LMA or vivipary? Wheat grain can germinate precociously during grain maturation under the cool conditions used to induce late maturity alpha-amylase (LMA).

Introduction: This study found that wheat (Triticum aestivum) grain can germinate precociously during the maturation phase of grain development, a phenomenon called vivipary that was associated with alpha-amylase induction. Farmers receive severe discounts for grain with low falling number (FN), an indicator that grain contains sufficiently elevated levels of the starch-digesting enzyme alpha-amylase to pose a risk to end-product quality. High grain alpha-amylase can result from: preharvest sprouting (PHS)/germination when mature wheat is rained on before harvest, or from late maturity alpha-amylase (LMA) when grain experiences cool temperatures during the soft dough stage of grain maturation (Zadoks growth stage 85). An initial LMA-induction experiment found that low FN was associated with premature visible germination, suggesting that cool and humid conditions caused vivipary. Methods: To examine whether LMA and vivipary are related, controlled environment experiments examined the conditions that induce vivipary, whether LMA could be induced without vivipary, and whether the pattern of alpha-amylase expression during vivipary better resembled PHS or LMA. Results: Vivipary was induced in the soft to hard dough stages of grain development (Zadok's stages 83-87) both on agar and after misting of the mother plant. This premature germination was associated with elevated alpha-amylase activity. Vivipary was more strongly induced under the cooler conditions used for LMA-induction (18°C day/7.5°C night) than warmer conditions (25°C day/18°C night). Cool temperatures could induce LMA with little or no visible germination when low humidity was maintained, and susceptibility to vivipary was not always associated with LMA susceptibility in a panel of 8 varieties. Mature grain preharvest sprouting results in much higher alpha-amylase levels at the embryo-end of the kernel. In contrast, vivipary resulted in a more even distribution of alpha-amylase that was reminiscent of LMA. Discussion: Vivipary can occur in susceptible varieties under moist, cool conditions, and the resulting alpha-amylase activity may result in low FN problems when a farm experiences cool, rainy conditions before the crop is mature. While there are genotypic differences in LMA and vivipary susceptibility, overlapping mechanisms are likely involved since they are similarly controlled by temperature and growth stage, and result in similar patterns of alpha-amylase expression.

Biogenic VOCs Emission Profiles Associated with Plant-Pest Interaction for Phenotyping Applications.

Pest attacks on plants can substantially change plants' volatile organic compounds (VOCs) emission profiles. Comparison of VOC emission profiles between non-infected/non-infested and infected/infested plants, as well as resistant and susceptible plant cultivars, may provide cues for a deeper understanding of plant-pest interactions and associated resistance. Furthermore, the identification of biomarkers-specific biogenic VOCs-associated with the resistance can serve as a non-destructive and rapid tool for phenotyping applications. This research aims to compare the VOCs emission profiles under diverse conditions to identify constitutive (also referred to as green VOCs) and induced (resulting from biotic/abiotic stress) VOCs released in potatoes and wheat. In the first study, wild potato Solanum bulbocastanum (accession# 22; SB22) was inoculated with Meloidogyne chitwoodi race 1 (Mc1), and Mc1 pathotype Roza (SB22 is resistant to Mc1 and susceptible to pathotype Roza), and VOCs emission profiles were collected using gas chromatography-flame ionization detection (GC-FID) at different time points. Similarly, in the second study, the VOCs emission profiles of resistant ('Hollis') and susceptible ('Alturas') wheat cultivars infested with Hessian fly insects were evaluated using the GC-FID system. In both studies, in addition to variable plant responses (susceptibility to pests), control treatments (non-inoculated or non-infested) were used to compare the VOCs emission profiles resulting from differences in stress conditions. The common VOC peaks (constitutive VOCs) between control and infected/infested samples, and unique VOC peaks (induced VOCs) presented only in infected/infested samples were analyzed. In the potato-nematode study, the highest unique peak was found two days after inoculation (DAI) for SB22 inoculated with Mc1 (resistance response). The most common VOC peaks in SB22 inoculated with both Mc1 and Roza were found at 5 and 10 DAI. In the wheat-insect study, only the Hollis showed unique VOC peaks. Interestingly, both cultivars released the same common VOCs between control and infected samples, with only a difference in VOC average peak intensity at 22.4 min retention time where the average intensity was 4.3 times higher in the infested samples of Hollis than infested samples of Alturas. These studies demonstrate the potential of plant VOCs to serve as a rapid phenotyping tool to assess resistance levels in different crops.

Reliable DNA Markers for a Previously Unidentified, Yet Broadly Deployed Hessian Fly Resistance Gene on Chromosome 6B in Pacific Northwest Spring Wheat Varieties.

Hessian fly [Mayetiola destructor (Say)] is a major pest of wheat (Triticum aestivum L.) throughout the United States and in several other countries. A highly effective and economically feasible way to control Hessian fly is with resistant cultivars. To date, over 37 Hessian fly resistance genes have been discovered and their approximate locations mapped. Resistance breeding is still limited, though, by the genes' effectiveness against predominant Hessian fly biotypes in a given production area, genetic markers that are developed for low-throughput marker systems, poorly adapted donor germplasm, and/or the inadequacy of closely linked DNA markers to track effective resistance genes in diverse genetic backgrounds. The purposes of this study were to determine the location of the Hessian fly resistance gene in the cultivar "Kelse" (PI 653842) and to develop and validate Kompetitive Allele Specific PCR (KASP) markers for the resistance locus. A mapping population was genotyped and screened for Hessian fly resistance. The resulting linkage map created from 2,089 Single Nucleotide Polymorphism SNP markers placed the resistance locus on the chromosome 6B short arm, near where H34 has been reported. Three flanking SNPs near the resistance locus were converted to KASP assays which were then validated by fine-mapping and testing a large panel of breeding lines from hard and soft wheat germplasm adapted to the Pacific Northwest. The KASP markers presented here are tightly linked to the resistance locus and can be used for marker-assisted selection by breeders working on Hessian fly resistance and allow confirmation of this Hessian fly resistance gene in diverse germplasm.

Combining Genomic and Phenomic Information for Predicting Grain Protein Content and Grain Yield in Spring Wheat.

Genomics and high throughput phenomics have the potential to revolutionize the field of wheat (Triticum aestivum L.) breeding. Genomic selection (GS) has been used for predicting various quantitative traits in wheat, especially grain yield. However, there are few GS studies for grain protein content (GPC), which is a crucial quality determinant. Incorporation of secondary correlated traits in GS models has been demonstrated to improve accuracy. The objectives of this research were to compare performance of single and multi-trait GS models for predicting GPC and grain yield in wheat and to identify optimal growth stages for collecting secondary traits. We used 650 recombinant inbred lines from a spring wheat nested association mapping (NAM) population. The population was phenotyped over 3 years (2014-2016), and spectral information was collected at heading and grain filling stages. The ability to predict GPC and grain yield was assessed using secondary traits, univariate, covariate, and multivariate GS models for within and across cycle predictions. Our results indicate that GS accuracy increased by an average of 12% for GPC and 20% for grain yield by including secondary traits in the models. Spectral information collected at heading was superior for predicting GPC, whereas grain yield was more accurately predicted during the grain filling stage. Green normalized difference vegetation index had the largest effect on the prediction of GPC either used individually or with multiple indices in the GS models. An increased prediction ability for GPC and grain yield with the inclusion of secondary traits demonstrates the potential to improve the genetic gain per unit time and cost in wheat breeding.

Deep Learning for Predicting Complex Traits in Spring Wheat Breeding Program.

Genomic selection (GS) is transforming the field of plant breeding and implementing models that improve prediction accuracy for complex traits is needed. Analytical methods for complex datasets traditionally used in other disciplines represent an opportunity for improving prediction accuracy in GS. Deep learning (DL) is a branch of machine learning (ML) which focuses on densely connected networks using artificial neural networks for training the models. The objective of this research was to evaluate the potential of DL models in the Washington State University spring wheat breeding program. We compared the performance of two DL algorithms, namely multilayer perceptron (MLP) and convolutional neural network (CNN), with ridge regression best linear unbiased predictor (rrBLUP), a commonly used GS model. The dataset consisted of 650 recombinant inbred lines (RILs) from a spring wheat nested association mapping (NAM) population planted from 2014-2016 growing seasons. We predicted five different quantitative traits with varying genetic architecture using cross-validations (CVs), independent validations, and different sets of SNP markers. Hyperparameters were optimized for DL models by lowering the root mean square in the training set, avoiding model overfitting using dropout and regularization. DL models gave 0 to 5% higher prediction accuracy than rrBLUP model under both cross and independent validations for all five traits used in this study. Furthermore, MLP produces 5% higher prediction accuracy than CNN for grain yield and grain protein content. Altogether, DL approaches obtained better prediction accuracy for each trait, and should be incorporated into a plant breeder's toolkit for use in large scale breeding programs.

Introgression of a Novel Ug99-Effective Stem Rust Resistance Gene into Wheat and Development of Dasypyrum villosum Chromosome-Specific Markers via Genotyping-by-Sequencing (GBS).

Dasypyrum villosum is a wild relative of common wheat (Triticum aestivum L.) with resistance to Puccinia graminis f. tritici, the causal agent of stem rust, including the highly virulent race TTKSK (Ug99). In order to transfer resistance, T. durum-D. villosum amphiploids were initially developed and used as a bridge to create wheat-D. villosum introgression lines. Conserved ortholog set (COS) markers were used to identify D. villosum chromosome introgression lines, which were then subjected to seedling P. graminis f. tritici resistance screening with race TTKSK. A COS marker-verified line carrying chromosome 2V with TTKSK resistance was further characterized by combined genomic in situ and fluorescent in situ analyses to confirm a monosomic substitution line MS2V(2D) (20″ + 1' 2V[2D]). This is the first report of stem rust resistance on 2V, which was temporarily designated as SrTA10276-2V. To facilitate the use of this gene in wheat improvement, a complete set of previously developed wheat-D. villosum disomic addition lines was subjected to genotyping-by-sequencing analysis to develop D. villosum chromosome-specific markers. On average, 350 markers per chromosome were identified. These markers can be used to develop diagnostic markers for D. villosum-derived genes of interest in wheat improvement.

The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping.

Recombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence-based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome-wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans-acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans-acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low-recombining pericentromeric regions of chromosomes.

A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat.

Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.

Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions.

BACKGROUND: The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90 K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations. RESULTS: Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons, and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust in all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) <0.10. GWAS also detected 9 additional genomic regions significantly associated (FDR-adjusted P < 0.10) with seedling resistance to stem rust in the Ethiopian wheat accessions. Many of the identified resistance loci were mapped close to previously identified rust resistance genes; however, three loci on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel. CONCLUSION: Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in this study should be useful in efficiently targeting the associated resistance loci in marker-assisted breeding for rust resistance in Ethiopia and other countries.

Multi-Locus Mixed Model Analysis Of Stem Rust Resistance In Winter Wheat.

Genome-wide association mapping is a powerful tool for dissecting the relationship between phenotypes and genetic variants in diverse populations. With the improved cost efficiency of high-throughput genotyping platforms, association mapping is a desirable method of mining populations for favorable alleles that hold value for crop improvement. Stem rust, caused by the fungus f. sp. is a devastating disease that threatens wheat ( L.) production worldwide. Here, we explored the genetic basis of stem rust resistance in a global collection of 1411 hexaploid winter wheat accessions genotyped with 5390 single nucleotide polymorphism markers. To facilitate the development of resistant varieties, we characterized marker-trait associations underlying field resistance to North American races and seedling resistance to the races TTKSK (Ug99), TRTTF, TTTTF, and BCCBC. After evaluating several commonly used linear models, a multi-locus mixed model provided the maximum statistical power and improved the identification of loci with direct breeding application. Ten high-confidence resistance loci were identified, including SNP markers linked to and and at least three newly discovered resistance loci that are strong candidates for introgression into modern cultivars. In the present study, we assessed the power of multi-locus association mapping while providing an in-depth analysis for its practical ability to assist breeders with the introgression of rare alleles into elite varieties.

Virulence Characterization of Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici in Ethiopia and Evaluation of Ethiopian Wheat Germplasm for Resistance to Races of the Pathogen from Ethiopia and the United States.

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases of wheat in Ethiopia. In total, 97 isolates were recovered from stripe rust samples collected in Ethiopia in 2013 and 2014. These isolates were tested on a set of 18 Yr single-gene differentials for characterization of races and 7 supplementary differentials for additional information of virulence. Of 18 P. striiformis f. sp. tritici races identified, the 5 most predominant races were PSTv-105 (21.7%), PSTv-106 (17.5%), PSTv-107 (11.3%), PSTv-76 (10.3%), and PSTv-41 (6.2%). High frequencies (>40%) were detected for virulence to resistance genes Yr1, Yr2, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27, Yr28, Yr31, Yr43, Yr44, YrExp2, and YrA. Low frequencies (<40%) were detected for virulence to Yr10, Yr24, Yr32, YrTr1, Hybrid 46, and Vilmorin 23. None of the isolates were virulent to Yr5, Yr15, YrSP, and YrTye. Among the six collection regions, Arsi Robe and Tiyo had the highest virulence diversities, followed by Bekoji, while Bale and Holeta had the lowest. Evaluation of 178 Ethiopian wheat cultivars and landraces with two of the Ethiopian races and three races from the United States indicated that the Ethiopian races were more virulent on the germplasm than the predominant races of the United States. Thirteen wheat cultivars or landraces that were resistant or moderately resistant to all five tested races should be useful for breeding wheat cultivars with resistance to stripe rust in both countries.

Association mapping of leaf rust resistance loci in a spring wheat core collection.

KEY MESSAGE: We identified 15 potentially novel loci in addition to previously characterized leaf rust resistance genes from 1032 spring wheat accessions. Targeted AM subset panels were instrumental in revealing interesting loci. Leaf rust is a common disease of wheat, consistently reducing yields in many wheat-growing regions of the world. Although fungicides are commonly applied to wheat in the United States (US), genetic resistance can provide less expensive, yet effective control of the disease. Our objectives were to map leaf rust resistance genes in a large core collection of spring wheat accessions selected from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection (NSGC), determine whether previously characterized race-nonspecific resistance genes could be identified with our panel, and evaluate the use of targeted panels to identify seedling and adult plant resistance (APR) genes. Association mapping (AM) detected five potentially novel leaf rust resistance loci on chromosomes 2BL, 4AS, and 5DL at the seedling stage, and 2DL and 7AS that conditioned both seedling and adult plant resistance. In addition, ten potentially novel race-nonspecific resistance loci conditioned field resistance and lacked seedling resistance. Analyses of targeted subsets of the accessions identified additional loci not associated with resistance in the complete core panel. Using molecular markers, we also confirmed the presence and effectiveness of the race-nonspecific genes Lr34, Lr46, and Lr67 in our panel. Although most of the accessions in this study were susceptible to leaf rust in field and seedling tests, many resistance loci were identified with AM. Through the use of targeted subset panels, more loci were identified than in the larger core panels alone.

Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain conferring resistance to Fusarium head blight.

Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating disease of wheat and barley that leads to reduced yield and mycotoxin contamination of grain, making it unfit for human consumption. FHB is a global problem, with outbreaks in the United States, Canada, Europe, Asia and South America. In the United States alone, total direct and secondary economic losses from 1993 to 2001 owing to FHB were estimated at $7.67 billion. Fhb1 is the most consistently reported quantitative trait locus (QTL) for FHB resistance breeding. Here we report the map-based cloning of Fhb1 from a Chinese wheat cultivar Sumai 3. By mutation analysis, gene silencing and transgenic overexpression, we show that a pore-forming toxin-like (PFT) gene at Fhb1 confers FHB resistance. PFT is predicted to encode a chimeric lectin with two agglutinin domains and an ETX/MTX2 toxin domain. Our discovery identifies a new type of durable plant resistance gene conferring quantitative disease resistance to plants against Fusarium species.

Markers Linked to Wheat Stem Rust Resistance Gene Sr11 Effective to Puccinia graminis f. sp. tritici Race TKTTF.

Wheat stem rust, caused by Puccinia graminis f. sp. tritici, can cause severe yield losses on susceptible wheat varieties and cultivars. Although stem rust can be controlled by the use of genetic resistance, population dynamics of P. graminis f. sp. tritici can frequently lead to defeat of wheat stem rust resistance genes. P. graminis f. sp. tritici race TKTTF caused a severe epidemic in Ethiopia on Ug99-resistant 'Digalu' in 2013 and 2014. The gene Sr11 confers resistance to race TKTTF and is present in 'Gabo 56'. We identified seven single-nucleotide polymorphism (SNP) markers linked to Sr11 from a cross between Gabo 56 and 'Chinese Spring' exploiting a 90K Infinium iSelect Custom beadchip. Five SNP markers were validated on a 'Berkut'/'Scalavatis' population that segregated for Sr11, using KBioscience competitive allele-specific polymerase chain reaction (KASP) assays. Two of the SNP markers, KASP_6BL_IWB10724 and KASP_6BL_IWB72471, were predictive of Sr11 among wheat genetic stocks, cultivars, and breeding lines from North America, Ethiopia, and Pakistan. These markers can be utilized to select for Sr11 in wheat breeding and to detect the presence of Sr11 in uncharacterized germplasm.

Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat.

Aegilops tauschii, the diploid progenitor of the wheat D genome, is a readily accessible germplasm pool for wheat breeding as genes can be transferred to elite wheat cultivars through direct hybridization followed by backcrossing. Gene transfer and genetic mapping can be integrated by developing mapping populations during backcrossing. Using direct crossing, two genes for resistance to the African stem rust fungus race TTKSK (Ug99), were transferred from the Ae. tauschii accessions TA10187 and TA10171 to an elite hard winter wheat line, KS05HW14. BC2 mapping populations were created concurrently with developing advanced backcross lines carrying rust resistance. Bulked segregant analysis on the BC2 populations identified marker loci on 6DS and 7DS linked to stem rust resistance genes transferred from TA10187 and TA10171, respectively. Linkage maps were developed for both genes and closely linked markers reported in this study will be useful for selection and pyramiding with other Ug99-effective stem rust resistance genes. The Ae. tauschii-derived resistance genes were temporarily designated SrTA10187 and SrTA10171 and will serve as valuable resources for stem rust resistance breeding.

Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat.

Wheat production is currently threatened by widely virulent races of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, that are part of the TTKSK (also known as 'Ug99') race group. The diploid D genome donor species Aegilops tauschii (2n = 2x = 14, DD) is a readily accessible source of resistance to TTKSK and its derivatives that can be transferred to hexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD). To expedite transfer of TTKSK resistance from Ae. tauschii, a direct hybridization approach was undertaken that integrates gene transfer, mapping, and introgression into one process. Direct crossing of Ae. tauschii accessions with an elite wheat breeding line combines the steps of gene transfer and introgression while development of mapping populations during gene transfer enables the identification of closely linked markers. Direct crosses were made using TTKSK-resistant Ae. tauschii accessions TA1662 and PI 603225 as males and a stem rust-susceptible T. aestivum breeding line, KS05HW14, as a female. Embryo rescue enabled recovery of F1 (ABDD) plants that were backcrossed as females to the hexaploid recurrent parent. Stem rust-resistant BC1F1 plants from each Ae. tauschii donor source were used as males to generate BC2F1 mapping populations. Bulked segregant analysis of BC2F1 genotypes was performed using 70 SSR loci distributed across the D genome. Using this approach, stem rust resistance genes from both accessions were located on chromosome arm 1DS and mapped using SSR and EST-STS markers. An allelism test indicated the stem rust resistance gene transferred from PI 603225 is Sr33. Race specificity suggests the stem rust resistance gene transferred from TA1662 is unique and this gene has been temporarily designated SrTA1662. Stem rust resistance genes derived from TA1662 and PI 603225 have been made available with selectable molecular markers in genetic backgrounds suitable for stem rust resistance breeding.

Development and characterization of a compensating wheat-Thinopyrum intermedium Robertsonian translocation with Sr44 resistance to stem rust (Ug99).

The emergence of the highly virulent Ug99 race complex of the stem rust fungus (Puccinia graminis Pers. f. sp. tritici Eriks. and Henn.) threatens wheat (Triticum aestivum L.) production worldwide. One of the effective genes against the Ug99 race complex is Sr44, which was derived from Thinopyrum intermedium (Host) Barkworth and D.R. Dewey and mapped to the short arm of 7J (designated 7J#1S) present in the noncompensating T7DS-7J#1L∙7J#1S translocation. Noncompensating wheat-alien translocations are known to cause genomic duplications and deficiencies leading to poor agronomic performance, precluding their direct use in wheat improvement. The present study was initiated to produce compensating wheat-Th. intermedium Robertsonian translocations with Sr44 resistance. One compensating RobT was identified consisting of the wheat 7DL arm translocated to the Th. intermedium 7J#1S arm resulting in T7DL∙7J#1S. The T7DL∙7J#1S stock was designated as TA5657. The 7DL∙7J#1S stock carries Sr44 and has resistance to the Ug99 race complex. This compensating RobT with Sr44 resistance may be useful in wheat improvement. In addition, we identified an unnamed stem rust resistance gene located on the 7J#1L arm that confers resistance not only to Ug99, but also to race TRTTF, which is virulent to Sr44. However, the action of the second gene can be modified by the presence of suppressors in the recipient wheat cultivars.

Spring Wheat Tolerance and Resistance to Heterodera avenae in the Pacific Northwest.

The cereal cyst nematode Heterodera avenae reduces wheat yields in the Pacific Northwest. Previous evaluations of cultivar resistance had been in controlled environments. Cultivar tolerance had not been evaluated. Seven spring wheat trials were conducted in naturally infested fields in three states over 2 years. A split-plot design was used for all trials. Five trials evaluated both tolerance and resistance in 1.8-by-9-m plots treated or not treated with nematicides. Two trials evaluated resistance in 1-m head rows where each wheat entry was paired with an adjacent row of a susceptible cultivar. Cultivars with the Cre1 resistance gene ('Ouyen' and 'Chara') reduced the postharvest density of H. avenae under field conditions, confirming Cre1 parents as useful for germplasm development. Ouyen was resistant but it was also intolerant, producing significantly lower grain yield in controls than in plots treated with nematicides. Susceptible cultivars varied in tolerance. Undefined resistance was identified in one commercial cultivar ('WB-Rockland) and four breeding lines (UC1711, SO900163, SY-B041418, and SY-97621-05). This research was the first systematic field demonstration of potential benefits to be derived through development and deployment of cultivars with resistance plus tolerance to cereal cyst nematode in North America.

Discovery and molecular mapping of a new gene conferring resistance to stem rust, Sr53, derived from Aegilops geniculata and characterization of spontaneous translocation stocks with reduced alien chromatin.

This study reports the discovery and molecular mapping of a resistance gene effective against stem rust races RKQQC and TTKSK (Ug99) derived from Aegilops geniculata (2n = 4x = 28, U(g)U(g)M(g)M(g)). Two populations from the crosses TA5599 (T5DL-5M(g)L·5M(g)S)/TA3809 (ph1b mutant in Chinese Spring background) and TA5599/Lakin were developed and used for genetic mapping to identify markers linked to the resistance gene. Further molecular and cytogenetic characterization resulted in the identification of nine spontaneous recombinants with shortened Ae. geniculata segments. Three of the wheat-Ae. geniculata recombinants (U6154-124, U6154-128, and U6200-113) are interstitial translocations (T5DS·5DL-5M(g)L-5DL), with 20-30% proximal segments of 5M(g)L translocated to 5DL; the other six are recombinants (T5DL-5M(g)L·5M(g)S) have shortened segments of 5M(g)L with fraction lengths (FL) of 0.32-0.45 compared with FL 0.55 for the 5M(g)L segment in the original translocation donor, TA5599. Recombinants U6200-64, U6200-117, and U6154-124 carry the stem rust resistance gene Sr53 with the same infection type as TA5599, the resistance gene donor. All recombinants were confirmed to be genetically compensating on the basis of genomic in situ hybridization and molecular marker analysis with chromosome 5D- and 5M(g)-specific SSR/STS-PCR markers. These recombinants between wheat and Ae. geniculata will provide another source for wheat stem rust resistance breeding and for physical mapping of the resistance locus and crossover hot spots between wheat chromosome 5D and chromosome 5M(g)L of Ae. geniculata.

Development and characterization of wheat-Ae. searsii Robertsonian translocations and a recombinant chromosome conferring resistance to stem rust.

The emergence of a new highly virulent race of stem rust (Puccinia graminis tritici), Ug99, rapid evolution of new Ug99 derivative races overcoming resistance of widely deployed genes, and spread towards important wheat growing areas now potentially threaten world food security. Exploiting novel genes effective against Ug99 from wild relatives of wheat is one of the most promising strategies for the protection of the wheat crop. A new source of resistance to Ug99 was identified in the short arm of the Aegilops searsii chromosome 3S(s) by screening wheat- Ae. searsii introgression libraries available as individual chromosome and chromosome arm additions to the wheat genome. For transferring this resistance gene into common wheat, we produced three double-monosomic chromosome populations (3A/3S(s), 3B/3S(s) and 3D/3S(s)) and then applied integrated stem rust screening, molecular maker analysis, and cytogenetic analysis to identify resistant wheat-Ae. searsii Robertsonian translocation. Three Robertsonian translocations (T3AL·3S(s)S, T3BL·3S(s)S and T3DL·3S(s)S) and one recombinant (T3DS-3S(s)S·3S(s)L) with stem rust resistance were identified and confirmed to be genetically compensating on the basis of genomic in situ hybridization, analysis of 3A, 3B, 3D and 3S(s)S-specific SSR/STS-PCR markers, and C-banding. In addition, nine SSR/STS-PCR markers of 3S(s)S-specific were developed for marker-assisted selection of the resistant gene. Efforts to reduce potential linkage drag associated with 3S(s)S of Ae. searsii are currently under way.