Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species

Yadav, Chandra Bhan; Muthamilarasan, Mehanathan; Pandey, Garima; Khan, Yusuf

doi:10.1007/s11032-014-0137-9

Cited by 67 publications

(60 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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

View full text Add to dashboard Cite

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.

show abstract

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

View full text Add to dashboard Cite

show abstract

“…Most of the above candidate genes from millet crops are transcription factors (TFs) as they can regulate the expression of downstream stress responsive genes and thus play important role in imparting stress tolerance. Of note, several candidate TFs including AP2/ERFs, NAC, C 2 H 2 zinc finger and MYB were analyzed in foxtail millet to identify suitable candidate genes which can be used for further characterization using transgene-based approaches towards engineering stress resistance (Lata et al, 2014;Puranik et al, 2013;Muthamilarasan et al, 2014b;Muthamilarasan et al, 2014c). In addition to TFs, several stress-responsive genes such as WD40, Dicer-like (DCL), Argonaute (AGO) and RNAdependent RNA polymerases (RDR) have been studied in foxtail millet to identify potential candidate genes for downstream characterization (Mishra et al, 2014;Yadav et al, 2014c).…”

Section: Functional Genomicsmentioning

confidence: 99%

“…Extensive genome-wide investigation and expression profiling studies of various TF families such as AP2/ERFs, NAC, C 2 H 2 zinc finger and MYB (Lata et al, 2014;Puranik et al, 2013;Muthamilarasan et al, 2014b;Muthamilarasan et al, 2014c) and stress responsive genes such as WD40, DCL, AGO and RDR polymerases and ALDH (Mishra et al, 2014;Yadav et al, 2014c;Zhu et al, 2014) have also been carried out in foxtail millet for analyzing gene families implicated in stress tolerance, identifying suitable candidate genes and delineating gene regulatory networks and molecular cross talks for abiotic stress responses.…”

Section: Foxtail Milletmentioning

confidence: 99%

“…Several other researchers also reported on identification of several microsatellite repeat motifs (Pandey et al, 2013;Zhang et al, 2014), eSSRs , and transposable elements (TE)-based markers (Yadav et al, 2014a) using Setaria genome sequence data. In another interesting study, 176 microRNA (miRNA)-based molecular markers have been developed (Yadav et al, 2014b) from a set of 335 mature miRNAs (Khan et al, 2014). SNPs are single base substitution, insertion or deletion commonly found in a population and have recently been developed into powerful molecular markers.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Advances in Omics for Enhancing Abiotic Stress Tolerance in Millets

Lata¹

2015

Proceedings of the Indian National Science Academy

View full text Add to dashboard Cite

Millets are small-seeded annual cereal crops which are mostly grown in marginal soils of arid and semi-arid regions, and consequently have to face several abiotic constraints that lead to reduction in the yield. Advanced biotechnological applications, particularly 'omics' approaches could serve as the most immediate and prospective strategies for improving abiotic stress tolerance in millet crops. Omics approaches lead to understand the mechanism of stress response and tolerance at molecular level through insights into gene, protein or metabolite profile and their phenotypic effects. Among millet crops, foxtail millet has been more intensively studied and characterized under abiotic stress conditions owing to its small genome size and diploidy. Genome-wide investigation and expression profiling studies have been extensively carried out in foxtail millet. However proteomic and metabolomic studies in response to abiotic stress in millets are still very limited. Some of the major quantitative trait loci (QTLs) controlling abiotic stress tolerance in millets have also been identified and mapped as for instance a major QTL for terminal drought tolerance in pearl millet and a major QTL for dehydration tolerance in foxtail millet. Gene manipulation for enhanced abiotic stress tolerance involving regulatory genes have proved to be more useful than using single or multiple stress responsive genes. Consequently, the recent advances in 'omics' technologies and accessibility to the genome sequences extend huge potential to enhance stress tolerance of millets. This review thus attempts to summarize various omics strategies and their applications in abiotic stress research in important millet crops namely foxtail millet, pearl millet and finger millet.

show abstract

“…Khan et al (2014a,b) constructed Foxtail millet miRNA Database (FmMiRNADb: http://59.163.192.91/FmMiRNADb/index.html) which provides miRNA marker information and also studied expression profiling under diverse abiotic stress conditions. Novel microRNAbased genetic markers in Foxtail millet has been constructed which promises the genotyping applications at crop improvement (Yadav et al, 2014). Owing to the important roles played by miRNAs in gene regulatory networks, it is important to identify the miRNAs in Finger millet (Eleusine coracana L.), a cereal grass grown mostly for its grain and belongs to the family Poaceae.…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

Usha

Jyothi

Sharadamma

et al. 2015

Gene

View full text Add to dashboard Cite

a b s t r a c t a r t i c l e i n f oMicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development.

show abstract

Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species

Cited by 67 publications

References 18 publications

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

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

Advances in Omics for Enhancing Abiotic Stress Tolerance in Millets

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

Contact Info

Product

Resources

About