This research aimed to identify quantitative trait loci (QTLs) associated with seed protein concentration in a recombinant inbred line (RIL) population of pea and aimed to validate the identified QTLs using chromosome segment-introgressed lines developed by recurrent backcrossing. PR-25, an RIL population consisting of 108 F7 bulked lines derived from a cross between CDC Amarillo (yellow cotyledon) and CDC Limerick (green cotyledon), was used in this research. The RIL population was genotyped using an Axiom 90K SNP array. A total of 10,553 polymorphic markers were used for linkage map construction, after filtering for segregation distortion and missing values. The linkage map represents 901 unique loci on 11 linkage groups which covered a map distance of 855.3 Centimorgans. Protein concentration was assessed using near-infrared (NIR) spectroscopy of seeds harvested from field trials in seven station-years in Saskatchewan, Canada, during the 2019–2021 field seasons. Three QTLs located on chromosomes 2, 3 and 5 were identified to be associated with seed protein concentration. These QTLs explained 22%, 11% and 17% of the variation for protein concentration, respectively. The identified QTLs were validated by introgression lines, developed by marker-assisted selection of backcross lines for introgression of corresponding chromosome segments (~1/4 chromosome) harboring the QTL regions. Introgression line PR-28-7, not carrying any protein-related QTLs identified in this study, was 4.7% lower in protein concentration than CDC Amarillo, the lower protein parent of PR-25 which carried one identified protein-related QTL. The SNP markers located at the peak of the three identified QTLs will be converted into breeder-friendly KASP assays, which will be used for the selection of high-protein lines from segregating populations.

No abstract

With the expanding interest in plant-based proteins in the food industry, increasing emphasis is being placed on breeding for protein concentration and quality. Two protein quality traits i.e., amino acid profile and protein digestibility, were assessed in replicated, multi-location field trials from 2019 to 2021 in pea recombinant inbred line population PR-25. This RIL population was targeted specifically for the research of protein related traits and its parents, CDC Amarillo and CDC Limerick, had distinct variations in the concentration of several amino acids. Amino acid profile was determined using near infrared reflectance analysis, and protein digestibility was through an in vitro method. Several essential amino acids were selected for QTL analysis, including lysine, one of the most abundant essential amino acids in pea, and methionine, cysteine, and tryptophan, the limiting amino acids in pea. Based on phenotypic data of amino acid profiles and in vitro protein digestibility of PR-25 harvested in seven location-years, three QTLs were associated with methionine + cysteine concentration, among which, one was located on chromosome 2 (R2 = 17%, indicates this QTL explained 17% phenotypic variation of methionine + cysteine concentration within PR-25), and two were located on chromosome 5 (R2 = 11% and 16%). Four QTLs were associated with tryptophan concentration and are located on chromosome 1 (R2 = 9%), chromosome 3 (R2 = 9%), and chromosome 5 (R2 = 8% and 13%). Three QTLs were associated with lysine concentration, among which, one was located on chromosome 3 (R2 = 10%), the other two were located on chromosome 4 (R2 = 15% and 21%). Two QTLs were associated with in vitro protein digestibility, one each located on chromosomes 1 (R2 = 11%) and 2 (R2 = 10%). QTLs associated with in vitro protein digestibility, and methionine + cysteine concentration on chromosome 2 were identified to be co-localized with known QTL for total seed protein concentration in PR-25. QTLs associated with tryptophan and methionine + cysteine concentration co-localized on chromosome 5. The identification of QTLs associated with pea seed quality is an important step towards marker-assisted selection of breeding lines with improved nutritional quality, which will further boost the competitiveness of pea in plant-based protein markets.