Mapping genes a faster route to crop improvement

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Genetic linkage maps help breeders to identify where desirable traits are located on the genome – a trait located close to a genetic marker is more likely to be inherited when breeders select for the genetic marker. ASMap genetic linkage mapping software has helped identify molecular markers for heat tolerance in wheat.

PHOTO: Nick Collins

Plant breeders have enthusiastically embraced an Australian software program that maps plant genomes to drive efficiency gains in the breeding pipeline.

The ASMap software program has been widely adopted by researchers at the University of Adelaide’s (UA) Waite campus, who are now using it to identify molecular markers linked to economically important traits for wheat and chickpea breeding.

ASMap is a linkage mapping program developed by Statistics for the Australian Grains Industry (SAGI) in conjunction with research staff from the Australian Wheat and Barley Molecular Marker Program. 

Breeders use linkage mapping to identify genetic markers that have a close proximity on the chromosome to a desirable, but as yet unidentified, gene. DNA sequences that are closely located are more likely to be inherited together.

Markers

Markers are commonly used to help identify genomic regions linked to important industry-driven traits such as grain yield, grain quality and disease resistance. They give breeders the ability to select varieties containing such favourable genetic characteristics.

The advent of high-throughput genotyping technology has allowed plant researchers to collate an enormous number of genetic markers for analysis. Keeping track of all this data requires sophisticated software.

Until recently, genetic map construction software has been plagued with challenges including very slow computational times and inaccurate algorithms. While inaccuracy is the biggest threat to success, slow analysis can prevent breeders from making selections in time for the next growing season, delaying the breeding process.

Enter ASMap – a flexible, efficient and accurate genetic linkage map construction algorithm coupled with graphical tools for simple diagnosis of construction issues.

Improved traits

Throughout its development SAGI directly consulted plant research staff to ensure the ASMap software was functional and efficient. ASMap was immediately embraced by researchers with the Molecular Marker Program when it dramatically increased efficiency of their analysis pipeline and improved the delivery time of important wheat and barley disease-related genetic markers to breeders.

The software has now been widely adopted within UA plant research groups, where it has been used to help identify markers in wheat associated with abiotic stressors such as drought, salt, heat and frost.

It has also played a key role at UA in accurately identifying genomic regions related to disease and drought resistance in chickpeas. 

The timely identification and accurate quantification of important genomic regions relies heavily on the software used to construct the genetic map for the underlying crop genome.

ASMap’s quality, efficiency and diagnostic capabilities have ensured it plays a pivotal role in the analysis pipeline used by plant research groups working on delivering high-quality marker information to breeders. 

Building on the widespread use of ASMap, SAGI developers have formed strong collaborative links with multiple research groups and private breeding companies, ensuring the fast delivery of important genetic information so that breeders can efficiently select better crop varieties.

More information:

Dr Julian Taylor,
University of Adelaide,
08 8313 2077,

julian.taylor@adelaide.edu.au;

Dr David Butler,
University of Wollongong,
0437 188 853,
dbutler@uow.edu.au

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LMA defect detection enhances new wheat varieties

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The science of picking winners

GRDC Project Code UA00143

Region National