Genome-wide identification, characterization, and expression profiling of SPX gene family in wheat.

The SPX gene family, ubiquitous in all vascular plants, plays a critical role in plant development and growth as well as in response to phosphorus stress. Based on genomic census, 46 TaSPX genes were identified in the wheat genome. All of them are evenly distributed on 13 of the 21 wheat chromosomes and chromosome 7A contains the largest members. As many as 57 gene specific SSRs were discovered among genomic sequences of identified TaSPXs. MicroRNA target analysis revealed that TaSPX genes were targeted by 9 different miRNAs including tae-miR1120a, tae-miR1120b-3p, tae-miR1120c-5p, tae-miR1122b-3p, tae-miR1122c-3p, tae-miR1130a, tae-miR1130b-3p, tae-miR1137a, and tae-miR1137b-5p. Expression profiles derived from transcriptome data and real-time quantitative PCR revealed that TaSPX genes were significantly induced by Pi starvation. The modeled 3D structure of wheat SPX proteins shared high level of homology with template structures, providing information to understand their functions at proteomic level. We have also refined the modeled 3D structures on 10 ns using molecular dynamics simulations for conformational stability. The discovered members of SPX gene family and their targeting miRNAs may provide resource for genetic improvement and promote P use efficiency in cereals.

Functional and structural insights into candidate genes associated with nitrogen and phosphorus nutrition in wheat (Triticum aestivum L.).

An extensive bioinformatics based study has been performed to gain insight into the structural and functional aspects of candidate genes involved in Nitrogen and Phosphorus nutrition in wheat. Based on our study, 37 N and P nutrition candidate genes were identified (24 NUE and 13 inorganic phosphate transporters) in wheat genome. 23 gene specific novel microsatellites were discovered using genomic sequences of identified N and P nutrition genes. We also identified the microRNAs that target ten candidate genes including TaAS1-3A, TaAS1-3D, TaASN2-1A, TaASN2-1B, TaANR1-6A, TaANR1-6B, TaNRT2.4-6A, TaNRT2.6-6A, TaNRT2.6-6B and TaPHT1.5-5B. Expression profiling of identified genes showed altered expression under N and P starvation. The proposed 3D structure of wheat N and P nutrition proteins shared high level homology with known experimental structures providing information to understand their functions at the biochemical level. Molecular dynamics simulations of refined modeled structures of wheat N and P nutrition proteins show conformational stability. The identified N and P nutrition candidate genes and their targeting miRNAs may provide resources for the genetic improvement and promote N and P use efficiency. Our study provides first-hand structural prospective of N and P nutrition candidate genes towards development of wheat varieties resilient to N and P stress.

---A web resource for nutrient use efficiency-related genes, quantitative trait loci and microRNAs in important cereals and model plants.

Cereals are key contributors to global food security. Genes involved in the uptake (transport), assimilation and utilization of macro- and micronutrients are responsible for the presence of these nutrients in grain and straw. Although many genomic databases for cereals are available, there is currently no cohesive web resource of manually curated nutrient use efficiency (NtUE)-related genes and quantitative trait loci (QTLs). In this study, we present a web-resource containing information on NtUE-related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops (wheat ( Triticum aestivum), rice ( Oryza sativa), maize ( Zea mays), barley ( Hordeum vulgare)), two alien species related to wheat ( Triticum urartu and Aegilops tauschii), and two model species ( Brachypodium distachyon and Arabidopsis thaliana). Gene annotations integrated in the current web resource were manually curated from the existing databases and the available literature. The primary goal of developing this web resource is to provide descriptions of the NtUE-related genes and their functional annotation. MicroRNAs targeting some of the NtUE related genes and the QTLs for NtUE-related traits are also included. The genomic information embedded in the web resource should help users to search for the desired information.

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress.