Most important traits in wheat are complex, quantitatively inherited, and controlled by many minor effect genes. This poses a significant challenge to characterize these traits. Linkage and linkage disequilibrium mapping approaches have limitations that a multi-parent population approach such as nested association mapping (NAM) can overcome to unlock the genetic basis of complex traits. We established a bread wheat NAM population with more than 5000 lines that takes into consideration genetic diversity, disease resistance and agronomically important traits. A high quality haplotype map for accurately imputing genotypes across wheat genome was assembled by more than 1.4 millions SNPs uncovered by high depth whole genome exome capture sequence approach. With a population exome capture sequencing (Pop-ECS) approach, we generated  159,011 high quality SNPs for 24440 NAM  recombinant inbred lines (RILs).  Genomic analysis demonstrated the success of our strategy to use synthetic hexaploid wheat (SHWs) to increase the genetic diversity of the D genome, with an average 27.0 increase  SNP rates for D genome. This validated the utilization of novel genetic variations of the D genome to improve wheat performance. Phenotypic analysis demonstrated that broad phenotypic variations were captured by this NAM population for disease  and agronomic traits. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for these traits and identified 491 QTL in total. We precisely mapped several known genes for these traits with a great number of additional QTL. These new QTL features would make them good targets to improve wheat performance by breeding program.  These findings demonstrated this NAM resource as a powerful tool to  dissect complex traits. In addition, 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 diversity of bread wheat. More applications for wheat genetic, genomic and evolutionary research exist for this unique resource.

Extension Messages:

• Establishment of a powerful wheat genetic resource for the wheat research community, A NAM genetic resource with more than 5000 lines captured a broad phenotypic variation.
• A high density haplotype was generated with more than 1.4 million SNPs, allowing accurately imputing genotypes for low coverage or low resolution genotyping platforms.
• Synthetic wheat introduces substantial increase in D genome variation, provided opportunities to improve wheat performance with the utilization of D genome
• Joint linkage mapping identified novel and valuable new genetic variations for key disease traits of wheat, providing new beneficial alleles for the breeding program.
• This established Canadian wheat NAM genetic and genomics resources will be a valuable source of novel genetic variations for Canadian spring wheat breeding wheat programs.