Genome-wide association study for morphological traits and resistance to Peryonella pinodes in the USDA pea single plant plus collection

Abstract

Peas (Pisum sativum) are the second most cultivated pulse crop in the world. They can serve as human food, fodder, and cover crop. The most serious foliar disease of pea cultivars worldwide is Ascochyta blight, which can be caused by several pathogens. Of these, Peyronella pinodes is the most aggressive and prevalent worldwide. Several traits, including resistance to Peyronella pinodes, stem diameter, internode length between nodes 2-3 and 5-6, and area of 7th leaf, were measured in 269 entries of the pea single plant plus collection. The heritability (H2) of the morphological traits was relatively high, while disease resistance had low heritability. Using 53,196 single-nucleotide polymorphism markers to perform a genome-wide association study to identify genomic loci associated with variation in all the traits measured, we identified 27 trait-locus associations, 5 of which were associated with more than 1 trait.

Keywords: Peryonella pinodes; Pisum sativum; Ascochyta blight; GWAS; USDA-PSPP; genome-wide association study; peas.

Fig. 1.

Distribution, correlations, and scatter plots of each trait BLUPs. Line for the best fit of data is displayed. *** correspond to P-value <0.001.

Fig. 2.

Manhattan plots and the corresponding Q–Q plots for the traits indicated. a, e) sAUDPC for P. pinodes. b, f) Internode length between nodes 2 and 3. c, g) Internode length between nodes 5 and 6. d, h) Area of 6th leaf. e, i) Stem diameter between nodes 5 and 6. In the Manhattan plots, the −log₁₀P-values adjusted for FDR (y-axis) are plotted against the position of each chromosome (x-axis), each circle represents an SNP, solid green line represents FDR adjusted P-value threshold of 0.005 and dotted line threshold of 0.05.