Association mapping for agronomic and seed quality traits of field pea (Pisum sativum, L)

Authors: GALI, K - University Of Saskatchewan; SACKVILLE, A - University Of Saskatchewan; TAFESSE, E - University Of Saskatchewan; LACHAGARI, R - University Of Hyderabad; MCPHEE, KEVIN - Montana State University; HYBL, M - Crop Research Institute - Czech Republic; MIKIC, A - Institute Of Field And Vegetable Crops; SMYKAL, P - Palacky University; McGee, Rebecca; BUSTIN, J - Inland Northwest Research Alliance, Inra; DOMONEY, C - John Innes Center; ELLIS, T - University Of Auckland; WARKENTIN, T - University Of Saskatchewan

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2019
Publication Date: 11/25/2019
Citation: Gali, K.K., Sackville, A., Tafesse, E.G., Lachagari, R.V., McPhee, K., Hybl, M., Mikic, A., Smykal, P., McGee, R.J., Bustin, J., Domoney, C., Ellis, T.N., Warkentin, T.D. 2019. Association mapping for agronomic and seed quality traits of field pea (Pisum sativum, L). Frontiers in Plant Science. 10. Article 1538. https://doi.org/10.3389/fpls.2019.01538.
DOI: https://doi.org/10.3389/fpls.2019.01538

Interpretive Summary: Pea is an important pulse crop grown in more than 100 countries on over 12 million hectares worldwide. Pea seeds are considered as a nutritional powerhouse because they are rich in protein, complex carbohydrates, vitamins, minerals and phytochemicals. Pea seeds are about 25% protein and have high levels of the amino acids, lysine and tryptophan, which are relatively low in cereal grains. To enhance productivity of pea production and meet global demand for pea consumption, over the last three decades pea breeding programs worldwide have made significant improvement in yield, disease resistance, and ease of harvestability. Pea breeding must focus both on crop productivity and improving seed quality to meet new market demands. In order to help meet these demands, this research investigated genetic diversity for desirable agronomic and seed quality traits in a panel of 136 pea cultivars and breeding lines from breeding programs around the world. The lines were grown in multiple locations between 2013-2017 and data were collected on days to flowering and maturity, plant height, seed yield, seed weight, seed shape, and seed quality. The lines were also genotyped using modern techniques and more than 14,000 molecular markers were identified. We were able to identify associations between these complex desirable traits, their underlying genes, and the molecular markers. These results can be directly translated into tools for pea breeding programs.

Technical Abstract: We used a Genome-Wide Association Study (GWAS) to map loci linked to agronomic traits (days to flowering, days to maturity, plant height, seed yield and seed weight ), seed morphology (seed shape and seed dimpling) and seed quality (protein, starch and fibre concentrations) traits in field pea (Pisum sativum L.). A collection of 175 pea accessions from Australia, Europe (Czech Republic, France, Netherlands, United Kingdom) and North America (Canada and USA) was used for GWAS. Accessions were genotyped using Genotyping-by-Sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 14,379 SNP loci were selected to determine population structure and trait associations. The GWAS accessions were clustered into nine major groups. The accessions were phenotyped in multi-year and multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Saskatoon, Saskatchewan (Canada) from 2013 to 2017, and each trait was evaluated at a minimum of five trials. We detected a total of 332 significantly associated loci (P < 0.05) for the evaluated traits. Significantly linked SNP markers (P <0.05, after Bonferroni correction) were identified for all traits in repeated trials. This research identified phylogenetic relationships among the 136 pea accessions in the GWAS panel, and trait-linked markers that can be used by pea breeding to accelerate cultivar improvement.