Canadian Wheat-NAM (CAN-NAM): Capturing genetic variation for Canadian wheat improvement

Funding Partners: Alberta Wheat Commission (AWC), Manitoba Wheat and Barley Growers Association (MWBGA), Western Grains Research Foundation (WGRF), Saskatchewan Ministry of Agriculture – Agriculture Development Fund (ADF)

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Project Description

This research builds on the application of a powerful combination of advanced genomics approaches and a newly available Can-NAM resource, allowing detection of novel alleles with high resolution and high-precision, thus enabling the rapid delivery of outcomes to the breeding program and facilitating cultivar release. Central to this project is the utilization of our unique Can-NAM population, which combines high genetic diversity and high levels of recombination events, with a genome wide approach, to characterize novel rust and FHB alleles for Canadian wheat improvement.

With consultation from breeders, many important traits for local producers, including agronomics traits, quality, and disease and pest resistance, drought and heat tolerance have been introduced into the Can-NAM population. As phenotyping of this large population is costly, here, this project will focus on some high impact traits for local producers. The researchers will phenotype seedling rust resistant genes (leaf, stripe and stem) at NRC-Saskatoon, with multiple races and adult plant leaf rust resistance (APR) in the field in Year 3 and Year 4 of this project in Manitoba. Field phenotyping focusing only on leaf rust will be carried out, due to the limited capacity of disease nursery field sites to screen such a large population. The population is also a rich resource for novel stripe rust and stem rust resistant genes and with the successful model from the leaf rust test, the researchers hope that more phenotyping efforts on stripe and stem rust will be promoted in the Can-NAM by potential public and private partners. This would identify novel stripe and stem rust resistant genes to protect Canadian wheat production.

In addition to rust, fusarium head blight (FHB) is another major disease threatening the wheat production in the Prairie region. Compared to rusts, FHB is a more complicated and challenging issue for wheat production. It is controlled by multiple genes with minor effects and also affected by the interaction of genotype and environment. Therefore, here, the researchers will phenotype FHB resistance from the Can-NAM population in years 3, 4 of this project. FHB response will be scored by growing replicated trials at sites in Manitoba for Type I and Type III resistance. For Type I resistance, FHB incidence and severity will be scored. At the same time, the anthesis dates and plant heights will be phenotyped, due to spurious correlations of growth stage and or plant height with FHB resistance. Type III resistance (resistance to DON or mycotoxin accumulation) will be determined using the enzyme-linked immunosorbent assay (ELISA) method to quantify the toxins. Due to the large size of the Can-NAM population, only targeted sub-populations will be phenotyped for resistance to DON or mycotoxin accumulation.

Research Results

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.