Research Objective

Project Description

To identifiy trait linked SNP markers for multiple phenotypes; to validate identified trait linked markers; to fine map QTL’s for identification of markers closely linked to traits; to convert key SNP markers to Taqman assays for routine screening of breeding lines; to breed for high seed protein concentration.

The goal of the project was to identify single nucleotide polymorphism (SNP) markers linked to various agronomic and seed quality traits important for pea breeding using diverse mapping populations. We assembled a panel of 34 unique SNP markers associated with 18 traits of pea.
The selected traits include:
1) Agronomic – days to flowering, days to maturity, lodging resistance, plant height, seed dimpling, seed weight, and grain yield;
2) Heat stress – SPAD (chlorophyll measurement), leaf wax, and stem thickness;
3) Seed quality – concentration of Iron (Fe), zinc (Zn), phytate, starch, and protein, and;
4) Disease resistance – Aphanomyces root rot, Mycosphaerella blight, and powdery mildew, for use in marker-assisted selection (MAS) in a breeding program.

The identified SNP markers were converted to Kompetitive allele specific PCR (KASP) assays and the assays were validated under laboratory conditions. We have used the SNP markers for MAS of high seed protein concentration and other traits in two mapping populations. The panel of SNP markers reported in this project will be useful for MAS in pea breeding as they will enrich the germplasm reaching yield trials with fixed alleles of importance.

Outcome

The goal of this research was to improve pea breeding efficiency through the identification of single nucleotide polymorphism (SNP) markers that could be linked back to various seed quality and agronomic characteristics and subsequently be used in marker-assisted selection (MAS) in a pea breeding program.  

This panel of SNP markers will be utilized to select breeding lines for the introgression of specific desired traits into the genetic backgrounds of other cultivars. It will also expedite the breeding process by supporting the selection of homozygous alleles in early generations, which mitigates the risk of losing a desired trait through subsequent recombination events. Traits of interest for this research included those related to nutritional quality, resistance to biotic stresses, agronomic considerations, and seed coat colour. This research involved genotyping and phenotyping (multi-location/multi-year field studies) endeavours on pea lines from around the world to improve the breeding program at the Crop Development Centre (CDC) at the University of Saskatchewan.  

Through this research, high-density linkage maps were developed and used to identify quantitative trait loci (QTL) on three pea recombinant inbred line (RIL) populations from the CDC. These QTLs are associated with a number of pea seed quality and agronomic traits. An additional RIL population was developed to map resistance to Aphanomyces root rot and validate a known QTL (Ae-Ps-7.6). 

A genome-wide association study (GWAS) was also executed, gathering a collection of 135 pea accessions from 23 different breeding programs worldwide. The lines were phenotyped and genotyped, and then association mapping was conducted on the collection. 

Cross-comparisons were performed on highly significant trait-linked markers from both the RIL mapping populations and the GWAS panel. The markers for seed zinc concentration included in the SNP panel were validated. SNP markers for disease resistance against Aphanomyces were also verified through a parallel introgression study, wherein the introgressed lines confirmed improvement in disease resistance.  

A panel of 34 unique SNP markers was assembled and converted to Kompetitive allele specific PCR (KASP) assays for routine laboratory use and is now being used in the marker-assisted selection (MAS) breeding program. The markers are associated with 18 phenotypic traits, including agronomic performance characteristics and disease resistance, specifically against Aphanomyces root rot, Mycosphaerella blight, and powdery mildew.  

Some markers for more complex agronomic traits and seed protein concentration require additional validation, which is currently underway in further mapping populations, referred to as the GWAS-2 panel. 

Through MAS and using the SNP panel developed, multiple crosses were performed on the elite CDC pea cultivar, CDC Lewochko, to introduce novel alleles for high seed protein concentration into the cultivar’s genetic background. Two of the crosses have been tested for the markers of the SNP panel and have yielded positive results in producing lines with favourable alleles for multiple of the selected traits. 

These outcomes are expected to accelerate the pea breeding process through the enhanced capabilities of MAS. Further research will continue to identify markers associated with additional quantitative traits related to heat stress tolerance and seed protein concentration. 

Related Research