Genetic variation within and between winter wheat genotypes from Turkey, Kazakhstan, and Europe as determined by nucleotide-binding-site profiling

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 419-430 ◽  
Author(s):  
Muge Sayar-Turet ◽  
Susanne Dreisigacker ◽  
Hans-J. Braun ◽  
Arne Hede ◽  
Ruth MacCormack ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Winter Wheat ◽  
Binding Site ◽  
Nucleotide Binding ◽  
Wheat Breeding ◽  
Nucleotide Binding Site ◽  
R Genes ◽  
Breeding Programs ◽  
Wheat Genotypes ◽  
Nbs Profiling

The genetic diversity within wheat breeding programs across Turkey and Kazakhstan was compared with a selection of European cultivars that represented the genetic diversity across eight European countries and six decades of wheat breeding. To focus the measure of genetic diversity on that relevant to disease-resistant phenotypes, nucleotide-binding-site (NBS) profiling was used to detect polymorphisms associated with the NBS motifs found within the NBS – leucine-rich repeat (LRR) class of resistance (R) genes. Cereal-specific NBS primers, designed specifically to the conserved NBS motifs found within cereal R-genes, provided distinct NBS profiles. Although the genetic diversity associated with NBS motifs was only slightly higher within the Eastern wheat genotypes, the NBS profiles produced by Eastern and European wheat lines differed considerably. Structure analysis divided the wheat genotypes into four groups, which compared well with the origin of the wheat genotypes. The highest levels of genetic diversity were seen for the wheat genotypes from the Genetic Resource Collection held in Ankara, Turkey, as wheat genotypes within breeding programs were genetically more similar. The wheat genotypes from Kazakhstan were the most similar to the European cultivars, reflecting the significant number of eastern European cultivars used in the breeding program in Kazakhstan. In general, the NBS profiles suggested that NBS–LRR R-gene usage in winter wheat breeding in Turkey and Kazakhstan differed from that deployed in European cultivars.

scholarly journals Consequences of geographical habitats on population structure and genetic diversity in Campanula spp.

2010 ◽  
Vol 1 (1) ◽  
pp. 5 ◽  
Author(s):  
Matteo Caser ◽  
Valentina Scariot ◽  
Paul Arens
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Binding Site ◽  
Geographical Location ◽  
Nucleotide Binding ◽  
Nonparametric Test ◽  
Nucleotide Binding Site ◽  
Gene Profiling ◽  
R Gene ◽  
Nbs Profiling

Characterization of populations by means of DNA techniques provides a tool for precise identification and a quantitative estimate of genetic diversity, crucial in evaluation of genetic fragmentation within and among populations. NBS profiling are PCR-based approaches that sample genetic variation in resistance genes (R-gene), and R gene analogs (RGA). To date, myb patterns have not been used for evaluating genetic diversity in other species. NBS primers are homologous to the conserved sequences in the Nucleotide-Binding-Site of the NBS-LRR class of R-genes. A total of 12 populations from five Campanula species (C. barbata L., C. latifolia L., C. rapunculoides L., C. spicata L. and C. trachelium L.), autochthonous of the West Italian Alps, were genotyped via nucleotide-binding site (NBS) and myb gene profiling. The selected markers produced a total of 361 bands, showing high levels of polymorphism. Genetic diversity among and within species and population structure was evaluated by different statistical analyses performed using TREECON software, Mantel Nonparametric Test, NTSYS package, AMOVA and STRUCTURE. The correlation between genetic variability and geographical location suggests that the five Campanula species have been subjected to long-term evolutionary processes consistent with the natural fragmentation of continuous mountains areas.

Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat

Genome ◽  
2006 ◽  
Vol 49 (11) ◽  
pp. 1473-1480 ◽  
Author(s):  
Paola Mantovani ◽  
Gerard van der Linden ◽  
Marco Maccaferri ◽  
Maria Corinna Sanguineti ◽  
Roberto Tuberosa
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Binding Site ◽  
Effective Means ◽  
Restriction Enzymes ◽  
Nucleotide Binding ◽  
Genetic Distances ◽  
Nucleotide Binding Site ◽  
Aflp Data ◽  
Nbs Profiling

Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a PCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme–primer combination was equal to 23.8 ± 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.

scholarly journals Isolation and Characterization of Nucleotide-Binding Site Resistance Gene Homologues in Common Bean (Phaseolus vulgaris)

2013 ◽  
Vol 103 (2) ◽  
pp. 156-168 ◽  
Author(s):  
Luz N. Garzón ◽  
Oscar A. Oliveros ◽  
Benjamin Rosen ◽  
Gustavo A. Ligarreto ◽  
Douglas R. Cook ◽  
...  
Keyword(s):  
Common Bean ◽  
Binding Site ◽  
Resistance Gene ◽  
Focal Point ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
R Genes ◽  
Degenerate Primers ◽  
Model Legume ◽  
Isolation And Characterization

Common bean production is constrained by many fungal, viral, and bacterial pathogens. Thus, the identification of resistance (R) genes is an important focal point of common bean research. The main goal of our study was to identify resistance gene homologues (RGH) in the crop, using degenerate primers designed from conserved sequences in the nucleotide-binding site (NBS) domains of R-genes from the model legume Medicago truncatula. Total DNA of the Andean common bean genotype G19833 was used for amplification of over 500 primer combinations. Sequencing of amplicons showed that 403 cloned fragments had uninterrupted open reading frames and were considered representative of functional RGH genes. The sequences were grouped at two levels of nucleotide identity (90 and 80%) and representative sequences of each group were used for phylogenetic analyses. The RGH sequence diversity of common bean was divided into TIR and non-TIR families, each with different clusters. The TIR sequences grouped into 14 clades while non-TIR sequences grouped into seven clades. Pairwise comparisons showed purifying selection, although some sequences may have been the result of diversifying selection. Knowledge about RGH genes in common bean can allow the design of molecular markers for pyramiding of resistance genes against various pathogens.

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.

Disease resistance gene analogs as candidates for QTLs involved in pepper-pathogen interactions

Genome ◽  
1999 ◽  
Vol 42 (6) ◽  
pp. 1100-1110 ◽  
Author(s):  
S Pflieger ◽  
V Lefebvre ◽  
C Caranta ◽  
A Blattes ◽  
B Goffinet ◽  
...  
Keyword(s):  
Binding Site ◽  
Quantitative Resistance ◽  
Nucleotide Binding ◽  
Kinase Domain ◽  
Nucleotide Binding Site ◽  
R Gene ◽  
R Genes ◽  
Unique Region ◽  
Hydrophobic Domain ◽  
Trait Loci

Whereas resistance genes (R-genes) governing qualitative resistance have been isolated and characterized, the biological roles of genes governing quantitative resistance (quantitave trait loci, QTLs) are still unknown. We hypothesized that genes at QTLs could share homologies with cloned R-genes. We used a PCR-based approach to isolate R-gene analogs (RGAs) with consensus primers corresponding with conserved domains of cloned R-genes: (i) the nucleotide binding site (NBS) and hydrophobic domain, and (ii) the kinase domain. PCR-amplified fragments were sequenced and mapped on a pepper intraspecific map. NBS-containing sequences of pepper, most similar to the N gene of tobacco, were classified into seven families and all mapped in a unique region covering 64 cM on the Noir chromosome. Kinase domain containing sequences and cloned R-gene homologs (Pto, Fen, Cf-2) were mapped on four different linkage groups. A QTL involved in partial resistance to cucumber mosaic virus (CMV) with an additive effect was closely linked or allelic to one NBS-type family. QTLs with epistatic effects were also detected at several RGA loci. The colocalizations between NBS-containing sequences and resistance QTLs suggest that the mechanisms of qualitative and quantitative resistance may be similar in some cases.Key words: Capsicum annuum, candidate gene, nucleotide binding site, kinase domain, quantitative trait loci.

Assessment of Genetic Diversity in Zingiberaceae Through Nucleotide Binding Site-Based Motif-Directed Profiling

2012 ◽  
Vol 50 (7-8) ◽  
pp. 642-656 ◽  
Author(s):  
Raj Kumar Joshi ◽  
Sujata Mohanty ◽  
Basudeba Kar ◽  
Sanghamitra Nayak
Keyword(s):  
Genetic Diversity ◽  
Binding Site ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site

Computational Identification of MicroRNA-targeted Nucleotide-Binding Site-Leucine-Rich Repeat Genes in Plants

BIO-PROTOCOL ◽  
2015 ◽  
Vol 5 (21) ◽  
Author(s):  
Zhu-Qing Shao ◽  
Yan-Mei Zhang ◽  
Bin Wang ◽  
Jian-Qun Chen
Keyword(s):  
Binding Site ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Leucine Rich Repeat ◽  
Computational Identification
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