Genetic diversity of thrips populations on Allium species around the world.

Thrips are a serious pest in many crops. In onion cultivation, Thrips tabaci is the most important, but not the only thrips species causing damage. We investigated which thrips species affects onion and related species worldwide, how much genetic variation there is within T. tabaci populations, and how this evolves. Furthermore, we determined the reproductive mode and the correlation between the genetic and geographic distances. Thrips samples from infested onions or related species were obtained from 14 different locations worldwide. Species and haplotypes were determined through DNA barcoding with the mitochondrial Cytochrome Oxidase subunit I (COI) gene. Thrips tabaci was the most commonly observed species, but Scirtothrips dorsalis, Thrips palmi, Frankliniella intonsa, Frankliniella occidentalis and Frankliniella tenuicornis were also found, especially at the beginning of the growing seasons and depending on the location. The Nei's genetic distance within T. tabaci was less than 5% and the haplotypes were clustered into two phylogenetic groups, each linked to a specific mode of reproduction, thelytokous or arrhenotokous. Thelytokous thrips were more common and more widely distributed than arrhenotokous thrips. A high percentage of heteroplasmy was detected in the arrhenotokous group. Heteroplasmic thrips were only found in populations where thelytokous and arrhenotokous were present in sympatry. Some T. tabaci haplotypes were present in high frequency at several sampled locations. No correlation was found between the genetic and geographic distances, which points to anthropic activities spreading thrips haplotypes throughout the world.

Cytotoxic activity of Nep1-like proteins on monocots.

Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are found throughout several plant-associated microbial taxa and are typically considered to possess cytolytic activity exclusively on dicot plant species. However, cytolytic NLPs are also produced by pathogens of monocot plants such as the onion (Allium cepa) pathogen Botrytis squamosa. We determined the cytotoxic activity of B. squamosa BsNep1, as well as other previously characterized NLPs, on various monocot plant species and assessed the plant plasma membrane components required for NLP sensitivity. Leaf infiltration of NLPs showed that onion cultivars are differentially sensitive to NLPs, and analysis of their sphingolipid content revealed that the GIPC series A : series B ratio did not correlate to NLP sensitivity. A tri-hybrid population derived from a cross between onion and two wild relatives showed variation in NLP sensitivity within the population. We identified a quantitative trait locus (QTL) for NLP insensitivity that colocalized with a previously identified QTL for B. squamosa resistance and the segregating trait of NLP insensitivity correlated with the sphingolipid content. Our results demonstrate the cytotoxic activity of NLPs on several monocot plant species and legitimize their presence in monocot-specific plant pathogens.

Visualization of Three Sclerotiniaceae Species Pathogenic on Onion Reveals Distinct Biology and Infection Strategies.

Botrytis squamosa, Botrytis aclada, and Sclerotium cepivorum are three fungal species of the family Sclerotiniaceae that are pathogenic on onion. Despite their close relatedness, these fungi cause very distinct diseases, respectively called leaf blight, neck rot, and white rot, which pose serious threats to onion cultivation. The infection biology of neck rot and white rot in particular is poorly understood. In this study, we used GFP-expressing transformants of all three fungi to visualize the early phases of infection. B. squamosa entered onion leaves by growing either through stomata or into anticlinal walls of onion epidermal cells. B. aclada, known to cause post-harvest rot and spoilage of onion bulbs, did not penetrate the leaf surface but instead formed superficial colonies which produced new conidia. S. cepivorum entered onion roots via infection cushions and appressorium-like structures. In the non-host tomato, S. cepivorum also produced appressorium-like structures and infection cushions, but upon prolonged contact with the non-host the infection structures died. With this study, we have gained understanding in the infection biology and strategy of each of these onion pathogens. Moreover, by comparing the infection mechanisms we were able to increase insight into how these closely related fungi can cause such different diseases.

Peeling the Onion: Towards a Better Understanding of Botrytis Diseases of Onion.

Onion is cultivated worldwide for its bulbs, but production is threatened by pathogens and pests. Three distinct diseases of onion are caused by species that belong to the fungal genus Botrytis. Leaf blight is a well-known foliar disease caused by B. squamosa that can cause serious yield losses. Neck rot is a postharvest disease that manifests in bulbs after storage and is associated with three species: B. aclada, B. allii, and B. byssoidea. The symptomless infection of onion plants in the field makes it difficult to predict the incidence of neck rot in storage, although progress on the detection of latent infection has been made. In onion cultivation for seed production, blighting of the inflorescence is caused by all four onion-specific Botrytis species plus the broad host range pathogen B. cinerea. Flower blight can reduce seed yield and contaminate seed. In this review, the long history of Botrytis diseases of onion is discussed, as well as recent and future approaches to acquire a better understanding of the biology and ecology of Botrytis spp. pathogenic on onion. New fundamental insights in the genetic, biochemical, and physiological aspects of Botrytis-onion interactions are essential to improve the breeding of Botrytis-resistant onion cultivars.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis.

Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.

SNP-markers in Allium species to facilitate introgression breeding in onion.

BACKGROUND: Within onion, Allium cepa L., the availability of disease resistance is limited. The identification of sources of resistance in related species, such as Allium roylei and Allium fistulosum, was a first step towards the improvement of onion cultivars by breeding. SNP markers linked to resistance and polymorphic between these related species and onion cultivars are a valuable tool to efficiently introgress disease resistance genes. In this paper we describe the identification and validation of SNP markers valuable for onion breeding. RESULTS: Transcriptome sequencing resulted in 192 million RNA seq reads from the interspecific F1 hybrid between A. roylei and A. fistulosum (RF) and nine onion cultivars. After assembly, reliable SNPs were discovered in about 36 % of the contigs. For genotyping of the interspecific three-way cross population, derived from a cross between an onion cultivar and the RF (CCxRF), 1100 SNPs that are polymorphic in RF and monomorphic in the onion cultivars (RF SNPs) were selected for the development of KASP assays. A molecular linkage map based on 667 RF-SNP markers was constructed for CCxRF. In addition, KASP assays were developed for 1600 onion-SNPs (SNPs polymorphic among onion cultivars). A second linkage map was constructed for an F2 of onion x A. roylei (F2(CxR)) that consisted of 182 onion-SNPs and 119 RF-SNPs, and 76 previously mapped markers. Markers co-segregating in both the F2(CxR) and the CCxRF population were used to assign the linkage groups of RF to onion chromosomes. To validate usefulness of these SNP markers, QTL mapping was applied in the CCxRF population that segregates for resistance to Botrytis squamosa and resulted in a QTL for resistance on chromosome 6 of A. roylei. CONCLUSIONS: Our research has more than doubled the publicly available marker sequences of expressed onion genes and two onion-related species. It resulted in a detailed genetic map for the interspecific CCxRF population. This is the first paper that reports the detection of a QTL for resistance to B. squamosa in A. roylei.

Genetic analysis of the interaction between Allium species and arbuscular mycorrhizal fungi.

The response of Allium cepa, A. roylei, A. fistulosum, and the hybrid A. fistulosum × A. roylei to the arbuscular mycorrhizal fungus (AMF) Glomus intraradices was studied. The genetic basis for response to AMF was analyzed in a tri-hybrid A. cepa × (A. roylei × A. fistulosum) population. Plant response to mycorrhizal symbiosis was expressed as relative mycorrhizal responsiveness (R') and absolute responsiveness (R). In addition, the average performance (AP) of genotypes under mycorrhizal and non-mycorrhizal conditions was determined. Experiments were executed in 2 years, and comprised clonally propagated plants of each genotype grown in sterile soil, inoculated with G. intraradices or non-inoculated. Results were significantly correlated between both years. Biomass of non-mycorrhizal and mycorrhizal plants was significantly positively correlated. R' was negatively correlated with biomass of non-mycorrhizal plants and hence unsuitable as a breeding criterion. R and AP were positively correlated with biomass of mycorrhizal and non-mycorrhizal plants. QTLs contributing to mycorrhizal response were located on a linkage map of the A. roylei × A. fistulosum parental genotype. Two QTLs from A. roylei were detected on chromosomes 2 and 3 for R, AP, and biomass of mycorrhizal plants. A QTL from A. fistulosum was detected on linkage group 9 for AP (but not R), biomass of mycorrhizal and non-mycorrhizal plants, and the number of stem-borne roots. Co-segregating QTLs for plant biomass, R and AP indicate that selection for plant biomass also selects for enhanced R and AP. Moreover, our findings suggest that modern onion breeding did not select against the response to AMF, as was suggested before for other cultivated species. Positive correlation between high number of roots, biomass and large response to AMF in close relatives of onion opens prospects to combine these traits for the development of more robust onion cultivars.

Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands.

Diversity and colonization levels of naturally occurring arbuscular mycorrhizal fungi (AMF) in onion roots were studied to compare organic and conventional farming systems in the Netherlands. In 2004, 20 onion fields were sampled in a balanced survey between farming systems and between two regions, namely, Zeeland and Flevoland. In 2005, nine conventional and ten organic fields were additionally surveyed in Flevoland. AMF phylotypes were identified by rDNA sequencing. All plants were colonized, with 60% for arbuscular colonization and 84% for hyphal colonization as grand means. In Zeeland, onion roots from organic fields had higher fractional colonization levels than those from conventional fields. Onion yields in conventional farming were positively correlated with colonization level. Overall, 14 AMF phylotypes were identified. The number of phylotypes per field ranged from one to six. Two phylotypes associated with the Glomus mosseae-coronatum and the G. caledonium-geosporum species complexes were the most abundant, whereas other phylotypes were infrequently found. Organic and conventional farming systems had similar number of phylotypes per field and Shannon diversity indices. A few organic and conventional fields had larger number of phylotypes, including phylotypes associated with the genera Glomus-B, Archaeospora, and Paraglomus. This suggests that farming systems as such did not influence AMF diversity, but rather specific environmental conditions or agricultural practices.

[Analysis of major QTL for Fusarium head blight resistance on the short arm of chromosome 3B in wheat].

Three recombinant inbred populations, Ning894037/Alondra, Wangshuibai/Alondra and Sumai3/Alondra, were analyzed for QTLs associated with Fusarium head blight resistance by interval mapping and composite interval mapping in this study. The result showed that the major QTLs were detected on the short arm of chromosome 3B of all three resistant parents using the data of FHB resistance evaluated in greenhouse or field. They were located in the interval of 5.0 cM between BARC133 and Xgwm493 in Ning894037, 11.5 cM between BARC147 and Xgwm493 in Wangshuibai, and 13.0 cM between Xgwm533a and Xgwm493 in Sumai3, explaining 42.8%, 15.1% and 10.6% of the phenotypic variance for Type II resistance (spread within the spike), respectively. Some of the SSR markers linking to the major QTLs tightly can be used directly in marker-assisted breeding to improve FHB resistance in wheat.