Ravish Chatrath

Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops

Wheat yields globally will depend increasingly on good management to conserve rainfall and new varieties that use water efficiently for grain production. Here we propose an approach for developing new varieties to make better use of deep stored water. We focus on water-limited wheat production in the summer-dominant rainfall regions of India and Australia, but the approach is generally applicable to other environments and root-based constraints. Use of stored deep water is valuable because it is more predictable than variable in-season rainfall and can be measured prior to sowing. Further, this moisture is converted into grain with twice the efficiently of in-season rainfall since it is taken up later in crop growth during the grain-filling period when the roots reach deeper layers. We propose that wheat varieties with a deeper root system, a redistribution of branch root density from the surface to depth, and with greater radial hydraulic conductivity at depth would have higher yields in rainfed systems where crops rely on deep water for grain fill. Developing selection systems for mature root system traits is challenging as there are limited high-throughput phenotyping methods for roots in the field, and there is a risk that traits selected in the lab on young plants will not translate into mature root system traits in the field. We give an example of a breeding programme that combines laboratory and field phenotyping with proof of concept evaluation of the trait at the beginning of the selection programme. This would greatly enhance confidence in a high-throughput laboratory or field screen, and avoid investment in screens without yield value. This approach requires careful selection of field sites and years that allow expression of deep roots and increased yield. It also requires careful selection and crossing of germplasm to allow comparison of root expression among genotypes that are similar for other traits, especially flowering time and disease and toxicity resistances. Such a programme with field and laboratory evaluation at the outset will speed up delivery of varieties with improved root systems for higher yield.

Insights of interaction between small and large subunits of ADP-glucose pyrophosphorylase from bread wheat (Triticum aestivum L.)

Lack of knowledge of three dimensional structures of small and large subunits of ADP- glucose pyrophosphorylase (AGPase) in wheat has hindered efforts to understand the binding specifities of substrate and catalytic mechanism. Thus, to understand the structure activity relationship, 3D structures were built by homology modelling based on crystal structure of potato tuber ADP-glucose pyrophosphorylase. Selected models were refined by energy minimization and further validated by Procheck and Prosa-web analysis. Ramachandran plot showed that overall main chain and side chain parameters are favourable. Moreover, Z-score of the models from Prosa-web analysis gave the conformation that they are in the range of the template. Interaction analysis depicts the involvement of six amino acids in hydrogen bonding (AGP-SThr422-AGP-LMet138, AGP- SArg420-AGP-LGly47, AGP-SSer259-AGP-LSer306, AGP-SGlu241-AGP-LIle311, AGPSGln113- AGP-LGlu286 and AGP-SGln70-AGP-LLys291). Fifteen amino acids of small subunit were able to make hydrophobic contacts with seventeen amino acids of large subunit. Furthermore, decrease in the solvent accessible surface area in the amino acids involved in interaction were also reported. All the distances were formed in between 2.27 to 3.78Å. The present study focussed on heterodimeric structure of (AGPase). This predicted complex not only enhance our understanding of the interaction mechanism between these subunits (AGP-L and AGP-S) but also enable to further study to obtain better variants of this enzyme for the improvement of the plant yield.

Evaluation of root characteristics, canopy temperature depression and stay green trait in relation to grain yield in wheat under early and late sown conditions

Forty wheat varieties was evaluated for grain yield in the field for two successive crop seasons (2009–10 and 2010–11), with 2 dates of sowing, viz., early (last week of October) and late (first week of December). Based on the yield potential, five high yielding and five low yielding varieties were selected to study the relationship between grain yield and root characteristics along with canopy temperature depression (CTD) and flag leaf drying under early and late sown conditions. It was observed that under early sown restricted irrigation conditions the high yielding varieties utilized energy in increasing the root length and root density to deeper soil depths instead of accumulating root weight, compared to low yielding varieties. In contrast, under late sown condition, the high yielding varieties had more root weight and density in their upper soil depths, compared to low yielding varieties. Hence, it can be suggested to select wheat varieties with high root density and more root length in the lower depths of the soil for rainfed/restricted irrigation conditions to mitigate the early heat effects, and varieties having high root density and more root length in the upper layers of the soil for late sown conditions to tolerate the late or terminal heat. Further, high CTD scores at 1st stage (vegetative) and high leaf score at fourth stage (post flowering) were found to be important selection parameters, which help in reducing the evapo-transpiration and increase 1000 grain weight under early sown limited irrigation condition, and thereby increase the grain yield; whereas, CTD at 3rd stage (flowering stage) contribute to maintain the stay green trait for longer period and reduce the loss due to evapo-transpiration and in-turn increase the grain yield under late sown conditions. These traits can be used as selection tools for physiological breeding programme to increase the production and productivity of wheat.

Mining and survey of simple sequence repeats in wheat rust Puccinia sp

The abundance and inherent potential for extensive allelic variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in eukaryotes. In this study, we analyzed and compared the abundance and organisation of SSR in the genome of two important fungal pathogens of wheat, brown or leaf rust (Puccinia triticina) and black or stem rust (Puccinia graminis f. sp. tritici). P. triticina genome with two fold genome size as compared to P. graminis tritici has lower relative abundance and SSR density. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of dinucleotide followed by trinucleotide repeats. More than two-hundred different types of repeat motifs were observed in the genomes. The longest SSR motifs varied in both genomes and some of the repeat motifs are found in higher frequency. The information about survey of relative abundance, relative density, length and frequency of different repeat motifs in Puccinia sp. will be useful for developing SSR markers that could find several applications in analysis of fungal genome such as genetic diversity, population genetics, race identification and acquisition of new virulence.

Modeling and phylogeny analysis of bread wheat MnSOD.

Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn(III) at the active site. Therefore, it is of interest to study MnSOD from bread wheat (a grain crop). However, a structure model is not yet solved for bread wheat MnSOD. Hence, we describe the structure model of bread wheat MnSOD developed using homology model. The model provides molecular insight to metal binding molecular function towards the understanding of oxidative stress resistance in plants. The distinction of bread wheat (a monocot) MnSOD from dicots is also shown using phylogenetic analysis.

Comparative computational analysis of ADP Glucose Pyrophosphorylase in plants.

ADP-glucose pyrophosphorylase (AGPase), a key enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Ample evidence has shown that the AGPase catalyzes the rate limiting step in starch biosynthesis in higher plants. In this study, we compiled detailed comparative information about ADP glucose pyrophosphorylase in selected plants by analyzing their structural features e.g. amino acid content, physico-chemical properties, secondary structural features and phylogenetic classification. Functional analysis of these proteins includes identification of important 10 to 20 amino acids long motifs arise because specific residues and regions proved to be important for the biological function of a group of proteins, which are conserved in both structure and sequence during evolution. Phylogenetic analysis depicts two main clusters. Cluster I encompasses large subunits (LS) while cluster II contains small subunits (SS).

Genetic dissection of grain zinc concentration in spring wheat for mainstreaming biofortification in CIMMYT wheat breeding

Wheat is an important staple that acts as a primary source of dietary energy, protein, and essential micronutrients such as iron (Fe) and zinc (Zn) for the world’s population. Approximately two billion people suffer from micronutrient deficiency, thus breeders have crossed high Zn progenitors such as synthetic hexaploid wheat, T. dicoccum, T. spelta, and landraces to generate wheat varieties with competitive yield and enhanced grain Zn that are being adopted by farmers in South Asia. Here we report a genome-wide association study (GWAS) using the wheat Illumina iSelect 90 K Infinitum SNP array to characterize grain Zn concentrations in 330 bread wheat lines. Grain Zn phenotype of this HarvestPlus Association Mapping (HPAM) panel was evaluated across a range of environments in India and Mexico. GWAS analysis revealed 39 marker-trait associations for grain Zn. Two larger effect QTL regions were found on chromosomes 2 and 7. Candidate genes (among them zinc finger motif of transcription-factors and metal-ion binding genes) were associated with the QTL. The linked markers and associated candidate genes identified in this study are being validated in new biparental mapping populations for marker-assisted breeding.

Framework for doubling the income of wheat producers’ by 2022: trends, pathway and drivers

Indian agriculture is at crossroads owing to the agrarian distress which manifests itself in various forms affecting farmers’ welfare. The present paper tracks the trend in wheat producers’ income between 2006–07 and 2013–14 followed by suggesting framework for doubling farmers’ income (DFI) by 2022. Convergence between science & technology, institutions and policy with emphasis on potential drivers like productivity enhancement through improved genotypes coupled with adoption of cost reduction technologies, diversification, irrigation, price realisation under efficient markets, terms of trade, risk adaptation, public-private partnership, skilling and land use governed by strong policies and leadership at all levels will enable an environment for DFI.

Molecular modeling and dynamics study of nonsynonymous SNP in bread wheat HSP16.9B gene

An ubiquitous molecular chaperon, small heat shock proteins (sHSP) maintain protein homeostasis under stress conditions. Single nucleotide polymorphism was predicted in HSP16.9B gene but so far its impact on protein structure has not been extensively studied. Keeping this point in mind, we applied computational methods and performed molecular dynamics simulation to examine the effect of aspartic acid substitution for asparagine at 11th position (D11N) in HSP16.9B. Furthermore, the secondary structural analysis revealed an addition of beta sheet before the mutation point in the mutant protein. Three dimensional protein structure modeling, validation of structures and molecular dynamics were performed to study the mechanism of the non-synonymous single nucleotide polymorphism on structural changes. The root mean square deviation (RMSD) result showed the stability of the mutated structure throughout simulations. Moreover, root mean square fluctuation (RMSF) of atoms and Hydrogen-bond patterns further supported our results.

Yield stability of wheat genotypes for Northern western plains zone of India

In this investigation 23 genotypes of wheat were tested for stability in 19 locations of North Western plains of the country, Yield data generated from the trials were analysed using AMMI analysis. The distribution of genotype by AMMI revealed that the genotypes 10,13, 20,12,15 and 14 scattered close to the origin, indicating minimal interaction of these genotypes with environments. Studied environments explained 57.2% of the total variation, whereas G and GxE captured 6.2% and 24.3%, respectively. First two principal components (PC1 and PC2) were used to create a 2dimensional GGE biplot and explained 26.4% and 14.3% of GGE sum of squares (SS), respectively. Environments of Karnal, Ludhiana and Gurdaspur fall in same sector with genotypes 23 & 16. The spearman correlations calculated based on ranks by stability methods varied from positive value 0.97 to negative correlation of 0.759. The cultivar superiority estimate (Pi) maintained negative correlation with other estimates ranking.