life tall fescue population and apply different breeding practices and mathematical models that we use empirically on this simulated population.

As polyploid evolved differently, they have special mode of inheritance and evolutionary diagram. There are currently over 50 software to simulate genomes but none of them fit the complex polyploid characters. For this reason, in my PhD I had to develop the first software (PolySim) that can closely simulate polyploid populations considering all complexities associated with polyploid genomes. I used PolySim to compare wide range of evolutionary scenarios against different values for polyploid-related parameters. Having PolySim and the thorough understanding of the effect of different parameters on the simulation of polyploid populations allowed for running a robust simulation study to compare different tall fescue breeding schemes that utilise both genomic selection and speed breeding. The efficiency of different recommended schemes was compared to the efficiency of the conventional breeding scheme and the effect of discarding different time-consuming conventional stages to achieve faster breeding cycles was also tested.

Science outcomes:

PolySim is a very useful tool to help researchers answer different fundamental research questions related to polyploid population genetics and evolution. The results in my thesis help researchers to precisely set their simulation parameters allowing them to develop simulated populations that closely match their experimental populations. The breeding schemes simulated in my PhD are the first to test the efficiency of combining genomic selection and speed breeding for tall fescue, which can be generalised to all cross-pollinated crops. One journal article from my PhD has been published and another one required revision to be accepted in reputable journals. I also authored and co-authored another 14 journal articles during my PhD. I have also been selected by Frontiers in Ecology and Evolution journal, under its mentorship program for PhD students, to curate and assist in editing an open access article volume of papers on my proposed research topic: Polyploid population genetics and evolution – from theory to practice.

Industry impact:

PolySim can be used for simulating other polyploid pasture crops for different industrial purposes. Moreover, this study provides recommendations of the optimal breeding scheme that combine genomic selection and speed breeding as an alternative to the current conventional breeding programs.

Education program:

The Dairy Futures CRC and Dairybio education program provided opportunities for personal and professional development. Funding the attendance of courses and international conferences as well as their mentoring program which connected me with a dairy farmer Ron Paynter. Enabling me to better understand the industry needs and have more focused research on solving practical problems.