Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

Capistrano-Goßmann, Gina; Ries, David; Holtgräwe, Daniela; Minoche, André E.; Kraft, Thomas; Frerichmann, Sebastian Leo Max; Soerensen, Thomas Rosleff; Dohm, Juliane C.; González, Irene González; Schilhabel, Markus B.; Varrelmann, Mark; Tschoep, Hendrik; Uphoff, Helmut; Schütze, Karin; Borchardt, Dietrich; Toerjek, O; Mechelke, W.; Lein, Jens Christoph LeinJ.C.; Schechert, Axel; Frèse, L.; Himmelbauer, Heinz; Weißhaar, Bernd; Kopisch‐Obuch, Friedrich J.

doi:10.1038/ncomms15708

Cited by 57 publications

(56 citation statements)

References 45 publications

(74 reference statements)

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“…maritima (Gidner et al., ; Lewellen et al., ). Recently, the candidate gene for Rz2 has been identified by mapping‐by‐sequencing and appears to represent a typical plant R gene encoding a coiled‐coil nucleotide‐binding leucine‐rich repeat (CC‐NB‐LRR) protein (Capistrano‐Gossmann et al., ).…”

Section: Introductionmentioning

confidence: 99%

Massive up‐regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease

Gil

Liebe²,

Thiel³

et al. 2018

Molecular Plant Pathology

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Rhizomania of sugar beet, caused by Beet necrotic yellow vein virus (BNYVV), is characterized by excessive lateral root (LR) formation leading to dramatic reduction of taproot weight and massive yield losses. LR formation represents a developmental process tightly controlled by auxin signaling through AUX/IAA-ARF responsive module and LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcriptional network. Several LBD transcription factors play central roles in auxin-regulated LR development and act upstream of EXPANSINS (EXPs), cell wall (CW)-loosening proteins involved in plant development via disruption of the extracellular matrix for CW relaxation and expansion. Here, we present evidence that BNYVV hijacks these auxin-regulated pathways resulting in formation LR and root hairs (RH). We identified an AUX/IAA protein (BvAUX28) as interacting with P25, a viral virulence factor. Mutational analysis indicated that P25 interacts with domains I and II of BvAUX28. Subcellular localization of co-expressed P25 and BvAUX28 showed that P25 inhibits BvAUX28 nuclear localization. Moreover, root-specific LBDs and EXPs were greatly upregulated during rhizomania development. Based on these data, we present a model in which BNYVV P25 protein mimics action of auxin by removing BvAUX28 transcriptional repressor, leading to activation of LBDs and EXPs. Thus, the evidence highlights two pathways operating in parallel and leading to uncontrolled formation of LRs and RHs, the main manifestation of the rhizomania syndrome.

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Section: Introductionmentioning

confidence: 99%

Massive up‐regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease

Gil

Liebe²,

Thiel³

et al. 2018

Molecular Plant Pathology

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“…The Rz2 gene in EL10 showed approximately 8 kb of Gypsy and Helitron elements inserted, as reported by Capistrano‐Gossmann et al . (). The Bv.nbarc.0121 domain associated with Rz2 was part of Sf.…”

Section: Resultsmentioning

confidence: 97%

“…The Rz2 gene sequence (Capistrano‐Gossmann et al ., ) overlapped Bv.nbarc.0121 at 9.3 MB on Chromosome 3 (Figure ). Previous estimates of the genetic distance between Rz1 and Rz2 resistance loci range from 5 to 20 cM (Barzen et al ., ; Stevanato et al ., ).…”

Section: Resultsmentioning

confidence: 98%

“…Generation of molecular markers across the Rz region has been ongoing for over two decades (Barzen et al ., , ; Scholten et al ., ; Francis and Luterbacher, ; Gidner et al ., ; Grimmer et al ., ; Stevanato and Trebbi, ; Stevanato et al ., ). Long after being reported as a separate source of resistance, a specific CC‐NB‐LRR gene associated with Rz2 was identified (Capistrano‐Gossmann et al ., ). The molecular basis of Rz1 resistance is still poorly understood (Lewellen, ; Biancardi and Tamada, ).…”

Section: Discussionmentioning

confidence: 97%

“…The molecular basis of Rz1 resistance is unknown. The nucleotide sequence of Rz2 shows a classic CC‐NLR located on Chromosome 3 (Capistrano‐Gossmann et al ., ). Other published sources of resistance also co‐locate to the chromosomal region (Gidner et al ., ; Grimmer et al ., , ).…”

Section: Introductionmentioning

confidence: 97%

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Nucleotide‐binding resistance gene signatures in sugar beet, insights from a new reference genome

2018

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Nucleotide-binding (NB-ARC), leucine-rich-repeat genes (NLRs) account for 60.8% of resistance (R) genes molecularly characterized from plants. NLRs exist as large gene families prone to tandem duplication and transposition, with high sequence diversity among crops and their wild relatives. This diversity can be a source of new disease resistance, but difficulty in distinguishing specific sequences from homologous gene family members hinders characterization of resistance for improving crop varieties. Current genome sequencing and assembly technologies, especially those using long-read sequencing, are improving resolution of repeat-rich genomic regions and clarifying locations of duplicated genes, such as NLRs. Using the conserved NB-ARC domain as a model, 231 tentative NB-ARC loci were identified in a highly contiguous genome assembly of sugar beet, revealing diverged and truncated NB-ARC signatures as well as full-length sequences. The NB-ARC-associated proteins contained NLR resistance gene domains, including TIR, CC and LRR, as well as other integrated domains. Phylogenetic relationships of partial and complete domains were determined, and patterns of physical clustering in the genome were evaluated. Comparison of sugar beet NB-ARC domains to validated R-genes from monocots and eudicots suggested extensive Beta vulgaris-specific subfamily expansions. The NLR landscape in the rhizomania resistance conferring Rz region of Chromosome 3 was characterized, identifying 26 NLR-like sequences spanning 20 MB. This work presents the first detailed view of NLR family composition in a member of the Caryophyllales, builds a foundation for additional disease resistance work in B. vulgaris, and demonstrates an additional nucleic-acid-based method for NLR prediction in non-model plant species.

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Sugar Beet Breeding

McGrath

Panella

2018

Plant Breeding Reviews

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Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes

Cited by 57 publications

References 45 publications

Massive up‐regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease

Massive up‐regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease

Nucleotide‐binding resistance gene signatures in sugar beet, insights from a new reference genome

Sugar Beet Breeding

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