The lupin time warp
Current narrow-leafed lupin (NLL) varieties either flower too early or too late for most cropping regions, limiting their cultivation primarily to the northern wheatbelt of Western Australia.
There is simply nothing in the domesticated gene pool that can provide in-between flowering times. As such, the flowering time gene, and its variants within the wider wild lupin population, which can modify when a crop flowers, is viewed by pre-breeder Dr Matthew Nelson as central to lifting nature’s current embargo on where NLL can be grown.
During 2014, a breakthrough was made in Dr Nelson’s laboratory by a 22-year-old GRDC undergraduate honours student, Candy Taylor, who at the time was completing the fourth year of a genetics and breeding undergraduate course at the University of WA.
With the support of a GRDC Undergraduate Honours Scholarship and supervised by Dr Nelson, she provided evidence indicating the identity of the key genetic regulator of flowering time and also implicated a mutation that can shift the gene’s ‘too-late’ setting into ‘too-early’ mode.
It was an impressive achievement for a student attempting research of any kind for the first time.
The lupin clock
About 80 per cent of flowering-time variation in Australian varieties has previously been genetically mapped, leading researchers to pinpoint one discrete region of the genome that was named ‘Ku’.
“The Ku region contains a gene that controls responsiveness to cold temperatures, also known as vernalisation,” Dr Nelson says. “Previously, I had identified within this region a strong candidate for the flowering-time gene, called FTc1, and handed it to Ms Taylor for analysis.”
Over the course of a year, she compared the way the gene behaves in early versus late-flowering NLL varieties. She extracted – from individual plant tissues – the molecules produced when a gene is expressed (called messenger RNA or mRNA). These molecules can be converted back into DNA (using a viral enzyme) so that they are amenable to analysis using the full suite of DNA biotechnologies.
She found that early and late-flowering varieties produce exactly the same mRNA molecules, with no discernible difference in their sequence. However, the levels of these molecules – which reflect how strongly the gene is expressed – were found to vary dramatically. Overall she saw three expression patterns that corresponded with differences in flowering-time behaviour.
“In early-flowering plants that do not require vernalisation to flower, the FTc1 (flowering-time) gene was expressed at high levels at all times and throughout the plant,” Ms Taylor says. “FTc1 gene expression in those early plants was unaffected by exposure to cold.”
The late-flowering (cold-sensitive) NLL lines produced two additional patterns of expression, depending on whether they had been exposed to cold.
“In the absence of cold, the late-flowering lupins expressed FTc1 at low levels that increased slowly as the plant matured, but never reaching the same levels seen in the early-flowering plants,” she says.
“In contrast, when exposed to cold, the FTc1 gene in the same varieties responded strongly to cold treatment, with gene expression reaching levels as high as those in the early-flowering variety.”
All of this means that the researchers now know what to look for in the wild gene pool to find a diverse spread of flowering times.
Gene expression is typically controlled by DNA located adjacent to the gene, referred to as the ‘promoter’.
To analyse and compare promoter sequences requires working with genomic DNA (not mRNA). Fortunately, Ms Taylor’s project occurred within a network of genome-related research activities, particularly Dr Nelson’s GRDC project to develop markers, as well as the genome sequencing project headed by CSIRO’s Dr Karam Singh.
Already a large deletion has been identified in the FTc1 promoter of the early-flowering variety. Ms Taylor speculates that within the deleted DNA are control elements that impose the cold-sensitive, late-flowering gene behaviours.
The process of making these discoveries – and the important implication for breeders and growers – has captivated Ms Taylor. She has now set aside her original choice of career as a nurse and is instead enrolled to continue working with the lupin pre-breeders as a PhD student.
“I went to university with the idea of becoming a nurse but whenever I needed to select a course, I find that my intellectual curiosity always draws me to plant biology, particularly genetics,” she says.
As of mid-2015, she joined a new GRDC project led by lupin breeder Dr Jon Clements at the Department of Agriculture and Food, WA, who is exploiting the new genomic data developed in WA to improve NLL varieties.
To that team, Ms Taylor brings the means to understand how to create nuances in NLL flowering time, a prerequisite for expanding where in Australia NLL can be grown.
More information:Candy Taylor,
GRDC Project Code UHS10659, DAN00237