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Leaf rust (LR) and stripe rust (YR) are important diseases in wheat producing areas worldwide and cause severe yield losses under favorable environmental conditions when susceptible varieties are grown. We determined the genetic basis of resistance to LR and YR in variety Borlaug 100 by developing and phenotyping a population of 198 F6 recombinant inbred lines derived from a cross with the susceptible parent Apav#1. LR and YR phenotyping were conducted for 4 and 3 seasons, respectively, at CIMMYT research stations in Mexico under artificial epidemics. Mendelian segregation analyses indicated that 3–5 LR and 2 YR genes conferred resistance in Borlaug 100. Lr46/Yr29 (1BL), Yr17 (2AS) and Yr30 (3BS) were present in the resistant parent and segregated in the RIL population based on characterization by molecular markers linked to these genes. When present alone, Lr46/Yr29 caused average 13% and 16% reductions in LR and YR severities, respectively, in RILs. Similarly, Yr17 and Yr30 reduced YR severities by 57% and 11%, respectively. The Yr30 and the Yr17 translocation were also associated with 27% and 14% reductions, respectively, in LR severity, indicating that the 3BS and 2AS chromosomal regions likely carry new slow rusting LR resistance genes, temporarily designated as LrB1 and LrB2, respectively. Additive effects of Yr30*Yr17, Yr29*Yr17 and Yr29*Yr30 on YR and LR were significant and reduced YR severities by 56%, 55%, and 45%, respectively, and LR severities by 34%, 40%, and 45%, respectively. Furthermore, interaction between the three genes was also significant, with mean reductions of 70% for YR and 54% for LR severities. Borlaug 100, or any one of the 21 lines with variable agronomic traits but carrying all three co-located resistance loci, can be used as resistance sources in wheat breeding programs.

Spot blotch (SB), caused by Bipolaris sorokiniana, is a major fungal disease of wheat in South Asia and South America. Two biparental mapping populations with 232 F2:7 progenies each were generated, with CIMMYT breeding lines CASCABEL and KATH as resistant parents and CIANO T79 as the common susceptible parent. The two populations were evaluated for field SB resistance in CIMMYT’s Agua Fria station for three consecutive cropping seasons, with artificial inoculation. Genotyping was done with the DArTseq platform and approximately 1,500 high quality and nonredundant markers were used for quantitative trait loci (QTL) mapping. In both populations, a major QTL was found on chromosome 5A in the Vrn-A1 region, explaining phenotypic variations of 13.5 to 25.9%, which turned up to be less- or nonsignificant when days to heading and plant height were used as covariates in the analysis, implying a disease escape mechanism. Another major QTL was located on chromosome 5B in CASCABEL, accounting for 8.9 to 21.4% of phenotypic variation. Minor QTL were found on 4A and 4B in CASCABEL; 1B, 4B, and 4D in KATH; and 1B, 2B, and 4B in CIANO T79. Through an analysis of QTL projection onto the IWGSC Chinese Spring reference genome, the 5B QTL in CASCABEL was mapped in the Sb2 region, delimited by the single nucleotide polymorphism marker wsnp_Ku_c50354_55979952 and the simple sequence repeat marker gwm213, with a physical distance of about 14 Mb to the Tsn1 locus.

Key message The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. Abstract The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, ‘Jagger’ and ‘CDC Stanley,’ and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.

Fusarium head blight (FHB) and stem rust are among the most devastating diseases of wheat worldwide. Fhb1 is the most widely utilized and the only isolated gene for FHB resistance, while Sr2 is a durable stem rust resistance gene used in rust-prone areas. The two loci are closely linked on the short arm of chromosome 3B and the two genes are in repulsion phase among cultivars. With climate change and the shift in Fusarium populations, it is imperative to develop wheat cultivars resistant to both diseases. The present study was dedicated to developing wheat germplasm combining Fhb1 and Sr2 resistance alleles in the International Maize and Wheat Improvement Center (CIMMYT)’s elite cultivars’ backgrounds. Four recombinant inbred lines (RILs) in Hartog background that have the resistant Fhb1 and Sr2 alleles in coupled phase linkage were crossed with seven CIMMYT bread wheat lines, resulting in 208 lines. Molecular markers for both genes were employed in addition to the use of pseudo-black chaff (PBC) as a phenotypic marker for the selection of Sr2. At various stages of the selection process, progeny lines were assessed for FHB index, Fusarium damaged kernels (FDK), stem rust, and PBC expression as well as other diseases of interest (stripe rust and leaf spotting diseases). The 25 best lines were selected for CIMMYT’s wheat breeding program. In addition to expressing resistance to FHB, most of these 25 lines have an acceptable level of resistance to other tested diseases. These lines will be useful for wheat breeding programs worldwide and potentially speed up the resistance breeding efforts against FHB and stem rust.

Stripe or yellow rust (YR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss. is a persistent biotic-stress threatening global wheat production. To broaden our understanding of the shared genetic basis of YR resistance across multi-site and multi-year evaluations, we performed a large genome-wide association study using 43,706 YR observations on 23,346 wheat lines from the International Maize and Wheat Improvement Center evaluated between 2013 and 2019 at sites in India, Kenya and Mexico, against predominant races prevalent in the countries. We identified 114 repeatable markers tagging 20 quantitative trait loci (QTL) associated with YR on ten chromosomes including 1D, 2A, 2B, 2D, 3A, 4A, 4D, 5A, 5B and 6B, among which four QTL, QYr.cim-2DL.2, QYr.cim-2AS.1, QYr.cim-2BS.2 and QYr.cim-2BS.3 were significant in more than ten datasets. Furthermore, we report YR-associated allelic fingerprints for the largest panel of wheat breeding lines (52,067 lines) till date, creating substantial opportunities for YR favorable allele enrichment using molecular markers. Overall, the markers and fingerprints reported in this study provide excellent insights into the genetic architecture of YR resistance in different geographical regions, time-periods and wheat germplasm and are a huge resource to the global wheat breeding community for accelerating YR resistance breeding efforts.

Wheat head blast (WHB), caused by the fungus Magnaporthe oryzae pathotype triticum, is a devastating disease affecting South America and South Asia. Despite 30 years of intensive effort, the 2NVS translocation from Aegilops ventricosa contains the only useful source of resistance to WHB effective against M. oryzae triticum isolates. The objective of this study was to identify non-2NVS sources of resistance to WHB among elite cultivars, breeding lines, landraces, and wild-relative accessions. Over 780 accessions were evaluated under field and greenhouse conditions in Bolivia, greenhouse conditions in Brazil, and at two biosafety level-3 laboratories in the United States. The M. oryzae triticum isolates B-71 (2012), 008 (2015), and 16MoT001 (2016) were used for controlled experiments, while isolate 008 was used for field experiments. Resistant and susceptible checks were included in all experiments. Under field conditions, susceptible spreaders were inoculated at the tillering stage to guarantee sufficient inoculum. Disease incidence and severity were evaluated as the average rating for each 1-m-row plot. Under controlled conditions, heads were inoculated after full emergence and individually rated for percentage of diseased spikelets. The diagnostic marker Ventriup-LN2 was used to test for the presence of the 2NVS translocation. Four non-2NVS spring wheat International Maize and Wheat Improvement Center breeding lines (CM22, CM49, CM52, and CM61) and four wheat wild-relatives (A. tauschii TA10142, TA1624, TA1667, and TA10140) were identified as resistant (VS-based varieties. The low frequency of WHB resistance and the increase in aggressiveness of newer M. oryzae triticum isolates highlight the threat that the disease poses to wheat production worldwide and the urgent need to identify and characterize new resistance genes that can be used in breeding for durably resistant varieties.

Fluorescence-capable pyrazine-based polycyclic heteroaromatics for application in bioimaging were synthesized via a simple and concise methodology, and investigation on their fluorescence properties, including the effect of pH on the fluorescence behaviour, and MTT assays were carried out. Interestingly, the fluorescence of the substituted phenanthrenes and triphenylene compounds showed emission in the green to red region and had robust emission that did not get dramatically affected in the biologically relevant pH range. The MTT assay of these compounds on HeLa cells (a human cervical carcinoma cell line) revealed that the compound was well tolerated by cells and was cytocompatible. The molecules were internalized and can be easily used for imaging mammalian cells.

Farmers in northwestern and central India have been exploring to sow their wheat much earlier (October) than normal (November) to sustain productivity by escaping terminal heat stress and to utilize the available soil moisture after the harvesting of rice crop. However, current popular varieties are poorly adapted to early sowing due to the exposure of juvenile plants to the warmer temperatures in the month of October and early November. Therefore, a study was undertaken to identify wheat genotypes suited to October sowing under warmer temperatures in India. A diverse collection of 3322 bread wheat varieties and elite lines was prepared in CIMMYT, Mexico, and planted in the 3rd week of October during the crop season 2012–2013 in six locations (Ludhiana, Karnal, New Delhi, Indore, Pune and Dharwad) spread over northwestern plains zone (NWPZ) and central and Peninsular zone (CZ and PZ, designated as CPZ) of India. Agronomic traits data from the seedling stage to maturity were recorded. Results indicated substantial diversity for yield and yield-associated traits, with some lines showing indications of higher yields under October sowing. Based on agronomic performance and disease resistance, the top 48 lines (and two local checks) were identified and planted in the next crop season (2013–2014) in a replicated trial in all six locations under October sowing (third week). High yielding lines that could tolerate higher temperature in October sowing were identified for both zones, however, performance for grain yield was more promising in the NWPZ. Hence, a new trial of 30 lines was planted only in NWPZ under October sowing. Lines showing significantly superior yield over the best check and the most popular cultivars in the zone were identified. The study suggested that agronomically superior wheat varieties with early heat tolerance can be obtained that can provide yield up to 8 t/ha by planting in the third to fourth week of October.

Bread wheat (Triticum aestivum L.) cultivars adapted to specific environments and resistant to prevalent pathogens are preferred for obtaining high yield. This study aimed to identify wheat genotypes with superior grain yield (GY) and yield associated traits from 168 genotypes of International Maize and Wheat Improvement Center’s 13th Stem Rust Resistance Screening Nursery evaluated over two seasons during 2019 and 2020 under high disease pressure of both stem rust (SR) and yellow rust (YR) in a 21 × 8 α-lattice design with 3 replications in Kenya. Effects due to seasons were significant for YRAud, SRAud, 1000-kernel weight (TKW), days to heading (DH), plant height (PH) and number of spikelets spike−1 (SS), while genotypes and genotypes × season interaction effects were significant for all traits except number of kernels spike−1. Respectively, heritability values of 0.95, 0.93, 0.87, 0.86, 0.77 and 0.75 were observed for area under disease progress curve for SR (SRAud), YR (YRAud), TKW, DH, biomass (BM) and GY. Path analysis showed positive direct effects on GY via PH, SS, BM, and TKW. Biplot analysis identified 16 genotypes with superior desirable traits GY, BM and harvest index. The SR contributed the highest reduction in GY and TKW while YR contributed the most reduction in BM. These identified genotypes with superior GY combined with adequate resistance to both SR and YR are potentially valuable resources for improvement of locally adapted wheat cultivars.

Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line ‘Copio’. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent ‘Apav’ with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37, and Yr17. Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non–race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.

Wheat (Triticum aestivum L.) is the most widely grown cereal crop in the world and is staple food to half the world’s population. The current world population is expected to reach 9.8 billion people by 2050, but food production is not expected to keep pace with demand in developing countries. Significant opportunities exist for traditional grain exporters to produce and export greater amounts of wheat to fill the gap. Karnal bunt, however, is a major threat, due to its use as a non-tariff trade barrier by several wheat-importing countries. The cultivation of resistant varieties remains the most cost-effective approach to manage the disease, but in countries that are free of the disease, genetic improvement is difficult due to quarantine restrictions. Here we report a study on pre-emptive breeding designed to identify linked molecular markers, evaluate the prospects of genomic selection as a tool, and prioritise wheat genotypes suitable for use as parents. In a genome-wide association (GWAS) study, we identified six DArTseq markers significantly linked to Karnal bunt resistance, which explained between 7.6 and 29.5% of the observed phenotypic variation. The accuracy of genomic prediction was estimated to vary between 0.53 and 0.56, depending on whether it is based solely on the identified Quantitative trait loci (QTL) markers or the use of genome-wide markers. As genotypes used as parents would be required to possess good yield and phenology, further research was conducted to assess the agronomic value of Karnal bunt resistant germplasm from the International Maize and Wheat Improvement Center (CIMMYT). We identified an ideal genotype, ZVS13_385, which possessed similar agronomic attributes to the highly successful Australian wheat variety, Mace. It is phenotypically resistant to Karnal bunt infection (

Races belonging to the Ug99 (TTKSK) lineage of the wheat stem rust fungus, carrying complex virulence combinations, and their migration to countries in Africa, Middle East and Asia continue to pose a significant threat to global wheat production. The rapid spread of additional races, e.g., TKTTF or the Digalu lineage, in several countries causing localized epidemics reminds us of the vulnerability of wheat germplasm to stem rust disease, a formidable foe referenced as early as biblical times. A global rust monitoring system reflecting increased surveillance efforts has identified 13 races within the Ug99 lineage in 13 countries and unrelated lineages are emerging, spreading and posing serious threats to wheat production. Race TKTTF has caused localized epidemics in Ethiopia and its variants have been recently implicated in stem rust outbreaks in Europe. Concerted research efforts have resulted in the identification of several new resistance genes and gene combinations for use in breeding. Combining multiple adult plant resistance (APR) genes in high-yielding backgrounds and discovery of new quantitative trait loci conferring stem rust resistance has progressed in the recent years, enhancing the durability of resistance. Effective gene stewardship and new generation breeding materials and cultivars that combine multiple race-specific or minor to intermediate effect APR genes, complemented by active surveillance and monitoring, have helped to limit major epidemics and increase grain yield potential in key target environments.

This paper applies reflectance spectroscopy and Advanced Space borne thermal emission reflection radiometer (ASTER) data processing to delineate dolomite-hosted rock phosphate around Udaipur City, Western India, using visible-near infrared (VNIR) and short wave infrared (SWIR) bands of the ASTER sensor. A number of ASTER image spectra and field spectra (resampled to ASTER bands) of pure dolomite and rock phosphate are compared and found to be consistent in terms of the presence of absorption minima at 2.3 µm for dolomite and the absence of the same feature in the spectra of the rock-phosphate. Before attempting spectral mapping, ASTER SWIR band data are clipped using the spatial extent of host rock; which has been prepared from the reference geological map and consequently updated using VNIR-SWIR derived image enhanced products at selected part of the study areas. Two sub-pixel spectral methods namely adaptive coherence estimator (ACE) and matched filtering (MF) methods are applied to ASTER SWIR bands to delineate rock-phosphate-rich zones within dolomite. The output images of the above algorithms are integrated in a principal component (PC) image to delineate phosphate pixels. A principal component; which has similar sign of Eigen vector loading for ACE and MF abundance image is used to delineate rock phosphate within dolomite. The results are validated in the field using a qualitative colorimetric method and also by comparing image spectra of spectrally anomalous zone with the ASTER resampled laboratory spectra of rock phosphate samples. A number of sporadic but important patches of phosphate rich zones in addition to the main surface exposures of the Jhamar Kotra Mine are confirmed in the field. The proposed method is a novel application of spectral mapping of phosphate deposits in dolomitic and carbonatic rocks and present approach of ASTER data processing can be used to delineate phosphate rich zones occurring within similar geological provinces in any parts of the world.

Key message Two QTL with major effects on DON content reduction were identified on chromosomes 3BL and 3DL, with the former showing minor and the latter showing no effects on FHB resistance. Abstract Deoxynivalenol (DON) contamination in food and feed is a major concern regarding Fusarium head blight (FHB) infection in wheat. However, relatively less attention has been paid on DON compared to FHB. In this study, a FHB-susceptible cultivar ‘NASMA’ was hybridized with a FHB-resistant CIMMYT breeding line ‘IAS20*5/H567.71’ to generate 197 recombinant inbred lines. The population was phenotyped for FHB and associated traits including DON accumulation in spray-inoculated field experiments at CIMMYT-Mexico across four years. Genotyping was performed by using the Illumina Infinium 15 K Beadchip and SSR markers. QTL mapping results indicated that the field FHB resistance was mainly controlled by QTL at Rht-D1 and Vrn-A1, along with a few minor QTL. For DON content, two major QTL were identified: the first located on chromosome 3BL (R2 of 16–24%), showing minor effects on FHB, and the second was on chromosome 3DL (R2 of 10–15%), exhibiting no effect on FHB resistance. It is likely that both DON QTL are new based on comparison with previous studies. This study indicates that resistance to DON accumulation and FHB disease could involve different genes, and the utilization of the two DON QTL in breeding could be helpful in further reducing DON contamination in food and feed. Electronic supplementary material The online version of this article (10.1007/s00122-019-03362-9) contains supplementary material, which is available to authorized users.

Wheat (Triticum aestivum L.) crop health assumes unprecedented significance in being the second most important staple crop of the world. It is host to an array of fungal pathogens attacking the plant at different developmental stages and accrues various degrees of yield losses owing to these. Tilletia indica that causes Karnal bunt (KB) disease in wheat is one such fungal pathogen of high quarantine importance restricting the free global trade of wheat besides the loss of grain yield as well as quality. With global climate change, the disease appears to be shifting from its traditional areas of occurrence with reports of increased vulnerabilities of new areas across the continents. This KB vulnerability of new geographies is of serious concern because once established, the disease is extremely difficult to eradicate and no known instance of its complete eradication using any management strategy has been reported yet. The host resistance to KB is the most successful as well as preferred strategy for its mitigation and control. However, breeding of KB resistant wheat cultivars has proven to be not so easy, and the low success rate owes to the scarcity of resistance sources, extremely laborious and regulated field screening protocols delaying identification/validation of putative resistance sources, and complex quantitative nature of resistance with multiple genes conferring only partial resistance. Moreover, given a lack of comprehensive understanding of the KB disease epidemiology, host-pathogen interaction, and pathogen evolution. Here, in this review, we attempt to summarize the progress made and efforts underway toward a holistic understanding of the disease itself with a specific focus on the host-pathogen interaction between T. indica and wheat as key elements in the development of resistant germplasm. In this context, we emphasize the tools and techniques being utilized in development of KB resistant germplasm by illuminating upon the genetics concerning the host responses to the KB pathogen including a future course. As such, this article could act as a one stop information primer on this economically important and re-emerging old foe threatening to cause devastating impacts on food security and well-being of communities that rely on wheat.

Rust diseases continuously threaten global wheat production: stem rust, leaf rust, and yellow rust caused by Puccinia graminis f. sp. tritici, Puccinia triticina, and Puccinia striiformis f. sp. tritici, respectively. Recent studies indicated that the average losses from all these three rusts reached up to 15.04 million tons per year, which is equivalent to an annual average loss of around US $2.9 billion per year. The major focus of Mexican and worldwide breeding programs is the release of rust resistant cultivars, as this is considered the best option for controlling rust diseases. In Mexico, the emphasis has been placed on genes that confer partial resistance in the adult plant stage and against a broad spectrum of rust races since the 1970s. In this study, a set of the first-generation tall varieties developed and released in the 1940s and 1950s, the first semi-dwarfs, and other releases in Mexico, all of which showed different levels of rust resistance have been phenotyped for the three rust diseases and genotyped. Results of the molecular marker detection indicated that Lr34, Lr46, Lr67, and Lr68 alone or in different gene combinations were present among the wheat cultivars. Flag leaf tip necrosis was present in all cultivars and most were positive for brown necrosis or Pseudo Black Chaff associated with the Sr2 stem rust resistance complex. The phenotypic responses to the different rust infections indicate the presence of additional slow rusting and race-specific resistance genes. The study reveals the association of the slow rusting genes with durable resistance to the three rusts including Ug99 in cultivars bred before the green revolution such as Frontera, Supremo 211, Chapingo 48, Yaqui 50, Kentana 52, Bajio 52, Bajio 53, Yaqui 53, Chapingo 53, Yaktana Tardio 54, and Mayo 54 and their descendants after intercrossing and recombination. These slow rusting genes are the backbone of the resistance in the current Mexican germplasm.

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.

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.

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.

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.

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.

Zhang, J. X., Singh, R. P., Kolmer, J. A., Huerta-Espino, J., Jin, Y., and Anderson, J. A. 2008. Genetics of leaf rust resistance in Brambling wheat. Plant Dis. 92:1111-1118. The CIMMYT-developed spring wheat ‘Brambling’ has a high level of adult-plant resistance (APR) to leaf rust caused by Puccinia triticina. Our objectives were to determine the genetic basis of resistance in seedlings and adult plants and the magnitude of genotype × environment effects on the expression of APR. Brambling was crossed with spring wheat ‘Jupateco 73S’ that is highly susceptible to current predominant P. triticina races in Mexico and the United States. The F1, F2:3, F4:5, F4:6, and F5:7 recombinant inbred lines (RILs) were evaluated under artificial field epidemics in Mexico and St. Paul, MN. The RILs also were tested with five races of P. triticina in greenhouse seedling experiments. A DNA marker was used to postulate the presence of slow-rusting gene Lr34 in the RILs. F1 data suggested strong dominant effect of the APR genes in Brambling. The proportion of homozygous susceptible lines in each generation indicated the presence of three effective resistance genes in adult plants of Brambling in tests in Mexico and three or four genes in tests in St. Paul. The RILs segregated for seedling genes Lr14a and Lr23 and adult-plant slow-rusting gene Lr34 derived from Brambling and Lr17a from Jupateco 73S. Gene Lr23 conditioned APR to P. triticina races present in the St. Paul nursery and accounted for the additional effective gene at this location. Expression of APR was influenced by the environment in the RILs, even though Brambling displayed a consistent response, indicating that stability of APR can be achieved by combinations of slow-rusting resistance genes.

Leaf rust caused by Puccinia triticina Eriks. was observed during the 2007–2008 crop season in the state of Sonora, Mexico on previously resistant durum wheat (Triticum turgidum L.) cvs. Jupare C2001 (Lr27 + 31) and Banamichi C2004. Single uredinial isolates were made from disease samples collected in the field and tested mostly on ‘Thatcher’ differentials at seedling or adult-plant stages (1). The isolates were identified as a new race, BBG/BP, resembling race BBG/BN predominant on durum wheat (2), but with additional virulences to resistance genes Lr27 + Lr31 in Gatcher and adult-plant resistance gene Lr12. The new race was also identified in samples collected from durum wheat in the State of Nuevo Leon during the same season. The avirulence/virulence formula of race BBG/BP is Lr1, 2a, 2b, 2c, 3, 3ka, 3bg, 9, 13, 14a, 15, 16, 17, 18, 19, 21, 22a, 24, 25, 26, 28, 29, 30, 32, 35, 37/Lr10, 11, 12, 14b, 20, 23, 27 + 31, 33. Although virulences to Lr27 + Lr31 and Lr12 is known to occur in P. triticina races predominant on bread wheat (T. aestivum L.) (1), to our knowledge, this is the first report of such virulences in the pathogen population on durum wheat. Pure isolates of race BBG/BP are stored in the CIMMYT leaf rust collection. References: (1) R. P. Singh. Plant Dis. 75:790, 1991. (2) R. P. Singh et al. Plant Dis. 88:703, 2004.

In 2007, new reports of stem rust caused by Puccinia graminis Pers. f. sp. tritici Eriks. in Lorestan and Hamadan provinces of Iran were considered unusual because stem rust had not been recorded previously in the Hamadan area where winter habit wheat cultivars are grown. Detailed investigations in these areas showed significant levels of stem rust in experimental plots and occasionally in farmers' fields, some that showed moderate to high levels of infection. Race analysis of four stem rust samples collected from Borujerd, Hamadan, and Poldokhtar (southwest) and Kelardasht (north) in 2007 was conducted using a modified North American Pgt differential set representing the resistance genes Sr5, 6, 7b, 8a, 9a, 9b, 9d, 9e, 9g, 10, 11, 17, 21, 24, 30, 31, 36, 38, Tmp, and McN, commercial cultivars, and genotypes known to carry the 1B.1R translocation. A race collected from Borujerd in 1997 was also included for comparison. Tests were carried out under standard controlled conditions (1,2). Two isolates from samples collected from Borujerd and Hamadan in 2007 showed high infection types (ITs 33+ to 4) on differential lines carrying resistance genes Sr5, 6, 7b, 8a, 9a, 9b, 9d, 9e, 9g, 10, 11, 17, 21, 30, 31, 38, and McN, and low ITs of ;C1= to 2=, ;C to ;N1=, and 2+ on lines carrying Sr24, Sr36, and SrTmp, respectively. On the basis of the high/low ITs on the 20 differentials in the modified Pgt differential set of North America, the two isolates of Pgt collected from Borujerd and Hamadan in 2007 were identified as race TTKSK. The two isolates from samples collected from Poldokhtar and Kelardasht in 2007 and the isolate collected from Borujerd in 1997 were identified as races TRFSC, TTJQC, and RRHSC, respectively. Race TTKSK identified in the current study produced high ITs of 3+ to 4 on the wheat genotypes Line E*4/Kavkaz, Fed.*4/Kavkaz, Clement, and Mildress and commercial cultivars Falat (Seri 82), Shiroodi (CIMMYT name Attila and Indian name PBW343), Atrak (Kauz), and MV17, all carrying the 1BL.1RS translocation and further confirming virulence for Sr31. The spread of Ug99 to Kenya (1999 to 2002), Ethiopia (2003), and Yemen (2006) suggests progressive migration from Uganda, following the pattern believed to have occurred for the spread of wheat stripe rust pathogen from East Africa in 1986 to India in 1998 (3). Our results are consistent with the TTKSK race identified in Iran migrating from the new African population. Seedling evaluation of Iranian wheat cultivars and advanced lines to isolates of TTKSK from Iran confirmed full susceptibility. These results reinforce the serious threat of race TTKSK to wheat production in Iran. In conclusion, the occurrence of race TTKSK in Iran, the susceptibility of Iranian wheat cultivars to this race, the presence of environmental conditions conducive to disease epidemics in different parts of the country, and the occurrence of the alternate host barberry in many of the mountainous areas of Iran, indicate a new and serious threat to wheat production in Iran and a potentially serious threat to neighboring countries. References: (1) Y. Jin et al. Plant Dis. 91:1096, 2007. (2) Z. A. Pretorius et al. Plant Dis. 84:203, 2000. (3) R. P. Singh et al. CAB Rev. 1 (No. 054), 2006.

Wheat is one of the most important cereal crops in the world. It is the main source of calories and protein for human consumption, especially in developing countries. Over 700 million tons of wheat is produced annually from around 215 million hectares of land worldwide. However, there is a continuous increase in demand for wheat owing to the rise in human population and changes in dietary habits resulting from rising economies in developing countries. Wheat has become an integral part of the daily diet in many developing countries, accounting for 20–60% of daily calorie intake; therefore, to meet the challenge of increasing demand, there is a continuous need to increase wheat yield and production. Recent reports have indicated that at least a 60% increase in wheat production will be required to meet the global demand for wheat by 2050. One of the major limiting factors in achieving increased yields is the yield losses caused by pests and diseases. Out of a documented list of 200 diseases and pests of wheat, about 50 have been considered significant in major wheat-growing regions of the world. Among these, fungal diseases rank the highest in causing considerable damage to wheat, thus hindering wheat production. Pathogenic fungi can be broadly classified as biotrophic or necrotrophic on the basis of their lifestyles. Rust pathogens and powdery mildews are classified as biotrophic, as they survive on living plants, whereas necrotrophs such as Fusarium head blight, Septoria tritici blotch, tan spot, spot blotch, Stagonospora nodorum blotch, and wheat blast can derive nutrition from dead tissue when live plants are not available. Overall, diseases and pests cause 13% actual losses in wheat. In the case of rust pathogens and powdery mildews, new races of these pathogens with new degrees of virulence continue to evolve, thus rendering resistance genes ineffective. Although populations of the pathogens that cause other nonrust diseases remain somewhat constant, there seems to be rather frequent evolution of rust races, largely due to their asexual or sexual modes of reproduction. Although race-specific genes have been deployed widely in breeding, this has resulted in frequent “boom and bust” cycles; therefore, deployment of combinations of race non-specific resistance genes is considered an alternative to enhance the durability of resistance. Overall, significant achievements in breeding resistant wheat cultivars have been made since the onset of the Green Revolution. However, there is still a need to explore and mobilize genetic diversity for disease resistance in modern wheat cultivars through use of advanced biotechnological interventions. Marker-assisted selection, genomic selection, and genome editing are promising tools. Continual emergence of new virulent races of pathogens should be monitored. A combination of molecular breeding and phenotypic evaluations is required for development of high-yielding wheat cultivars with resistance to multiple diseases. This chapter describes wheat diseases caused by biotrophic and necrotrophic fungi, the losses incurred, the current situation, and potential options for resistance breeding.

Despite extensive genetics and breeding research, effective control of leaf rust caused by Puccinia triticina Eriks. and an important foliar disease of wheat, has not been achieved. This is mainly due to the widespread use of race-specific seedling resistance genes, which are rapidly overcome by new virulent races. There is increased emphasis now on the use of race-nonspecific adult plant resistance (APR) genes for durable control of leaf rust. The objective of this study was the evaluation of Aegilops tauschii Coss. (the D-genome donor of bread wheat) for APR, previously known to be a rich source of seedling resistance genes to leaf rust. A geographically diverse collection of A. tauschii maintained by the Wheat Genetics Resource Center was evaluated for APR in the field with a leaf rust composite culture of predominant races. Out of a total of 371 A. tauschii accessions, 50 with low to moderate levels of disease severity were subsequently tested at the seedling stage in the greenhouse with four races and one composite culture of leaf rust. Nine accessions displayed moderate resistance to one or more races of leaf rust at the seedling stage. The remaining 41 seedling-susceptible accessions are potential sources of new APR genes. Accessions from Afghanistan only displayed APR whereas both seedling resistance and APR were common in the Caspian Sea region (Iran and Azerbaijan). The APR in these newly identified A. tauschii accessions will be further characterized for novelty, effectiveness, and race-specificity.

Wheat blast caused by Magnaporthe oryzae pathotype Triticum (MoT) is a threat to wheat production especially in the warmer-humid environments. In Zambia, wheat blast symptoms were observed for the first time on wheat (Triticum aestivum L.) grown in experimental plots and five farmers' fields in Mpika district of Muchinga Province during the 2017-18 rainy season. Infected plants showed the typical wheat blast symptoms with the spike becoming partially or completely bleached with the blackening of the rachis in a short span of time. Incidence of blast symptoms on nearly all wheat heads was high and ranged from 50 to 100%. Examination of diseased plant leaves showed the presence of elliptical, grayish to tan necrotic lesions with dark borders on the leaf often mixed with other foliar diseases. A study was conducted to isolate and identify the causal pathogen(s) using classical and molecular methods and determine the pathogenicity of the detected disease causal agent. Morphobiometrical determination of causal pathogen revealed conidia with characteristic pear shaped 2-septate hyaline spores associated with M. oryzae species. Preliminary polymerase chain reaction screening of six isolates obtained from wheat blast infected samples with diagnostic primers (MoT3F/R) was conducted at ZARI, Zambia, and subsequent analysis of two isolates with MoT3F/R and C17F/R was performed at USDA-ARS, USA. Both experiments confirmed that MoT is the causal agent of wheat blast in Zambia. Further, pathogenicity tests performed with pure culture isolates from samples WS4 and WS5 produced typical blast symptoms on all the six inoculated wheat genotypes. Results of this study indicate that MoT is causing wheat blast in rain-fed wheat grown in Zambia, thus making it the first report of MoT in Zambia and Africa. This inter-continental movement of the pathogen (disease) has serious implication for wheat production and trade that needs to be urgently addressed.

Races belonging to Ug99 lineage of stem rust fungus Puccinia graminis f. sp. tritici (Pgt) continue to pose a threat to wheat (Triticum aestivum L.) production in various African countries. Growing resistant varieties is the most economical and environmentally friendly control measure. Recombinant inbred line (RIL) populations from the crosses of susceptible parent ‘Cacuke’ with the resistant parents ‘Huhwa’ and ‘Yaye’ were phenotyped for resistance at the seedling stage to Pgt race TTKSK (Ug99) and in adult plants in field trials at Njoro, Kenya for two seasons in 2016. Using the Affymetrix Axiom breeders SNP array, two stem rust resistance genes, temporarily designated as SrH and SrY, were identified and mapped on chromosome arm 2BL through selective genotyping and bulked segregant analysis (BSA), respectively. Kompetitive allele specific polymorphism (KASP) markers and simple sequence repeat (SSR) markers were used to saturate chromosome arm 2BL in both RIL populations. SrH mapped between markers cim109 and cim114 at a distance of 0.9 cM proximal, and cim117 at 2.9 cM distal. SrY was flanked by markers cim109 and cim116 at 0.8 cM proximal, and IWB45932 at 1.9 cM distal. Two Ug99-effective stem rust resistance genes derived from bread wheat, Sr9h and Sr28, have been reported on chromosome arm 2BL. Infection types and map position in Huhwa and Yaye indicated that Sr28 was absent in both the parents. However, susceptible reactions produced by resistant lines from both populations against Sr9h-virulent race TTKSF+ confirmed the presence of a common resistance locus Sr9h in both lines. Test of allelism is required to establish genetic relationships between genes identified in present study and Sr9h. Marker cim117 linked to SrH was genotyped on set of wheat lines with Huhwa in the pedigree and is advised to be used for marker assisted selection for this gene, however, a combination of phenotypic and genotypic assays is desirable for both genes especially for selection of Sr9h in breeding programs.

Karnal bunt (KB) of wheat, caused by Tilletia indica, is one of the greatest challenges to grain industry, not because of yield loss, but quarantine regulations that restrict international movement and trade of affected stocks. Genetic resistance is the best way to manage this disease. Although several different sources of resistance have been identified to date, very few of those have been subjected to genetic analyses. Understanding the genetics of resistance, characterization and mapping of new resistance loci can help in development of improved germplasm. The objective of this study was to identify and characterize resistance loci (QTL) in two independent recombinant inbred lines (RILs) populations utilizing different wheat lines as resistance donors. Elite CIMMYT wheat lines Blouk#1 and Huirivis#1 were used as susceptible female parents and WHEAR/KUKUNA/3/C80.1/3∗BATAVIA//2∗WBLL1 (WKCBW) and Mutus as moderately resistant male parents in Pop1 and Pop2 populations, respectively. Populations were evaluated for KB resistance in 2015–16 and 2016–17 cropping seasons at two seeding dates (total four environments) in Cd. Obregon, Mexico. Two stable QTL from each population were identified in each environment: QKb.cim-2B and QKb.cim-3D (Pop1), QKb.cim-3B1 and QKb.cim-5B2 (Pop2). Other than those four QTL, other QTL were detected in each population which were specific to environments: QKb.cim-5B1, QKb.cim-6A, and QKb.cim-7A (Pop1), QKb.cim-3B2, QKb.cim-4A1, QKb.cim-4A2, QKb.cim-4B, QKb.cim-5A1, QKb.cim-5A2, and QKb.cim-7A2 (Pop2). Among the four stable QTL, all but QKb.cim-3B1 were derived from the resistant parent. QKb.cim-2B and QKb.cim-3D in Pop1 and QKb.cim-3B1 and QKb.cim-5B2 in Pop2 explained 5.0–11.4% and 3.3–7.1% phenotypic variance, respectively. A combination of two stable QTL in each population reduced KB infection by 24–33%, respectively. Transgressive resistant segregants lines derived with resistance alleles from both parents in each population were identified. Single nucleotide polymorphism (SNP) markers flanking these QTL regions may be amenable to marker-assisted selection. The best lines from both populations (in agronomy, end-use quality and KB resistance) carrying resistance alleles at all identified loci, may be used for inter-crossing and selection of improved germplasm in future. Markers flanking these QTL may assist in selection of such lines.

Development of novel antivirals, which requires knowledge of the viral life cycle in molecular detail, is a daunting task, involving extensive investments, and frequently resulting in failure. As there exist significant commonalities among virus families in the manner of host interaction, identifying and targeting common rather than specific features may lead to the development of broadly useful antivirals. Here, we have targeted the 3C protease of Hepatitis A Virus (HAV), a feco‐orally transmitted virus of the family Picornaviridae, for identification of potential antivirals. The 3C protease is a viable drug target as it is required by HAV, as well as by other picornaviruses, for post‐translational proteolysis of viral polyproteins and for inhibiting host innate immune pathways. Computational screening, followed by chemical synthesis and experimental validation resulted in identification of a few compounds which, at low micromolar concentrations, could inhibit HAV 3C activity. These compounds were further tested experimentally against the 3C protease of Human Rhinovirus, another member of the Picornaviridae family, with comparable results. Computational studies on 3C proteases from other members of the picornavirus family have indicated that the compounds identified could potentially be generic inhibitors for picornavirus 3C proteases., The active site residues of 3C proteases show a significant intraspecies overlap among most common members of the picornavirus family. The similarity of the interacting residues could be utilized for designing broad‐range generic inhibitors against the 3C proteases of the picornavirus family.

Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production. Clare Lewis et al. report the first identification in nearly 60 years of a cultivated wheat plant infected with the fungal pathogen Puccinia graminis f.sp. tritici (wheat stem rust) in the United Kingdom. They find that only 20% of UK wheat varieties are resistant to this strain and urge growers to resume resistance breeding programs.

Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is a serious problem in oilseed rape and mustard worldwide. Locating effective sources of host resistance to this disease offers the best long term prospects for its improved management. For this reason, 19 Brassica napus genotypes from Australia (6), China (7) and India (6) and 34 Brassica juncea genotypes from Australia (6), China (3) and India (25), were screened for resistance to SSR under field conditions using a stem inoculation test. There were significant differences ( P B. napus and B. juncea test genotypes in relation to the stem lesion length. The most resistant B. napus genotypes were Oscar from Australia, Zhongyou-za No. 8, Fan 168 and Ding 110 from China, all with stem lesion lengths ≤4.1 cm. The most susceptible B. napus were GSL2 from India, and 03-p74-11 from China, with stem lesion lengths ≥12 cm. The most resistant B. juncea genotypes were Aravali and Bio-902 from India with stem lesion lengths ≤5.7 cm; while the most susceptible were JM018 from Australia, Xinyou 8 and Xinyou 9 from China, Sanjucta Ascsh and Basanti from India, all with stem lesion lengths >10 cm. In particular, this high level resistance in B. napus Oscar from Australia, Zhongyou-za No. 8, Fan 168 and Ding 110 from China provides sources of resistance for oilseed Brassica breeding programs in Australia; particularly resistance to pathotype 76, the dominant prevailing S. sclerotiorum pathotype. It is noteworthy that progenies from B. napus crosses of Oscar with Ding 110 express isolate-independent host resistance, making Oscar and Ding 110, and potentially their progenies, an ideal target to exploit in developing new commercial rapeseed cultivars that not only have more effective resistance to SSR, but resistance that is effective across multiple pathotypes of this pathogen. These findings ensure successful management of SSR based on host resistance rather than fungicides is now possible providing breeders take the opportunities now presented.

Tan spot, a major foliar disease of wheat, is caused by an ascomycete Pyrenophora tritici-repentis (PTR). Association mapping on germplasm collection is a novel approach for the discovery and validation of major genes/QTLs for a trait. Linkage disequilibrium, the genetic basis of association mapping, can be an important tool to identify genomic regions associated with tan spot resistance. Association analysis utilizing the population structure and additive genetic covariance between relatives was conducted for tan spot resistance on a set of historical bread wheat germplasm comprising of 170 lines developed at CIMMYT, Mexico with the genotypic data generated with 1644 molecular markers. Tan spot resistance data was obtained by screening the germplasm with PTR race 1 isolate Ptr-1. Two weeks old seedlings were inoculated and rated 8 days later on a lesion type disease scale. Three experiments were conducted in the greenhouse with each experiment as arranged in completely randomized design with two replicates. Over half of the entries were resistant to tan spot induced by PTR race 1. The genome-wide scan revealed significant marker-phenotype associations on the short arm of chromosomes 1A, 1B, and 6B and long arm of chromosomes 4A, 6A1, 6A2, 2B, 3B, 5B, and 7B that play an important role in conferring resistance to tan spot. Although some genomic regions contributing to tan spot resistance have been previously identified; novel regions on long arm of chromosomes 6A1, 6A2, and 7B, were identified in this study. Findings of this study reveal that a high proportion of CIMMYT wheat germplasm is resistant to tan spot caused by PTR race 1 and genetic base of CIMMYT germplasm resistance involves race specific and non-race specific resistance genes.

Spot blotch (SB) caused by Cochliobolus sativus is a serious biotic stress to wheat in warm and humid areas, particularly South Asia (SA). In order to support South Asian farmers to combat SB, International Maize and Wheat Improvement Center (CIMMYT) established an efficient SB screening system at Agua Fria, Mexico and developed a nursery under the project - Cereal Systems Initiative for South Asia (CSISA). The materials used to form CSISA-SB nursery were selected from advanced breeding lines from different wheat breeding programs at CIMMYT. Seed of CSISA-SB nursery was produced at disease-free plots at El Batan and Mexicali, and distributed to SA after rigorous seed health checks. The 4th CSISA-SB, made available in 2012, comprised 50 entries including two resistant and two susceptible checks. The nursery was evaluated in seven locations in Mexico, India, and Bangladesh in the 2012–13 cropping season. The results indicated that although few lines exhibited stable resistance across locations due to strong G × E interaction, promising lines with SB resistance and good agronomy can still be identified in each location. The two most promising lines showing consistent spot blotch resistance across the regions were CHUKUI#1 (CIMMYT germplasm bank identification number, GID 6178575) and VAYI#1 (GID 6279248). These lines could be promoted as sources of SB resistance or directly released as cultivars in SA.

Stripe rust, caused by Puccinia striiformis f. sp. tritici W., is a devastating disease of wheat worldwide. A new stripe rust resistance gene with moderate seedling and adult plant resistance was mapped using an F5 recombinant inbred line (RIL) population developed from the cross of the resistant parent ‘Almop’ with the susceptible parent ‘Avocet’. The parents and RILs were phenotyped for seedling stripe rust response variation in a greenhouse and in field trials at Toluca, Mexico for 2 years. Almop showed moderate levels of resistance at both seedling and adult plant stages compared with the highly susceptible response of Avocet. The distribution of homozygous resistant, homozygous susceptible, and segregating RILs conformed to segregation at a single locus. Seedlings and adult plant responses were correlated, indicating that the same gene conferred resistance at both stages. A bulk segregant analysis approach with widely distributed simple sequence repeat (SSR) markers mapped the resistance gene to the distal region of the long arm of chromosome 4A. The SSR marker wmc776 cosegregated with this gene, whereas markers wmc219 and wmc313 were tightly linked and both located at 0.6 centimorgans. The resistance locus was designated Yr60.

As an important cereal disease in humid and semi-humid areas, Fusarium head blight (FHB) has caused severe epidemics on wheat (Triticum aestivum L.) in different countries worldwide. By causing both yield loss and quality degradation, FHB presents a two-fold threat to farmers and consumers. Since the beginning of FHB research at the International Maize and Wheat Improvement Centre (CIMMYT) in the early 1980s, a large-scale FHB screening has been conducted to identify and incorporate new resistance genes into elite CIMMYT germplasm. Candidates of the 15th Fusarium head blight screening nursery (FHBSN) were derived from different CIMMYT wheat breeding programs and were tested for 3 years successively in El Batan, Mexico, before being included in the 15th FHBSN set. From 2010 to 2012, a set of 44 out of 2794 lines were gradually selected depending on their FHB indices, pedigree information, and phenological traits like plant height and days to heading. The performance of these lines varied across years under different disease pressure, but they all showed high level of resistance compared to the susceptible checks. In 2013, the nursery was again evaluated in El Batan, as well as in artificially inoculated field trials in Norway, Uruguay, the Netherlands, and Japan (2014), and in naturally infected experiments in Toluca, Mexico, and Canada. Although not all lines demonstrated strong resistance across environments, promising lines with good FHB resistance can still be identified in each location. The genotypes were haplotyped with PCR-based markers for ten loci on seven chromosomes associated with known FHB resistance, and the results suggested that 24 of the genotypes (55 %) carried the 4BS QTL as in Wuhan 1, which was the most frequent QTL in this nursery, and the 7A QTL as in T. dicoccoides was noticed in five (11 %) of the genotypes. The resistance QTLs on chromosomes 3B, 5A and 6B as in Sumai 3 and 3A as in T. dicoccoides were not detected in any of the genotypes denoting the uniqueness of these lines. Fifteen (34 %) of the genotypes may not carry any of the ten QTLs examined. The results provide valuable information that could be successfully utilized by breeders to select resistant parents for crosses since novel resistance sources were detected for better targeted crosses toward diversifying and/or pyramiding FHB resistance.

© 2017 Lan, Hale, Herrera-Foessel, Basnet, Randhawa, Huerta-Espino, Dubcovsky and Singh. Growing resistant wheat varieties is a key method of minimizing the extent of yield losses caused by the globally important wheat leaf rust (LR) and stripe rust (YR) diseases. In this study, a population of 186 F8recombinant inbred lines (RILs) derived from a cross between a synthetic wheat derivative (PI610750) and an adapted common wheat line (cv. “UC1110”) were phenotyped for LR and YR response at both seedling and adult plant stages over multiple seasons. Using a genetic linkage map consisting of single sequence repeats and diversity arrays technology markers, in combination with inclusive composite interval mapping analysis, we detected a new LR adult plant resistance (APR) locus, QLr.cim-2DS, contributed by UC1110. One co-located resistance locus to both rusts, QLr.cim-3DC/QYr.cim-3DC, and the known seedling resistance gene Lr26 were also mapped. QLr.cim-2DS and QLr.cim-3DC showed a marginally significant interaction for LR resistance in the adult plant stage. In addition, two previously reported YR APR loci, QYr.ucw-3BS and Yr48, were found to exhibit stable performances in rust environments in both Mexico and the United States and showed a highly significant interaction in the field. Yr48 was also observed to confer intermediate seedling resistance against Mexican YR races, thus suggesting it should be re-classified as an allstage resistance gene. We also identified 5 and 2 RILs that possessed all detected YR and LR resistance loci, respectively. With the closely linked molecular markers reported here, these RILs could be used as donors for multiple resistance loci to both rusts in wheat breeding programs.

The leaf spotting diseases in wheat that include Septoria tritici blotch (STB) caused by , Stagonospora nodorum blotch (SNB) caused by , and tan spot (TS) caused by pose challenges to breeding programs in selecting for resistance. A promising approach that could enable selection prior to phenotyping is genomic selection that uses genome-wide markers to estimate breeding values (BVs) for quantitative traits. To evaluate this approach for seedling and/or adult plant resistance (APR) to STB, SNB, and TS, we compared the predictive ability of least-squares (LS) approach with genomic-enabled prediction models including genomic best linear unbiased predictor (GBLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes Cπ (BC), Bayesian least absolute shrinkage and selection operator (BL), and reproducing kernel Hilbert spaces markers (RKHS-M), a pedigree-based model (RKHS-P) and RKHS markers and pedigree (RKHS-MP). We observed that LS gave the lowest prediction accuracies and RKHS-MP, the highest. The genomic-enabled prediction models and RKHS-P gave similar accuracies. The increase in accuracy using genomic prediction models over LS was 48%. The mean genomic prediction accuracies were 0.45 for STB (APR), 0.55 for SNB (seedling), 0.66 for TS (seedling) and 0.48 for TS (APR). We also compared markers from two whole-genome profiling approaches: genotyping by sequencing (GBS) and diversity arrays technology sequencing (DArTseq) for prediction. While, GBS markers performed slightly better than DArTseq, combining markers from the two approaches did not improve accuracies. We conclude that implementing GS in breeding for these diseases would help to achieve higher accuracies and rapid gains from selection.

Leaf rust, stripe rust, and stem rust pose a significant threat to global wheat production. Growing rust resistant cultivars is the most efficient and environment friendly method to reduce yield losses. Genetic analysis is undertaken to identify genes and study their roles in conferring rust resistance in a given wheat background. This chapter summarizes the protocol for genetic analysis of rust resistance at both seedling and adult plant stages. Additionally, it examines statistical analysis and related software to characterize quantitative trait loci (QTL) linked with rust resistance.