Journal Article•
Molecular cloning, characterization and transcriptional variability study of resistance gene candidates from wild Curcuma spp. for resistance against Pythium aphanidermatum.
TL;DR: A PCR mediated approach has been made using degenerate primers designed on conserved region (P-loop and GLPL) of the NBS domain from R-genes that provides the source for cloning analogous sequences called resistance gene candidates (RGCs) from three wild turmeric plants resistant or susceptible to Pythium aphanidermatum.
Abstract: The genetic base of preferred turmeric (Curcuma longa L.) genotypes has eroded due to their continuous domestication through exclusive vegetative routes thus making them highly susceptible to various pests and pathogens. Molecular cloning of resistance related sequences from wild genotypes can result in efficient turmeric improvement by evolving more effective resistance specificities compared to cultigens. In this study, a PCR mediated approach has been made using degenerate primers designed on conserved region (P-loop and GLPL) of the NBS domain from R-genes that provides the source for cloning analogous sequences called resistance gene candidates (RGCs) from three wild turmeric- Curcuma aromatica, Curcuma angustifolia and Curcuma zedoaria. Twenty-one wild turmeric RGCs were isolated and grouped into four phenetic classes. A strong amino acid identity ranging from 41 to 53% together with presence of internal conserved motifs provided evidence that the isolated RGCs belong to the non-toll interleukin receptor (non-TIR) NBS-LRR R-gene sub-family. Southern hybridization showed a high copy representation of turmeric RGCs. Expression variability of wild turmeric RGCs was analyzed through reverse transcription PCR in root tissues of the three wild turmeric plants resistant or susceptible to Pythium aphanidermatum. Cap12 and Can12 showed a constitutive expression in both resistant and susceptible plants of Curcuma aromatica and Curcuma angustifolia respectively while Czp11 expression was realized only in Pythium aphanidermatum resistant lines of Curcuma zedoaria as well as Curcuma longa L. This result can pave way towards the identification and characterization of a potential Pythium aphanidermatum resistance gene in turmeric.
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TL;DR: Structural and phylogenetic analyses grouped CzR1 within the non-TIR (homology to Toll/interleukin-1 receptors) subclass of NBS-LRR R-genes and semi quantitative RT-PCR analysis showed constitutive expression of CZR1 which gets significantly upregulated in response to infection by different strains of P. aphanidermatum.
18 citations
TL;DR: In this article , degenerate primers were used for cloning and characterization of NBS-LRR type resistant gene from betelvine against anthracnose disease, and a strong amino acid identity ranging from 90.38 to 97.75% and the presence of internal conserved motifs, provided evidence that the identified resistance gene analogs (RGAs) belong to the non-TIR NBS LRR class of R genes.
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TL;DR: A cluster analysis based on the deduced amino acid sequence and carried out on grape NBS-sequences, together with several analogous domains of known R-genes, classified grape sequences into three major groups and showed a clear-cut separation between resistant species and susceptible varieties.
Abstract: A set of NBS-containing sequences was isolated from genomic DNA of two grape species (Vitis amurensis and Vitis riparia) and characterised in a panel of Vitis genotypes carrying different levels of resistance against downy mildew and other diseases. A PCR-mediated approach made use of degenerate primers designed on conserved regions encoding known R-genes, and provided the source for cloning grape analogous sequences. Cloned sequences were digested with ten endonucleases and 29 out of 71 putative recombinant clones, which showed unique restriction patterns, were sequenced. Using a threshold value of 40% identity, at least 12 grape NBS-sequences had a high overall similarity with known R-genes, such as the Arabidopsis gene RPS5 and the tobacco gene N. The presence of internal conserved motifs provided evidence that sequences isolated from grape may belong to the NBS-LRR gene family. A cluster analysis based on the deduced amino acid sequence and carried out on grape NBS-sequences, together with several analogous domains of known R-genes, classified grape sequences into three major groups. A grape sequence of each group was used as a probe on Southern blots with digested genomic DNA from resistant and susceptible grapes. One of the NBS-containing probes showed a clear-cut separation between resistant species and susceptible varieties. This evidence makes the probe a candidate marker for disease resistance genes in Vitis germplasm.
75 citations
TL;DR: Genomic DNA sequences sharing homology with the NBS-LRR resistance genes were isolated and cloned from apricot using a PCR approach with degenerate primers designed from conserved regions ofThe NBS domain led to the identification of 43 unique amino acid sequences grouped into six families of resistance gene analogs (RGAs).
Abstract: Genomic DNA sequences sharing homology with the NBS-LRR (nucleotide binding site-leucine-rich repeat) resistance genes were isolated and cloned from apricot (Prunus armeniaca L.) using a PCR approach with degenerate primers designed from conserved regions of the NBS domain. Restriction digestion and sequence analyses of the amplified fragments led to the identification of 43 unique amino acid sequences grouped into six families of resistance gene analogs (RGAs). All of the RGAs identified belong to the Toll-Interleukin receptor (TIR) group of the plant disease resistance genes (R-genes). RGA-specific primers based on non-conserved regions of the NBS domain were developed from the consensus sequences of each RGA family. These primers were used to develop amplified fragment length polymorphism (AFLP)-RGA markers by means of an AFLP-modified procedure where one standard primer is substituted by an RGA-specific primer. Using this method, 27 polymorphic markers, six of which shared homology with the TIR class of the NBS-LRR R-genes, were obtained from 17 different primer combinations. Of these 27 markers, 16 mapped in an apricot genetic map previously constructed from the self-pollination of the cultivar Lito. The development of AFLP-RGA markers may prove to be useful for marker-assisted selection and map-based cloning of R-genes in apricot.
62 citations
"Molecular cloning, characterization..." refers background in this paper
...Many numbers of RGC classes have also been identified in other plant species such as six classes in apricot (Soriano et al., 2005), five classes in ginger (Nair and Thomas, 2007) and four classes in Kaempferia galanga (Joshi et al....
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...Many numbers of RGC classes have also been identified in other plant species such as six classes in apricot (Soriano et al., 2005), five classes in ginger (Nair and Thomas, 2007) and four classes in Kaempferia galanga (Joshi et al., 2012)....
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TL;DR: Sequence analysis revealed that RGA are abundant and highly diverged in the cotton genome and could be categorized into 10 distinct subfam families based on the similarities of their nucleotide sequences, and gene index analysis showed that each of the subfamilies is at a different stage of RGA family evolution.
Abstract: The nucleotide-binding site-leucine-rich repeat (NBS-LRR)-encoding gene family has attracted much research interest because approximately 75% of the plant disease resistance genes that have been cloned to date are from this gene family. We cloned the NBS-LRR-encoding genes from polyploid cotton by a polymerase chain reaction-based approach. A sample of 150 clones was selected from the NBS-LRR gene sequence library and was sequenced, and 61 resistance gene analogs (RGA) were identified. Sequence analysis revealed that RGA are abundant and highly diverged in the cotton genome and could be categorized into 10 distinct subfamilies based on the similarities of their nucleotide sequences. The numbers of members vary many fold among different subfamilies, and gene index analysis showed that each of the subfamilies is at a different stage of RGA family evolution. Genetic mapping of a selection of RGA indicates that the RGA reside on a limited number of the cotton chromosomes, with those from a single subfamily tending to cluster and two of the RGA loci being colocalized with the cotton bacterial blight resistance genes. The distribution of RGA between the two subgenomes A and D of cotton is uneven, with RGA being more abundant in the A subgenome than in the D subgenome. The data provide new insights into the organization and evolution of the NBS-LRR-encoding RGA family in polyploid plants.
61 citations
"Molecular cloning, characterization..." refers background in this paper
...…full-length resistance genes conferring both qualitative and quantitative resistance to different pathogens but also provide vital information about the organization, expression and evolution of R-genes (Pan et al., 2000; Bai et al., 2002; Meyers et al., 2003; Deng et al., 2003; He et al., 2004)....
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01 Nov 2013
TL;DR: Traditional Unani and pharmacological activities of this herb reported till date are explored, which are useful for the treatment of various gastrointestinal, pulmonary, cardiovascular and sexual disorders.
Abstract: Ginger (Zingiber officinale) belonging to the family Zingiberaceae is a perennial herb. It is widely distributed in tropical Asia. In India, it is cultivated mainly in Kerala, Andhra Pradesh, Uttar Pradesh, West Bengal and Maharashtra. It is one of the most common spices, which is in use since centuries for its versatile medicinal actions like antiemetic, stomachic, expectorant, anti-inflammatory, aphrodisiac etc in traditional system of medicine (Unani, Ayurveda, and Chinese medicine). It is useful for the treatment of various gastrointestinal, pulmonary, cardiovascular and sexual disorders. The phytochemical study of ginger showed the presence of many volatile oils and oleo-resins like gingerol, zingerone, zingiberol etc. Numerous experimental and clinical trials have proven ginger for its range of therapeutic activities such as antibacterial, antidiabetic, antiemetic, hypolipidaemic, hepatoprotective etc properties. The present article aims to explore traditional Unani and pharmacological activities of this herb reported till date.
54 citations
TL;DR: The isolation and characterization of RGCs from ginger and its wild relatives are reported for the first time, which will serve as a potential resource for future improvement of this important vegetatively propagated spice crop.
Abstract: Ginger (Zingiber officinale Rosc.) production is seriously affected by many fungal and bacterial diseases to which no resistant source is available in the cultivated germplasm. Degenerate primers based on conserved motifs of plant resistance (R) genes were used to isolate analogous sequences called resistance gene candidates (RGCs) from cultivated and wild Zingiber species. Cloning and sequence characterization identified 42 Zingiber RGCs, which could be classified into five classes following phenetic analysis. Deduced amino acid sequences of Zingiber RGCs showed strong identity, ranging from 16 to 43%, to non-toll interleukin receptor (non-TIR) R-gene subfamily. Non-synonymous to synonymous nucleotide substitution (dN/dS) ratio for the NBS domains of Zingiber RGC classes showed evidence of purifying selection. RT-PCR analysis with 15 Zingiber RGC-specific primers demonstrated 8 of the 15 Zingiber RGCs to be expressed. The present study reports for the first time the isolation and characterization of RGCs from ginger and its wild relatives, which will serve as a potential resource for future improvement of this important vegetatively propagated spice crop.
52 citations
"Molecular cloning, characterization..." refers background or methods or result in this paper
...Curcuma NBS clone GenBank protein accession from Zingiberaceae showing the highest similarity Amino acid identity (...
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..., 2000) ginger (Nair and Thomas, 2007) and alfalfa (Cordero and Skinner, 2002) showed that 75%, 49%, and 55% of sequence characterized were RGCs respectively....
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..., 2005), five classes in ginger (Nair and Thomas, 2007) and four classes in Kaempferia galanga (Joshi et al....
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...No TIR-RGCs were obtained in wild Curcuma genotypes in the present study, which is in accordance with the earlier reports on the absence of such groups among the Rgenes/RGCs of Zingiberaceae (Nair and Thomas, 2007; Joshi et al., 2010; Joshi et al., 2012)....
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...This strategy have been successfully employed in many plant species for the isolation of homologous resistance sequences by heterologous amplification (Leister et al., 1996; Kanazin et al., 1996; Mago et al., 1999; Xiao et al., 2006; Nair and Thomas, 2007)....
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