Genome-wide analysis and identification of genes related to potassium transporter families in rice (Oryza sativa L.)

Potassium (K+) is an important macronutrient and the most abundant cation in higher plants which plays a key role in various cellular processes. Its accumulation from soil and its distribution throughout diverse plant tissues is mediated by transporter proteins. In plants, different transport systems are known to be involved in the uptake and release of K+ from the cells. Though most of the information about the putative K+ transporters and their phylogenetic relationships is available in Arabidopsis, it is not the best model for plants with agronomic applications. Recent completion of rice genome sequencing project offered the opportunity to make an inventory of all putative K+ transporter proteins. More than 5% of the rice genome appears to encode membrane transport proteins. Unfortunately, several hundreds of putative transporter proteins have not yet been assigned to any families or subfamilies or functions. Therefore, phylogenetic relationships of many K+ transporters in rice are analyzed since rice is considered as a model plant because of its high degree of co-linearity with other cereals. Phylogenetic analysis of all K+ transporters in rice revealed that they fall into five major branches. Phylogenetic trees of each family define the evolutionary relationships of the members to each other. In each family, closely related isoforms and separate subfamilies existed, indicating possible redundancies and specialized functions. The HAK family is represented by 26 genes and formed the tightest and most distinct branch in the phylogenetic tree. Around 14 genes with conserved P-loop were found in K+ channel family out of which 11 genes belong to 1P/6TM (Shaker-type), and three genes to the 2P/4TM (ORK-type). On searching rice genome, it was found that nine genes belonged to Trk family. In rice, K+/H+ antiporter family is represented by a single gene. Comparative analysis of rice K+ channels with that of Arabidopsis, wheat and maize revealed that while cereals are closely related, Arabidopsis appeared quite distant from rice

Mining functional information from cereal genomes–the utility of expressed sequence tags

The vast number of expressed sequence tags (ESTs) generated from cereals with large genome size is an important complement method to the whole genome sequencing projects. As technology-driven revolution sweeps through, we are submerged in an avalanche of new information about genes and their function. To accomplish functional roles to the available ESTs, proper annotation of EST data is crucial, which could be achieved through the employment of tools of bioinformatics generated in the recent past. In this review, the critical steps involved in EST-based gene discovery and the employment of available web-based bioinformatic tools for annotation of ESTs is discussed. The current status of application of EST clones in the development of molecular markers in cereal species and utilizing ESTs as a resource for the construction of arrays is summarized as well. We also focus on large-scale gene expression data analysis methods and the challenges for computational biologists to extract functional information from such large-scale gene expression data

Development of transgenic tomato (Solanum lycoperscicum L.) by heterologous expression of osmotin-like protein (OLP) and chitinase (Chi11) genes for salt and drought stress tolerance

Tomato (Solanum lycopersicum L.) is the second most produced and consumed vegetable, next to potato. Pusa early dwarf (PED) variety of tomato is sensitive to salinity and drought which reduces the yield and fruit quality in tomato. In the present study, tomato transgenics were developed with osmotin-like protein (OLP) and chitinase (Chi11) genes via in vitro and in planta transformation methods. Transgene integration and transcript levels were confirmed by multiplex PCR, DNA blot, and multiplex reverse transcriptase PCR. Homozygous T2 transgenics, when evaluated for salt and drought stress, showed enhanced tolerance compared to wild-type plants. Transgenics showed enhanced root biomass under normal conditions. Transformants also displayed higher proline content, K+, relative water content, chlorophyll fluorescence, total biomass, vascular conductivity, and fruit yield compared to the wild-type plants under stress conditions. Co-immunoprecipitation revealed that Chi11 co-expresses with phosphofructokinase2 (PFK2), which may play a role in enhanced root biomass. qPCR analysis resulted in higher transcript levels of OLP, Chi11, and PFK2 in transgenics as compared to the wild-type plants

Genomics and molecular breeding in lesser explored pulse crops: Current trends and future opportunities

Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields

Overexpression of a plasma membrane bound Na+/H+ Antiporter-Like Protein (SbNHXLP) confers salt tolerance and improves fruit yield in tomato by maintaining Ion homeostasis

A Na+/H+ antiporter-like protein (NHXLP) was isolated from Sorghum bicolor L. (SbNHXLP) and validated by overexpressing in tomato for salt tolerance. Homozygous T2 transgenic lines when evaluated for salt tolerance, accumulated low Na+ and displayed enhanced salt tolerance compared to wild-type plants (WT). This is consistent with the amiloride binding assay of the protein. Transgenics exhibited higher accumulation of proline, K+, Ca2+, improved cambial conductivity, higher PSII, and antioxidative enzyme activities than WT. Fluorescence imaging results revealed lower Na+ and higher Ca2+ levels in transgenic roots. Co-immunoprecipitation experiments demonstrate that SbNHXLP interacts with a Solanum lycopersicum cation proton antiporter protein2 (SlCHX2). qRT-PCR results showed upregulation of SbNHXLP and SlCHX2 upon treatment with 200 mM NaCl and 100 mM potassium nitrate. SlCHX2 is known to be involved in K+ acquisition, and the interaction between these two proteins might help to accumulate more K+ ions, and thus maintain ion homeostasis. These results strongly suggest that plasma membrane bound SbNHXLP involves in Na+ exclusion, maintains ion homeostasis in transgenics in comparison with WT and alleviates NaCl stress

Genotyping-by-sequencing based intra-specific genetic map refines a ‘‘QTL-hotspot” region for drought tolerance in chickpea

To enhance the marker density in the “QTL-hotspot” region, harboring several QTLs for drought tolerance-related traits identified on linkage group 04 (CaLG04) in chickpea recombinant inbred line (RIL) mapping population ICC 4958 × ICC 1882, a genotyping-by-sequencing approach was adopted. In total, 6.24 Gb data from ICC 4958, 5.65 Gb data from ICC 1882 and 59.03 Gb data from RILs were generated, which identified 828 novel single-nucleotide polymorphisms (SNPs) for genetic mapping. Together with these new markers, a high-density intra-specific genetic map was developed that comprised 1,007 marker loci spanning a distance of 727.29 cM. QTL analysis using the extended genetic map along with precise phenotyping data for 20 traits collected over one to seven seasons identified 49 SNP markers in the “QTL-hotspot” region. These efforts have refined the “QTL-hotspot” region to 14 cM. In total, 164 main-effect QTLs including 24 novel QTLs were identified. In addition, 49 SNPs integrated in the “QTL-hotspot” region were converted into cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers which can be used in marker-assisted breeding