Performance Story: Canadian Wheat-NAM (Can-NAM): Capturing genetic variation for Canadian wheat improvement
The advent of advanced genome sequence technologies has revealed an enormous amount of genetic variation in major crops. Most important traits in wheat are quantitatively inherited and controlled by many minor effect genes. There is still a significant gap in connecting the genetic variation (genotypes) to phenotypes. Linkage and linkage disequilibrium (LD) mapping approaches have limitations to address this challenge. The multi-parent population approach holds great potential to unlock the genetic basis of these complex traits.
Here, we reported using a structured multi-parent population (MPP) approach, an approach that can enrich genetic diversity, and have high statistical power and resolution, to bridge this gap and unlock the basis of complex traits in bread wheat. This large-scale MPP of bread wheat was developed by the nested association mapping (NAM) approach with more than 5000 recombinant inbred lines (RILS) from 50 subpopulations. This NAM population is comprised not only of progeny derived from parents of an elite panel of Canadian cultivars from the nineteenth century to current, but also a synthetic hexaploid wheat (SHW) panel that captures divergent D genomes from Aegilops tauschii, the D genome progenitor. A high-quality haplotype map was assembled with more than 1.4 million SNPs uncovered by high-depth genome-wide exome capture sequencing. With a population exome capture sequencing (Pop-ECS) approach and the haplotype-map as reference, missing data was imputed and finally, 159,011 high-quality SNPs for 2440 NAM RILs were generated, allowing the development of a high-resolution NAM based linkage map. Genomic analysis revealed an average 27.0% increase in polymorphism in the SHW panel over the elite panel D genomes, demonstrating the value of using SHWs to increase the sampled diversity of D genomes. Phenotypic analysis demonstrated that broad phenotypic variations were captured by this NAM population for disease and agronomic traits. We performed a joint linkage mapping analysis of these traits and identified 491 QTL in total, with a few QTL precisely mapped to known genes for plant height, flower time, rust and fusarium head blight resistance. These previously not reported new QTL would be good targets to improve wheat performance by breeding.
The broad phenotypic variation captured by the NAM population provided valuable novel genetic variations for the Canadian spring wheat breeding program. The high-quality haplotype map generated from this project could allow breeders to accurately impute genotypes with a low-resolution genotyping platform in their breeding program. Novel genetic variations for disease and agronomic traits identified by the NAM analysis provide new targets and breeder-friendly markers for wheat improvement. These established NAM genomic resources may also serve as a cost-efficient platform for Canadian wheat breeding programs to identify genetic markers of their targeted traits, as only phenotyping is required. In addition, the unique design of this NAM enables us to uncover the solid genetic foundations underlying elite Canadian cultivars, and the mechanism of the D genome in shaping the bread wheat performance. Finally, this NAM resource can also allow a combination of top-down (quantitative genetics) and bottom-up (population genomics) approaches to characterize genetic architecture of complex traits in wheat and identify functional variants contributing to the phenotypic variation. More applications for wheat genetic, genomic and evolutionary research exist for this unique resource.
These findings demonstrated the success of NAM resources as a powerful tool to dissect complex traits. This CanNAM resource can potentially become a key resource to apply quantitative genetic and genomic approaches and population genomics approaches to improve wheat performance. To achieve this, there is a need to promote more phenotyping analysis and collaboration on these NAM resources, allowing it to become a core community resource for wheat research. There is also a need for collaborative efforts across the wheat community to maintain this genetic resource, allowing it to be accessed by more public/or private wheat research communities.