Genomic prediction for grain zinc and iron concentrations in spring wheat.

KEY MESSAGE: Predictability estimated through cross-validation approach showed moderate to high level; hence, genomic selection approach holds great potential for biofortification breeding to enhance grain zinc and iron concentrations in wheat. Wheat (Triticum aestivum L.) is a major staple crop, providing 20 % of dietary energy and protein consumption worldwide. It is an important source of mineral micronutrients such as zinc (Zn) and iron (Fe) for resource poor consumers. Genomic selection (GS) approaches have great potential to accelerate development of Fe- and Zn-enriched wheat. Here, we present the results of large-scale genomic and phenotypic data from the HarvestPlus Association Mapping (HPAM) panel consisting of 330 diverse wheat lines to perform genomic predictions for grain Zn (GZnC) and Fe (GFeC) concentrations, thousand-kernel weight (TKW) and days to maturity (DTM) in wheat. The HPAM lines were phenotyped in three different locations in India and Mexico in two successive crop seasons (2011-12 and 2012-13) for GZnC, GFeC, TKW and DTM. The genomic prediction models revealed that the estimated prediction abilities ranged from 0.331 to 0.694 for Zn and from 0.324 to 0.734 for Fe according to different environments, whereas prediction abilities for TKW and DTM were as high as 0.76 and 0.64, respectively, suggesting that GS holds great potential in biofortification breeding to enhance grain Zn and Fe concentrations in bread wheat germplasm.

QTL for yield and associated traits in the Seri/Babax population grown across several environments in Mexico, in the West Asia, North Africa, and South Asia regions.

Heat and drought adaptive quantitative trait loci (QTL) in a spring bread wheat population resulting from the Seri/Babax cross designed to minimize confounding agronomic traits have been identified previously in trials conducted in Mexico. The same population was grown across a wide range of environments where heat and drought stress are naturally experienced including environments in Mexico, West Asia, North Africa (WANA), and South Asia regions. A molecular genetic linkage map including 475 marker loci associated to 29 linkage groups was used for QTL analysis of yield, days to heading (DH) and to maturity (DM), grain number (GM2), thousand kernel weight (TKW), plant height (PH), canopy temperature at the vegetative and grain filling stages (CTvg and CTgf), and early ground cover. A QTL for yield on chromosome 4A was confirmed across several environments, in subsets of lines with uniform allelic expression of a major phenology QTL, but not independently from PH. With terminal stress, TKW QTL was linked or pleiotropic to DH and DM. The link between phenology and TKW suggested that early maturity would favor the post-anthesis grain growth periods resulting in increased grain size and yields under terminal stress. GM2 and TKW were partially associated with markers at different positions suggesting different genetic regulation and room for improvement of both traits. Prediction accuracy of yield was improved by 5 % when using marker scores of component traits (GM2 and DH) together with yield in multiple regression. This procedure may provide accumulation of more favorable alleles during selection.

Harnessing High Yield Potential in Wheat (Triticum aestivum L.) under Climate Change Scenario.

Wheat is a major staple food crop for food security in India and South Asia. The current rate (0.8-1.2%) of genetic gain in wheat is significantly shorter than the 2.4% needed to meet future demand. The changing climate and increased yield loss due to factors such as terminal heat stress necessitate the need for climate-resilient practices to sustain wheat production. At ICAR-Indian Institute of Wheat and Barley Research in Karnal, Haryana, India, a new High Yield Potential Trial (HYPT) was conceptualized and subsequently conducted at six locations in the highly productive North Western Plain Zone (NWPZ). An attempt was made to harness higher wheat yields through the best pipeline genotypes suitable for early sowing and modified agronomic practices to explore the feasibility of a new approach that is profitable to farmers. The modified agronomic practices included like early sowing, application of 150% recommended dose of fertilizers, and two sprays of growth regulators (Chlormaquate chloride and Tebuconazole) to prevent lodging. The mean yield in the HYPT was 19.4% superior compared to the best trials conducted during the normal sowing time. A highly positive and significant correlation of grain yield with grain filling duration (0.51), biomass (0.73), harvest index (0.75), normalized difference vegetation Index (0.27), chlorophyll content index (0.32), and 1000-grain weight (0.62) was observed. An increased return of USD 201.95/ha was realized in the HYPT when compared to normal sowing conditions. This study proves that new integrated practices have the potential to provide the best profitable yields in wheat in the context of climate change.

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.

Correction to: Strategic crossing of biomass and harvest index-source and sink-achieves genetic gains in wheat.

[This corrects the article DOI: 10.1007/s10681-017-2040-z.].

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).

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.

Analysis of simple sequence repeats (SSRs)dynamics in fungus Fusarium graminearum.

The abundance and inherent potential for variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in eukaryotes. We describe the organization and abundance of SSRs in fungus Fusarium graminearum (causative agent for Fusarium head blight or head scab of wheat). We identified 1705 SSRs of various nucleotide repeat motifs in the sequence database of F. graminearum. It is observed that mononucleotide repeats (62%) were most abundant followed by di- (20%) and trinucleotide repeats (14%). It is noted that tetra-, penta- and hexanucleotide repeats accounted for only 4% of SSRs. The estimated frequency of Class I SSRs (perfect repeats ≥20 nucleotides) was one SSR per 124.5 kb, whereas the frequency of Class II (perfect repeats >10 nucleotides and ≫20 nucleotides) was one SSR per 25.6 kb. The dynamics of SSRs will be a powerful tool for taxonomic, phylogenetic, genome mapping and population genetic studies as SSR based markers show high levels of allelic variation, codominant inheritance and ease of analysis.

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.

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.