Validation of Diaporthe toxica resistance markers in European Lupinus angustifolius germplasm and identification of novel resistance donors for marker-assisted selection

Abstract

The fungus, Diaporthe toxica, anamorph Phomopsis sp., previously classified as P. leptostromiformis, is a plant endophyte and occasional pathogen, causing Phomopsis stem blight. This disease is damaging not only to lupins but also to the animals grazing on infected plants, due to the toxic secondary metabolites called phomopsins. The aim of this work was to validate markers for resistance to Phomopsis stem blight in narrow-leafed lupins and identify novel germplasm with increased levels of resistance to the disease. Plant inoculations were performed using ten isolates of D. toxica, originating from Australia and Poland. The European core collection of L. angustifolius was evaluated both in a controlled environment and with field experiments to classify the accessions based on their resistance to the disease. Simultaneously, the accessions were assayed with disease resistance markers to identify donors of hypothetical resistance alleles. We have found that the European lupin germplasm collection preserves wild and domesticated donors of at least two resistance genes to Phomopsis stem blight, including Phr1 and PhtjR. Molecular markers PhtjM7, InDel2, and InDel10, tagging PhtjR gene, were applicable for marker-assisted selection targeting the European gene pool with an expected accuracy of 95%. None of diagnostic markers for the Phr1 locus was found useful for European breeding programs; two existing markers Ph258M1 and Ph258M2 were unreliable, due to a high percentage of false-positive results (up to 58%) and a high recombination rate between markers (~30%).

The Resistance of Narrow-Leafed Lupin to Diaporthe toxica Is Based on the Rapid Activation of Defense Response Genes

“…In field conditions, the latent phase lasts until plant maturity [ 20 , 21 , 28 , 29 ]. However, in a greenhouse, with the high humidity favoring fungal development, full disease symptoms are observed on susceptible plants no later than 30 dpi, indicating a considerable reduction of the latent phase [ 30 ]. Termination of the latent phase, which is expected to occur in a greenhouse about 15–20 dpi, would explain this sudden surge in defense response, resulting in the final arrest of the pathogen.…”

“…It resulted in the creation of a highly resistant breeding line, 75A:258 [ 23 ]. This genotype was successfully implemented in Australian breeding programs and is still considered as a reference in phytopathological assays because its resistance to D. toxica has never been broken [ 24 , 25 , 26 , 27 , 28 , 29 , 30 ]. It was later revealed that D. toxica resistance in 75A:258 is conferred by a single dominant allele, subsequently named Phr1 [ 29 ].…”

“…The PhtjR gene was provided with PhtjM4, PhtjM5, and PhtjM7 single nucleotide polymorphism markers [ 27 ], as well as with a pair of InDel2 and InDel10 insertion–deletion markers that were developed using high-throughput genome sequencing [ 25 ]. The European L. angustifolius germplasm collection was recently genotyped with markers tagging Phr1 and PhtjR alleles and phenotyped for D. toxica resistance using several strains of fungi originating from Poland and Australia [ 30 ]. That study confirmed that the resistance conferred by Phr1 and PhtjR alleles was retained in both field and controlled environment conditions.…”

Photoperiod and Vernalization Control of Flowering-Related Genes: A Case Study of the Narrow-Leafed Lupin (Lupinus angustifolius L.)

“…As seed alkaloid content was reduced by breeding below 0.01% of seed dry weight, a bitter taste, a typical feature of lupins, was fully eliminated from modern cultivars (Kamel et al, 2016). Additionally, the postharvest stubble can be now safety grazed by livestock, because the risk of lupinosis disease was diminished by the introduction of Phomospis stem blight resistance genes (Mulholland et al, 1976;Jago et al, 1982;Cowling et al, 1987;Williamson et al, 1994;Shankar et al, 2002;Ksiażkiewicz et al, 2020). Furthermore, L. angustifolius is currently being promoted in human food markets as a result of its nutritional, metabolomic, and other health benefits (Foyer et al, 2016;Kouris-Blazos and Belski, 2016).…”

Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.)

“…Mass sequencing has been exploited in narrow-leafed lupin, to provide several markers linked to anthracnose and Phomopsis stem blight resistance genes. Some of these SNPs were revealed to have a lower recombination rate between the particular trait and marker loci than the previously developed SSR-based markers, and were implemented into breeding practice (Książkiewicz et al 2020 ; Książkiewicz and Yang 2020 ; Yang et al 2015a ; Yang et al 2015b ; Yang et al 2013a ; Yang et al 2013b ; Zhou et al 2018 ). All of these molecular resources have greatly contributed to the improvement of narrow-leafed lupin as a crop.…”