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 (SPPC). The heritability (H2) of the morphological traits was relatively high, while disease resistance had low heritability. Using 53,196 single nucleotide polymorphism (SNPs) 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 one trait.

Breeding for Biotic Stress Resistance in Pea

“…Out of these species, P. pinodes appears to be the most widespread and damaging. Only moderate levels of quantitative resistance are available [5][6][7][8][9][10][11]. Several quantitative trait loci (QTLs) associated with partial resistance to ascochyta blight have been reported (Table 2) [7][8][9][10][11].…”

“…Only moderate levels of quantitative resistance are available [5][6][7][8][9][10][11]. Several quantitative trait loci (QTLs) associated with partial resistance to ascochyta blight have been reported (Table 2) [7][8][9][10][11]. However, these QTLs explain only a limited percentage of the phenotypic variation.…”

The Exceptionally Large Genomes of the Fabeae Tribe: Comparative Genomics and Applications in Abiotic and Biotic Stress Studies

“…After the publication of the first pea genome [13], several studies on legume biotic stresses have been favored by the availability of a pea reference genome. Genetic and genomic studies on legume fungal diseases have been performed in aerial fungal diseases, such as powdery mildew [61][62][63], white mold [69], rust [71,72], ascochyta blight [93,94], and also in root diseases, like fusarium wilt and root rot [76,77,95] and Aphanomyces root rot (caused by oomycetes) [79][80][81]. In these studies, the Caméor pea genome was used for SNP calling, location of SNP physical positions, identification of candidate genes underlying QTLs, and syntenic studies aiming at genetic linkage maps validation and location of ortholog genes of interest by comparative mapping.…”

Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study

“…However, GWAS typically requires a panel of inbred lines with multiple individuals for phenotypic analysis in crops, which necessitates time for population development. Single-plant GWAS (sp-GWAS) has been successfully applied in maize [ 32 ], wheat [ 33 ], lentil [ 34 ], and pea [ 35 ], demonstrating its ability to identify candidate genes associated with phenotype variation by performing GWAS on individual plants. This approach reduces the time and resources required to complete the GWAS [ 32 ].…”