LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

Helft, Laura; Reddy, V. Dashwantha; Chen, Xiyang; Koller, Teresa; Federici, L.; Fernández‐Recio, Juan; Gupta, Rishabh; Bent, Andrew F.

doi:10.1371/journal.pone.0021614

Cited by 49 publications

(62 citation statements)

References 90 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Different domains of the NLR were identified based the homology to the annotated RPM1 protein 44 . The most probable LRR motifs were predicted using the LRR conservation mapping tool v2.0 (www.plantpath.wisc.edu/RCM) 45 .…”

Section: Lr22a Protein Domain Predictionmentioning

confidence: 99%

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

et al. 2017

View full text Add to dashboard Cite

Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago longrange linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.DOI: https://doi.org/10.1038/nbt.3877Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-144182 Journal Article Accepted Version Originally published at: Thind, Anupriya Kaur; Wicker, Thomas; Šimková, Hana; Fossati, Dario; Moullet, Odile; Brabant, Cécile; Vrána, Jan; Doležel, Jaroslav; Krattinger, Simon G (2017). Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nature Biotechnology, 35(8) Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene using molecular marker information and EMS mutants and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis RPM1 protein.While the world population continues to grow, the arable land per capita is decreasing 6 . To ensure food security, agriculture will require high-yielding crops that can withstand diseases, pests and adverse climatic conditions. A better understanding of genes that control these important traits may enable breeding of crop cultivars capable of feeding the 9-10 billion people expected by 2050. triticina isolates [13][14][15][16] . The Lr22a-mediated resistance is not present in young seedlings (<20 days) but is only visible in wheat plants from ~25 days of age.First, in order to evaluate the effectiveness of Lr22a against Swiss P. triticina isolates we inoculated the Lr22a-containing backcross line RL6044 ('Thatcher Lr22a') and the spring wheat cultivar 'Thatcher' with ten P. triticina isolates that were collected in Switzerland. The first leaves of RL6044 developed leaf rust pustules of similar size as the susceptible control 'Thatcher', while we observed complete to moderate resistance on the third leaves of 30-dayold RL6044 plants in comparison to 'Thatcher' (Fig. 1, Supplementary Fig. 1).Lr22a was previously mapped to the short arm of wheat chromosome 2D using microsatellite analysis of the Lr22a-containing wheat line 98B34-T4B 13 . In order to...

show abstract

Section: Lr22a Protein Domain Predictionmentioning

confidence: 99%

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

et al. 2017

View full text Add to dashboard Cite

show abstract

“…The extracellular LRR of EFR is highly glycosylated, which seems to be important for ligand binding as mutation of a single predicted glycosylation site compromises elf18 binding despite correct localization of the mutated protein to the plasma membrane (85). Elf18 most likely binds to the concave surface of the horseshoe-like LRR as mutations of predicted ligand-binding sites identified by several computational methods compromise EFR-mediated immune responses (89).…”

Section: Innate Immunity Mediated By Efrmentioning

confidence: 99%

Plant Innate Immunity: Perception of Conserved Microbial Signatures

Schwessinger

Ronald

2012

Annu. Rev. Plant Biol.

306

252

View full text Add to dashboard Cite

Plants and animals sense conserved microbial signatures through receptors localized to the plasma membrane and cytoplasm. These receptors typically carry or associate with non-arginine-aspartate (non-RD) kinases that initiate complex signaling networks cumulating in robust defense responses. In plants, coregulatory receptor kinases have been identified that not only are critical for the innate immune response but also serve an essential function in other regulatory signaling pathways.

show abstract

“…Leucine-rich repeats (LRR) are ligand interaction domains found in various types of proteins. The ubiquity of the domain may be due to its ability to interact with a wide range of substrates (Helft et al 2011). LRR are particularly important for protein-protein interactions (Bella et al 2008) and mechanism of ice-recrystallisation inhibition might be guided by the presence of LRR and IRI patterns in protein sequences (Muthukumaran et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Association of single nucleotide polymorphisms in LpIRI1 gene with freezing tolerance traits in perennial ryegrass

et al. 2014

View full text Add to dashboard Cite

Perennial ryegrass is an important agricultural crop, however, it is susceptible to winterkill. Freezing injury is caused primarily by ice formation. The LpIRI1 protein has the potential to inhibit ice recrystallization, thus minimize the damage. An association study was conducted using single nucleotide polymorphisms obtained through allele sequencing of the LpIRI1 gene and phenotypic data were collected using two phenotyping platforms in a perennial ryegrass association mapping population of 76 diverse genotypes. Winter survival (FWS) was evaluated under field conditions, while tiller survival (PTS) and electrolyte leakage (EL) at -8 and -12°C were determined under controlled-environment conditions. Proline content (PC) in cold-acclimated plants was measured prior to the freezing test. Significant variation in FWS, PTS, EL and PC was observed among genotypes in our panel. EL and PTS revealed significant negative correlations at -8°C (r s = -0.40) and -12°C (r s = -0.49). PC, however, did not show significant correlations with any of the measured traits, while FWS was correlated (r s = -0.48) with EL at -12°C. The LpIRI1 gene was found to be highly polymorphic with an average SNP frequency of 1 SNP per 16 bp. Association analysis revealed two non-synonymous SNPs being associated with increased EL, both located in the LpIRI1 leucinerich repeat. The results indicate that allelic variation in the LpIRI1 gene plays an important role in the cell membrane integrity of perennial ryegrass during freezing, and can be exploited for developing more freezing tolerant cultivars.

show abstract

LRR Conservation Mapping to Predict Functional Sites within Protein Leucine-Rich Repeat Domains

Cited by 49 publications

References 90 publications

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

Plant Innate Immunity: Perception of Conserved Microbial Signatures

Association of single nucleotide polymorphisms in LpIRI1 gene with freezing tolerance traits in perennial ryegrass

Contact Info

Product

Resources

About