SRA’s breeding program is about to change radically. From next year, General Manager Variety Development Garry Rosewarne, will be based in Meringa. He and his team will be using words like DNA, genomics, phenomics, and Big Data on a daily basis.

The aim is to introduce genomics selection into the breeding program which will mean newly crossed seeds will tick all the quality boxes from the get-go.

“We will be recombining the existing genes from parents through crossing programs like we have always done but now we will be able to select our parents and their progeny much more efficiently and based on data collected from the best lines,” Dr Rosewarne said.

“Using genomic selection we will be able to check for quality and disease resistance right from the beginning so that everything coming through the pipeline will succeed at the end of the PATs, CATs and FATs in the field for traits such as tonnes of cane per hectare, CCS,  fibre, and resistance to Pachymetra and smut.”

The change has been coming on the back of about eight years of work by the research program. Next year this work will be deployed throughout the breeding program.

A genotypic platform has been put together which can collect 54,000 data points from the genome of every sugarcane plant processed.

Eight thousand clones, including all the parents in the crossing plot at Meringa, and all FAT clones for the past 10 years, have been genotyped – their DNA extracted and analysed.

That data and the selected clones have been used to make up what is called ‘training populations’ in the field in order to make prediction equations on the quality of the traits the lines will show.

“We genotype these lines and then we test them in the field for tonnes of cane per hectare, CCS scores, smut resistance, for fibre and for Pachymetra resistance.

“From this work we have a prediction equation which enables us to analyse brand new germplasm straight out of the honeymoon suite by taking a DNA sample from the baby leaves. Thanks to the genotypic database we will be able to reasonably predict how these seeds will perform for our five traits,” Dr Rosewarne said.

“In the future we will work on developing more prediction equations for a further 10-15 traits e.g. resistance to other diseases, plant height, tiller number, maturity and so on.”

Garry has worked on implementing a genomic-based breeding strategy before with Agriculture Victoria.

“The impact it has on a breeding program is a complete game changer.

“We are not doing any genetic modification or transformation. We are just recombining the existing genes through our crossing programs like we have always done but now we are able to select our parents and progeny much better.

“We make 100,000 lines a year. How do we select the 10,000 that go into the next stage of the pipeline? Up until now it has all been done by experienced breeders looking at individual plants. The breeders can identify the really bad lines and get rid of them but even the best breeders find it hard to differentiate between the really good lines.

“The other difficulty is we often don’t trial the selected lines in a glasshouse for diseases such as smut or Pachymetra until 8 or 10 years along in the breeding program. Or fibre quality until 10 or 12 years later. But with genomic selection we can test for these traits when we first generate it as new seed.”