Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa)

Mondal, Tapan Kumar; Ganie, Showkat Ahmad

doi:10.1016/j.gene.2013.11.033

Cited by 99 publications

(84 citation statements)

References 33 publications

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“…Based on published literature (Gregorio et al 1997;Mohammadi-Nejad et al 2008;Islam et al 2012;Mondal and Ganie 2014) as well as preliminary testing, we selected eight highly polymorphic markers that are tightly linked with Saltol QTL for using in the present study. The details of the primers, retrieved from Gramene (Jaiswal et al 2006), are given in Table 1.…”

Section: Markers Used For Genotypingmentioning

confidence: 99%

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Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.

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Section: Markers Used For Genotypingmentioning

confidence: 99%

“…PCR amplification and the data analysis were performed according to Mondal and Ganie (2014). Haplotype analysis was conducted according to Liu and Anderson (2003) with four most polymorphic SSR markers, i.e., RM8094, RM3412, RM562 and RM1287 using FL478 genotype as a reference.…”

Section: Pcr Amplification and Data Analysismentioning

confidence: 99%

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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“…This feature distinguishes miRNAs from other sRNAs, such as small interfering RNAs, which originate from double-stranded RNAs derived from the inter-molecular hybridization of two complementary RNA molecules (Bej and Basak, 2014;Barvkar et al, 2013;Gursanscky et al, 2011). The application of miRNA as a novel type of genetic markers has been developed for genotyping applications in foxtail millet (Setaria italica L.) and related grass species (Yadav et al, 2014), in combination with the SSR markers in Oryza sativa (Mondal and Ganie, 2014) with the aim to identify the salt responsive miRNA-SSR markers and in the genotyping of Brassica species (Fu et al, 2013). The application of those markers based on miRNA has not been used in genotyping within a single plant species.…”

Section: Introductionmentioning

confidence: 99%

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

Ražná¹,

Hlavačková

Bežo

et al. 2015

Acta fytotechn zootechn

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Two types of molecular markers based on randomly amplified DNA by RAPD-based assay and amplified microRNA by miRNA-based assay were applied for the genotyping of five accessions of Silybum marianum (L.) Gaertn. It was also verified the effectiveness of the isolation of genomic DNA by three commercially available isolation kits and two similar complex methods and their applicability for this medicinal herb. None of the commercial isolation kits provided the genomic DNA of sufficient quality and quantity. Applied originally designed CTAB method and modified CTAB method for purpose of DNA isolation from medicinal plants allowed to isolate DNA of required quality and of sufficient yield. RAPD-based DNA fingerprints, allowed to distinguish the individual genotypes of Silybum marianum. MicroRNA-based markers showed the cross-genera transferability potential and displayed sufficient level of polymorphism. Both types of molecular markers could be used as suitable tool for genotyping of milk thistle. However, because of the size of miRNA amplicons is the efficiency of miRNA-based markers PCR amplifications preferred and consequently less DNA quality-dependent which may be advantageous in view of the content of undesirable secondary metabolites in medicinal plants.

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“…Although these findings contributed greatly to identify a large source of stress-related miRNAs, further efforts are needed to advance current understanding of the interrelated molecular pathways controlling miRNA biogenesis and action (Borges and Martienssen, 2015;Reis et al, 2015). Progress in this direction was made recently by the identification of stressresponsive regulatory sequences located within the MIR gene promoters (Devi et al, 2013) and by the discovery of salt stress-responsive miR-SSR markers (Mondal and Ganie, 2014).…”

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confidence: 99%

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

et al. 2017

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Grapevine (Vitis vinifera) is routinely grafted, and rootstocks inducing drought tolerance represent a source for adapting vineyards to climate change in temperate areas. Our goal was to investigate drought stress effects on microRNA (miRNA) abundance in a drought-resistant grapevine rootstock, M4 (Vitis vinifera 3 Vitis berlandieri), compared with a commercial cultivar, Cabernet Sauvignon, using their autografts and reciprocal grafts. RNA extracted from roots and leaves of droughted and irrigated plants of different graft combinations was used to prepare cDNA libraries for small RNA sequencing and to analyze miRNAs by quantitative real-time polymerase chain reaction (RT-qPCR). Measurements of leaf water potential, leaf gas exchange, and root hydraulic conductance attested that, under irrigation, M4 reduced water loss in comparison with cultivar Cabernet Sauvignon mostly through nonhydraulic, root-specific mechanisms. Under drought, stomatal conductance decreased at similar levels in the two genotypes. Small RNA sequencing allowed the identification of 70 conserved miRNAs and the prediction of 28 novel miRNAs. Different accumulation trends of miRNAs, observed upon drought and in different genotypes and organs, were confirmed by RT-qPCR. Corresponding target transcripts, predicted in silico and validated by RT-qPCR, often showed opposite expression profiles than the related miRNAs. Drought effects on miRNA abundance differed between the two genotypes. Furthermore, the concentration of drought-responsive miRNAs in each genotype was affected by reciprocal grafting, suggesting either the movement of signals inducing miRNA expression in the graft partner or, possibly, miRNA transport between scion and rootstock. These results open new perspectives in the selection of rootstocks for improving grapevine adaptation to drought.

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Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa)

Cited by 99 publications

References 33 publications

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

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