Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi

Abstract

Grass pea (Lathyrus sativus L.) is an annual legume species, phylogenetically close to pea (Pisum sativum L.), that may be infected by Fusarium oxysporum f. sp. pisi (Fop), the causal agent of fusarium wilt in peas with vast worldwide yield losses.A range of responses varying from high resistance to susceptibility to this pathogen has been reported in grass pea germplasm. Nevertheless, the genetic basis of that diversity of responses is still unknown, hampering its breeding exploitation. To identify genomic regions controlling grass pea resistance to fusarium wilt, a genomewide association study approach was applied on a grass pea worldwide collection of accessions inoculated with Fop race 2. Disease responses were scored in this collection that was also subjected to high-throughput based single nucleotide polymorphisms (SNP) screening through genotyping-by-sequencing. A total of 5,651 highquality SNPs were considered for association mapping analysis, performed using mixed linear models accounting for population structure.

Association Mapping of Lathyrus sativus Disease Response to Uromyces pisi Reveals Novel Loci Underlying Partial Resistance

“…The disease reaction of a worldwide germplasm collection of 182 grass pea accessions was evaluated in response to U. pisi . This germplasm collection was the same as described by Sampaio et al (2021a) to identify genomic regions controlling resistance for fusarium wilt in grass pea. Two main ecotypes have been defined in grass pea related to their seed morphological traits, mostly composed of accessions with Mediterranean (big and light-colored seeds) or Asian origin (small and dark-colored seeds) ( Przybylska et al, 2000 ).…”

“…Both the genotypic datasets constituted 5,651 SNP markers after quality control, and the pea genome marker positions previously described by Sampaio et al (2021a) were retrieved to perform the present association analysis. This genotypic dataset was obtained from two high-throughput genotyping-by-sequence providers [Dart-Seq™ genotyping ( Kilian et al, 2012 ) and BGI, Beijing Genomic Institute, Beijing, China] using genomic DNA extracted from young leaves.…”

“…Three linear mixed models, as described in the study of Sampaio et al (2021a) , were tested to control for false-positive SNP-trait associations: a naïve model, not accounting for population structure or family relatedness (Phenotype = SNP + Error ); a model accounting for population structure (Q), using 15 principal components from the principal component analysis (PCA) ( Phenotype = Q + SNP + Error ); and a model accounting for familial relatedness ( K ), using kinship matrix K ( Phenotype = SNP + Accession + Error ), with Accession random effects structured following a kinship matrix K ( Malosetti et al, 2007 ).…”

“…Grass pea accessions can be classified into two main ecotypes, mostly considering their seed morphological features: one ecotype with accessions with larger and light-colored seeds usually originated from Mediterranean countries, and the other ecotype with accessions with smaller and dark-colored seeds, mostly from Asian countries ( Przybylska et al, 2000 ). The genetic structure analysis was performed using molecular markers of a worldwide germplasm collection of grass pea accessions ( Sampaio et al, 2021a ). Moreover, further phenotypic characterization revealed that accessions from the Mediterranean region showed higher resistance to Fusarium oxysporum Schl.…”

“…GWAS is a powerful methodology for harnessing the natural variation occurring in plant germplasm collections to dissect the allelic variants controlling complex traits (e.g., partial resistance to biotic stress). This approach has proven successful in better characterizing the response of a worldwide diverse grass pea germplasm collection (the same targeted in this study) against biotic constraints, namely, fusarium blight ( Sampaio et al, 2021a ). Although the absence of a fully assembled grass pea reference genome imposed some challenges to the interpretation of GWAS results, a comparative approach with the pea reference genome ( Kreplak et al, 2019 ), highly macrosyntenic to grass pea ( Santos et al, 2021 ), has shown to be a reliable strategy to propose candidate genes.…”