scholarly journals NLR Diversity and Candidate Fusiform Rust Resistance Genes in Loblolly Pine

2021 ◽  
Author(s):  
Daniel Ence ◽  
Katherine E Smith ◽  
Shenghua Fan ◽  
Leandro Gomide Neves ◽  
Robin Paul ◽  
...  
Keyword(s):  
Gene Family ◽  
Resistance Gene ◽  
Loblolly Pine ◽  
Resistance Genes ◽  
Rust Resistance ◽  
De Novo ◽  
Gene Diversity ◽  
Gene Family Evolution ◽  
Fusiform Rust ◽  
Geographic Diversity

Abstract Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently SNP markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for an NLR protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family-evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified ten SNPs and two QTL associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family-evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.

scholarly journals Mapping Fusiform Rust Resistance Genes within a Complex Mating Design of Loblolly Pine

Forests ◽  
2014 ◽  
Vol 5 (2) ◽  
pp. 347-362 ◽  
Author(s):  
Tania Quesada ◽  
Marcio Resende Jr. ◽  
Patricio Muñoz ◽  
Jill Wegrzyn ◽  
David Neale ◽  
...  
Keyword(s):  
Loblolly Pine ◽  
Resistance Genes ◽  
Rust Resistance ◽  
Fusiform Rust ◽  
Mating Design ◽  
Rust Resistance Genes

scholarly journals Metagenomics Analysis Reveals the Microbial Communities, Antimicrobial Resistance Gene Diversity and Potential Pathogen Transmission Risk of Two Different Landfills in China

Diversity ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 230
Author(s):  
Shan Wan ◽  
Min Xia ◽  
Jie Tao ◽  
Yanjun Pang ◽  
Fugen Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Diversity ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Pathogen Transmission ◽  
Transmission Risk ◽  
Antimicrobial Resistance Gene

In this study, we used a metagenomic approach to analyze microbial communities, antibiotic resistance gene diversity, and human pathogenic bacterium composition in two typical landfills in China. Results showed that the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were predominant in the two landfills, and archaea and fungi were also detected. The genera Methanoculleus, Lysobacter, and Pseudomonas were predominantly present in all samples. sul2, sul1, tetX, and adeF were the four most abundant antibiotic resistance genes. Sixty-nine bacterial pathogens were identified from the two landfills, with Klebsiella pneumoniae, Bordetella pertussis, Pseudomonas aeruginosa, and Bacillus cereus as the major pathogenic microorganisms, indicating the existence of potential environmental risk in landfills. In addition, KEGG pathway analysis indicated the presence of antibiotic resistance genes typically associated with human antibiotic resistance bacterial strains. These results provide insights into the risk of pathogens in landfills, which is important for controlling the potential secondary transmission of pathogens and reducing workers’ health risk during landfill excavation.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

Genome ◽  
1997 ◽  
Vol 40 (5) ◽  
pp. 659-665 ◽  
Author(s):  
Evans S. Lagudah ◽  
Odile Moullet ◽  
Rudi Appels
Keyword(s):  
Disease Resistance ◽  
Gene Family ◽  
Binding Site ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Gene Sequence ◽  
Nucleotide Binding ◽  
Disease Resistance Gene ◽  
Leucine Rich Repeat ◽  
Rich Region

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS – leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.Key words: cereal cyst nematode, disease resistance genes, nucleotide-binding site, leucine-rich repeat.

scholarly journals Identification and Molecular Characterization of Leaf Rust Resistance Gene Lr14a in Durum Wheat

Plant Disease ◽  
2008 ◽  
Vol 92 (3) ◽  
pp. 469-473 ◽  
Author(s):  
S. A. Herrera-Foessel ◽  
R. P. Singh ◽  
J. Huerta-Espino ◽  
H. M. William ◽  
V. Garcia ◽  
...  
Keyword(s):  
Durum Wheat ◽  
Leaf Rust ◽  
Resistance Gene ◽  
Ssr Markers ◽  
Common Wheat ◽  
Resistance Genes ◽  
Rust Resistance ◽  
Leaf Rust Resistance ◽  
Rust Resistance Gene ◽  
Leaf Rust Resistance Gene

Leaf rust, caused by Puccinia triticina, is an important disease of durum wheat (Triticum turgidum subsp. durum) and only a few designated resistance genes are known to occur in this crop. A dominant leaf rust resistance gene in the Chilean durum cv. Llareta INIA was mapped to chromosome arm 7BL through bulked segregant analysis using the amplified fragment length polymorphism (AFLP) technique, and by mapping three polymorphic markers in the common wheat (T. aestivum) International Triticeae Mapping Initiative population. Several simple sequence repeat (SSR) markers, including Xgwm344-7B and Xgwm146-7B, were associated with the leaf rust resistance gene. Resistance response and chromosomal position indicated that this gene is likely to be Lr14a. The SSR markers Xgwm344-7B and Xgwm146-7B and one AFLP marker also differentiated common wheat cv. Thatcher from the near-isogenic line with Lr14a, as well as durum ‘Altar C84’ from durum wheat with Lr14a. This is the first report of the presence of Lr14a in durum wheat, although the gene originally was transferred from emmer wheat ‘Yaroslav’ to common wheat. Lr14a is also present in CIMMYT-derived durum ‘Somateria’ and effective against Mexican and other P. triticina races of durum origin. Lr14a should be deployed in combination with other effective leaf rust resistance genes to prolong its effectiveness in durum wheat.

Monoterpene composition and fusiform rust resistance in slash and loblolly pines

1995 ◽  
Vol 25 (2) ◽  
pp. 193-197 ◽  
Author(s):  
M. Michelozzi ◽  
T.L. White ◽  
A.E. Squillace ◽  
W.J. Lowe
Keyword(s):  
Loblolly Pine ◽  
Rust Resistance ◽  
Slash Pine ◽  
Cortical Tissue ◽  
Fusiform Rust ◽  
Breeding Values ◽  
Loblolly Pines ◽  
Monoterpene Composition

Monoterpene composition of cortical tissue was analyzed in slash pine (Pinuselliottii Engelm. var. elliottii) and loblolly pine (Pinustaeda L.) clones with known breeding values for fusiform rust resistance. Trees having a relatively high content of β-phellandrene tend to be more resistant than trees with a low β-phellandrene content. Such results confirm previous data and suggest the utilization of β-phellandrene content as an aid in selecting relatively rust resistant slash and loblolly pines.

Indirect selection and clonal propagation of loblolly pine seedlings enhance resistance to fusiform rust

1989 ◽  
Vol 19 (4) ◽  
pp. 534-537 ◽  
Author(s):  
G. S. Foster ◽  
R. L. Anderson
Keyword(s):  
Loblolly Pine ◽  
Rust Resistance ◽  
Clonal Propagation ◽  
Indirect Selection ◽  
Artificial Inoculation ◽  
Fusiform Rust ◽  
Rooted Cutting ◽  
Pine Seedlings ◽  
Susceptible Control ◽  
High Degree

A population of loblolly pine (Pinustaeda L.) seedlings without fusiform rust (Cronartiumquercuum (Berk.) Miyabe ex Shirai f.sp. fusiforme) galls was developed by controlled-cross matings of parent trees with known rust resistance, and subsequent screening of the seedling offspring through artificial inoculation. The seedlings without rust galls then entered a vegetative propagation system using rooted cuttings. A second round of rust testing by artificial inoculation, using a random sample of 20 clones from the program, revealed a high degree of rust resistance (4% galled) compared with that of seedlings from either a resistant control seedlot (50% galled) or a susceptible control seedlot (81% galled). This apparently high degree of rust resistance may be due to genetic effects, rooted cutting morphology, or both.

scholarly journals Apple Contains Receptor-like Genes Homologous to the Cladosporium fulvum Resistance Gene Family of Tomato with a Cluster of Genes Cosegregating with Vf Apple Scab Resistance

2001 ◽  
Vol 14 (4) ◽  
pp. 508-515 ◽  
Author(s):  
Boris A. Vinatzer ◽  
Andrea Patocchi ◽  
Luca Gianfranceschi ◽  
Stefano Tartarini ◽  
Hong-Bin Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Transmembrane Domain ◽  
Venturia Inaequalis ◽  
Scab Resistance ◽  
Common Disease ◽  
Resistance Locus ◽  
Cladosporium Fulvum ◽  
High Quality

Scab caused by the fungal pathogen Venturia inaequalis is the most common disease of cultivated apple (Malus × domestica Borkh.). Monogenic resistance against scab is found in some small-fruited wild Malus species and has been used in apple breeding for scab resistance. Vf resistance of Malus floribunda 821 is the most widely used scab resistance source. Because breeding a high-quality cultivar in perennial fruit trees takes dozens of years, cloning disease resistance genes and using them in the transformation of high-quality apple varieties would be advantageous. We report the identification of a cluster of receptor-like genes with homology to the Cladosporium fulvum (Cf) resistance gene family of tomato on bacterial artificial chromosome clones derived from the Vf scab resistance locus. Three members of the cluster were sequenced completely. Similar to the Cf gene family of tomato, the deduced amino acid sequences coded by these genes contain an extracellular leucine-rich repeat domain and a transmembrane domain. The transcription of three members of the cluster was determined by reverse transcription-polymerase chain reaction to be constitutive, and the transcription and translation start of one member was verified by 5′ rapid amplification of cDNA ends. We discuss the parallels between Cf resistance of tomato and Vf resistance of apple and the possibility that one of the members of the gene cluster is the Vf gene. Cf homologs from other regions of the apple genome also were identified and are likely to present other scab resistance genes.

scholarly journals Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana

2020 ◽  
Vol 16 ◽  
pp. 117693432091105
Author(s):  
Huawei Wei ◽  
Jia Liu ◽  
Qinwei Guo ◽  
Luzhao Pan ◽  
Songlin Chai ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Phylogenetic Analysis ◽  
Gene Family ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Chromosome Mapping ◽  
Gene Families ◽  
Gene Clusters ◽  
Motif Analysis ◽  
Solanum Pimpinellifolium

NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.

scholarly journals Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

2020 ◽  
Vol 12 (3) ◽  
pp. 185-202
Author(s):  
Xia Han ◽  
Jindan Guo ◽  
Erli Pang ◽  
Hongtao Song ◽  
Kui Lin
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Genome Phylogeny ◽  
Partial Homology

Abstract How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.

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