Lupin breeding breaks genetic bottleneck

Key points

  • New lupin research is addressing a chronic shortage of viable break crops in certain cereal farming systems
  • Molecular breeding tools are being developed to tap the adaptive diversity of lupins’ wild relatives

Tools are being developed in Western Australia to breed hardier lupin varieties better suited as break crops across more Australian agro-climatic growing regions

Image of Dr Matthew Nelson

CSIRO researcher Dr Matthew Nelson has worked on lupin genome sequencing and development of molecular markers for crop improvement.

PHOTO: Evan Collis

Western Australian scientists are developing molecular breeding tools to finally expand the regions in which Australian lupins can be grown – and in so doing, increasing break-crop options.

About 85 per cent of the world’s commercial lupins are grown on the acidic soils of WA’s northern grainbelt. While many benefits accrue from the inclusion of narrowed-leafed lupin (NLL) varieties in crop rotations, their suitability elsewhere is limited.

Pre-breeder Dr Matthew Nelson explains that as the most recently domesticated of the major agricultural crops, commercial lupins suffer from the tight genetic bottleneck that resulted from the domestication process, which was undertaken only in the past century. Selection for the all-important domestication traits reduced the founder gene pool to just a handful of parents.

The too-narrow ancestry of commercial NLL varieties is the main obstruction to a wider cropping zone. However, the adaptive traits needed to expand that zone exist in the wild gene pool.

“Particularly limiting is the lack of diversity in traits related to the timing of life events – what we call phenology – with the quintessentially important example being flowering time diversity,” Dr Nelson says.

However, two recently completed GRDC projects are making it possible to close the gap between NLL’s current status and its perceived potential as a break crop.

These projects were based on developing an understanding of the NLL genome as the springboard to develop tools – particularly markers – that can accelerate genetic improvement of NLL commercial varieties by drawing on the diversity of the wild gene pool.

Taking part are the University of Western Australia (UWA), CSIRO and the Department of Agriculture and Food, WA (DAFWA).

Marker breakthrough

Of the two completed projects, one recently announced it had developed a suite of new markers that are directly applicable in DAFWA’s lupin breeding program. This project was headed by Dr Nelson, until recently with the UWA’s School of Plant Biology and now at the Royal Botanic Gardens, Kew, in the UK.

Dr Nelson says the new cache of about 600 markers targets the gene-rich regions of the genome and they can also detect variation in genes within the wild and domesticated gene pools for agronomically important traits.

“We developed these markers for DAFWA’s lupin breeders and they are designed to home in on the genetic variation needed to improve commercial varieties, such as the flowering time gene,” Dr Nelson says.

His markers narrow the search to just those genes expressed in the flowers and leaves, thereby ignoring the vast amount of DNA in the genome that is not relevant to breeding programs, enabling a big lift in pre-breeding efficiency – a stated early goal.

This targeting was achieved by purifying molecules called messenger RNA (mRNA). These molecules represent the expressed portion of the genome, which is called a transcriptome.

For the lupin project, the transcriptomes from leaves and flowers were combined and analysed in 16 different wild and domesticated NLL lines. Also available for comparison was the full genome sequence of the commercial variety TanjilA (which is the subject of the second GRDC lupin project headed by CSIRO’s Dr Karam Singh).

Those sequence comparisons made it possible to design markers that can distinguish NLL germplasm whose genes vary due to disparate genetic ancestry.

This ancestry broadly clusters into three groups. There is the domesticated group that is the least diverse but does possess its own distinguishing genetic characteristics. Then there are wild lines originating from the western Mediterranean region (Morocco, Portugal and Spain), which proved the most diverse, and then material originating from the eastern Mediterranean region (Greece, Italy and Turkey).

“The markers are so good that given anonymous NLL lines we can accurately determine their origin,” Dr Nelson says.

The markers were then used to map the variety MandelupA and eight wild lines in DAFWA’s collection prior to crossing wild and domesticated lines to create the starting material to diversify the lupin breeding genepool as part of a new GRDC project headed by DAFWA breeder Dr Jon Clements.

“These are markers that can be associated with differences in agronomically important lupin traits, not just flowering time, but also drought tolerance and disease resistance,” Dr Nelson says.

Why lupins matter

The NLL is a legume with much to offer Australian agriculture through its adaptation to nitrogen and phosphorus-deficient, acidic, sandy soils, Dr Nelson says. “In WA this crop is an important part of sustainable farming systems, reducing the need for nitrogenous fertiliser, providing valuable disease breaks and boosting cereal yields.”

NLL fixes nitrogen through symbiotic interactions with bacteria such as Bradyrhizobium lupini and Kribbella lupini.

In addition, the grain has a broad range of food and feed applications, matching (and potentially exceeding) soybeans in versatility.

“Breeders recall a story about a ‘lupine dinner’ held in Hamburg in 1918 (by the Association for Applied Botany) that captures the breadth of lupin’s versatility and the reason that Germany spearheaded efforts to domesticate lupins,” Dr Nelson says. “Everything consumed at the dinner was made from lupin beans – the soup, steak, margarine, cheese, aperitifs and after-dinner coffee.”

The six genes that domesticate lupins

Among the newly developed molecular breeding tools are markers associated with the six genes that had to change in order to domesticate narrowed-leafed lupin. These have been identified as genes that regulate:

  • pod shattering (two genes are involved);
  • alkaloid content (the degree of bitter taste associated with the grain);
  • pod dormancy;
  • vernalisation; and
  • flower colour (white for domesticated narrowed-leafed lupins and blue for wild).

NLL beans contain similar protein to soybean but less fat and have an extremely low glycaemic index, which has attracted attention from nutritionists dealing with the increasing global incidence of obesity and diabetes.

The beans are also gluten-free and high in dietary fibre, amino acids and antioxidants.

The first steps to truly transform the lupin into a domesticated crop, undertaken in Germany, involved cultivating a ‘sweet’ variety (low in the seed’s alkaloids that are responsible for a bitter taste in wild lupin). The domestication process was completed by the now-retired breeder Dr John Gladstone at UWA, and then at DAFWA, during the 1950s and 1960s. As a result, WA today dominates world production of commercial lupins.

For Dr Nelson, the development of molecular breeding tools, such as the newly developed markers, creates exciting opportunities to expand where NLL can be grown in Australia, builds on existing market dominance and explores novel marketing opportunities for this versatile pulse.

More information:

Dr Matthew Nelson,


Positive lessons from the blackest day


Trials show cost of varieties mismatched with sowing time

GRDC Project Code UWA00151

Region Overseas, West