Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins

Sánchez‐Martín, Javier; Widrig, Victoria; Herren, Gerhard; Wicker, Thomas; Zbinden, Helen; Gronnier, Julien; Spörri, Laurin; Praz, Coraline R.; Heuberger, Matthias; Kolodziej, Markus C.; Isaksson, Jonatan; Steuernagel, Burkhard; Karafiátová, Miroslava; Doležel, Jaroslav; Zipfel, Cyril; Keller, Beat

doi:10.1038/s41477-021-00869-2

Cited by 105 publications

(119 citation statements)

References 116 publications

(134 reference statements)

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“…either complex pyramiding schemes or transgenic methods 11 under tight regulation in many countries. Moreover, resistance gene breeding takes advantage of a comparatively simple genetic architecture where single, easily transferable major genes confer large genetic gains 12 .…”

mentioning

confidence: 99%

GiPS: Genomics-informed parent selection uncovers the breeding value of wheat genetic resources

Schulthess

Kale

Liu

et al. 2021

Preprint

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The great efforts spent in the maintenance of past diversity in genebanks are rationalized by the potential role of plant genetic resources in future crop improvement – a concept whose practical implementation has fallen short of expectations. Here, we implement genomics-informed parent selection to expedite pre-breeding without discriminating against non-adapted germplasm. We collect dense genetic profiles for a large winter wheat collection and evaluate grain yield and resistance to yellow rust in representative coresets. Genomic prediction within and across genebanks identified the best parents for PGR x elite derived crosses that outyielded current elite cultivars in multiple field trials.

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mentioning

confidence: 99%

GiPS: Genomics-informed parent selection uncovers the breeding value of wheat genetic resources

Schulthess

Kale

Liu

et al. 2021

Preprint

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“…reported two cloned genes Pm2 and Pm4, the latter of which encoded a putative chimeric protein of a serine/threonine kinase and multiple C2 domains and transmembrane regions (Sánchez-Martín et al, 2016;Sánchez-Martín et al, 2021). Pm21, encoding a typical coiled-coil nucleotide binding siteleucine-rich repeat protein, confers broad-spectrum resistance to powdery mildew disease in wheat (He et al, 2018).…”

Section: Core Ideasmentioning

confidence: 99%

Section: Core Ideasmentioning

confidence: 99%

RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat

et al. 2021

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Powdery mildew causes considerable yield losses in common wheat (Triticum aestivum L.) production. Mapping and cloning powdery mildew-resistant quantitative trait loci can benefit stable yield production by facilitating the breeding of resistant varieties. In this study, we used the powdery mildew resistance introgression line 'CH7087' (harboring the resistance gene PmCH7087) and developed a large F 2 population and a corresponding F 2:3 segregation population containing 2,000 family lines for molecular mapping of PmCH7087. Genetic analysis demonstrated that the resistance phenotype was controlled by a single dominant gene. According to the performance exhibited by the F 2:3 lines, 50 resistant lines and 50 susceptible lines without phenotype segregation were chosen for pooling and bulked segregant RNA sequencing (BSR-Seq) analysis. A region spanning 42.77 Mb was identified, and genotyping of an additional 183 F 2:3 lines with extreme phenotypes using 20 kompetitive allele-specific polymerase chain reaction (KASP) markers in the BSR-Seq mapping regions confirmed this region and narrowed it to 9.68 Mb, in which 45 genes were identified and annotated. Five of these transcripts harbored nonsynonymous single nucleotide polymorphisms between the two parents, with the transcripts of TraesCS2B01G302800 being involved in signal transduction. Furthermore, TraesCS2B01G302800.2 was annotated as the closest homologue of serine/threonine-protein kinase PBS1, a typical participant in the plant disease immune response, indicating that TraesCS2B01G302800 was the candidate gene of PmCH7087. Our results may facilitate future research attempting to improve powdery mildew resistance in wheat and to identify candidate genes for further verification and gene cloning.

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“…However, not all R genes enclose the canonical disease-resistance domains. A putative chimeric protein with serine/threonine kinase and several C2 domains has been recently cloned through MutChromSeq [60]. The underlying gene, Pm4, has a unique domain architecture and confers resistance to wheat powdery mildew.…”

Section: Mutchromseqmentioning

confidence: 99%

Bioinformatic-Based Approaches for Disease-Resistance Gene Discovery in Plants

Fernandez-Gutierrez¹,

Gutiérrez-González²

2021

Agronomy

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Pathogens are among the most limiting factors for crop success and expansion. Thus, finding the underlying genetic cause of pathogen resistance is the main goal for plant geneticists. The activation of a plant’s immune system is mediated by the presence of specific receptors known as disease-resistance genes (R genes). Typical R genes encode functional immune receptors with nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) domains, making the NBS-LRRs the largest family of plant resistance genes. Establishing host resistance is crucial for plant growth and crop yield but also for reducing pesticide use. In this regard, pyramiding R genes is thought to be the most ecologically friendly way to enhance the durability of resistance. To accomplish this, researchers must first identify the related genes, or linked markers, within the genomes. However, the duplicated nature, with the presence of frequent paralogues, and clustered characteristic of NLRs make them difficult to predict with the classic automatic gene annotation pipelines. In the last several years, efforts have been made to develop new methods leading to a proliferation of reports on cloned genes. Herein, we review the bioinformatic tools to assist the discovery of R genes in plants, focusing on well-established pipelines with an important computer-based component.

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Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins

Cited by 105 publications

References 116 publications

GiPS: Genomics-informed parent selection uncovers the breeding value of wheat genetic resources

GiPS: Genomics-informed parent selection uncovers the breeding value of wheat genetic resources

RNA‐seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat

Bioinformatic-Based Approaches for Disease-Resistance Gene Discovery in Plants

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