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Key message The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5AmS, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22. Abstract The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7AmL, completely linked to Sr22. SrTm5 displayed a different race specificity compared to Sr22 indicating that they are distinct. Sequencing of the Sr22 homolog in PI 306540 revealed a novel haplotype. Characterization of the segregating populations with Pgt race QFCSC revealed an additional resistance gene on chromosome arm 5AmS that was assigned the official name Sr60. This gene was also effective against races QTHJC and SCCSC but not against TTKSK (a Ug99 group race). Using two large mapping populations (4046 gametes), we mapped Sr60 within a 0.44 cM interval flanked by sequenced-based markers GH724575 and CJ942731. These two markers delimit a 54.6-kb region in Brachypodium distachyon chromosome 4 and a 430-kb region in the Chinese Spring reference genome. Both regions include a leucine-rich repeat protein kinase (LRRK123.1) that represents a potential candidate gene. Three CC–NBS–LRR genes were found in the colinear Brachypodium region but not in the wheat genome. We are currently developing a Bacterial Artificial Chromosome library of PI 306540 to determine which of these candidate genes are present in the T. monococcum genome and to complete the cloning of Sr60. Electronic supplementary material The online version of this article (doi:10.1007/s00122-017-3024-z) contains supplementary material, which is available to authorized users.

We detected the deletion breakpoints of wheat ph1b mutant and the actual size of the deletion. Also, we developed ph1b deletion-specific markers useful for ph1b-mediated gene introgression and genome studies. The Ph1 (pairing homoeologous) locus has been considered a major genetic system for the diploidized meiotic behavior of the allopolyploid genome in wheat. It functions as a defense system against meiotic homoeologous pairing and recombination in polyploid wheat. A large deletion of the genomic region harboring Ph1 on the long arm of chromosome 5B (5BL) led to the ph1b mutant in hexaploid wheat ‘Chinese Spring,’ which has been widely used to induce meiotic homoeologous recombination for gene introgression from wild grasses into wheat. However, the breakpoints and physical size of the deletion remain undetermined. In the present study, we first anchored the ph1b deletion on 5BL by the high-throughput wheat 90K SNP assay and then delimited the deletion to a genomic region of 60,014,523 bp by chromosome walking. DNA marker and sequence analyses detected the nucleotide positions of the distal and proximal breakpoints (DB and PB) of the ph1b deletion and the deletion junction as well. This will facilitate understanding of the genomic region harboring the Ph1 locus in wheat. In addition, we developed user-friendly DNA markers specific for the ph1b deletion. These new ph1b deletion-specific markers will dramatically improve the efficacy of the ph1b mutant in the meiotic homoeologous recombination-based gene introgression and genome studies in wheat and its relatives.

A new gene for adult plant leaf rust resistance in wheat was mapped to chromosome 3BL. This gene was designated as Lr77. ‘Santa Fe’ is a hard red winter cultivar that has had long-lasting resistance to the leaf rust fungus, Puccinia triticina. The objective of this study was to determine the chromosome location of the adult plant leaf rust resistance in Santa Fe wheat. A partial backcross line of ‘Thatcher’ (Tc) wheat with adult plant leaf rust resistance derived from Santa Fe was crossed with Thatcher to develop a Thatcher//Tc*2/Santa Fe F6 recombinant inbred line (RIL) population. The RIL population and parental lines were evaluated for segregation of leaf rust resistance in three field plot tests and in an adult plant greenhouse test. A genetic map of the RIL population was constructed using 90,000 single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. A significant quantitative trait locus for reduction of leaf rust severity in all four tests was found on chromosome 3BL that segregated as a single adult plant resistance gene. The RILs with the allele from the resistant parent for SNP marker IWB10344 had lower leaf rust severity and a moderately resistant to moderately susceptible response compared to the susceptible RILs and Thatcher. The gene derived from Santa Fe on chromosome 3BL was designated as Lr77. Kompetitive allele-specific polymerase chain reaction assay markers linked to Lr77 on 3BL should be useful for selection of wheat germplasm with this gene.

Oat crown rust is one of the most damaging diseases of oat. We identified a new source of resistance and developed KASP and TaqMan markers for selection in breeding programs. A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plants are resistant with no virulent isolates encountered in over 8 years of testing. Resistance was incorporated into hexaploid oat by embryo rescue, colchicine chromosome doubling followed by backcrosses with a hexaploid parent, and selection for stable transmission of resistance. To mitigate flag leaf and panicle chlorosis/necrosis associated with the resistance, crosses were made with derived resistant lines to breeding lines of divergent parentage followed by selection. Subsequently, two F2 sister lines, termed MNBT1020-1 and MNBT1021-1, were identified in which the chlorosis/necrosis was reduced. These two lines performed well in replicated multi-location state trials in 2015 and 2016 out-yielding all cultivar entries. Segregating F2:3 plants resulting from crosses of MNBT lines to susceptible parents were genotyped with the oat 6K SNP array, and SNP loci with close linkage to the resistance were identified. KASP assays generated from linked SNPs showed accurate discrimination of the resistance in derivatives of the resistant MNBT lines crossed to susceptible breeding lines. A TaqMan marker was developed and correctly identified homozygous resistance in over 95% of 379 F4 plants when rust was scored in F4:5 plants in the field. Thus, a novel highly effective resistance and associated molecular markers are available for use in breeding, genetic analysis, and functional studies.

A gene for Ug99 resistance from wheat landrace CItr 4311 was detected on the long arm of chromosome 2B. Wheat landrace CItr 4311 has seedling resistance to stem rust caused by Puccinia graminis f. sp. tritici race TTKSK and field resistance to the Ug99 race group. Parents, F1 seedlings, 121 doubled haploid (DH) lines, and 124 recombinant inbred lines (RILs) developed from a cross between CItr 4311 and the susceptible line LMPG-6 were evaluated for seedling resistance to race TTKSK. Goodness-of-fit tests indicated that a single dominant gene in CItr 4311 conditioned the TTKSK resistance. The 90 K wheat iSelect SNP platform was used to genotype parents and the DH population. The seedling resistance locus was mapped to the chromosome arm 2BL. Parents and the DH population were evaluated for field resistance in Kenya. One major QTL for the field resistance was consistently detected in the same region on 2BL as the seedling resistance. Using KASP assays, five linked SNP markers were used to verify the result in the 124 RIL, 35 wheat accessions, 46 DH lines from the LMPG-6/PI 165194 cross and F1 seedlings, and susceptible bulks derived from crosses between six resistant landraces with LMPG-6. Race specificity, mapping results, and haplotype similarity with lines with Sr9h (Gabo 56, Timstein, and PI 670015), support the hypothesis that the Sr gene in CItr 4311 and the landraces is Sr9h. The KASP assays developed in this study will be useful for pyramiding the TTKSK resistance from CItr 4311 with other Sr genes effective against Ug99.

This research characterized the genetics of resistance of wild barley accession PI 466423 to a widely virulent pathotype of Cochliobolus sativus . Breeding lines were identified that combine the Midwest Six-rowed Durable Resistance Haplotype and resistance to the virulent isolate ND4008. Spot blotch, caused by Cochliobolus sativus, is a historically important foliar disease of barley (Hordeum vulgare L.) in the Upper Midwest region of the USA. However, for the last 50 years this disease has been of little consequence due to the deployment of resistant six-rowed malting cultivars. These durably resistant cultivars carry the Midwest Six-rowed Durable Resistant Haplotype (MSDRH) comprised of three Quantitative Trait Loci (QTL) on chromosomes 1H, 3H and 7H, originally contributed by breeding line NDB112. Recent reports of C. sativus isolates (e.g. ND4008) with virulence on NDB112 indicate that widely grown cultivars of the region are vulnerable to spot blotch epidemics. Wild barley (H. vulgare ssp. spontaneum), the progenitor of cultivated barley, is a rich source of novel alleles, especially for disease resistance. Wild barley accession PI 466423 is highly resistant to C. sativus isolate ND4008. To determine the genetic architecture of resistance to isolate ND4008 in PI 466423, we phenotyped and genotyped an advanced backcross population (N = 244) derived from the wild accession and the recurrent parent ‘Rasmusson’, a Minnesota cultivar with the MSDRH. Disease phenotyping was done on BC2F4 seedlings in the greenhouse using isolate ND4008. The Rasmusson/PI 466423 population was genotyped with 7842 single nucleotide polymorphic markers. QTL analysis using composite interval mapping revealed four resistance loci on chromosomes 1H, 2H, 4H and 5H explaining 10.3, 7.4, 6.4 and 8.4 % of the variance, respectively. Resistance alleles on chromosomes 1H, 4H and 5H were contributed by PI 466423, whereas the one on chromosome 2H was contributed by Rasmusson. All four resistance QTL are likely coincident with previously identified QTL. Agronomically advanced two- and six-rowed lines combining the MSDRH and resistance alleles to isolate ND4008 have been identified and are being utilized in breeding. These results reaffirm the value of using wild relatives as a source of novel resistance alleles.

New molecular markers were developed and mapped to the FHB resistance QTL region in high resolution. Micro-collinearity of the QTL region with rice and Brachypodium was revealed for a better understanding of the genomic region. The wild emmer wheat (Triticum dicoccoides)-derived Fusarium head blight (FHB) resistance quantitative trait locus (QTL) Qfhs.ndsu-3AS previously mapped to the short arm of chromosome 3A (3AS) in a population of recombinant inbred chromosome lines (RICLs). This study aimed to attain a better understanding of the genomic region harboring Qfhs.ndsu-3AS and to improve the utility of the QTL in wheat breeding. Micro-collinearity of the QTL region with rice chromosome 1 and Brachypodium chromosome 2 was identified and used for marker development in saturation mapping. A total of 42 new EST-derived sequence tagged site (STS) and simple sequence repeat (SSR) markers were developed and mapped to the QTL and nearby regions on 3AS. Further comparative analysis revealed a complex collinearity of the 3AS genomic region with their collinear counterparts of rice and Brachypodium. Fine mapping of the QTL region resolved five co-segregating markers (Xwgc1186/Xwgc716/Xwgc1143/Xwgc501/Xwgc1204) into three distinct loci proximal to Xgwm2, a marker previously reported to be closely linked to the QTL. Four other markers (Xwgc1226, Xwgc510, Xwgc1296, and Xwgc1301) mapped farther proximal to the above markers in the QTL region with a higher resolution. Five homozygous recombinants with shortened T. dicoccoides chromosomal segments in the QTL region were recovered by molecular marker analysis and evaluated for FHB resistance. Qfhs.ndsu-3AS was positioned to a 5.2 cM interval flanked by the marker Xwgc501 and Xwgc510. The recombinants containing Qfhs.ndsu-3AS and new markers defining the QTL will facilitate utilization of this resistance source in wheat breeding.

A compensating, recombined Lr59 translocation with greatly reduced alien chromatin was identified. Microsatellite locus Xdupw217 occurs within the remaining segment and can be used as a co-dominant marker for Lr59. In earlier studies, leaf rust (caused by Puccinia triticina Eriks.) resistance gene Lr59 was transferred from Aegilops peregrina (Hackel) Maire et Weiler to chromosome arm 1AL of common wheat (Triticum aestivum L.). The resistance gene was then genetically mapped on the translocated chromosome segment following homoeologous pairing induction. Eight recombinants that retained the least alien chromatin apparently resulted from crossover within a terminal region of the translocation that was structurally different from 1AL. These recombinants could not be differentiated by size, and it was not clear whether they were compensating in nature. The present study determined that the distal part of the original translocation has group 6 chromosome homoeology and a 6BS telomere (with the constitution of the full translocation chromosome being 1AS·1LP·6SP ·6BS). During the allosyndetic pairing induction experiment to map and shorten the full size translocation, a low frequency of quadrivalents involving 1A, the 1A translocation, and two 6B chromosomes was likely formed. Crossover within such quadrivalents apparently produced comparatively small compensating alien chromatin inserts within the 6BS satellite region on chromosome 6B of seven of the eight recombinants. It appears that the Gli-B2 storage protein locus on 6BS has not been affected by the recombination events, and the translocations are therefore not expected to affect baking quality. Simple sequence repeat marker results showed that Lr59-151 is the shortest recombinant, and it will therefore be used in breeding. Marker DUPW217 detects a homoeo-allele within the remaining alien chromatin that can be used for marker-assisted selection of Lr59.

A new gene for Ug99 resistance from wheat landrace PI 374670 was detected on the long arm of chromosome 7A. Wheat landrace PI 374670 has seedling and field resistance to stem rust caused by Puccinia graminis f. sp tritici Eriks. & E. Henn (Pgt) race TTKSK. To elucidate the inheritance of resistance, 216 BC1F2 families, 192 double haploid (DH) lines, and 185 recombinant inbred lines (RILs) were developed by crossing PI 374670 and the susceptible line LMPG-6. The parents and progeny were evaluated for seedling resistance to Pgt races TTKSK, MCCFC, and TPMKC. The DH lines were tested in field stem rust nurseries in Kenya and Ethiopia. The DH lines were genotyped with the 90K wheat iSelect SNP genotyping platform. Goodness-of-fit tests indicated that a single dominant gene in PI 374670 conditioned seedling resistance to the three Pgt races. The seedling resistance locus mapped to the long arm of chromosome 7A and this result was verified in the RIL population screened with the flanking SNP markers using KASP assays. In the same region, a major QTL for field resistance was detected in a 7.7 cM interval and explained 34–54 and 29–36 % of the variation in Kenya and Ethiopia, respectively. Results from tests with specific Pgt races and the csIH81 marker showed that the resistance was not due to Sr22. Thus, a new stem rust resistance gene or allele, either closely linked or allelic to Sr15, is responsible for the seedling and field resistance of PI 374670 to Ug99.

We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange. This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16 % of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange.

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today’s fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.

This manuscript reports a new gene (Yr62) and a small-effect QTL for potentially durable resistance to stripe rust and usefulness of Yr62 markers for marker-assisted selection. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease of wheat worldwide. Spring wheat germplasm PI 192252 showed a high level of high-temperature adult-plant (HTAP) resistance to stripe rust in germplasm evaluation over 8 years in the State of Washington. To elucidate the genetic basis of resistance, PI 192252 was crossed with ‘Avocet susceptible’. A mapping population of 150 F5 recombinant inbred lines was developed using single-seed descent. Stripe rust tests were conducted with selected Pst races in a greenhouse and in field conditions under natural infections. The relative area under the disease progress curve (rAUDPC) data showed continuous distributions, indicating that HTAP resistance of PI 192252 was controlled by quantitative trait loci (QTL). Two QTL were identified in PI 192252, explaining 74.2 % of the total phenotypic variation for rAUDPC. These two QTL were mapped to chromosomes 4BL (QYrPI192252.wgp-4BL) and 5BS (QYrPI192252.wgp-5BS) with SSR and SNP markers and explained 40–60 and 22–27 %, respectively, of the phenotypic variation across the four environments. Because the major-effect QTL on 4BL is different from previously named Yr genes and inherited as a single gene, it is named Yr62. The SSR marker alleles Xgwm192 222 and Xgwm251 133 flanking Yr62 were different from the alleles in various wheat varieties, suggesting that these markers could be useful in marker-assisted selection for incorporating Yr62 into commercial cultivars.

This is the first report on genetic analysis and genome mapping of major dominant genes for near non-host resistance to barley crown rust ( Puccinia coronata var. hordei ) in common wheat. Barley crown rust, caused by Puccinia coronata var. hordei, primarily occurs on barley (Hordeum vulgare L.) in the Great Plain regions of the United States. However, a few genotypes of common wheat (Triticum aestivum L.) were susceptible to this pathogen among 750 wheat accessions evaluated. To investigate the genetics of crown rust resistance in wheat, a susceptible winter wheat accession PI 350005 was used in crosses with two resistant wheat varieties, Chinese Spring and Chris. Analysis of F1 plants and F2 populations from these two crosses indicated that crown rust resistance is controlled by one and two dominant genes in Chris and Chinese Spring, respectively. To determine the chromosome location of the resistance gene Cr1 in Chris, a set of 21 monosomic lines derived from Chris was used as female parents to cross with a susceptible spring type selection (SSTS35) derived from the PI 350005/Chris cross. Monosomic analysis indicated that Cr1 is located on chromosome 5D in Chris and one of the crown rust resistance genes is located on chromosome 2D in Chinese Spring. The other gene in Chinese Spring is not on 5D and thus is different from Cr1. Molecular linkage analysis and QTL mapping using a population of 136 doubled haploid lines derived from Chris/PI 350005 further positioned Cr1 between SSR markers Xwmc41-2 and Xgdm63 located on the long arm of chromosome 5D. Our study suggests that near non-host resistance to crown rust in these different common wheat genotypes is simply inherited.

Genome-wide association studies (GWAS) provide an opportunity to examine the genetic architecture of quantitatively inherited traits in breeding populations. The objectives of this study were to use GWAS to identify chromosome regions governing traits of importance in six-rowed winter barley (Hordeum vulgare L.) germplasm and to identify single-nucleotide polymorphisms (SNPs) markers that can be implemented in a marker-assisted breeding program. Advanced hulled and hulless lines (329 total) were screened using 3,072 SNPs as a part of the US. Barley Coordinated Agricultural Project (CAP). Phenotypic data collected over 4 years for agronomic and food quality traits and resistance to leaf rust (caused by Puccinia hordei G. Otth), powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal], net blotch (caused by Pyrenophora teres), and spot blotch [caused by Cochliobolus sativus (Ito and Kuribayashi) Drechsler ex Dastur] were analyzed with SNP genotypic data in a GWAS to determine marker-trait associations. Significant SNPs associated with previously described quantitative trait loci (QTL) or genes were identified for heading date on chromosome 3H, test weight on 2H, yield on 7H, grain protein on 5H, polyphenol oxidase activity on 2H and resistance to leaf rust on 2H and 3H, powdery mildew on 1H, 2H and 4H, net blotch on 5H, and spot blotch on 7H. Novel QTL also were identified for agronomic, quality, and disease resistance traits. These SNP-trait associations provide the opportunity to directly select for QTL contributing to multiple traits in breeding programs.

The durum wheat cultivar 'Golden Ball' (GB) is a source of resistance to wheat sawfly due to its superior solid stem. In the late 1980s, Dr. Leonard Joppa developed a complete set of 14 'Langdon' (LDN)-GB disomic substitution (DS) lines by using GB as the chromosome donor and LDN as the recipient. However, these substitution lines have not been previously characterized and reported in the literature. The objectives of this study were to confirm the authenticity of the substituted chromosomes and to analyze the genetic background of the 14 LDN-GB DS lines with the aid of molecular markers, and to further use the substitution lines for chromosomal localization of DNA markers and genes conferring the superior stem solidness in GB. Results from simple sequence repeat marker analysis validated the authenticity of the substituted chromosomes in 14 LDN-GB DS lines. Genome-wide scans using the target region amplification polymorphism (TRAP) marker system produced a total of 359 polymorphic fragments that were used to compare the genetic background of substitution lines with that of LDN. Among the polymorphic TRAP markers, 134 (37.3%) and 185 (51.5%) were present in LDN and GB, respectively, with only 10 (2.8%) derived from Chinese Spring. Therefore, marker analysis demonstrated that each LDN-GB DS line had a pair of chromosomes from GB with a genetic background similar to that of LDN. Of the TRAP markers generated in this study, 200 were successfully assigned to specific chromosomes based on their presence or absence in the corresponding LDN-GB DS lines. Also, evaluation of stem solidness in the substitution lines verified the presence of a major gene for stem solidness in chromosome 3B. Results from this research provides useful information for the utilization of GB and LDN-GB DS lines for genetic and genomic studies in tetraploid wheat and for the improvement of stem solidness in both durum and bread wheat.

The wheat stem rust resistance gene Sr6, present in several wheat cultivars, confers a high level of resistance against a wide range of races of Puccinia graminis f. sp. tritici. Resistance conferred by Sr6 is influenced by temperature, light intensity, and genetic background of the recipient genotype. Here, we report the identification and validation of molecular markers linked to Sr6 that can be used for the detection of this gene in wheat breeding programs. A mapping population of 136 F2 plants and their F2:3 families derived from a cross between near-isogenic lines, ‘Chinese Spring’ and ISr6-Ra, were screened for stem rust reaction in the seedling stage. Bulked segregant analysis (BSA) based on seedling tests was used to screen 418 SSR markers that covered the entire genome of wheat. Four markers, Xwmc453, Xcfd43, Xcfd77, and Xgwm484, were mapped within a chromosome region that spanned 9.7 cM from Sr6. The closest markers, Xwmc453 and Xcfd43, were linked to Sr6 at a distance of 1.1 and 1.5 cM, respectively. The markers Xwmc453 and Xcfd43 amplified Sr6-specific marker alleles that were diagnostic for Sr6 in a diverse set of 46 wheat accessions and breeding lines developed and/or collected in Australia, Canada, China, Egypt, Ethiopia, Kenya, Mexico, South Africa, and USA. These markers can now be used for marker-assisted selection of Sr6 and for pyramiding it with other stem rust resistance genes.

Bright yellow color, firmness and low cooking loss are important factors for the production of good-quality pasta products. However, the genetic factors underlying those traits are still poorly understood. To fill this gap we developed a population of 93 recombinant inbred lines (RIL) from the cross between experimental line UC1113 (intermediate pasta quality) with the cultivar Kofa (excellent pasta quality). A total of 269 markers, including 23 SNP markers, were arranged on 14 linkage groups covering a total length of 2,140 cM. Samples from each RIL from five different environments were used for complete pasta quality testing and the results from each year were used for QTL analyses. The combined effect of different loci, environment and their interactions were analyzed using factorial ANOVAs for each trait. We identified major QTLs for pasta color on chromosomes 1B, 4B, 6A, 7A and 7B. The 4B QTL was linked to a polymorphic deletion in the Lpx-B1.1 lipoxygenase locus, suggesting that it was associated with pigment degradation during pasta processing. The 7B QTL for pasta color was linked to the Phytoene synthase 1 (Psy-B1) locus suggesting difference in pigment biosynthesis. QTLs affecting pasta firmness and cooking loss were detected on chromosomes 5A and 7B, and in both cases they were overlapping with QTL for grain protein content and wet gluten content. These last two parameters were highly correlated with pasta firmness (R > 0.71) and inversely correlated to cooking loss (R < -0.37). The location and effect of other QTLs affecting grain size and weight, gluten strength, mixing properties, and ash content are also discussed. Fil: Zhang, W.. University of California; Estados Unidos Fil: Chao, S.. United States Department of Agriculture. Agricultural Research Service; Estados Unidos Fil: Manthey, F.. North Dakota State University. Department of Plant Sciences; Estados Unidos Fil: Chicaiza, O.. University of California; Estados Unidos Fil: Brevis, J. C.. University of California; Estados Unidos Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina Fil: Dubcovsky, J.. University of California; Estados Unidos

End-use quality is one of the priorities of modern wheat (Triticum aestivum L.) breeding. Even though quality is a complex trait, high molecular weight (HMW) glutenins play a major role in determining the bread making quality of wheat. DNA markers developed from the sequences of HMW glutenin genes were reported in several previous studies to facilitate marker-assisted selection (MAS). However, most of the previously available markers are dominant and amplify large DNA fragments, and thus are not ideal for high throughput genotyping using modern equipment. The objective of this study was to develop and validate co-dominant markers suitable for high throughput MAS for HMW glutenin subunits encoded at the Glu-A1 and Glu-D1 loci. Indels were identified by sequence alignment of allelic HMW glutenin genes, and were targeted to develop locus-specific co-dominant markers. Marker UMN19 was developed by targeting an 18-bp deletion in the coding sequence of subunit Ax2* of Glu-A1. A single DNA fragment was amplified by marker UMN19, and was placed onto chromosome 1AL. Sixteen wheat cultivars with known HMW glutenin subunits were used to validate marker UMN19. The cultivars with subunit Ax2* amplified the 362-bp fragment as expected, and a 344-bp fragment was observed for cultivars with subunit Ax1 or the Ax-null allele. Two co-dominant markers, UMN25 and UMN26, were developed for Glu-D1 by targeting the fragment size polymorphic sites between subunits Dx2 and Dx5, and between Dy10 and Dy12, respectively. The 16 wheat cultivars with known HMW glutenin subunit composition were genotyped with markers UMN25 and UMN26, and the genotypes perfectly matched their subunit types. Using an Applied Biosystems 3130xl Genetic Analyzer, four F(2) populations segregating for the Glu-A1 or Glu-D1 locus were successfully genotyped with primers UMN19, UMN25 and UMN26 labeled with fluorescent dyes.