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Background: Sulphotransferase (SOT) enzyme (encoded by a conserved family of SOT genes) is involved in sulphonation of a variety of compounds, through transfer of a sulphuryl moiety from 3'phosphoadenosine- 5'phosphosulphate (PAPS) to a variety of secondary metabolites. The PAPS itself is derived from 3'adenosine-5'phosphosulphate (APS) that is formed after uptake of sulphate ions from the soil. The process provides tolerance against abiotic stresses like drought and heat in plants. Therefore, a knowledge of SOT genes in any crop may help in designing molecular breeding methods for improvement of tolerance for drought and heat., Methods: Sequences of rice SOT genes and SOT domain (PF00685) of corresponding proteins were both used for identification of SOT genes in wheat and six related species (T. urartu, Ae. tauschii, T. turgidum, Z. mays, B. distachyon and Hordeum vulgare), although detailed analysis was conducted only in wheat. The wheat genes were mapped on individual chromosomes and also subjected to synteny and collinearity analysis. The proteins encoded by these genes were examined for the presence of a complete SOT domain using 'Conserved Domain Database' (CDD) search tool at NCBI., Results: In wheat, 107 TaSOT genes, ranging in length from 969 bp to 7636 bp, were identified and mapped onto individual chromosomes. SSRs (simple sequence repeats), microRNAs, long non-coding RNAs (lncRNAs) and their target sites were also identified in wheat SOT genes. SOT proteins were also studied in detail. An expression assay of TaSOT genes via wheat RNA-seq data suggested engagement of these genes in growth, development and responses to various hormones and biotic/abiotic stresses., Conclusions: The results of the present study should help in further functional characterization of SOT genes in wheat and other related crops., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Drought-tolerant transgenic [genetically modified (GM)] HB4® wheat carrying the drought-responsive sunflower gene Hahb4 was first developed in Argentina in 2019 and has already been approved for marketing and consumption as food/feed in at least ten countries. It has also been approved in Argentina and Brazil for commercial cultivation., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

In bread wheat, a literature search gave 228 QTLs for six traits, including resistance against spot blotch and the following five other related traits: (i) stay green; (ii) flag leaf senescence; (iii) green leaf area duration; (iv) green leaf area of the main stem; and (v) black point resistance. These QTLs were used for metaQTL (MQTL) analysis. For this purpose, a consensus map with 72,788 markers was prepared; 69 of the above 228 QTLs, which were suitable for MQTL analysis, were projected on the consensus map. This exercise resulted in the identification of 16 meta-QTLs (MQTLs) located on 11 chromosomes, with the PVE ranging from 5.4% (MQTL7) to 21.8% (MQTL5), and the confidence intervals ranging from 1.5 to 20.7 cM (except five MQTLs with a range of 36.1-57.8 cM). The number of QTLs associated with individual MQTLs ranged from a maximum of 17 in MQTL3 to 8 each in MQTL5 and MQTL8 and 5 each in MQTL7 and MQTL14. The 16 MQTLs, included 12 multi-trait MQTLs; one of the MQTL also overlapped a genomic region carrying the major spot blotch resistance gene Sb1. Of the total 16 MQTLs, 12 MQTLs were also validated through marker-trait associations that were available from earlier genome-wide association studies. The genomic regions associated with MQTLs were also used for the identification of candidate genes (CGs) and led to the identification of 516 CGs encoding 508 proteins; 411 of these proteins are known to be associated with resistance against several biotic stresses. In silico expression analysis of CGs using transcriptome data allowed the identification of 71 differentially expressed CGs, which were examined for further possible studies. The findings of the present study should facilitate fine-mapping and cloning of genes, enabling Marker Assisted Selection., (© 2024. The Author(s).)

In wheat, genomic prediction accuracy (GPA) was assessed for three micronutrient traits (grain iron, grain zinc, and β-carotenoid concentrations) using eight Bayesian regression models. For this purpose, data on 246 accessions, each genotyped with 17,937 DArT markers, were utilized. The phenotypic data on traits were available for 2013-2014 from Powerkheda (Madhya Pradesh) and for 2014-2015 from Meerut (Uttar Pradesh), India. The accuracy of the models was measured in terms of reliability, which was computed following a repeated cross-validation approach. The predictions were obtained independently for each of the two environments after adjusting for the local effects and across environments after adjusting for the environmental effects. The Bayes ridge regression (BayesRR) model outperformed the other seven models, whereas BayesLASSO (BayesL) was the least efficient. The GPA increased with an increase in the size of the training set as well as with an increase in marker density. The GPA values differed for the three traits and were higher for the best linear unbiased estimate (BLUE) (obtained after adjusting for the environmental effects) relative to those for the two environments. The GPA also remained unaffected after accounting for the population structure. The results of the present study suggest that only the best model should be used for the estimations of genomic estimated breeding values (GEBVs) before their use for genomic selection to improve the grain micronutrient contents., (© 2023 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Recombination UVB (sensitivity) like (RuvBL) helicase genes represent a conserved family of genes, which are known to be involved in providing tolerance against abiotic stresses like heat and drought. We identified nine wheat RuvBL genes, one each on nine different chromosomes, belonging to homoeologous groups 2, 3, and 4. The lengths of genes ranged from 1647 to 2197 bp and exhibited synteny with corresponding genes in related species including Ae. tauschii, Z. mays, O. sativa, H. vulgare, and B. distachyon. The gene sequences were associated with regulatory cis-elements and transposable elements. Two genes, namely TaRuvBL1a-4A and TaRuvBL1a-4B, also carried targets for a widely known miRNA, tae-miR164. Gene ontology revealed that these genes were closely associated with ATP-dependent formation of histone acetyltransferase complex. Analysis of the structure and function of RuvBL proteins revealed that the proteins were localized mainly in the cytoplasm. A representative gene, namely TaRuvBL1a-4A, was also shown to be involved in protein-protein interactions with ten other proteins. On the basis of phylogeny, RuvBL proteins were placed in two sub-divisions, namely RuvBL1 and RuvBL2, which were further classified into clusters and sub-clusters. In silico studies suggested that these genes were differentially expressed under heat/drought. The qRT-PCR analysis confirmed that expression of TaRuvBL genes differed among wheat cultivars, which differed in the level of thermotolerance. The present study advances our understanding of the biological role of wheat RuvBL genes and should help in planning future studies on RuvBL genes in wheat including use of RuvBL genes in breeding thermotolerant wheat cultivars., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Epigenetic regulation of the activity of defense genes during onset of diseases or resistance against diseases in plants is an active area of research. In the present study, a pair of wheat NILs for leaf rust resistance gene Lr28 (R) in the background of an Indian cultivar HD2329 (S) was used for a study of DNA methylation mediated regulation of gene expression. Leaf samples were collected at 0 h before (S0 and R0) and 96 h after inoculation (S96 and R96). The DNA samples were subjected to BS-Seq and sequencing data were used for identification of differentially methylated/demethylated regions/genes (DMRs and DMGs). Following four pairs of comparisons were used for this purpose: S0 vs S96; S0 vs R0; R0 vs R96; S96 vs R96. Major role of CHH methylation relative to that of CG and CHG methylation was observed. Some important observations include the following: (i) abundance of CHH methylation among DMRs; (ii) predominance of DMRs in intergenic region, relative to other genomic regions (promoters, exons, introns, TSS and TTS); (iii) abundance of transposable elements (TEs) in DMRs with CHH context; (iv) demethylation mediated high expression of genes during susceptible reaction (S0 vs S96) and methylation mediated low expression of genes during resistant reaction (R0 vs R96 and S96 vs R96); (v) major genes under regulation encode proteins, which differ from those encoded by genes regulated during susceptible reaction and (vi) ~ 500 DMGs carried differential binding sites for H3K4/K27me3 marks suggesting joint involvement of DNA and H3 methylation. Thus, CHH methylation either alone or in combination with histone methylation plays a major role in regulating the expression of genes involved in wheat-leaf rust interaction., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

In bread wheat, meta-QTL analysis was conducted using 353 QTLs that were available from earlier studies. When projected onto a dense consensus map comprising 76,753 markers, only 184 QTLs with the required information, could be utilized leading to identification of 61 MQTLs spread over 18 of the 21 chromosomes (barring 5D, 6D and 7D). The range for mean R 2 (PVE %) was 1.9% to 48.1%, and that of CI was 0.02 to 11.47 cM; these CIs also carried 37 Yr genes. Using these MQTLs, 385 candidate genes (CGs) were also identified. Out of these CGs, 241 encoded known R proteins and 120 showed differential expression due to stripe rust infection at the seedling stage; the remaining 24 CGs were common in the sense that they encoded R proteins as well as showed differential expression. The proteins encoded by CGs carried the following widely known domains: NBS-LRR domain, WRKY domains, ankyrin repeat domains, sugar transport domains, etc. Thirteen breeders' MQTLs (PVE > 20%) including four pairs of closely linked MQTLs are recommended for use in wheat molecular breeding, for future studies to understand the molecular mechanism of stripe rust resistance and for gene cloning., (© 2021. The Author(s).)

During the last three decades, QTL analysis in wheat has been conducted for a variety of individual traits, so that thousands of QTL along with the linked markers, their genetic positions and contribution to phenotypic variation (PV) for concerned traits are now known. However, no exhaustive database for wheat QTL is currently available at a single platform. Therefore, the present database was prepared which is an exhaustive information resource for wheat QTL data from the published literature till May, 2020. QTL data from both interval mapping and genome-wide association studies (GWAS) have been included for the following classes of traits: (i) morphological traits, (ii) N and P use efficiency, (iii) traits for biofortification (Fe, K, Se, and Zn contents), (iv) tolerance to abiotic stresses including drought, water logging, heat stress, pre-harvest sprouting and salinity, (v) resistance to biotic stresses including those due to bacterial, fungal, nematode and insects, (vi) quality traits, and (vii) a variety of physiological traits, (viii) developmental traits, and (ix) yield and its related traits. For the preparation of the database, literature was searched for data on QTL/marker-trait associations (MTAs), curated and then assembled in the form of WheatQTLdb. The available information on metaQTL, epistatic QTL and candidate genes, wherever available, is also included in the database. Information on QTL in this WheatQTLdb includes QTL names, traits, associated markers, parental genotypes, crosses/mapping populations, association mapping panels and other useful information. To our knowledge, WheatQTLdb prepared by us is the largest collection of QTL (11,552), epistatic QTL (107) and metaQTL (330) data for hexaploid wheat to be used by geneticists and plant breeders for further studies involving fine mapping, cloning, and marker-assisted selection (MAS) during wheat breeding., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

SET domain genes (SDGs) that are involved in histone methylation have been examined in many plant species, but have never been examined in bread wheat; the histone methylation caused due to SDGs is associated with regulation of gene expression at the transcription level. We identified a total of 166 bread wheat TaSDGs, which carry some interesting features including the occurrence of tandem/interspersed duplications, SSRs (simple sequence repeats), transposable elements, lncRNAs and targets for miRNAs along their lengths and transcription factor binding sites (TFBS) in the promoter regions. Only 130 TaSDGs encoded proteins with complete SET domain, the remaining 36 proteins had truncated SET domain. The TaSDG encoded proteins were classified into six classes (I-V and VII). In silico expression analysis indicated relatively higher expression (FPKM > 20) of eight of the 130 TaSDGs in different tissues, and downregulation of 30 TaSDGs under heat and drought at the seedling stage. qRT-PCR was also conducted to validate the expression of seven genes at the seedling stage in pairs of contrasting genotypes in response to abiotic stresses (water and heat) and biotic stress (leaf rust). These genes were generally downregulated in response to the three stresses examined.

Key Message: A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.

Genome-wide transcriptome analysis was undertaken in a leaf-rust resistant bread wheat line CSP44 (selected from Australian cv. Condor) carrying the adult plant resistance (APR) gene Lr48. Two pre-adult plant (P-AP) susceptible stages (S48 and S96) and two adult plant (AP) resistant stages (R48 and R96) were used for RNA-seq. At the susceptible P-AP stage (during S48 to S96), expression increased in 2062 genes, and declined in 130 genes; 1775 of 2062 differentially expressed genes (DEGs) also exhibited high expression during early incompatible stage R48. Comparison of S96 with R96 showed that the expression of 80 genes was enhanced and that of 208 genes declined at the AP stage. At the resistant AP stage (during R48 to R96), expression of mere 25 genes increased and that of 126 genes declined. Apparently, the resistance during late adult stage (R96) is caused by regulation of the expression of relatively fewer genes, although at pre-adult stage (S48 to S96), expression of large number of genes increased; expression of majority of these genes kept on increasing during adult stage at R48 also. These and other results of the present study suggest that APR may mimic some kind of systemic acquired resistance (SAR). The host-specific DEGs belonged to 10 different classes including genes involved in defence, transport, epigenetics, photosynthesis, genes encoding some transcription factors etc. The pathogen (Puccinia triticina) specific DEGs (including three genes encoding known biotrophic effectors) seem to help the pathogen in infection/growth through large-scale stage-specific enhanced expression of host's genes. A putative candidate gene for Lr48 containing protein kinase domain (its ortholog in rice encoding OsWAK8) was also identified.

Genetic control of grain yield and phenology was examined in the Excalibur/Kukri doubled haploid mapping population grown in 32 field experiments across the climatic zones of southern Australia, India and north-western Mexico where the wheat crop experiences drought and heat stress. A total of 128 QTL were identified for four traits: grain yield, thousand grain weight (TGW), days to heading and grain filling duration. These QTL included 24 QTL for yield and 27 for TGW, showing significant interactions with the environment (Q * E). We also identified 14 QTL with a significant, small main effects on yield across environments. The study focussed on a region of chromosome 1B where two main effect QTL were found for yield and TGW without the confounding effect of phenology. Excalibur was the source of favourable alleles: QYld.aww-1B.2 with a peak at 149.5-150.1 cM and QTgw.aww-1B at 168.5-171.4 cM. We developed near isogenic lines (NIL) for the interval including QYld.aww-1B.2 and QTgw.aww-1B and evaluated them under semi-controlled conditions. Significant differences in four pairs of NIL were observed for grain yield but not for TGW, confirming a positive effect of the Excalibur allele for QYld.aww-1B.2. The interval containing QYld.aww-1B.2 was narrowed down to 2.9 cM which corresponded to a 2.2 Mbp genomic region on the chromosome 1B genomic reference sequence of cv. Chinese Spring and contained 39 predicted genes.

The ToxA - Tsn1 system is an example of an inverse gene-for-gene relationship. The gene ToxA encodes a host-selective toxin (HST) which functions as a necrotrophic effector and is often responsible for the virulence of the pathogen. The genomes of several fungal pathogens (e.g., Pyrenophora tritici-repentis, Parastagonospora nodorum, and Bipolaris sorokiniana ) have been shown to carry the ToxA gene. Tsn1 is a sensitivity gene in the host, whose presence generally helps a ToxA -positive pathogen to cause spot blotch in wheat. Cultivars lacking Tsn1 are generally resistant to spot blotch; this resistance is attributed to a number of other known genes which impart resistance in the absence of Tsn1 . In the present study, 110 isolates of B. sorokiniana strains, collected from the ME 5 A and ME 4 C megaenvironments of India, were screened for the presence of the ToxA gene; 77 (70%) were found to be ToxA positive. Similarly, 220 Indian wheat cultivars were screened for the presence of the Tsn1 gene; 81 (36.8%) were found to be Tsn1 positive. When 20 wheat cultivars (11 with Tsn1 and 9 with tsn1 ) were inoculated with ToxA -positive isolates, seedlings of only those carrying the Tsn1 allele (not tsn1 ) developed necrotic spots surrounded by a chlorotic halo. No such distinction between Tsn1 and tsn1 carriers was observed when adult plants were inoculated. This study suggests that the absence of Tsn1 facilitated resistance against spot blotch of wheat. Therefore, the selection of wheat genotypes for the absence of the Tsn1 allele can improve resistance to spot blotch.

Key Message: The review outlines past failures, present status and future prospects of hybrid wheat, and includes information on CMS/CHA/transgenic approaches for male sterility, heterotic groups and cost-effective hybrid seed production. Hybrid varieties give increased yield and improved grain quality in both cross- and self-pollinated crops. However, hybrid varieties in self-pollinated crops (particularly cereals) have not been very successful, except for hybrid rice in China. In case of hybrid wheat, despite the earlier failures, renewed efforts in recent years have been made and hybrid varieties with desirable attributes have been produced and marketed in some European countries. This review builds upon previous reviews, with a new outlook and improved knowledge base, not covered in earlier reviews. New technologies have been described, which include the Hordeum chilense-based CMS-fertility restorer system, chromosomal XYZ-4E-ms system and the following transgenic technologies: (1) conditional male sterility involving use of tapetum-specific expression of a gene that converts a pro-toxin into a phytotoxin causing male sterility; (2) barnase-barstar SeedLink system of Bayer CropScience; (3) split-barnase system that obviates the need of a barstar-based male restorer line; and (4) seed production technology of DuPont-Pioneer that makes use of transgenes in production of male-sterile lines, but gives hybrid seed with no transgenes. This review also includes a brief account of studies for discovery of heterotic QTL, genomic prediction of hybrid vigour and the development of heterotic groups/patterns and their importance in hybrid wheat production. The problem of high cost of hybrid seed due to required high seed rate in wheat relative to hybrid rice has also been addressed. The review concludes with a brief account of the current efforts and future possibilities in making hybrid wheat a commercial success.

RWP-RKs represent a small family of transcription factors (TFs) that are unique to plants and function particularly under conditions of nitrogen starvation. These RWP-RKs have been classified in two sub-families, NLPs (NIN-like proteins) and RKDs (RWP-RK domain proteins). NLPs regulate tissue-specific expression of genes involved in nitrogen use efficiency (NUE) and RKDs regulate expression of genes involved in gametogenesis/embryogenesis. During the present study, using in silico approach, 37 wheat RWP-RK genes were identified, which included 18 TaNLPs (2865 to 7340 bp with 4/5 exons), distributed on 15 chromosomes from 5 homoeologous groups (with two genes each on 4B,4D and 5A) and 19 TaRKDs (1064 to 5768 bp with 1 to 6 exons) distributed on 12 chromosomes from 4 homoeologous groups (except groups 1, 4 and 5); 2-3 splice variants were also available in 9 of the 37 genes. Sixteen (16) of these genes also carried 24 SSRs (simple sequence repeats), while 11 genes had targets for 13 different miRNAs. At the protein level, MD simulation analysis suggested their interaction with nitrate-ions. Significant differences were observed in the expression of only two (TaNLP1 and TaNLP2) of the nine representative genes that were used for in silico expression analysis under varying levels of N at post-anthesis stage (data for other genes was not available for in silico expression analysis). Differences in expression were also observed during qRT-PCR, when expression of four representative genes (TaNLP2, TaNLP7, TaRKD6 and TaRKD9) was examined in roots and shoots of seedlings (under different conditions of N supply) in two contrasting genotypes which differed in NUE (C306 with low NUE and HUW468 with high NUE). These four genes for qRT-PCR were selected on the basis of previous literature, level of homology and the level of expression (in silico study). In particular, the TaNLP7 gene showed significant up-regulation in the roots and shoots of HUW468 (with higher NUE) during N-starvation; this gene has already been characterized in Arabidopsis and tobacco, and is known to be involved in nitrate-signal transduction pathway., Competing Interests: The authors have declared that no competing interests exist.

Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions. The libraries were sequenced on Sequencing by Oligonucleotide Ligation and Detection (SOLiD) system generating 37-48 million reads. After mapping and gene expression analysis of ~6-12 million trimmed reads/library, we revealed five major categories comprised of Lr28 controlled transcripts in resistant (+Lr28) isoline (39), transcripts specific to susceptible (-Lr28) isoline (785), transcripts specific to hypersensitive-response (HR) (375), transcripts specific for basal-defense (153) and transcripts for establishment of pathogen (1616). We estimated the impact of specific genes and pathways through mapping on plant resistant gene database (PRGdb), reactive oxygen species (ROS) and phytohormone database. Functional annotation results revealed, receptor binding, homeostatic processes and cytoskeletal components as the major discriminating factors between susceptibility and resistance. We validated 28 key genes using qRT-PCR and found positive results. These findings were projected on hypothetical interaction model to demonstrate interaction mechanism. The study might have significant impact on future rust-resistance breeding through knowledge based smart genetic selection of quantitative resistance genes besides major effect R-gene., (Copyright © 2017 Elsevier B.V. All rights reserved.)

In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat.

Key Message: TFs involved in drought tolerance in plants may be utilized in future for developing drought tolerant cultivars of wheat and some other crops. Plants have developed a fairly complex stress response system to deal with drought and other abiotic stresses. These response systems often make use of transcription factors (TFs); a gene encoding a specific TF together with -its target genes constitute a regulon, and take part in signal transduction to activate/silence genes involved in response to drought. Since, five specific families of TFs (out of >80 known families of TFs) have gained widespread attention on account of their significant role in drought tolerance in plants, TFs and regulons belonging to these five multi-gene families (AP2/EREBP, bZIP, MYB/MYC, NAC and WRKY) have been described and their role in improving drought tolerance discussed in this brief review. These TFs often undergo reversible phosphorylation to perform their function, and are also involved in complex networks. Therefore, some details about reversible phosphorylation of TFs by different protein kinases/phosphatases and the co-regulatory networks, which involve either only TFs or TFs with miRNAs, have also been discussed. Literature on transgenics involving genes encoding TFs and that on QTLs and markers associated with TF genes involved in drought tolerance has also been reviewed. Throughout the review, there is a major emphasis on wheat as an important crop, although examples from the model cereal rice (sometimes maize also), and the model plant Arabidopsis have also been used. This knowledge base may eventually allow the use of TF genes for development of drought tolerant cultivars, particularly in wheat.

Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910-2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method.

TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in 'CGCG' motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).

Wheat genotype CSP44 carrying a recessive gene Lr48 exhibits adult plant resistance (APR; incompatible reaction) but gives a compatible reaction (susceptibility) at the seedling stage against leaf rust. A comparative gene expression analysis involving cDNA-amplified fragment length polymorphism (cDNA-AFLP) and quantitative PCR (qPCR) was carried out for incompatible and compatible reactions in the genotype CSP44. cDNA-AFLP analysis was conducted using RNA samples that were isolated from flag leaves following inoculation with leaf rust race 77-5 (the most virulent race) and also after mock inoculation. As many as 298 of a total of 493 expressed transcript-derived fragments (TDFs) exhibited differential expression (262 upregulated and 36 downregulated). Of these 298 TDFs, 48 TDFs were eluted from gels, re-amplified, cloned, and sequenced. Forty two of these 48 TDFs had homology with known genes involved in the following biological processes: energy production, metabolism, transport, signaling, defense response, plant-pathogen interaction, transcriptional regulation, translation, and proteolysis. The functions of the remaining six TDFs could not be determined; apparently, these represented some novel genes. The qPCR analysis for 18 TDFs (with known and unknown functions, but showing major differences in expression) was conducted using RNA isolated from the seedlings as well as from the adult plants. The expression of at least 11 TDFs was induced and that of 4 other TDFs attenuated or remained near normal in adult plants following leaf rust inoculations. The remaining three TDFs had non-specific/developmental stage-specific expression. Functional annotation of TDFs that were upregulated suggest that the APR was supported by transient recruitment and reprogramming of processes like perception and recognition of pathogen effector by receptors, followed by CDPK and MAPK signaling, transport, metabolism, and energy release.

Wheat is an important staple crop, and its productivity is severely constrained by drought stress (DS). An understanding of the molecular basis of drought tolerance is necessary for genetic improvement of wheat for tolerance to DS. The two-component system (TCS) serves as a common sensor-regulator coupling mechanism implicated in the regulation of diverse biological processes (including response to DS) not only in prokaryotes, but also in higher plants. In the latter, TCS generally consists of two signalling elements, a histidine kinase (HK) and a response regulator (RR) associated with an intermediate element called histidine phosphotransferase (HPT). Keeping in view the possible utility of TCS in developing water use efficient (WUE) wheat cultivars, we identified and characterized 62 wheat genes encoding TCS elements in a silico study; these included 7 HKs, 45 RRs along with 10 HPTs. Twelve of the 62 genes showed relatively higher alterations in the expression under drought. The quantitative RT-PCR (qRT-PCR)-based expression analysis of these 12 TCS genes was carried out in wheat seedlings of a drought sensitive (HD2967) and a tolerant (Dharwar Dry) cultivar subjected to either dehydration stress or cytokinin treatment. The expression of these 12 genes under dehydration stress differed in sensitive and tolerant genotypes, even though for individual genes, both showed either up-regulation or down-regulation. In response to the treatment of cytokinin, the expression of type-A RR genes was higher in the tolerant genotype, relative to that in the sensitive genotype, the situation being reverse for the type-B RRs. These results have been discussed in the context of the role of TCS elements in drought tolerance in wheat.

Leaf rust, caused by the fungus Puccinia triticina, is the most devastating disease of wheat worldwide, which sometimes becomes epidemic. The pathogen evolves into new strains, making its control difficult. Though more than 60 leaf rust resistant genes are now known, only limited insight is available into the molecular mechanism involved in this host pathogen interaction. In the present study, quantitative real-time PCR based differential gene expression profiling was examined for five target genes encoding for chitinase3, β-1,3/1,4 glucanase, thaumatin-like protein, peroxidase2 and mitogen activated protein kinase1 to unravel their coordinated action during compatible and incompatible interaction, to inhibit the pathogen progression and to identify the time-period of maximum defense activity. Spatio-temporal expression profiling suggested that the maximum defense activity occurred at 12-24 hours post inoculation, whereas the state of infection and degree of resistance was predicted using coordinated unique expression signatures of target genes. The significant differences of targeted gene expression between resistant mock inoculated, resistant infected and susceptible infected plants were evaluated using t test at significance level of p < 0.01. The differences occurred can be attributed to the presence of seedling leaf rust resistance Lr28 gene, which facilitated prevention of leaf rust infection in resistant wheat plants.

Background: The uneven distribution of recombination across the length of chromosomes results in inaccurate estimates of genetic to physical distances. In wheat (Triticum aestivum L.) chromosome 3B, it has been estimated that 90% of the cross over events occur in distal sub-telomeric regions representing 40% of the chromosome. Radiation hybrid (RH) mapping which does not rely on recombination is a strategy to map genomes and has been widely employed in animal species and more recently in some plants. RH maps have been proposed to provide i) higher and ii) more uniform resolution than genetic maps, and iii) to be independent of the distribution patterns observed for meiotic recombination. An in vivo RH panel was generated for mapping chromosome 3B of wheat in an attempt to provide a complete scaffold for this ~1 Gb segment of the genome and compare the resolution to previous genetic maps., Results: A high density RH map with 541 marker loci anchored to chromosome 3B spanning a total distance of 1871.9 cR was generated. Detailed comparisons with a genetic map of similar quality confirmed that i) the overall resolution of the RH map was 10.5 fold higher and ii) six fold more uniform. A significant interaction (r = 0.879 at p = 0.01) was observed between the DNA repair mechanism and the distribution of crossing-over events. This observation could be explained by accepting the possibility that the DNA repair mechanism in somatic cells is affected by the chromatin state in a way similar to the effect that chromatin state has on recombination frequencies in gametic cells., Conclusions: The RH data presented here support for the first time in vivo the hypothesis of non-casual interaction between recombination hot-spots and DNA repair. Further, two major hypotheses are presented on how chromatin compactness could affect the DNA repair mechanism. Since the initial RH application 37 years ago, we were able to show for the first time that the iii) third hypothesis of RH mapping might not be entirely correct.

We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C(0)t fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences (e.g., transposable elements and simple sequence repeats), protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/exclusion in methylation-filtered (MF) library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags (ESTs) available in the public domain. Only a limited overlap among MF, high C(0)t (HC), and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space., (Copyright © 2011. Published by Elsevier Ltd.)

In bread wheat, a set of 527 simple sequence repeats (SSRs) were tried on 164 deletion lines, leading to a successful mapping of 270 SSRs on 313 loci covering all 21 chromosomes. A maximum of 119 loci (38%) were located on B subgenome, and a minimum of 90 loci (29%) mapped on D subgenome. Similarly, homoeologous group 7 carried a maximum of 61 loci (19%), and group 4 carried a minimum of 22 loci (7%). Of the cited 270 SSRs, 39 had multiple loci, but only eight of these detected homoeologous loci. Linear order of loci in physical maps largely corresponded with those in the genetic maps. Apparently, distances between each of only 26 pairs of loci significantly differed from the corresponding distances on genetic maps. Some loci, which were genetically mapped close to the centromere, were physically located distally, while other loci that were mapped distally in the genetic maps were located in the proximal bins in the physical maps. This suggested that although the linear order of the loci was largely conserved, variation does exist between genetic and physical distances.

In hexaploid wheat, single-locus and two-locus quantitative trait loci (QTL) analyses for grain protein content (GPC) were conducted using two different mapping populations (PI and PII). Main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL x environment interactions (QE, QQE) were detected using two-locus analyses in both the populations. Only a few QTLs were common in both the analyses, and the QTLs and the interactions detected in the two populations differed, suggesting the superiority of two-locus analysis and the need for using several mapping populations for QTL analysis. A sizable proportion of genetic variation for GPC was due to interactions (28.59% and 54.03%), rather than to M-QTL effects (7.24% and 7.22%), which are the only genetic effects often detected in the majority of QTL studies. Even E-QTLs made a marginal contribution to genetic variation (2.68% and 6.04%), thus suggesting that the major part of genetic variation is due to changes in gene networks rather than the presence or absence of specific genes. This is in sharp contrast to the genetic dissection of pre-harvest sprouting tolerance conducted by us earlier, where interaction effects were not substantial, suggesting that the nature of genetic variation also depends on the nature of the trait.