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 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.

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.

Td4IN2: A drought-responsive durum wheat (Triticum durum Desf.) gene coding for a resistance like protein with serine/threonine protein kinase, nucleotide binding site and leucine rich domains

2017 ◽  
Vol 120 ◽  
pp. 223-231 ◽  
Author(s):  
Patrizia Rampino ◽  
Mariarosaria De Pascali ◽  
Monica De Caroli ◽  
Andrea Luvisi ◽  
Luigi De Bellis ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Durum Wheat ◽  
Binding Site ◽  
Triticum Durum ◽  
Nucleotide Binding ◽  
Nucleotide Binding Site ◽  
Gene Coding ◽  
Triticum Durum Desf

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

Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

2021 ◽  
pp. 1-15
Author(s):  
Zengzhi Si ◽  
Yake Qiao ◽  
Kai Zhang ◽  
Zhixin Ji ◽  
Jinling Han
Keyword(s):  
Binding Site ◽  
Abiotic Stresses ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Nucleotide Binding ◽  
Regulatory Elements ◽  
Nucleotide Binding Site ◽  
Biotic And Abiotic Stresses ◽  
Encoding Genes

Sweetpotato, <i>Ipomoea batatas</i> (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that <i>IbNBS75</i>, <i>IbNBS219</i>, and <i>IbNBS256</i> respond to stem nematode infection; <i>Ib­NBS240</i>, <i>IbNBS90</i>, and <i>IbNBS80</i> respond to cold stress, while <i>IbNBS208</i>, <i>IbNBS71</i>, and <i>IbNBS159</i> respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

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