Einkorn genomics sheds light on history of the oldest domesticated wheat.

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat.

In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01357-5.

Meta-QTLs, ortho-meta QTLs and related candidate genes for yield and its component traits under water stress in wheat (Triticum aestivum L.).

Meta-QTLs (MQTLs), ortho-MQTLs, and related candidate genes (CGs) for yield and its seven component traits evaluated under water deficit conditions were identified in wheat. For this purpose, a high density consensus map and 318 known QTLs were used for identification of 56 MQTLs. Confidence intervals (CIs) of the MQTLs were narrower (0.7-21 cM; mean = 5.95 cM) than the CIs of the known QTLs (0.4-66.6 cM; mean = 12.72 cM). Forty-seven MQTLs were co-located with marker trait associations reported in previous genome-wide association studies. Nine selected MQTLs were declared as 'breeders MQTLs' for use in marker-assisted breeding (MAB). Utilizing known MQTLs and synteny/collinearity among wheat, rice and maize, 12 ortho-MQTLs were also identified. A total of 1497 CGs underlying MQTLs were also identified, which were subjected to in-silico expression analysis, leading to identification of 64 differentially expressed CGs (DECGs) under normal and water deficit conditions. These DECGs encoded a variety of proteins, including the following: zinc finger, cytochrome P450, AP2/ERF domain-containing proteins, plant peroxidase, glycosyl transferase, glycoside hydrolase. The expression of 12 CGs at seedling stage (3 h stress) was validated using qRT-PCR in two wheat genotypes, namely Excalibur (drought tolerant) and PBW343 (drought sensitive). Nine of the 12 CGs were up-regulated and three down-regulated in Excalibur. The results of the present study should prove useful for MAB, for fine mapping of promising MQTLs and for cloning of genes across the three cereals studied. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01301-z.

BS-Seq reveals major role of differential CHH methylation during leaf rust resistance in wheat (Triticum aestivum L.).

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.

WheatQTLdb V2.0: a supplement to the database for wheat QTL.

We recently developed a database for hexaploid wheat QTL (WheatQTLdb; www.wheatqtldb.net), which included 11,552 QTL affecting various traits of economic importance. However, that database did not include valuable QTL from other wheat species and/or progenitors of hexaploid wheat. Therefore, an updated and improved version of wheat QTL database (WheatQTLdb V2.0) was developed, which now includes information on hexaploid wheat (Triticum aestivum) and the following seven other related species: T. durum, T. turgidum, T. dicoccoides, T. dicoccum, T. monococcum, T. boeoticum, and Aegilops tauschii. WheatQTLdb V2.0 includes a much-improved list of QTL, including 27,518 main effect QTL, 202 epistatic QTL, and 1321 metaQTL. This newly released WheatQTLdb V2.0 also has additional valuable options to search and choose the QTL, category-wise, and trait-wise data for their use in research or breeding programs.

Meta-QTLs, ortho-MetaQTLs and candidate genes for grain Fe and Zn contents in wheat (Triticum aestivum L.).

Majority of cereals are deficient in essential micronutrients including grain iron (GFe) and grain zinc (GZn), which are therefore the subject of research involving biofortification. In the present study, 11 meta-QTLs (MQTLs) including nine novel MQTLs for GFe and GZn contents were identified in wheat. Eight of these 11 MQTLs controlled both GFe and GZn. The confidence intervals of the MQTLs were narrower (0.51-15.75 cM) relative to those of the corresponding QTLs (0.6 to 55.1 cM). Two ortho-MQTLs involving three cereals (wheat, rice and maize) were also identified. Results of MQTLs were also compared with the results of earlier genome wide association studies (GWAS). As many as 101 candidate genes (CGs) underlying MQTLs were also identified. Twelve of these CGs were prioritized; these CGs encoded proteins with important domains (zinc finger, RING/FYVE/PHD type, flavin adenine dinucleotide linked oxidase, etc.) that are involved in metal ion binding, heme binding, iron binding, etc. qRT-PCR analysis was conducted for four of these 12 prioritized CGs using genotypes which have differed for GFe and GZn. Significant differential expression in these genotypes was observed at 14 and 28 days after anthesis. The MQTLs/CGs identified in the present study may be utilized in marker-assisted selection (MAS) for improvement of GFe/GZn contents and also for understanding the molecular basis of GFe/GZn homeostasis in wheat. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01149-9.

WheatQTLdb: a QTL database for wheat.

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.

Meta-QTLs, ortho-MQTLs, and candidate genes for thermotolerance in wheat (Triticum aestivum L.).

Meta-QTL analysis for thermotolerance in wheat was conducted to identify robust meta-QTLs (MQTLs). In this study, 441 QTLs related to 31 heat-responsive traits were projected on the consensus map with 50,310 markers. This exercise resulted in the identification of 85 MQTLs with confidence interval (CI) ranging from 0.11 to 34.9 cM with an average of 5.6 cM. This amounted to a 2.96-fold reduction relative to the mean CI (16.5 cM) of the QTLs used. Seventy-seven (77) of these MQTLs were also compared and verified with the results of recent genome-wide association studies (GWAS). The 85 MQTLs included seven MQTLs that are particularly useful for breeding purposes (we called them breeders' MQTLs). Seven ortho-MQTLs between wheat and rice genomes were also identified using synteny and collinearity. The MQTLs were used for the identification of 1,704 candidate genes (CGs). In silico expression analysis of these CGs permitted identification of 182 differentially expressed genes (DEGs), which included 36 high confidence CGs with known functions previously reported to be important for thermotolerance. These high confidence CGs encoded proteins belonging to the following families: protein kinase, WD40 repeat, glycosyltransferase, ribosomal protein, SNARE associated Golgi protein, GDSL lipase/esterase, SANT/Myb domain, K homology domain, etc. Thus, the present study resulted in the identification of MQTLs (including breeders' MQTLs), ortho-MQTLs, and underlying CGs, which could prove useful not only for molecular breeding for the development of thermotolerant wheat cultivars but also for future studies focused on understanding the molecular basis of thermotolerance. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01264-7.

Genome-wide analysis of H3K4me3 and H3K27me3 modifications due to Lr28 for leaf rust resistance in bread wheat (Triticum aestivum).

KEY MESSAGE: Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.

Complex relationship between DNA methylation and gene expression due to Lr28 in wheat-leaf rust pathosystem.

Differential DNA methylation due to Lr28 was examined in susceptible (S) wheat cv. HD2329 and its resistant (R) near isogenic line (NIL) (HD2329+Lr28) using two approaches: methylation sensitive amplified polymorphism (MSAP) and methylated DNA immunoprecipitation (MeDIP). S/R lines each had a large number of hypomethylated genes and relatively fewer hypermethylated genes at 96 hai (hours after inoculation) relative to 0 hbi (hours before inoculation), suggesting activation of many genes during the passage of time (96 hai), although identity of genes may differ in S and R lines. When R NIL was compared with S cultivar, there were many hypermethylated and fewer hypomethylated genes in R NIL relative to S cultivar, suggesting that many genes that are active in S cultivar are silenced in R NIL, both at 0 hbi and at 96 hai. Level of methylation was generally abundant in intergenic regions followed by that in promoters, transcription termination sites (TTSs) and exons/introns. Hypermethylation in promoter and gene body regions was not always associated with inhibition of gene expression and vice-versa, indicating that more than one regulatory mechanisms may control the expression of genes due to pathogen attack in presence and absence of Lr28. MSAP analysis also showed abundance of mCG methylation in S cultivar and that of mCCG methylation in R NIL (at 96 hai), suggesting differences in methylation context in NILs with and without Lr28. The results of the present study improved our understanding of the epigenetic control of leaf rust resistance in wheat.

Meta-QTL analysis and identification of candidate genes for drought tolerance in bread wheat (Triticum aestivum L.).

Meta-QTL (MQTL) analysis for drought tolerance was undertaken in bread wheat to identify consensus and robust MQTLs using 340 known QTLs from 11 earlier studies; 13 MQTLs located on 6 chromosomes (1D, 3B, 5A, 6D, 7A and 7D) were identified, with maximum of 4 MQTLs on chromosome 5A. Mean confidence intervals for MQTLs were much narrower (mean, 6.01 cM; range 2.07-19.46 cM), relative to those in original QTLs (mean, 13.6 cM; range, 1.0-119.1 cM). Two MQTLs, namely MQTL4 and MQTL12, were major MQTLs with potential for use in marker-assisting breeding. As many as 228 candidate genes (CGs) were also identified using 6 of the 13 MQTLs. In-silico expression analysis of these 228 CGs allowed identification of 14 important CGs, with + 3 to - 8 fold change in expression under drought (relative to normal conditions) in a tolerant cv. named TAM107. These CGs encoded proteins belonging to the following families: NAD-dependent epimerase/dehydratase, protein kinase, NAD(P)-binding domain protein, heat shock protein 70 (Hsp70), glycosyltransferase 2-like, etc. Important MQTLs and CGs identified in the present study should prove useful for future molecular breeding and for the study of molecular basis of drought tolerance in cereals in general and wheat in particular.

H3K4/K9 acetylation and Lr28-mediated expression of six leaf rust responsive genes in wheat (Triticum aestivum).

Development of leaf rust-resistant cultivars is a priority during wheat breeding, since leaf rust causes major losses in yield. Resistance against leaf rust due to Lr genes is partly controlled by epigenetic modifications including histone acetylation that is known to respond to biotic/abiotic stresses. In the present study, enrichment of H3K4ac and H3K9ac in promoters of six defense responsive genes (N-acetyltransferase, WRKY 40, WRKY 70, ASR1, Peroxidase 12 and Sarcosine oxidase) was compared with their expression in a pair of near-isogenic lines (NILs) for the gene Lr28 following inoculation with leaf rust pathotype '77-5'; ChIP-qPCR was used for this purpose. The proximal and distal promoters of these genes contained a number of motifs that are known to respond to biotic stresses. The enrichment of two acetylation marks changed with passage of time; changes in expression of two of the six genes (N-acetyltransferase and peroxidase12), largely matched with changes in H3K4/H3K9 acetylation patterns of the two promoter regions. For example, enrichment of both the marks matched with higher expression of N-acetyltransferase gene in susceptible NIL and the deacetylation (H3K4ac) largely matched with reduced gene expression in resistant NIL. In peroxidase12, enrichment of H3K4ac and H3K9ac largely matched with higher expression in both the NILs. In the remaining four genes, changes in H3 acetylation did not always match with gene expression levels. This indicated complexity in the regulation of the expression of these remaining four genes, which may be controlled by other epigenetic/genetic regulatory mechanisms that need further analysis.

Hybrid wheat: past, present and future.

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.

Further studies on sugar transporter (SWEET) genes in wheat (Triticum aestivum L.).

SWEET proteins represent one of the largest sugar transporter family in the plant kingdom and play crucial roles in plant development and stress responses. In the present study, a total of 108 TaSWEET genes distributed on all the 21 wheat chromosomes were identified using the latest whole genome sequence (as against 59 genes reported in an earlier report). These 108 genes included 14 of the 17 types reported in Arabidopsis and also included three novel types. Tandem duplications (22) and segmental duplications (5) played a significant role in the expansion of TaSWEET family. A number of cis-elements were also identified in the promoter regions of TaSWEET genes, indicating response of TaSWEET genes during development and also during biotic/abiotic stresses. The TaSWEET proteins carried 4-7 trans-membrane helices (TMHs) showing diversity in structure. Phylogenetic analysis using SWEET proteins of wheat and 8 other species gave four well-known clusters. Expression analysis involving both in silico and in planta indicated relatively higher expression of TaSWEET genes in water/heat sensitive and leaf rust resistant genotypes. The results provided insights into the functional role of TaSWEETs in biotic and abiotic stresses, which may further help in planning strategies to develop high yielding wheat varieties tolerant to environmental stresses.

Genetic diversity and population structure analysis of Indian garlic (Allium sativum L.) collection using SSR markers.

Genetic diversity was assessed among 53 Indian garlic accessions using SSR markers. Initially, 24 SSR primer pairs were used for screening three selected garlic accessions. Out of 24 SSR primer pairs, 10 primer pairs which consistently showed good amplification and polymorphism were selected for DNA profiling. SSR primer pairs showed PIC values ranging from 0.30 to 0.99. Based on AMOVA we found that the greater part of the genetic diversity was expected due to intra population with 84% variation and only 16% of variation was due to among populations suggesting presence of genetic structure. The results of cluster analysis and principal component analysis largely correspond to each other. Population structure analysis revealed genetic differentiation of accessions. The results of present study revealed existence of significant variability in Indian garlic germplasm.

AGPase: its role in crop productivity with emphasis on heat tolerance in cereals.

KEY MESSAGE: AGPase, a key enzyme of starch biosynthetic pathway, has a significant role in crop productivity. Thermotolerant variants of AGPase in cereals may be used for developing cultivars, which may enhance productivity under heat stress. Improvement of crop productivity has always been the major goal of plant breeders to meet the global demand for food. However, crop productivity itself is influenced in a large measure by a number of abiotic stresses including heat, which causes major losses in crop productivity. In cereals, crop productivity in terms of grain yield mainly depends upon the seed starch content so that starch biosynthesis and the enzymes involved in this process have been a major area of investigation for plant physiologists and plant breeders alike. Considerable work has been done on AGPase and its role in crop productivity, particularly under heat stress, because this enzyme is one of the major enzymes, which catalyses the rate-limiting first committed key enzymatic step of starch biosynthesis. Keeping the above in view, this review focuses on the basic features of AGPase including its structure, regulatory mechanisms involving allosteric regulators, its sub-cellular localization and its genetics. Major emphasis, however, has been laid on the genetics of AGPases and its manipulation for developing high yielding cultivars that will have comparable productivity under heat stress. Some important thermotolerant variants of AGPase, which mainly involve specific amino acid substitutions, have been highlighted, and the prospects of using these thermotolerant variants of AGPase in developing cultivars for heat prone areas have been discussed. The review also includes a brief account on transgenics for AGPase, which have been developed for basic studies and crop improvement.

Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits.

Einkorn wheat (Triticum monococcum) is an ancient grain crop and a close relative of the diploid progenitor (T. urartu) of polyploid wheat. It is the only diploid wheat species having both domesticated and wild forms and therefore provides an excellent system to identify domestication genes and genes for traits of interest to utilize in wheat improvement. Here, we leverage genomic advancements for einkorn wheat using an einkorn reference genome assembly combined with skim-sequencing of a large genetic population of 812 recombinant inbred lines (RILs) developed from a cross between a wild and a domesticated T. monococcum accession. We identify 15,919 crossover breakpoints delimited to a median and average interval of 114 Kbp and 219 Kbp, respectively. This high-resolution mapping resource enables us to perform fine-scale mapping of one qualitative (red coleoptile) and one quantitative (spikelet number per spike) trait, resulting in the identification of small physical intervals (400 Kb to 700 Kb) with a limited number of candidate genes. Furthermore, an important domestication locus for brittle rachis is also identified on chromosome 7A. This resource presents an exciting route to perform trait discovery in diploid wheat for agronomically important traits and their further deployment in einkorn as well as tetraploid pasta wheat and hexaploid bread wheat cultivars.

An Update on Resistance Genes and Their Use in the Development of Leaf Rust Resistant Cultivars in Wheat.

Wheat is one of the most important cereal crops in the world. The production and productivity of wheat is adversely affected by several diseases including leaf rust, which can cause yield losses, sometimes approaching >50%. In the present mini-review, we provide updated information on (i) all Lr genes including those derived from alien sources and 14 other novel resistance genes; (ii) a list of QTLs identified using interval mapping and MTAs identified using GWAS (particular those reported recently i.e., after 2018) and their association with known Lr genes; (iii) introgression/pyramiding of individual Lr genes in commercial/prominent cultivars from 18 different countries including India. Challenges and future perspectives of breeding for leaf rust resistance are also provided at the end of this mini-review. We believe that the information in this review will prove useful for wheat geneticists/breeders, not only in the development of leaf rust-resistant wheat cultivars, but also in the study of molecular mechanism of leaf rust resistance in wheat.

Genome-wide characterization and identification of cyclophilin genes associated with leaf rust resistance in bread wheat (Triticum aestivum L.).

Cyclophilins (CYPs) are a group of highly conserved proteins involved in host-pathogen interactions in diverse plant species. However, the role of CYPs during disease resistance in wheat remains largely elusive. In the present study, the systematic genome-wide survey revealed a set of 81 TaCYP genes from three subfamilies (GI, GII, and GIII) distributed on all 21 wheat chromosomes. The gene structures of TaCYP members were found to be highly variable, with 1-14 exons/introns and 15 conserved motifs. A network of miRNA targets with TaCYPs demonstrated that TaCYPs were targeted by multiple miRNAs and vice versa. Expression profiling was done in leaf rust susceptible Chinese spring (CS) and the CS-Ae. Umbellulata derived resistant IL "Transfer (TR). Three homoeologous TaCYP genes (TaCYP24, TaCYP31, and TaCYP36) showed high expression and three homoeologous TaCYP genes (TaCYP44, TaCYP49, and TaCYP54) showed low expression in TR relative to Chinese Spring. Most of the other TaCYPs showed comparable expression changes (down- or upregulation) in both contrasting TR and CS. Expression of 16 TaCYPs showed significant association (p < 0.05) with superoxide radical and hydrogen peroxide abundance, suggesting the role of TaCYPs in downstream signaling processes during wheat-leaf rust interaction. The differentially expressing TaCYPs may be potential targets for future validation using transgenic (overexpression, RNAi or CRISPR-CAS) approaches and for the development of leaf rust-resistant wheat genotypes.