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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #350393
Title: Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome

Author
item FUNK, A - Michigan State University
item GALEWSKI, P - Michigan State University
item McGrath, Jon

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2018
Publication Date: 6/15/2018
Citation: Funk, A., Galewski, P., McGrath, J.M. 2018. Nucleotide-binding resistance gene signatures in sugar beet, insights from a new reference genome. Plant Journal. 95(4):659-671.

Interpretive Summary: Nucleotide-binding , leucine-rich-repeat (NLR) genes are key components for plant disease resistance. A recently characterized sugar beet gene is an NLR which confers resistance to the disease rhizomania caused by Beet Necrotic Yellow-Vein Virus. NLRs exist as large gene families that exhibit high levels of diversity among crops and their wild relatives. Difficulty in distinguishing specific sequences from homologous gene family members has hindered the understanding of resistance for improving crop varieties. Using a conserved NB-ARC gene model, 231 tentative NLRs were identified in the EL10 reference genome assembly of sugar beet. Comparison of sugar beet NLRs to those of other plants revealed numerous beet-specific genes. This work presents the first detailed view of NLR composition in this family of plants, and builds a foundation for additional disease resistance work in beet and other plants.

Technical Abstract: 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.