scholarly journals Disease Resistance Genetics and Genomics in Octoploid Strawberry

2019 ◽  
Author(s):  
Christopher Barbey ◽  
Seonghee Lee ◽  
Sujeet Verma ◽  
Kevin A. Bird ◽  
Alan E. Yocca ◽  
...  
Keyword(s):  
Disease Resistance ◽  
A Priori ◽  
Eqtl Analysis ◽  
R Gene ◽  
R Genes ◽  
Specialty Crop ◽  
Crop Disease ◽  
Strawberry Cultivar ◽  
Gene Collection ◽  
Resistance Genetics

ABSTRACTOctoploid strawberry (Fragaria × ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, eQTL analysis and RenSeq analysis in cultivars. Octoploid fruit transcript expression quantitative trait loci (eQTL) were identified for 77 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. × ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance towards exploiting variation for strawberry cultivar improvement.

scholarly journals Disease Resistance Genetics and Genomics in Octoploid Strawberry

2019 ◽  
Vol 9 (10) ◽  
pp. 3315-3332 ◽  
Author(s):  
Christopher R. Barbey ◽  
Seonghee Lee ◽  
Sujeet Verma ◽  
Kevin A. Bird ◽  
Alan E. Yocca ◽  
...  
Keyword(s):  
Disease Resistance ◽  
A Priori ◽  
Eqtl Analysis ◽  
R Gene ◽  
R Genes ◽  
Specialty Crop ◽  
Crop Disease ◽  
Strawberry Cultivar ◽  
Gene Collection ◽  
Resistance Genetics

Octoploid strawberry (Fragaria ×ananassa) is a valuable specialty crop, but profitable production and availability are threatened by many pathogens. Efforts to identify and introgress useful disease resistance genes (R-genes) in breeding programs are complicated by strawberry’s complex octoploid genome. Recently-developed resources in strawberry, including a complete octoploid reference genome and high-resolution octoploid genotyping, enable new analyses in strawberry disease resistance genetics. This study characterizes the complete R-gene collection in the genomes of commercial octoploid strawberry and two diploid ancestral relatives, and introduces several new technological and data resources for strawberry disease resistance research. These include octoploid R-gene transcription profiling, dN/dS analysis, expression quantitative trait loci (eQTL) analysis and RenSeq analysis in cultivars. Octoploid fruit eQTL were identified for 76 putative R-genes. R-genes from the ancestral diploids Fragaria vesca and Fragaria iinumae were compared, revealing differential inheritance and retention of various octoploid R-gene subtypes. The mode and magnitude of natural selection of individual F. ×ananassa R-genes was also determined via dN/dS analysis. R-gene sequencing using enriched libraries (RenSeq) has been used recently for R-gene discovery in many crops, however this technique somewhat relies upon a priori knowledge of desired sequences. An octoploid strawberry capture-probe panel, derived from the results of this study, is validated in a RenSeq experiment and is presented for community use. These results give unprecedented insight into crop disease resistance genetics, and represent an advance toward exploiting variation for strawberry cultivar improvement.

Arabidopsis thaliana: A source of candidate disease-resistance genes for Brassica napus

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 452-460 ◽  
Author(s):  
D Sillito ◽  
I AP Parkin ◽  
R Mayerhofer ◽  
D J Lydiate ◽  
A G Good
Keyword(s):  
Arabidopsis Thaliana ◽  
Disease Resistance ◽  
Brassica Napus ◽  
Resistance Genes ◽  
Plant Disease Resistance ◽  
Disease Resistance Genes ◽  
R Gene ◽  
R Genes ◽  
Rapid Divergence ◽  
Genomic Regions

Common structural and amino acid motifs among cloned plant disease-resistance genes (R genes), have made it possible to identify putative disease-resistance sequences based on DNA sequence identity. Mapping of such R-gene homologues will identify candidate disease-resistance loci to expedite map-based cloning strategies in complex crop genomes. Arabidopsis thaliana expressed sequence tags (ESTs) with homology to cloned plant R genes (R-ESTs), were mapped in both A. thaliana and Brassica napus to identify candidate R-gene loci and investigate intergenomic collinearity. Brassica R-gene homologous sequences were also mapped in B. napus. In total, 103 R-EST loci and 36 Brassica R-gene homologous loci were positioned on the N-fo-61-9 B. napus genetic map, and 48 R-EST loci positioned on the Columbia × Landsberg A. thaliana map. The mapped loci identified collinear regions between Arabidopsis and Brassica which had been observed in previous comparative mapping studies; the detection of syntenic genomic regions indicated that there was no apparent rapid divergence of the identified genomic regions housing the R-EST loci.Key words: RFLP mapping, candidate R genes, R-gene homologues, genomic collinearity, Arabidopsis ESTs.

scholarly journals In-silico identification and differential expression of putative disease resistance-related genes within the collinear region of Brassica napus blackleg resistance locus LepR2’ in Brassica oleracea

2020 ◽  
Vol 61 (5) ◽  
pp. 879-890 ◽  
Author(s):  
Mohammad Rashed Hossain ◽  
Mostari Jahan Ferdous ◽  
Jong-In Park ◽  
Arif Hasan Khan Robin ◽  
Sathishkumar Natarajan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Brassica Napus ◽  
Resistance Locus ◽  
R Gene ◽  
R Genes ◽  
Blackleg Resistance ◽  
B Genome ◽  
Expression Of Genes ◽  
C Genome ◽  
R Loci

Abstract Blackleg disease, caused by Leptosphaeria maculans, greatly affects the production of cabbage (Brassica oleracea). However, definitive R-gene(s) are yet to be identified in this crop. In contrast, a number of R-loci have been identified in A- or B-genome crops. Identification of few resistant cabbage genotypes indicates the presence of R-genes in this C-genome crop. High ancestral synteny between Brassica genomes suggests that the collinear regions of known A- or B-genome R-loci may also contain functional R-genes in the C-genome. Strong resistance was observed in the cotyledons of cabbage inbred line SCNU-98 against two L. maculans isolates, 03–02 s and 00–100 s. We investigated the collinear region of the Brassica napus blackleg resistance locus LepR2’ in B. oleracea since both isolates of L. maculans contain corresponding avirulence genes. The locus was collinear to a 5.8 Mbp genomic segment of B. oleracea chromosome C09 containing 13 genes that have putative disease resistance-related domains. High expression of genes Bo9g117290 and Bo9g111510 against isolate 00–100 s, and high expression of genes Bo9g126150 and Bo9g111490 against both isolates in the resistant-line SCNU-98 indicate their putative roles in blackleg resistance, which remained to be functionally verified. This work enhances our understanding of R-gene-mediated resistance to blackleg in cabbage.

scholarly journals Isolation, Characterization and Phylogenetic Analysis of Nucleotide Binding Site-encoding Disease-resistance Gene Analogues from European Aspen (Populus tremula)

2010 ◽  
Vol 59 (1-6) ◽  
pp. 68-77 ◽  
Author(s):  
Yong Zhang ◽  
Shougong Zhang ◽  
Liwang Qi ◽  
Tao Zhang ◽  
Chunguo Wang ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Binding Site ◽  
Resistance Gene ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Populus Tremula ◽  
R Gene ◽  
R Genes ◽  
Degenerate Primers ◽  
European Aspen

Abstract The majority of verified plant disease resistance genes (R genes) isolated to date was of the nucleotide binding site-leucine rich repeat (NBS-LRR) class. The conservation between different NBS-LRR R genes opens the avenue for the use of PCR based strategies in isolating and cloning other R gene family members or analogs (resistance gene analogue, RGA) using degenerate primers for these conserved regions. In this study, to better understand the R gene in European aspen (Populus tremula), a perennial tree, we used degenerate primers to amplify RGA sequences from European aspen. Cloning and sequence characterization identified 37 European aspen RGAs, which could be phylogenetically classified into seven subfamilies. Deduced amino acid sequences of European aspen RGAs showed strong identity, ranging from 30.41 to 46.63%, to toll interleukin receptor (TIR) R gene subfamily. BLAST searches with reference to the genomic sequence of P. trichocarpa found 209 highly homologous regions distributed in 28 genomic loci, suggesting the abundance and divergence of NBS-encoding R genes in European aspen genome. Although, numerous studies have reported that plant R genes are under diversifying selection for specificity to evolving pathogens, non-synonymous to synonymous nucleotide substitution (dN/dS) ratio were <1 for NBS domains of European aspen RGA, showing the evidence of purifying selection in this perennial tree. In further analysis, many intergenic exchanges were also detected among these RGAs, indicating a probable role in homogenising NBS domains. The present study permits insights into the origin, diversification, evolution and function of NBS-LRR R genes in perennial species like European aspen and will be useful for further R gene isolation and exploitation.

scholarly journals The Genetic Architecture of Disease Resistance in Maize: A Synthesis of Published Studies

2006 ◽  
Vol 96 (2) ◽  
pp. 120-129 ◽  
Author(s):  
Randall J. Wisser ◽  
Peter J. Balint-Kurti ◽  
Rebecca J. Nelson
Keyword(s):  
Disease Resistance ◽  
Genetic Architecture ◽  
Visual Inspection ◽  
Statistical Tests ◽  
R Gene ◽  
R Genes ◽  
Consensus Map ◽  
Maize Germplasm ◽  
Genome Wide ◽  
Breeding Schemes

Fifty publications on the mapping of maize disease resistance loci were synthesized. These papers reported the locations of 437 quantitative trait loci (QTL) for disease (dQTL), 17 resistance genes (R-genes), and 25 R-gene analogs. A set of rules was devised to enable the placement of these loci on a single consensus map, permitting analysis of the distribution of resistance loci identified across a variety of maize germplasm for a number of different diseases. The confidence intervals of the dQTL were distributed over all 10 chromosomes and covered 89% of the genetic map to which the data were anchored. Visual inspection indicated the presence of clusters of dQTL for multiple diseases. Clustering of dQTL was supported by statistical tests that took into account genome-wide variations in gene density. Several novel clusters of resistance loci were identified. Evidence was also found for the association of dQTL with maturity-related QTL. It was evident from the distinct dQTL distributions for the different diseases that certain breeding schemes may be more suitable for certain diseases. This review provides an up-to-date synthesis of reports on the locations of resistance loci in maize.

Investigation of variations in NBS motifs in alfalfa (Medicago sativa), M. edgeworthii, and M. ruthenica

2003 ◽  
Vol 83 (2) ◽  
pp. 371-376 ◽  
Author(s):  
T. A. Campbell
Keyword(s):  
Disease Resistance ◽  
Plant Disease Resistance ◽  
Open Reading Frames ◽  
R Gene ◽  
R Genes ◽  
Asian Species ◽  
Leucine Rich Repeats ◽  
Medicago Species ◽  
Plant Disease Resistance Genes ◽  
Reading Frames

Medicago edgeworthii Sirjaev and M. ruthenica (L.) Ledebour are allogamous, diploid (2n = 2x = 16) perennials from Asia, which have a remarkable ability to survive stress , but are genetically distant from cultivated alfalfa (M. sativa L., 2n = 4x = 32). In lieu of hybridization, potentially important genes from the Asian species could be transferred to alfalfa using transgenic techniques. Many plant disease resistance genes (R-genes) belong to the nucleotide binding site-leucine rich repeats (NBS-LRR) superfamily and have several highly conserved NBS region motifs, which can be used to identify them. Thus, genomic DNA of alfalfa and the two Asian species was primed with a degenerate forward P-loop primer paired with degenerate reverse primers designed for GLPLA, RNBS-C, or RNBS-D-non-Toll/Interleukin (RNBS-D-non-TIR) motifs. The P-Loop/GLPLA primer combination yielded the largest number of sequences without stop codons, and alfalfa had the greatest variation within the kinase and RNBS-C domains; however several kinase and RNBS-C sequences were unique to M. edgeworthii or M. ruthenica. Priming with the P-loop/RNBS-C primer pair resulted in some open reading frames, which apparently did not belong to the NBS-LRR superfamily. The only open reading frames for the P-loop/RNBS-D-non-TIR primer combination were for M. ruthenica. These non-TIR-type clones, and the only non-TIR-type clone from the P-loop/GLPLA PCR (alfalfa), had sequences that were markedly different from the TIR-type sequences. The RNBS-C region may be useful in identifying non-TIRtype R-gene analogs in future studies. Screening for unique R-gene analogs in genetically distant Medicago species may be a very effective way of isolating potential new R-genes for transfer to alfalfa. Key words: Alfalfa, disease resistance, kinase, Medicago edgeworthii, Medicago ruthenica, NBS-LRR, R-gene analog

scholarly journals Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1021-1031 ◽  
Author(s):  
Jianping Hu ◽  
Beth Anderson ◽  
Susan R Wessler
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Chromosome 1 ◽  
R Gene ◽  
R Genes ◽  
Helix Loop Helix ◽  
Isolation And Characterization ◽  
Undetermined Function ◽  
Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

scholarly journals Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives

2020 ◽  
Vol 22 (1) ◽  
pp. 313
Author(s):  
Aldrin Y. Cantila ◽  
Nur Shuhadah Mohd Saad ◽  
Junrey C. Amas ◽  
David Edwards ◽  
Jacqueline Batley
Keyword(s):  
Brassica Napus ◽  
Genetic Factors ◽  
Quantitative Resistance ◽  
Genetic Resistance ◽  
Leptosphaeria Maculans ◽  
Gene Interaction ◽  
R Gene ◽  
R Genes ◽  
Blackleg Resistance ◽  
Avr Gene

Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1961-1977
Author(s):  
Michelle A Graham ◽  
Laura Fredrick Marek ◽  
Randy C Shoemaker
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Developmental Stages ◽  
Gene Evolution ◽  
Pcr Amplification ◽  
Disease Resistance Genes ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

scholarly journals Multiyear Evaluation of the Durability of the Resistance Conferred by Ma and RMia Genes to Meloidogyne incognita in Prunus Under Controlled Conditions

2013 ◽  
Vol 103 (8) ◽  
pp. 833-840 ◽  
Author(s):  
Samira Khallouk ◽  
Roger Voisin ◽  
Ulysse Portier ◽  
Joël Polidori ◽  
Cyril Van Ghelder ◽  
...  
Keyword(s):  
Meloidogyne Incognita ◽  
Economic Losses ◽  
R Gene ◽  
R Genes ◽  
Tomato Plants ◽  
Controlled Conditions ◽  
Meloidogyne Spp ◽  
Resistance Breakdown ◽  
Susceptible Tomato ◽  
Prunus Spp

Root-knot nematodes (RKNs) (Meloidogyne spp.) are highly polyphagous pests that parasitize Prunus crops in Mediterranean climates. Breeding for RKN-resistant Prunus cultivars, as an alternative to the now-banned use of nematicides, is a real challenge, because the perennial nature of these trees increases the risk of resistance breakdown. The Ma plum resistance (R) gene, with a complete spectrum, and the RMia peach R gene, with a more restricted spectrum, both provide total control of Meloidogyne incognita, the model parthenogenetic species of the genus and the most important RKN in terms of economic losses. We investigated the durability of the resistance to this nematode conferred by these genes, comparing the results obtained with those for the tomato Mi-1 reference gene. In multiyear experiments, we applied a high and continuous nematode inoculum pressure by cultivating nematode-infested susceptible tomato plants with either Prunus accessions carrying Ma or RMia R genes, or with resistant tomato plants carrying the Mi-1 gene. Suitable conditions for Prunus development were achieved by carrying out the studies in a glasshouse, in controlled conditions allowing a short winter leaf fall and dormancy. We first assessed the plum accession ‘P.2175’, which is heterozygous for the Ma gene, in two successive 2-year evaluations, for resistance to two M. incognita isolates. Whatever the isolate used, no nematodes reproducing on P.2175 were detected, whereas galls and nematodes reproducing on tomato plants carrying Mi-1 were observed. In a second experiment with the most aggressive isolate, interspecific full-sib material (P.2175 × [‘Garfi’ almond × ‘Nemared’ peach]), carrying either Ma or RMia (from Nemared) or both (in the heterozygous state) or neither of these genes, was evaluated for 4 years. No virulent nematodes developed on Prunus spp. carrying R genes, whereas galling and virulent individuals were observed on Mi-1-resistant tomato plants. Thus, the resistance to M. incognita conferred by Ma in Prunus material in both a pure-plum and an interspecific genetic background, or by RMia in an interspecific background, appears to be durable, highlighting the value of these two genes for the creation of Prunus rootstock material.

Sign in / Sign up

Export Citation Format

Share Document