Identification of Novel Genes Associated with Partial Resistance to Aphanomyces Root Rot in Field Pea by BSR-Seq Analysis

Abstract

Aphanomyces root rot, caused by Aphanomyces euteiches, causes severe yield loss in field pea (Pisum sativum). The identification of a pea germplasm resistant to this disease is an important breeding objective. Polygenetic resistance has been reported in the field pea cultivar ‘00-2067’. To facilitate marker-assisted selection (MAS), bulked segregant RNA-seq (BSR-seq) analysis was conducted using an F8 RIL population derived from the cross of ‘Carman’ × ‘00-2067’. Root rot development was assessed under controlled conditions in replicated experiments. Resistant (R) and susceptible (S) bulks were constructed based on the root rot severity in a greenhouse study. The BSR-seq analysis of the R bulks generated 44,595,510~51,658,688 reads, of which the aligned sequences were linked to 44,757 genes in a reference genome. In total, 2356 differentially expressed genes were identified, of which 44 were used for gene annotation, including defense-related pathways (jasmonate, ethylene and salicylate) and the GO biological process. A total of 344.1 K SNPs were identified between the R and S bulks, of which 395 variants were located in 31 candidate genes. The identification of novel genes associated with partial resistance to Aphanomyces root rot in field pea by BSR-seq may facilitate efforts to improve management of this important disease.

Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea

“…We identified 75 DEGs at 6 hpi and 375 DEGs at 20 hpi (Table S 4 ) and retrieved the available information of the corresponding genes from the pea genome database ( https://urgi.versailles.inra.fr/download/pea/ ), including gene ontology (GO) terms for all genes (Tables S 5 and S 6 ). At the earliest time point, we identified three seed linoleate 9S-lipoxygenase-3-like genes that were previously associated with partial resistance to Aphanomyces root rot (ARR) and predicted to be involved in oxidation–reduction processes and jasmonic acid (JA) biosynthesis [ 27 ]. Additionally, Psat2g149200.1, Psat5g289880.1 and Psat5g291320.1 were all downregulated in ‘Linnea’ upon infection with SE51 (Table S 5 ).…”

“…The other three genes were associated with hormone metabolism where Psat3g026920.1 was predicted to be part of methylsalicylate degradation. Genes Psat5g289880.1 and Psat5g291320.1 were associated with oxidation–reduction processes and JA biosynthesis and were among the most downregulated genes in ‘PI180693’ [ 27 ] (Table S 5 ).…”

“…Differentially regulated genes at 48 hpi were cross-referenced with genes localized in genomic regions segregating with ARR resistance [ 26 , 27 ]. The 39 genes displayed in Fig.…”

“…A cross between a susceptible and resistant pea cultivar was used to identify QTL for partial resistance to ARR based on greenhouse and field experiments, and ultimately identified the gene content in the ARR resistance QTL [ 26 ]. Genes segregating with ARR resistance were further expanded using bulked segregant RNA-seq (BSR-seq) analysis and used for cross-referencing with differentially expressed genes (DEGs) [ 27 ].…”

A fine-tuned defense at the pea root caps: Involvement of border cells and arabinogalactan proteins against soilborne diseases

“…interact synergistically to infect the plant forming the pea root rot complex (PRRC) that aggravates pea root rot disease. The involvement of multi-species pathogens in the PRRC is a major limiting factor for plant breeding making complete pea resistance highly complex ( Chatterton et al., 2019 ; Wille et al., 2021 ; Wu et al., 2022 ). However, plant beneficial microorganisms such as arbuscular mycorrhizal fungi (AMF) Glomus intraradices and Glomus claroideum were reported to slightly increase pea tolerance to root rot development ( Thygesen et al., 2004 ).…”