Work by PhD candidate Thomas Noble has seeded a new era of research. Employed by Queensland University of Technology (QUT) and working within the National Mungbean Improvement Program's (NMIP) breeding program, Mr Noble has created a highly diversified population that allows valuable traits to be linked to DNA markers and the trait's underlying genes.
The new tools make marker-assisted breeding possible for a new generation of high-value mungbean traits. Concurrently, they open a pathway to eventually applying the most innovative and efficient breeding technology currently available - prediction-based genomic selection - to mungbean crops.
"High levels of genetic diversity are essential when it comes to developing tools that detect associations between traits and genes," Mr Noble says. "So, the project started by first mapping the population structure of Australian mungbean germplasm."
This was achieved using the mungbean genome sequence and DNA markers (called single nucleotide polymorphism or SNPs) that detect subtle genetic differences between mungbean genotypes.
Analysis of Australian mungbean germplasm was used to assemble the Australian Mungbean Diversity Set, which is composed of 466 lines that are representative of available phenotypic and genetic diversity.
The 30 most diverse lines were then selected to build the trait discovery platform. This involved crossing each of the 30 lines with the commercial variety, Crystal. The crosses resulted in over 2000 progeny that make up the mungbean Nested Association Mapping (NAM) population.
This population is currently undergoing screening in the paddock in order to analyse its trait characteristics and determine which to link back to markers and move into breeding lines.
Mungbean breeder and Department of Agriculture and Fisheries (DAF) principal research scientist Col Douglas says this exciting and unique genomic resource is being put to use for Australian growers in the DAF/GRDC NMIP. It is also being used in the International Mungbean Improvement Network.
While the project focused on the Australian germplasm, Mr Noble added a twist that makes the NAM population especially innovative.
As he explains: "Australian mungbeans are valued for their big, green, shiny morphology, but breeding for that morphology has somewhat constrained the diversity in the Australian gene pool."
To avoid limiting the resolution of his NAM population (due to too little diversity), Mr Noble found two ways to boost it.
First, he ensured a large contribution of germplasm from the World Vegetable Centre, which has the global mandate for mungbean improvement.
More importantly, he was aware Australia has the world's largest wild mungbean population in the form of native mungbean species that cross readily with commercial varieties.
Wanting to tap into that diversity, he contacted native mungbean expert Professor Bob Lawn at James Cook University. Together, they selected four native mungbeans whose genetics are now included in the NAM population. That inclusion vastly increases the potential to discover traits related to hardiness and disease resistance.
"I see native mungbeans as a potentially huge untapped resource sitting in our own backyard," Mr Noble says.
The natives are normally difficult to exploit in breeding programs, since they grow as crawling vines and produce tiny, rock-hard grain the size of sesame seed - the opposite of what is wanted by the high-value markets that Australia produces for. But including them in the NAM population allows their potentially valuable traits to be evaluated in an agronomically adapted background.
To push that capability even further - down to individual genes - Mr Noble visited the Taiwanese laboratory that intends to sequence hundreds of mungbean genomes. He convinced them to include the 31 parents used to create the NAM population.
"That will allow comparative analyses that are extremely useful in delineating which genetic differences matter in terms of traits and phenotypes," Mr Noble says. "Included is the variety Crystal, which means the mungbean industry gets a new reference genome based on DNA that is agronomically important to the Australian mungbean industry."
Mr Noble's work was undertaken while enrolled at QUT. Mr Douglas says the work has led to greater understanding of the biology and diversity of the Halo blight pathogen: "This PhD research has provided a foundation on which to inform breeding for bacterial resistance and industry-wide integrated approaches to combating bacterial disease," he says.
More information: Thomas Noble, t2.noble@qut.edu.au