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Summary The incorporation of resistance genes into wheat commercial varieties is the ideal strategy to combat stripe or yellow rust (YR). In a search for novel resistance genes, we performed a large‐scale genomic association analysis with high‐density 660K single nucleotide polymorphism (SNP) arrays to determine the genetic components of YR resistance in 411 spring wheat lines. Following quality control, 371 972 SNPs were screened, covering over 50% of the high‐confidence annotated gene space. Nineteen stable genomic regions harbouring 292 significant SNPs were associated with adult‐plant YR resistance across nine environments. Of these, 14 SNPs were localized in the proximity of known loci widely used in breeding. Obvious candidate SNP variants were identified in certain confidence intervals, such as the cloned gene Yr18 and the major locus on chromosome 2BL, despite a large extent of linkage disequilibrium. The number of causal SNP variants was refined using an independent validation panel and consideration of the estimated functional importance of each nucleotide polymorphism. Interestingly, four natural polymorphisms causing amino acid changes in the gene TraesCS2B01G513100 that encodes a serine/threonine protein kinase (STPK) were significantly involved in YR responses. Gene expression and mutation analysis confirmed that STPK played an important role in YR resistance. PCR markers were developed to identify the favourable TraesCS2B01G513100 haplotype for marker‐assisted breeding. These results demonstrate that high‐resolution SNP‐based GWAS enables the rapid identification of putative resistance genes and can be used to improve the efficiency of marker‐assisted selection in wheat disease resistance breeding.

The title compound, C25H22N2O2Se, crystallizes in the space groupP21/cwith one molecule in the asymmetric unit. The compound was synthesized by the addition of phenylselenyl bromide to a cyanamide. The phenylselenyl portion and the cyano group, as well as the ketone functional group in the cyclohexa-2,5-dien-1-one portion of the structure, are disordered, with occupancy factors of 0.555 (14) and 0.445 (14).

About two billion people suffer from micronutrient deficiencies worldwide especially with zinc (Zn) and iron (Fe) leading to various health impairments. Genetic biofortification strategies offer sustainable solution to improve the nutrition status of resource-poor people in developing countries. The wheat biofortification breeding program at CIMMYT has made significant progress in terms of development and deployment of Zn-enriched competitive wheat lines with increased yield potential, disease resistance and better processing quality. A decade of research and breeding efforts led to the release of several biofortified wheat varieties in target regions of South Asia and reached about 0.5 million consumers with biofortified wheat products. Breeding for high-Zn concentration has been diversified with progenitors from diverse genetic resources and mainstreaming of grain zinc in CIMMYT wheat breeding pipeline has been initiated to develop next generation of superior biofortified wheat varieties.

Key message Genome-wide association mapping in conjunction with population sequencing map and Ensembl plants was used to identify markers/candidate genes linked to leaf rust, stripe rust and tan spot resistance in wheat. Abstract Leaf rust (LR), stripe rust (YR) and tan spot (TS) are some of the important foliar diseases in wheat (Triticum aestivum L.). To identify candidate resistance genes for these diseases in CIMMYT’s (International Maize and Wheat Improvement Center) International bread wheat screening nurseries, we used genome-wide association studies (GWAS) in conjunction with information from the population sequencing map and Ensembl plants. Wheat entries were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. Using a mixed linear model, we observed that seedling resistance to LR was associated with 12 markers on chromosomes 1DS, 2AS, 2BL, 3B, 4AL, 6AS and 6AL, and seedling resistance to TS was associated with 14 markers on chromosomes 1AS, 2AL, 2BL, 3AS, 3AL, 3B, 6AS and 6AL. Seedling and adult plant resistance (APR) to YR were associated with several markers at the distal end of chromosome 2AS. In addition, YR APR was also associated with markers on chromosomes 2DL, 3B and 7DS. The potential candidate genes for these diseases included several resistance genes, receptor-like serine/threonine-protein kinases and defense-related enzymes. However, extensive LD in wheat that decays at about 5 × 107 bps, poses a huge challenge for delineating candidate gene intervals and candidates should be further mapped, functionally characterized and validated. We also explored a segment on chromosome 2AS associated with multiple disease resistance and identified seventeen disease resistance linked genes. We conclude that identifying candidate genes linked to significant markers in GWAS is feasible in wheat, thus creating opportunities for accelerating molecular breeding. Electronic supplementary material The online version of this article (10.1007/s00122-018-3086-6) contains supplementary material, which is available to authorized users.

Agronomic systems based on zero tillage and residue retention are becoming more important due to their potential for climate change adaptation through the reduction of soil erosion and improved water availability. Denser soil surface conditions and large amounts of crop residues, however, may be a constraint for early plant establishment, especially in irrigated production areas with high yield potential. Genotype by tillage interactions for yield are not well understood and it is unknown whether tillage should be an evaluation factor in breeding programs. Twenty-six CIMMYT bread ( Triticum aestivum ) and durum ( Triticum turgidum ) wheat genotypes, created between 1964 and 2009, were tested for yield and agronomic performance at CIMMYT’s experimental station near Ciudad Obregon, Mexico, over six years. Treatments included conventional and permanent raised beds with full and reduced irrigation. The objectives were to study breeding progress in distinct agronomic systems and to elucidate the importance of tillage and genotype by tillage interaction for yield and agronomic traits. Breeding progress was achieved irrespective of agronomic treatment. Tillage influenced plant growth and number of grains per m 2 in both wheat types. In bread wheat, genotype by tillage interaction was significant for yield, test weight, and growth parameters. However, no cross-over effects were detected and rank changes were small. In durum wheat, genotype by tillage interaction was only significant for plant growth. The results do not indicate the need for separate breeding programs. However, the question of a need for selection under zero tillage to increase breeding progress is yet to be answered.

Since 1984, the ‘Chilero’ spring wheat line developed by CIMMYT has proven to be highly resistant to leaf rust and stripe rust. Amid efforts to understand the basis of resistance of this line, a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero was studied. The parents and RILs were characterized in field trials for leaf rust and stripe rust in three locations in Mexico between 2012 and 2015 and genotyped with DArT-array, DArT-GBS, and SSR markers. A total of 6,168 polymorphic markers were used to construct genetic linkage maps. Inclusive composite interval mapping detected four colocated resistance loci to both rust diseases and two stripe rust resistant loci in the Avocet × Chilero population. Among these, the quantitative trait locus (QTL) on chromosome 1BL was identified as a pleotropic adult plant resistance gene Lr46/Yr29, whereas QLr.cim-5DS/QYr.cim-5DS was a newly discovered colocated resistance locus to both rust diseases in Chilero. Additionally, one new stripe rust resistance locus on chromosome 7BL was mapped in the current population. Avocet also contributed two minor colocated resistance QTLs situated on chromosomes 1DL and 4BS. The flanking SNP markers can be converted to breeder friendly Kompetitive Allele Specific PCR (KASP) markers for wheat breeding programs.

In this work, a method for producing highly reactive catalysed coke from medium and non-coking coal using low-grade iron ore fines as a catalyst through two different alternate routes, namely carbonisation in a stamp charge coke oven and carbonisation in a horizontal tube furnace was attempted. Phenolic resin and petroleum pitch were individually experimented as a binding material to get adequate strength. Effect of process parameters such as coal-to-iron ratio, briquetting load, binder quantity and coking to non-coking coal ratio on the coke properties such as reactivity and mechanical strength was investigated. The SEM and petrography analysis of catalysed coke were used to study the microstructure and its effects on reactivity.

The CIMMYT wheat breeding program aims to develop bread wheat (Triticum aestivum L.) genotypes that have superior grain yields, disease resistance and stress tolerance, along with appropriate quality to satisfy all stakeholders of the wheat value chain. Grain quality for wheat consists of a combination of many defined parameters including grain morphological characteristics, dough and final products properties, all of which are defined by the genotype, the environment and their interactions. Our current approach for improving grain quality is to study grain samples obtained under high yield potential environments with optimum management. To assess the effect of this strategy on quality under stressed environments, 54 genotypes were evaluated for two years under six environmental conditions, including drought and heat stress. Grain morphology (grain density and size), protein content and flour yield were severely affected by the environment, as drought and heat stress had a strong negative effect on all of these characteristics except protein content. Gluten quality (strength and extensibility) was defined more by the genotype, although the environmental effects and the interactions were also important, particularly for gluten extensibility. The current selection strategy for quality traits carried out under optimum conditions was found to be suitable to ensure high quality characteristics across several environments for most of the parameters with an overall positive outcome.

In genomic-enabled prediction, the task of improving the accuracy of the prediction of lines in environments is difficult because the available information is generally sparse and usually has low correlations between traits. In current genomic selection, although researchers have a large amount of information and appropriate statistical models to process it, there is still limited computing efficiency to do so. Although some statistical models are usually mathematically elegant, many of them are also computationally inefficient, and they are impractical for many traits, lines, environments, and years because they need to sample from huge normal multivariate distributions. For these reasons, this study explores two recommender systems: item-based collaborative filtering (IBCF) and the matrix factorization algorithm (MF) in the context of multiple traits and multiple environments. The IBCF and MF methods were compared with two conventional methods on simulated and real data. Results of the simulated and real data sets show that the IBCF technique was slightly better in terms of prediction accuracy than the two conventional methods and the MF method when the correlation was moderately high. The IBCF technique is very attractive because it produces good predictions when there is high correlation between items (environment–trait combinations) and its implementation is computationally feasible, which can be useful for plant breeders who deal with very large data sets.

Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype × environment (G × E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding.

Los esfuerzos recientes en el Campo Experimental Valle de Mexicali del Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, han permitido el desarrollo de variedades de trigo de alto rendimiento y calidad industrial. Entre estos genotipos superiores esta la nueva variedad de trigo harinero Ñipal F2016 que supera el rendimiento de Cachanilla F2000 con 8.1% además es resistente a roya lineal amarilla, resistente a roya de la hoja, septoria, tizón de la espiga y muestra buena calidad industrial. La semilla de Ñipal F2016 está disponible en el Campo Experimental Valle de Mexicali.

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

4-Methylidene substituted oxazolines are shown to be suitable substrates in thermal ene reactions with a variety of common enophiles. These pre-aromatic heterocycles provide access to a variety of adducts in modest to good yields. Interestingly, reaction with nitrosobenzene led to the formation of nitrones rather than the anticipated hydroxyl amine derivatives.

Novel electronic systems displaying exotic physical properties can be derived from complex topological materials through chemical doping. MoTe$_2$, the candidate type-II Weyl semimetal shows dramatically enhanced superconductivity up to 4.1 K upon Re doping in Mo sites. Based on bulk transport and local scanning tunneling microscopy (STM) here we show that Re doping also leads to the emergence of a possible charge density wave (CDW) phase in Re$_{0.2}$Mo$_{0.8}$Te$_2$. In addition, the tunneling $I-V$ characteristics display non-linearity and hysteresis which is commensurate with a hysteresis observed in the change in tip-height ($z$) as a function of applied voltage $V$. The observations indicate an electric field induced hysteretic switching consistent with piezoelectricity and possible ferroelectricity., Comment: To appear in Journal of Physics: Condensed Matter (JPCM)

An investigation of the dearomatization reactions of benzylic thioureas, ureas and guanidines using hypervalent iodine reagents is described. Initial attempts to perform this reaction with methyl aryl ethers was compromised by electrophilic addition leading to the formation of benzo[d]thiazoles. However, inverting the direction of the process and oxidizing the corresponding phenol delivered the desired spiro fused heterocycles in moderate to good yields for all three families.

A method for the Cu-catalyzed, intramolecular dehydrogenative cross-coupling of 3-substituted and 3,4-disubstituted pyrrole–azole systems was developed. The C–H bond in the C2 position was site-selectively activated over the C–H bond in the C5 position of unsymmetrically substituted pyrroles, and the six- and seven-membered annulated pyrrole products were directly accessed in moderate to good yields.

An efficient enantioselective vinylogous aldol reaction of 3-alkylidene oxindoles with -ketoesters by a bifunctional cinchona alkaloid derived thiourea catalyst has been disclosed here. The simultaneous H-bond directing dual activation of vinylogous nucleophile and electrophile afforded high yield (upto 92%) while obtaining excellent stereocontrol (upto 99% ee).

In this communication, the development of a highly enantioselective stereoablative protocol for the chemoselective aryloxylation of 3-bromooxindoles with aryl alcohols have been realized. Promoted by easily available cinchona alkaloid derivatives (C6'-OH) under air- and moisture-tolerant conditions, aryloxylation of a wide range of 3-bromooxindoles bearing a 3'-alkyl substituent proceeded in high yields and excellent enantioselectivities (up to 95% ee). The newly developed strategy expediently provided the 3-phenoxy analogue of the core of alkaloid CPC-1.

The Global Wheat Program, now managed by the CGIAR consortium and led by CIMMYT, initiated wheat breeding about 70 years ago in Mexico. Currently, the key objectives are to develop wheat cultivars that have superior grain yield, durable disease resistance, drought and heat tolerance and meet the processing and end-use quality needs for diverse worldwide processing conditions and products. In this study, the genetic gains in grain quality of semi-dwarf spring wheat cultivars developed from 1965 to 2015 by CIMMYT and related breeding programs of national partners in the target areas were examined. Genetic gains for test weight, thousand kernel weight, grain hardness, flour yield, gluten extensibility and protein content were non-significant, and these traits remained stable despite grain yield increase over years. Positive genetic gains were found for dough strength related parameters mixograph mixing time (0.026 min. per year), torque (0.93 per year) and alveograph W (2.31 J*10–4 per year), and bread-making quality (loaf volume, 1.32 mL per year). We concluded that genetic gains for grain yield of CIMMYT spring wheat cultivars demonstrated by previous studies were not at the expense of processing and end-use quality traits. Both types of traits have been improved in the last 50 years through direct selection ensuring the acceptability of CIMMYT germplasm in the target countries by all wheat value chain stakeholders.

Background Modern agriculture uses hyperspectral cameras that provide hundreds of reflectance data at discrete narrow bands in many environments. These bands often cover the whole visible light spectrum and part of the infrared and ultraviolet light spectra. With the bands, vegetation indices are constructed for predicting agronomically important traits such as grain yield and biomass. However, since vegetation indices only use some wavelengths (referred to as bands), we propose using all bands simultaneously as predictor variables for the primary trait grain yield; results of several multi-environment maize (Aguate et al. in Crop Sci 57(5):1–8, 2017) and wheat (Montesinos-López et al. in Plant Methods 13(4):1–23, 2017) breeding trials indicated that using all bands produced better prediction accuracy than vegetation indices. However, until now, these prediction models have not accounted for the effects of genotype × environment (G × E) and band × environment (B × E) interactions incorporating genomic or pedigree information. Results In this study, we propose Bayesian functional regression models that take into account all available bands, genomic or pedigree information, the main effects of lines and environments, as well as G × E and B × E interaction effects. The data set used is comprised of 976 wheat lines evaluated for grain yield in three environments (Drought, Irrigated and Reduced Irrigation). The reflectance data were measured in 250 discrete narrow bands ranging from 392 to 851 nm (nm). The proposed Bayesian functional regression models were implemented using two types of basis: B-splines and Fourier. Results of the proposed Bayesian functional regression models, including all the wavelengths for predicting grain yield, were compared with results from conventional models with and without bands. Conclusions We observed that the models with B × E interaction terms were the most accurate models, whereas the functional regression models (with B-splines and Fourier basis) and the conventional models performed similarly in terms of prediction accuracy. However, the functional regression models are more parsimonious and computationally more efficient because the number of beta coefficients to be estimated is 21 (number of basis), rather than estimating the 250 regression coefficients for all bands. In this study adding pedigree or genomic information did not increase prediction accuracy.

An efficient, metal-free approach to 3-substituted 3-hydroxyoxindole by DBU-mediated highly diastereoselective addition of aryl acetonitrile to N-protected isatin under mild conditions has been developed. The reaction proceeds smoothly to produce respective cyanomethylated adducts in good yield and excellent diastereoselectivity. Further transformation of the cyanide group allowed the synthesis of an advance intermediate of corresponding (±) CPC analogue. The mechanistic insight toward the aldol-type cyanomethylation of N-tritylisatin with benzyl cyanide was obtained by DFT calculations.

This research concerns the influence of contrasting tillage practices (Zero Tillage (ZT), Permanent Bed (PB) and Conventional tillage (CT)) in main plots and crop rotation (rice-wheat (R-W), rice-maize (R-M) and rice-lentil (R-L)) under rice based cropping system under split plot design with three replication, on soil microbial budgeting in terms of size and structure of microbial population, dehydrogenase activity (DHA), phosphatase activity and fluorescein diacetate (FDA) hydrolysis. Rice base cropping system is advocated as the dominant system prevailing in India due to the better suitability to its landforms and climatic conditions. Within tillage system, SOC was reported higher in zero tillage (0.67%), compared to permanent bed planting (0.66%) and CT (0.62%) at 0-15cm. At 15-30cm depth, zero tillage (0.57%) and PB (0.58%) registered significantly (P < 0.05) higher SOC compared to CT (0.52%). In this study, we estimated the microbial community size and structure, enzymatic activities, mychorrizal root infection and soil organic carbon (SOC). Root and rhizospheric soil samples were collected during two consecutive seasons from a 5 year old long term field experiment on conservation agriculture located at Research farm, Bihar Agricultural College, Sabour and still continuing. ZT treatment resulted higher soil organic carbon content (0.57%), viable microbial population (19.6% higher fungi, 10.63% bacteria, and 12.6% actinomycetes), dehydrogenase activity (5.3-9.11 %), phosphatase activity (9.3-10.57%) which was at par with PB and differed significantly to that of CT treatment. Thus tillage practices and crop diversifications are the important factors affecting soil microbial community size and structure.

Leaf rust (LR) and stripe rust (YR) are important diseases of wheat worldwide. We used 148 recombinant inbred lines (RIL) from the cross of Avocet × Kundan for determining and mapping the genetic basis of adult plant resistance (APR) loci. The population was phenotyped LR and YR for three seasons in field trials conducted in Mexico and genotyped with the diversity arrays technology sequencing (DArT-Seq) and simple sequence repeat markers. The final genetic map was constructed using 2,937 polymorphic markers with an average distance of 1.29 centimorgans between markers. Inclusive composite interval mapping identified two co-located APR quantitative trait loci (QTL) for LR and YR, two LR QTL, and three YR QTL. The co-located resistance QTL on chromosome 1BL corresponded to the pleiotropic APR gene Lr46/Yr29. QLr.cim-2BL, QYr.cim-2AL, and QYr.cim-5AS could be identified as new resistance loci in this population. Lr46/Yr29 contributed 49.5 to 65.1 and 49.2 to 66.1% of LR and YR variations, respectively. The additive interaction between detected QTL showed that LR severities for RIL combining four QTL ranged between 5.3 and 25.8%, whereas the lowest YR severities were for RIL carrying QTL on chromosomes 1BL + 2AL + 6AL. The high-density DArT-Seq markers across chromosomes can be used in fine mapping of the targeted loci and development SNP markers.

Functionalized polycyclic pyrrole-azole structures possessing fused six membered and seven membered rings were directly synthesized via ligand-enabled, Pd-catalyzed, site selective, intramolecular cross couplings of N-substituted pyrrole-azoles. C5-H activation in the presence of a reactive C2-H remains a challenge that needs to be addressed and this was targeted to be resolved through the present approach by specifically generating the cyclized products with 83-100% selectivity. The featured methodology provides a novel disconnection for the synthesis of pyrrole containing alkaloids and medicinal compounds.

New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds. CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5–60.8%, 9.0–14.3%, 2.8–13.9%, and 11.6–29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.

The International Center for Maize and Wheat Improvement (CIMMYT) leads the Global Wheat Program, whose main objective is to increase the productivity of wheat cropping systems to reduce poverty in developing countries. The priorities of the program are high grain yield, disease resistance, tolerance to abiotic stresses (drought and heat), and desirable quality. The Wheat Chemistry and Quality Laboratory has been continuously evolving to be able to analyze the largest number of samples possible, in the shortest time, at lowest cost, in order to deliver data on diverse quality traits on time to the breeders for making selections for advancement in the breeding pipeline. The participation of wheat quality analysis/selection is carried out in two stages of the breeding process: evaluation of the parental lines for new crosses and advanced lines in preliminary and elite yield trials. Thousands of lines are analyzed which requires a big investment in resources. Genomic selection has been proposed to assist in selecting for quality and other traits in breeding programs. Genomic selection can predict quantitative traits and is applicable to multiple quantitative traits in a breeding pipeline by attaining historical phenotypes and adding high-density genotypic information. Due to advances in sequencing technology, genome-wide single nucleotide polymorphism markers are available through genotyping-by-sequencing at a cost conducive to application for genomic selection. At CIMMYT, genomic selection has been applied to predict all of the processing and end-use quality traits regularly tested in the spring wheat breeding program. These traits have variable levels of prediction accuracy, however, they demonstrated that most expensive traits, dough rheology and baking final product, can be predicted with a high degree of confidence. Currently it is being explored how to combine both phenotypic and genomic selection to make more efficient the genetic improvement for quality traits at CIMMYT spring wheat breeding program.

Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R2≈0.16 at 0cM) due to germplasm peerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across all environments representing five QTL. The extensively short LD blocks required us to repeat the analysis with less diverse subset of 220 landraces in which R2 decayed below 0.2 at 0.3cM. The subset GWAS resulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detected in the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical origin of this germplasm through time have permitted for selecting novel resistance loci.

A general strategy for a one-pot stereoselective synthesis of 2-amino-4-(2-furanone)-4H-chromene-3-carbonitriles by reaction of salicylaldehyde, malononitrile and butenolides via a tandem Knoevenagel/Pinner/vinylogous Michael condensation is presented. The β,γ-butenolides gave a syn-selective MCR adduct with a dr up to 11.5 : 1. The mechanistic insight into the MCR was obtained by DFT calculations.

Synthetic hexaploid (SH) wheat (AABBD’D’) is developed by artificially generating a fertile hybrid between tetraploid durum wheat (Triticum turgidum, AABB) and diploid wild goat grass (Aegilops tauschii, D’D’). Over three decades, the International Maize and Wheat Improvement Center (CIMMYT) has developed and utilized SH wheat to bridge gene transfer from Ae. tauschii and durum wheat to hexaploid bread wheat. This is a unique example of success utilizing wild relatives in mainstream breeding at large scale worldwide. Our study aimed to determine the genetic contribution of SH wheat to CIMMYT’s global spring bread wheat breeding program. We estimated the theoretical and empirical contribution of D’ to synthetic derivative lines using the ancestral pedigree and marker information using over 1,600 advanced lines and their parents. The average marker-estimated D’ contribution was 17.5% with difference in genome segments suggesting application of differential selection pressure. The pedigree-based contribution was correlated with marker-based estimates without providing chromosome segment specific variation. Results from international yield trials showed that 20% of the lines were synthetic derived with an average D’ contribution of 15.6%. Our results underline the importance of SH wheat in maintaining and enhancing genetic diversity and genetic gain over years and is important for development of a more targeted introgression strategy. The study provides retrospective view into development and utilization of SH in the CIMMYT Global Wheat Program.

The International Maize and Wheat Improvement Center (CIMMYT)-derived durum wheat line Quetru is moderately resistant to leaf rust and displays disease severities of 15–30% at the adult plant stage. Atil C2000 is moderately susceptible to leaf rust at adult plant stage and displays severities of 20–60%. These two durum wheats were crossed with the susceptible line Atred#1, and the respective recombinant inbred line populations were phenotyped for resistance to leaf rust in field trials in four environments in Mexico. The phenotypic segregation in the Atred#1 × Atil C2000 population was attributed to the pleiotropic adult plant resistance (APR) gene Lr46 based on the closest marker cslv46G22 located within 1.4 cM. Lr46 reduced leaf rust severity by 19.6–35.5%, and it was also identified in the Atred#1 × Quetru population, where it reduced leaf rust severity by 28.5–57.7% depending on the environment. We also identified a putatively novel, race-specific APR gene LrQ in Quetru that is located on the Chromosome 6BL and flanked by SNP markers AX-95144243 and AX-95155193. These two markers have been converted into kompetitive allele–specific PCR (KASP) markers and validated in the population. LrQ was ineffective at the seedling stage but reduced leaf rust severity by 37.3% on average over four field trials. The combination of LrQ and Lr46 resulted in significantly reduced leaf rust severity in the field and could be used to breed improved durum wheat varieties.

Various insect pests attack wheat (Triticum aestivum L.) that can cause significant grain yield losses to the crop. Farmers usually depend on pesticides, however, smallholder farmers often have limited and ill-timed access to control methods, including insecticides. Host plant resistance is an alternative to protect grain yield and reduce costs to farmers. Three of the most serious pests of wheat are Diuraphis noxia (Kurdjumov), Mayetiola destructor (Say), and Cephus pygmeaus L. These pests occur in most of the wheat growing areas. However, they are of high importance in North Africa and West Asia. The aim of this study was to evaluate a set of wheat—alien translocations for resistance against D. noxia, M. destructor and C. pygmeaus. Genotypes of this germplasm set have already been reported to carry resistance against certain wheat aphid species. Genotypes 1RSam.1AL and MA1S.1RLe(1B), displayed high levels of resistance against D. noxia and C. pygmeaus, respectively. While three genotypes showed resistance reaction against M. destructor: 1Re(1D), 7A.7S-L5, and 7A.7S-Gb5. Except for the resistant genotype to C. pygmeaus, the other four genotypes were previously reported to carry resistance against Sitobion avenae Fabricius, Rhopalosiphum padi L. and Schizaphis graminum (Rondani). These five wheat—alien translocations are currently being used in the bread-wheat breeding programs at CIMMYT and ICARDA to transfer the multiple pest resistance in elite germplasm.

The greenbug, Schizaphis graminum Rondani, significantly reduces wheat, Triticum aestivum L., grain yields if not controlled. Host plant resistance (HPR) can protect yield, is environmentally friendly and easy to use. Our objectives were to: (1) identify genomic regions associated with S. graminum resistance in a recombinant inbred line (RIL) population derived from a cross of “Sokoll” (resistant) and “Weebill1” (moderately susceptible), (2) evaluate Sokoll derived breeding germplasm for resistance, and (3) conduct allelism tests between Sokoll and sources carrying resistance genes Gba, Gbb, and Gbd. Resistance was measured quantitatively and qualitatively using a SPAD meter and visual assessments, respectively. We identified a large effect resistance gene on chromosome arm 7DL of Sokoll, herein referred as GbSkl, which contributed up to 24% of the phenotypic variation. Other minor QTL on chromosomes 2B, 3A, and 7B were also identified. The QTL on 2B and 3A originated from Weebill1. Of the Sokoll derived germplasm, 13% displayed resistance. Allelism tests indicated that GbSkl could be allelic or tightly linked to the temporarily designated genes Gba, Gbb, and Gbd. Utility of SPAD to determine quantitative variation in resistance phenotyping is demonstrated and breeding efforts are underway to transfer the resistance from Sokoll to new CIMMYT elite germplasm.

Durum wheat (Triticum turgidum) cultivars developed by the International Maize and Wheat Improvement Center (CIMMYT) are currently grown on more than 8 million hectares worldwide. Because of the lack of information on the genetic basis of resistance to stripe rust (caused by Puccinia striiformis), crosses in a diallel arrangement (without reciprocals) were made among five worldwide resistant cultivars and the susceptible cultivar Local Red. Inheritance of resistance was investigated in seedling and adult plant growth stages of F2 populations, and F3lines. The low seedling infection type of each resistant cultivar, namely Kroub 76, Chonta Inia, Sna 3, Syros, and Arena, was based on the additive action of the same two genes. Each of these genes conferred intermediate infection types when present alone. The field resistance of the cultivars was based on the additive action of the two genes identified in the seedlings and one additional, partially effective adult resistance gene. Segregation for plants with stripe rust severities higher than that of the parents in intercrosses of resistant cultivars indicated that some genetic diversity exists for adult genes. The resistance of these cultivars may prove to be long-lasting, since it results from the combined action of at least three genes.

Smale, M., Singh, R. P., Sayre, K., Pinga li, P., Rajaram, S., and Dubin, H. J. 1998. Estimating the economic impact of breeding nonspecific resistance to leaf rust in modern bread wheats. Plant Dis. 82:1055-1061. Breeding for resistance to rust diseases in wheat is an example of productivity maintenance research. Productivity maintenance research is n ecessary to avoid contractions in the wheat supply curve that result from changes in the biological or physical environment. In this study, the benefits of incorporating nonspecific resistance to leaf rust caused by Puccinia recondita into modern bread wheats (Triticum aestivum) have been estimated using data on resistance genes identified in cultivars, trial data, and area sown to cultivar in the Yaqui Valley, Sonora State, Mexico. In the most pessimistic scenario, the gross benefits generated in the Yaqui Valley from 1970 to 1990 were 17 million U.S. dollars (in 1994 real terms). Even when costs were overstated and benefits were understated, the internal rate of return on capital invested was 13%, well within the range recommended for use in project evaluations by the World Bank. Substantial economic benefits likely are associated with deployment of nonspecific resistance in many wheat-producing areas of developing countries where farmers change cultivars slowly because of delays in cultivar release, incomplete seed markets, and ec onomic factors related to adoption or where disease pressure is heavy and the costs of treating disease outbreaks is high.

Leaf rust, caused by Puccinia triticina, is an important disease of wheat (Triticum aestivum) in China. Sixty-one spring and 102 facultative or winter growth habit wheat cultivars from China and a set of testers, carrying named Lr genes, were evaluated for resistance at the seedling growth stage with an array of Mexican Puccinia triticina races. Variation in seedling infection types of the cultivars was compared with that of the testers, and genes conferring low infection types were postulated. In total, nine named genes, Lr1 (in 13 cultivars), Lr3 (12), Lr3bg (2), Lr10 (1), Lr13 (4), Lr14a (1), Lr16 (49), Lr23 (9), and Lr26 (81), were identified. Thirty-one cultivars displayed intermediate reactions to one or more races that could not be attributed to any named gene. Twenty-eight spring cultivars were also evaluated at two field sites in Mexico using two common races. About half of them displayed good to moderate adult resistance that may be partly due to the presence of slow rusting gene Lr34 in at least seven cultivars. Diversity in adult plant responses of these wheats indicated the presence of additional slow rusting genes. Presence of 1B.1R translocation in 12 wheat cultivars, supposedly derived from intergeneric crosses involving T. durum, Haynaldia villosa, and Avena fatua, indicated that their pedigrees were incorrect.

In this study, we used genotype × environment interactions (G×E) models for hybrid prediction, where similarity between lines was assessed by pedigree and molecular markers, and similarity between environments was accounted for by environmental covariables. We use five genomic and pedigree models (M1-M5) under four cross-validation (CV) schemes: prediction of hybrids when the training set (i) includes hybrids of all males and females evaluated only in some environments (T2FM), (ii) excludes all progenies from a randomly selected male (T1M), (iii) includes all progenies from 20% randomly selected females in combination with all males (T1F), and (iv) includes one randomly selected male plus 40% randomly selected females that were crossed with it (T0FM). Models were tested on a total of 1888 wheat ( L.) hybrids including 18 males and 667 females in three consecutive years. For grain yield, the most complex model (M5) under T2FM had slightly higher prediction accuracy than the less complex model. For T1F, the prediction accuracy of hybrids for grain yield and other traits of the most complete model was 0.50 to 0.55. For T1M, Model M3 exhibited high prediction accuracies for flowering traits (0.71), whereas the more complex model (M5) demonstrated high accuracy for grain yield (0.5). For T0FM, the prediction accuracy for grain yield of Model M5 was 0.61. Including genomic and pedigree gave relatively high prediction accuracy even when both parents were untested. Results show that it is possible to predict unobserved hybrids when modeling genomic general combining ability (GCA) and specific combining ability (SCA) and their interactions with environments.

Inheritance of adult-plant resistance to leaf rust, caused by Puccinia triticina, was studied in the progeny of a one-way diallel cross involving five CIMMYT-derived adult-plant resistant wheat (Triticum aestivum) genotypes and a susceptible wheat ‘Avocet-YrA’. F1 progenies, F2 populations, F2-derived F3, and F4-derived F5 lines were field evaluated under artificial epidemics with leaf rust race MCJ/SP. Adult-plant resistance to leaf rust was incompletely dominant in crosses with the susceptible parent and was found to be controlled by additive interactions of Lr34 with at least two to three additional genes. Transgressive segregation giving rise to plants or lines with higher and lower levels of resistance than the parents was observed in all F2 and F5 derivatives of the resistant-parent intercrosses and suggested that, apart from Lr34, some of the other additive genes were nonallelic. Although specific combining ability was significant in some generations, general combining ability was found to be the major component of variation. Among generations, the estimates of the narrow-sense heritability of adult-plant resistance to leaf rust ranged from 0.67 to 0.97.

Leaf rust, caused by Puccinia triticina, is an important disease of durum wheat (Triticum turgidum subsp. durum) and only a few designated resistance genes are known to occur in this crop. A dominant leaf rust resistance gene in the Chilean durum cv. Llareta INIA was mapped to chromosome arm 7BL through bulked segregant analysis using the amplified fragment length polymorphism (AFLP) technique, and by mapping three polymorphic markers in the common wheat (T. aestivum) International Triticeae Mapping Initiative population. Several simple sequence repeat (SSR) markers, including Xgwm344-7B and Xgwm146-7B, were associated with the leaf rust resistance gene. Resistance response and chromosomal position indicated that this gene is likely to be Lr14a. The SSR markers Xgwm344-7B and Xgwm146-7B and one AFLP marker also differentiated common wheat cv. Thatcher from the near-isogenic line with Lr14a, as well as durum ‘Altar C84’ from durum wheat with Lr14a. This is the first report of the presence of Lr14a in durum wheat, although the gene originally was transferred from emmer wheat ‘Yaroslav’ to common wheat. Lr14a is also present in CIMMYT-derived durum ‘Somateria’ and effective against Mexican and other P. triticina races of durum origin. Lr14a should be deployed in combination with other effective leaf rust resistance genes to prolong its effectiveness in durum wheat.

The stem rust resistance gene Sr24 is effective against most races of Puccinia graminis f. sp. tritici, including race TTKS (syn. Ug99), and is used widely in commercial wheat cultivars worldwide. In 2006, susceptible infection responses were observed on wheat lines and cultivars carrying Sr24 in a field stem rust screening nursery at Njoro, Kenya. We derived 28 single-pustule isolates from stem rust samples collected from the 2006 Njoro nursery. The isolates were evaluated for virulence on 16 North American stem rust differential lines; on wheat lines carrying Sr24, Sr31, Sr38, and SrMcN; and on a wheat cultivar with a combination of Sr24 and Sr31. All isolates were identified as race TTKS with additional virulence on Sr31 and Sr38. These isolates were divided into two groups: group A (seven isolates and the two control isolates), producing a low infection type, and group B (21 isolates), producing a high infection type on Sr24, respectively. Isolates of group B represented a new variant of race TTKS with virulence to Sr24. Eighteen simple sequence repeat (SSR) markers were used to examine the genetic relationship between these two groups of isolates in race TTKS and five North American races (MCCF, QCCQ, RCRS, RTHS, and TPMK) that are representative of distinct lineage groups. All isolates of race TTKS shared an identical SSR genotype and were clearly different from North American races. The virulence and SSR data indicated that the new variant of race TTKS with Sr24 virulence likely has arisen via mutation within the TTKS genetic lineage. We propose to revise the North American stem rust nomenclature system by the addition of four genes (Sr24, Sr31, Sr38, and SrMcN) as the fifth set. This revision recognizes the virulence on Sr31 and differentiates isolates within race TTKS into two separate races: TTKSK and TTKST, with avirulence and virulence on Sr24, respectively. The occurrence of race TTKST with combined virulence on Sr24 and Sr31 has substantially increased the vulnerability of wheat to stem rust worldwide.