Syed M. Husain

Plant miRNAome and antiviral resistance: a retrospective view and prospective challenges.

MicroRNAs (miRNAs) are small regulatory RNAs that play a defining role in post-transcriptional gene silencing of eukaryotes by either mRNA cleavage or translational inhibition. Plant miRNAs have been implicated in innumerable growth and developmental processes that extend beyond their ability to respond to biotic and abiotic stresses. Active in an organism’s immune defence response, host miRNAs display a propensity to target viral genomes. During viral invasion, these virus-targeting miRNAs can be identified by their altered expression. All the while, pathogenic viruses, as a result of their long-term interaction with plants, have been evolving viral suppressors of RNA silencing (VSRs), as well as viral-encoded miRNAs as a counter-defence strategy. However, the gene silencing attribute of miRNAs has been ingeniously manipulated to down-regulate the expression of any gene of interest, including VSRs, in artificial miRNA (amiRNA)-based transgenics. Since we currently have a better understanding of the intricacies of miRNA-mediated gene regulation in plant–virus interactions, the majority of miRNAs manipulated to confer antiviral resistance to date are in plants. This review will share the insights gained from the studies of plant-virus combat and from the endeavour to manipulate miRNAs, including prospective challenges in the context of the evolutionary dynamics of the viral genome. Next generation sequencing technologies and bioinformatics analysis will further delineate the molecular details of host–virus interactions. The need for appropriate environmental risk assessment principles specific to amiRNA-based virus resistance is also discussed.

Molecular Diversity Analysis of Coat Protein Gene Encoded by Legume Begomoviruses and PCR Assay to Detect Yellow Mosaic Viruses Infecting Soybean in India

Aim: Coat protein (CP) genes encoded by Legume yellow mosaic viruses (LYMVs) were analysed to study molecular diversity and to devise effective PCR based assay to distinguish major Begomovirus species ( Mungbean yellow mosaic India virus and Mungbean yellow mosaic virus ) infecting soybean Design of the Study: All the known coat protein gene sequences encoded by begomoviruses causing yellow mosaic disease (YMD) in legumes were obtained from GenBank. YMD infected soybean leaf samples were collected from different parts of India during Kharif 2012 and species of virus infections identified using CP gene based primers in a PCR assay.

Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India

Molecular characterization and genetic diversity among 82 soybean accessions was carried out by using 44 simple sequence repeat (SSR) markers. Of the 44 SSR markers used, 40 markers were found polymorphic among 82 soybean accessions. These 40 polymorphic markers produced a total of 119 alleles, of which five were unique alleles and four alleles were rare. The allele number for each SSR locus varied between two to four with an average of 2.97 alleles per marker. Polymorphic information content values of SSRs ranged from 0.101 to 0.742 with an average of 0.477. Jaccard’s similarity coefficient was employed to study the molecular diversity of 82 soybean accessions. The pairwise genetic similarity among 82 soybean accessions varied from 0.28 to 0.90. The dendrogram constructed based on genetic similarities among 82 soybean accessions identified three major clusters. The majority of genotypes including four improved cultivars were grouped in a single subcluster IIIa of cluster III, indicating high genetic resemblance among soybean germplasm collection in India.

Viral Micro RNA Transcriptomics (miRNAomics)

In an era of small RNA (sRNA) transcriptomics, microRNAs (miRNAs) require little introduction. miRNAs are small non-coding RNAs (sncRNAs) that play vital role in post transcriptional gene silencing (PTGS) in nucleotide sequence dependent manner either by cleaving target mRNA or by repressing cognate mRNA translation. In plants, miRNAs have been implicated in regulating the expression of target mRNAs including transcriptional factors (TFs).

Physiological response to drought and Dehydration responsive transcripts(DRTs) from the leaves of water-deficit Indian soybean [Glycine max (L.)Merrill cv NRC7]

Drought is a major reason for reduced productivity in principal food crops including soybean. Development of drought tolerant varieties is imperative to tide over erratic rainfall conditions in Indian context. Here we studied molecular mechanism governing drought tolerance in Indian soybean cultivar NRC7 to identify drought responsive genic biomarkers. Drought associated physiological parameters like relative water content (RWC) and electrolytic leakage studies under water-deficit condition revealed very low water status in the stressed plants. In addition, membrane damage studies on electrolytic leakages revealed that the stressed plants exhibited greater membrane damage than control plants. Differential display RT-PCR (DD-RT-PCR) identified two drought responsive transcripts (gmDRT1 and gmDRT2) from the soybean cultivar NRC7. The identified transcripts were found to have sequence homology with dehydrin protein and ion ATPase transporters. These biomarkers identified for drought tolerance would also help in engineering drought tolerant soybean cultivars.

Advances in Soybean Genomics

Soybean is an agronomically important crop that is endowed with rich seed protein and oil. It enriches the soil by fixing nitrogen through symbiosis with bacteria. In addition to human consumption, soybean is a major protein source in animal feeds and is also becoming a major crop for biodiesel production. A major landmark in soybean genomics research was its draft genome sequence assembly (cultivar Williams 82) following whole-genome shot gun (WGS) approach. It revealed 950 Mb (megabases) of assembled and anchored sequence as against the predicted 1,115 Mb genome consequently representing 85 % of the whole genome. Development of comprehensive physical map employing chiefly Bacterial artificial chromosomes (BAC) and Binary large-insert BAC clones (BIBAC) have assisted in the whole genome sequencing venture and in targeted genetic marker development, accelerating positional cloning approaches along with the generation of rapid and robust EST maps. Comprehensive Expressed Sequence Tags (ESTs) repository and genome sequence of the crop have helped in sound integration of physical map with the genetic map. In order to perform genetic and genomic analysis various molecular markers like RFLP, RAPD, AFLP, SSR, SNP etc. have been employed on RIL or F2 populations. In addition the genome is typified with single nucleotide polymorphisms (SNPs) and its utilization in molecular breeding applications like QTL mapping, positional cloning and association mapping studies is gaining impetus. QTLs associated with foremost traits of agronomic interests including QTLs for Aphid resistance, Soybean Cyst Nematode (SCN) resistance among others have been identified and validated. Further molecular marker assisted QTL introgression and gene pyramiding for traits like enhanced seed protein concentration and Soybean Mosaic Virus (SMV) resistance, insect resistance etc. have been accomplished. Legume comparative genomics using orthologous genomic regions have addressed queries relating to Nucleotide binding-Leucine rich repeat (NB-LRRs) genes, polyploidy, and genome evolution. In the soybean functional genomics arena, in addition to the conventional assays involving qRT-PCR, Northern blotting, global gene expression analysis like Serial analysis of gene expression (SAGE), microarrays kind strategies are being widely employed. With the identification of micro RNAs (miRNAs) as ultimate gene effector molecules identification and characterization of novel miRNAs in soybean is gaining a momentum. Thus the rapid development of soybean genomics and transcriptomics has provided tremendous opportunity for the genetic improvement of soybean.