An interspecific barberry hybrid enables genetic dissection of non-host resistance to the stem rust pathogen Puccinia graminis

Bartaula, Radhika; Melo, Arthur T. O.; Connolly, Bryan A.; Jin, Yue; Hale, Iago

doi:10.1093/jxb/ery066

Cited by 5 publications

(11 citation statements)

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“…From the practical standpoint of breeding for improved resistance to wheat stem rust, the central questions regarding Pg -NHR concern the nature and modes of inheritance of the underlying genes. As previously observed in a natural interspecific barberry hybrid population [21], F 1 interspecific hybrids exhibit a range of reactions to Pg , from fully resistant to fully susceptible, with various intermediate forms. This range of reactions was similarly observed in the F 1 mapping population developed for this study (Fig.…”

Section: Discussionmentioning

confidence: 54%

“…Low marker density often results in inflated genetic distances [55], so it is expected that additional markers would reduce the overall length of B. vulgaris linkage map. The significantly lower number of markers available for B. vulgaris is likely a result of the relatively lower level of diversity observed in this species as a result of the severe genetic bottleneck presumed during its colonial introduction from Europe into North America [21].…”

Section: Discussionmentioning

confidence: 99%

“…To verify the putative F 1 status of the individuals in the mapping population, a PCR-based species-specific marker was designed based on available GBS data [21]. A universal primer pair was designed to amplify a short genomic sequence exhibiting a length polymorphism between the two parents.…”

Section: Methodsmentioning

confidence: 99%

“…Although some limited progression of Pg infection has been shown in rice, thus raising the possibility of dissecting Pg -NHR in that system, the infection process exhibits little variation, requires tedious microscopic studies to characterize, and ultimately fails to complete [13]. As an alternative to rice, the Berberis - Pg system was recently proposed as a tractable pathosystem for studying the genetics of Pg -NHR [21]. Numerous species within the highly diverse Berberis , or barberry, genus are susceptible to Pg infection (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid

et al. 2019

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Background Non-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis ( Pg )], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen’s alternate host, barberry ( Berberis spp.), to overcome this challenge. Results In this study, an interspecific mapping population derived from a cross between Pg -resistant Berberis thunbergii ( Bt ) and Pg -susceptible B. vulgaris was developed to investigate the Pg -NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance. Conclusions Foundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg -NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg -NHR in the alternate host of one of agriculture’s most devastating pathogens. Electronic supplementary material The online version of this article (10.1186/s12870-019-1893-9) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid

et al. 2019

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“…As a reference-optional (or de novo ) pipeline, GBS-SNP-CROP has proven useful to breeders of under-researched crop species for which the lack of a reference genome presented a barrier to the efficient use of GBS data (Cheng et al , 2017; Hale et al , 2018; Melo et al , 2017; Sogbohossou et al , 2018; Wang et al , 2017). The pipeline has facilitated studies of genetic diversity and population structure for natural populations of both plants (Arredondo et al , 2018; Bartaula et al , 2018; Sunseri et al , 2018) and animals (Drury et al , 2017; Xu et al , 2017) and has successfully supported molecular breeding analyses in a variety of crop and non-crop plant species (Adhikari et al , 2018; Chung et al , 2018; Holloway et al , 2018; Munjal et al , 2017). In presenting GBS-SNP-CROP v.4.0, this note describes the expanded functionality and enhanced performance of the pipeline relative to its original version.…”

Section: Introductionmentioning

confidence: 99%

Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP

Melo

Hale

2018

Bioinformatics

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Summary GBS-SNP-CROP is a bioinformatics pipeline originally developed to support the cost-effective genome-wide characterization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly in the absence of a reference genome. Since its 2016 release, the pipeline’s functionality has greatly expanded, its computational efficiency has improved, and its applicability to a broad set of genomic studies for both plants and animals has been demonstrated. This note details the suite of improvements to date, as realized in GBS-SNP-CROP v.4.0, with specific attention paid to a new integrated metric that facilitates reliable variant identification despite the complications of homologs. Using the new de novo GBS read simulator GBS-Pacecar, also introduced in this note, results show an improvement in overall pipeline accuracy from 66% (v.1.0) to 84% (v.4.0), with a time saving of ∼70%. Both GBS-SNP-CROP versions significantly outperform TASSEL-UNEAK; and v.4.0 resolves the issue of non-overlapping variant calls observed between UNEAK and v.1.0. Availability and implementation GBS-SNP-CROP source code and user manual are available at https://github.com/halelab/GBS-SNP-CROP . The GBS read simulator GBS-Pacecar is available at https://github.com/halelab/GBS-Pacecar . Supplementary information Supplementary data are available at Bioinformatics online.

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Genetic approaches to dissect plant nonhost resistance mechanisms

Sexton

Yang

et al. 2023

Molecular Plant Pathology

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Nonhost resistance (NHR) refers to the immunity of most tested genotypes of a plant species to most tested variants of a pathogen species. Thus, NHR is broad spectrum and durable in nature and constitutes a major safety barrier against invasion of a myriad of potentially pathogenic microbes in any plants including domesticated crops. Genetic study of NHR is generally more difficult compared to host resistance mainly because NHR is genetically more complicated and often lacks intraspecific polymorphisms. Nevertheless, substantial progress has been made towards the understanding of the molecular basis of NHR in the past two decades using various approaches. Not surprisingly, molecular mechanisms of NHR revealed so far encompasses pathogen‐associated molecular pattern‐triggered immunity and effector‐triggered immunity. In this review, we briefly discuss the inherent difficulty in genetic studies of NHR and summarize the main approaches that have been taken to identify genes contributing to NHR. We also discuss new enabling strategies for dissecting multilayered NHR in model plants with a focus on NHR against filamentous pathogens, especially biotrophic pathogens such as powdery mildew and rust fungi.

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An interspecific barberry hybrid enables genetic dissection of non-host resistance to the stem rust pathogen Puccinia graminis

Abstract: This study demonstrates for the first time the feasibility of dissecting the genetic mechanism of non-host resistance to the stem rust pathogen in its ancestral host genus Berberis.

Cited by 5 publications

References 55 publications

Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid

Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid

Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP

Genetic approaches to dissect plant nonhost resistance mechanisms

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