Wheat landraces provide a source of genetic variability for breeding. The emergence and spread of highly virulent races of the stem rust pathogen (Ug99 race group of Puccinia graminis f. sp. tritici) threaten wheat production globally. Spring wheat landraces were screened for resistance in eight field seasons at the Kenya Agricultural Research Institute, Njoro, where the Ug99 race group has become endemic. Accessions showing resistance in one season were retested and screened with molecular markers associated with resistance genes Sr2, Sr24, Sr36, and Lr34/Yr18; two height-reducing genes; and a photoperiod insensitivity allele. Of 2,509 accessions tested, 278 were categorized as resistant based on results from at least two seasons. Of these resistant accessions, 32 were positive for one or more markers for Sr2, Sr36, Rht-B1b, or Rht-D1b, indicating that they do not fit the definition of "landrace" because these genes were likely introduced via modern breeding practices. Thus, 246 resistant "landrace" accessions were identified. Of countries with more than five tested accessions, Afghanistan, Iran, Portugal, Ethiopia, Uzbekistan, Greece, Tajikistan, Bosnia and Herzegovina, and Serbia had at least 10% of tested accessions that were resistant to the Ug99 race group. Future research will characterize the resistance to determine its novelty and incorporate novel genes into improved lines.

Studies on the effects of β‐glucan on humans have shown that food containing high concentrations of β‐glucans from barley (Hordeum vulgare L.) reduced total cholesterol levels. β‐Glucan has been shown to be beneficial for the regulation of blood‐glucose levels, and high β‐glucan has been found to reduce glucose intolerance and insulin resistance. High β‐glucan barley varieties with good agronomic traits are few and have reduced yield potential compared with feed‐ and malting‐barley cultivars. ‘Transit’ (Reg. No. CV‐348, PI 660128), a two‐rowed, spring, high β‐glucan barley, was developed and submitted for release in 2009 by the USDA‐ARS, Aberdeen, ID in cooperation with the University of Idaho Agricultural Experiment Station. Transit is a selection from the cross 10/‘Azhul’//‘CDC Alamo’. 10 is a selection from composite cross XXXII. Azhul is a six‐rowed, high β‐glucan cultivar released by the ARS and Arizona Agricultural Experiment Station and is the progenitor of most high β‐glucan cultivars and germplasm. Azhul was developed by the mutation of line 76‐19‐7 with diethyl sulfate. Line 76‐19‐7 has the pedigree CCXXXII/‘Arimont’//‘Westbar’. CDC Alamo, tested as HB340, has the pedigree SB85750/Azhul. Transit has a reduced yield potential compared with the best feed and malting types, but its high level of β‐glucan provides enough added value to allow it to be economically competitive with current malting‐barley cultivars. The release of Transit will provide producers with a variety having improved yield potential and β‐glucan content compared with the current varieties CDC Alamo and Azhul. Transit is expected to be adapted to both irrigated and rainfed regions in Idaho.

Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD) are well recognized; however, seed protein levels are modest and resources for genetic improvement are scarce. The wild tetraploid, A. magna Murphy et Terrell (syn A. maroccana Gdgr., 2n = 4x = 28, CCDD), which contains approximately 31% seed protein, was hybridized with cultivated oat to produce a domesticated A. magna. Wild and cultivated accessions were crossed to generate a recombinant inbred line (RIL) population. Although these materials could be used to develop domesticated, high-protein oat, mapping and quantitative trait loci introgression is hindered by a near absence of genetic markers. Objectives of this study were to develop high-throughput, A. magna-specific markers; generate a genetic linkage map based on the A. magna RIL population; and map genes controlling oat domestication. A Diversity Arrays Technology (DArT) array derived from 10 A. magna genotypes was used to generate 2,688 genome-specific probes. These, with 12,672 additional oat clones, produced 2,349 polymorphic markers, including 498 (21.2%) from A. magna arrays and 1,851 (78.8%) from other Avena libraries. Linkage analysis included 974 DArT markers, 26 microsatellites, 13 SNPs, and 4 phenotypic markers, and resulted in a 14-linkage-group map. Marker-to-marker correlation coefficient analysis allowed classification of shared markers as unique or redundant, and putative linkage-group-to-genome anchoring. Results of this study provide for the first time a collection of high-throughput tetraploid oat markers and a comprehensive map of the genome, providing insights to the genome ancestry of oat and affording a resource for study of oat domestication, gene transfer, and comparative genomics.

Tan spot, caused by Pyrenophora tritici-repentis, is a major foliar disease of wheat worldwide. Host plant resistance is the best strategy to manage this disease. Traditionally, bi-parental mapping populations have been used to identify and map quantitative trait loci (QTL) affecting tan spot resistance in wheat. The association mapping (AM) could be an alternative approach to identify QTL based on linkage disequilibrium (LD) within a diverse germplasm set. In this study, we assessed resistance to P. tritici-repentis races 1 and 5 in 567 spring wheat landraces from the USDA-ARS National Small Grains Collection (NSGC). Using 832 diversity array technology (DArT) markers, QTL for resistance to P. tritici-repentis races 1 and 5 were identified. A linear model with principal components suggests that at least seven and three DArT markers were significantly associated with resistance to P. tritici-repentis races 1 and 5, respectively. The DArT markers associated with resistance to race 1 were detected on chromosomes 1D, 2A, 2B, 2D, 4A, 5B, and 7D and explained 1.3–3.1% of the phenotypic variance, while markers associated with resistance to race 5 were distributed on 2D, 6A and 7D, and explained 2.2–5.9% of the phenotypic variance. Some of the genomic regions identified in this study correspond to previously identified loci responsible for resistance to P. tritici-repentis, offering validation for our AM approach. Other regions identified were novel and could possess genes useful for resistance breeding. Some DArT markers associated with resistance to race 1 also were localized in the same regions of wheat chromosomes where QTL for resistance to yellow rust, leaf rust and powdery mildew, have been mapped previously. This study demonstrates that AM can be a useful approach to identify and map novel genomic regions involved in resistance to P. tritici-repentis.

Although microsatellites are an efficient and reliable genetic marker system, availability is limited in cultivated oat (Avena sativa L.). Previous research has suggested that microsatellites from related species may be adapted to oat. This study investigated the stability of existing oat microsatellites, sequenced polymorphic oat amplicons derived from wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) primers, and redesigned primers to develop oat-based markers. We evaluated 161 published oat microsatellites and identified 9 with polymorphism between mapping parents Ogle1040 and TAM O-301 (OT). We also studied 30 wheat, 1 Aegilops tauschii Coss., and 9 barley primers with reported oat polymorphism. Sixteen primers (1 A. tauschii, 10 wheat, 5 barley) amplified random oat sequences and were used to generate 28 new oat STS markers. Eight primers, 4 each from wheat and barley, amplified oat repetitive motifs, generating 10 new oat SSRs. Four additional SSRs were developed from characterization of thaumatin-like pathogenesis-related protein sequences formerly utilized as the Rast1-4 oat marker. These new markers, along with 9 existing oat SSRs and 6 previously identified disease resistance loci, were mapped in the OT population, joining 3 pairs of linkage groups. Map locations of multiallelic SSRs and disease-resistance QTL interactions suggested possible homoeologous relationships among the oat chromosomes.

Management of oat crown rust disease with host resistance is challenging because major gene resistance is generally short lived. Partially resistant oat cultivars could benefit oat growers by providing more durable resistance. The objective of this study was to validate and discover quantitative trait loci (QTL) affecting crown rust resistance in the partially resistant oat line MN841801-1 using conventional and molecular assessments of disease produced in single-race greenhouse inoculations, single-race polycyclic field tests, and under natural infection in disease-conducive environments. Crown rust was assessed on 150 F(6:9) MN841801-1/'Noble-2' recombinant inbred lines. In total, eight QTL associated with MN841801-1 alleles were detected. Of these, seven matched QTL previously identified while a new QTL (Prq8) was detected on linkage group MN13. Four QTL (Prq1a, Prq2, Prq7, and Prq8) were consistently detected and predicative genetic assays for these QTL should be developed for future validation in additional genetic backgrounds.

Crown rust is the most damaging disease of cultivated oat (Avena sativa) and genetic resistance is the primary means of controlling the disease. Quantitative trait loci (QTL) with major and minor effects have been identified in Ogle1040 and TAM O-301 (most notably, Pc58 and PcNQMG/LGCG from TAM O-301 and OT-27 from Ogle1040) through single-isolate greenhouse and field tests. To map loci and determine the effectiveness of previously identified QTL against naturally occurring pathogen populations in highly disease-conducive environments, the Ogle/TAM O-301 (OT) recombinant inbred line (RIL) population was grown in Texas and Louisiana over 2 years and in Manitoba, Canada. The genetic region characterized by the Pc58 resistance gene complex, particularly Pc58a, accounted for most of the diseased leaf area (DLA) and infection type (IT) variance in all five experiments. Additionally, the genetic region characterized by PcNQMG/LGCG accounted for a portion of the IT variance in three experiments. Although no QTL was detected on OT-27 in this study, all the markers on this linkage group were associated (P < 0.0001) with reducing both IT and DLA using single-marker analysis. Screening with 25 Puccinia coronata isolates from six different states indicated that Pc58abc and Pc58a were highly effective, while characterization using F(2) populations derived from OT RILs containing the two main genetic regions responsible for crown rust resistance in TAM O-301 (Pc58 and PcNQMG/LGCG) and a minor QTL in Ogle (OT-27) indicated that Pc58a, in combination with a locus in Ogle1040, provided high levels of resistance to natural races in Texas. This study provides new information and key loci in OT mapping population and may be useful for effective control of crown rust in North America.

Identification and genetic mapping of loci conferring resistance to polycyclic pathogens such as the rust fungi depends on accurate measurement of disease resistance. We converted an absolute quantification assay of Puccinia coronata DNA to a relative assay by adding a TaqMan (R) primers/probe set specific to the oat -actin gene to simplify and improve quantification of fungal infection. The new multiplex assay estimates the amount of fungal DNA in a sample relative to the amount of host DNA and requires fewer and less labour-intensive steps than previous assays. The relative fungal DNA assay (RFDNA) reliably detected and quantified both host and pathogen DNA over five orders of magnitude and was at least as sensitive as either digital image analysis (DLA) or absolute estimation of fungal DNA (AFDNA) in repeated greenhouse studies using 12 oat cultivars with different resistance responses to P. coronata isolate LGCG. Measuring crown rust resistance to LGCG using DLA, AFDNA and RFDNA in a P8669/P94163 recombinant inbred line population produced segregation ratios that did not differ from the 1:1 Mendelian ratio expected for a single gene. Compared to the AFDNA assessment method, the RFDNA assay is equally sensitive, yet faster and much easier to use than the AFDNA method for precise quantification of the crown rust pathogen in oat leaves. The method will be especially useful for streamlining measurement of partial resistance, since uncovering small differences in resistance requires phenotypic evaluation of large populations.

‘Endeavor’ (Reg. No. CV‐341, PI 654824), a two‐rowed winter malting barley (Hordeum vulgare L.), was developed and submitted for release in 2007 by the USDA–ARS, Aberdeen, ID, in cooperation with the University of Idaho Agricultural Experiment Station. Endeavor is a selection from the cross ORWM8406/‘Harrington’. ORWM8406 has the pedigree ‘Carstens’/‘Riso’ mutant 1508 (F1)//‘Cossack’. Riso mutant 1508 is an ethyleneimine‐induced mutant of ‘Bomi’. Progenitors of ORWM8406 are all European barleys. Harrington is a two‐rowed spring malting barley released by the Crop Development Centre, University of Saskatchewan, and is the current western two‐rowed malting industry standard. Endeavor was released because of its higher diastatic power compared with ‘Charles’, the most‐advanced two‐rowed winter malting barley adapted to Idaho.

‘Lenetah’ (Reg. No. CV‐338, PI 652440) two‐rowed spring feed barley (Hordeum vulgare L.) was developed by the Agricultural Research Service, Aberdeen, ID, in cooperation with the Idaho Agricultural Experimental Station and released in December 2007. Lenetah was selected from the cross 94Ab12981/91Ab3148. 94Ab12981 has the pedigree 85Ab2323/‘Camas’. 85Ab2323 has the pedigree 79Ab19042/‘Crystal’. 79Ab19042 is a selection from the cross ‘Klages’/‘Hector’. Camas is a selection from the cross ND5976/ND7159. ND5976 has the pedigree ‘Maris Concord’/Klages//ND2679‐4 and ND7159 has the pedigree Klages/ND1244/3/ND2685/ND1156//Hector. 91Ab3148 has the pedigree ‘Gallatin’/‘Targhee’//‘Bowman’. Lenetah was selected as an F5:6 line in 2001 and given the experimental designation 01Ab11107. It was released due to its superior yield and test weight compared to ‘Baronesse’, the most widely grown feed barley in Idaho and Montana. The yield advantage over Baronesse is especially pronounced in northern Idaho and eastern Washington and under dryland conditions.

The crown rust pathogen Puccinia coronata is an obligate biotroph with wind-disseminated propagules and numerous races. These characteristics make propagation of single-race cultures difficult. Genetic studies using single races in field and greenhouse environments are also problematic because pure cultures can easily become contaminated. In this study, we developed an isolated propagation system for P. coronata and tested its ability to assess host resistance. Oat (Avena sativa) leaf sections (10 cm each) were harvested, disinfested, and suspended in sterile plastic boxes by enclosing 3.5-cm linear sections of each leaf end between 4% agar blocks amended with various chemical constituents. The exposed sections (approximately 3 cm) were inoculated with P. coronata urediniospores suspended in water. Boxes were sealed and incubated in a lighted growth cabinet until the pathogen sporulated. Viable spores were produced on leaves in all treatments, whereas 6-benzylaminopurine (BAP) and kinetin treatments sustained the leaves longer and yielded the most viable spores. Based on these data, the BAP treatment was adopted and used for additional studies. Detached leaves of differential oat cultivars produced the same reactions as whole plants screened under standard conditions in a growth chamber. The proposed detached-leaf system should be useful for the propagation of numerous single-race cultures of P. coronata as well as evaluation of host resistance under highly controlled conditions.

Mapping disease resistance loci relies on the type and precision of phenotypic measurements. For crown rust of oat, disease severity is commonly assessed based on visual ratings of infection types (IT) and/or diseased leaf area (DLA) of infected plants in the greenhouse or field. These data can be affected by several variables including; (i) non-uniform disease development in the field; (ii) atypical symptom development in the greenhouse; (iii) the presence of multiple pathogenic races or pathotypes in the field, and (iv) rating bias. To overcome these limitations, we mapped crown rust resistance to single isolates in the Ogle/TAM O-301 (OT) recombinant inbred line (RIL) population using detailed measurements of IT, uredinia length (UL) and relative fungal DNA (FDNA) estimates determined by q-PCR. Measurements were taken on OT parents and recombinant inbred lines (RIL) inoculated with Puccinia coronata pathotypes NQMG and LGCG in separate greenhouse and field tests. Qualitative mapping identified an allele conferred by TAM O-301 on linkage group (LG) OT-11, which produced a bleached fleck phenotype to both NQMG and LGCG. Quantitative mapping identified two major quantitative trait loci (QTL) originating from TAM O-301 on LGs OT-11 and OT-32 which reduced UL and FDNA of both isolates in all experiments. Additionally, minor QTLs that reduced UL and FDNA were detected on LGs OT-15 and OT-8, originating from TAM O-301, and on LG OT-27, originating from Ogle. Detailed assessments of the OT population using two pathotypes in both the greenhouse and field provided comprehensive information to effectively map the genes responsible for crown rust resistance in Ogle and TAM O-301 to NQMG and LGCG.

Identifying polymerase chain reaction (PCR)‐based markers in crop genomes and amplifying them with specific primer pairs has provided convenient molecular markers for mapping projects. Oat (Avena sativa L.) lags behind other crops in the utilization of PCR‐based markers due to limited development of genomic and genetic resources in Avena species. We surveyed 356 genome‐derived simple sequence repeat (SSR) markers from wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), chosen on the basis of even dispersal across different chromosomes, to search for an alternate method of expanding the PCR‐based marker pool in oat. Primer pairs for these SSR markers were tested for amplification and polymorphism between parental lines from Ogle1040/TAM‐O‐301 (OT) and Kanota/Ogle157 (KO) mapping populations. Eighty‐nine of 210 wheat primer pairs (42%) and 56 of 146 barley primer pairs (38%) successfully amplified sequences in oat. Forty‐five percent of the amplified markers, representing 19% of the total markers, showed polymorphism between parental lines of at least one mapping population. The polymorphism was primarily the presence or absence of a product band. Fifteen PCR products from 10 primer pairs were tested for reproducibility by amplifying each marker in the OT population. When assayed with the same PCR conditions used in the survey, the segregation ratio of 14 markers did not differ from the 1:1 ratio expected for a single locus. This study indicates that genomic SSR primer pairs from wheat and barley may be a good way to efficiently generate PCR‐based DNA markers for oat genetics research.

ABSTRACT Resistance is the primary means of control for crown rust of oat (Avena sativa L.), caused by Puccinia coronata f. sp. avenae, and better knowledge of the genetics of resistance will enhance resistance breeding. Disease data were generated in the field and greenhouse for parents and recombinant inbred lines of the Ogle/TAM O-301 (OT) oat mapping population using (i) a new quantitative assay that employs quantitative real-time polymerase chain reaction (q-PCR) to estimate fungal growth in the host, (ii) digital image analysis, and (iii) visual ratings. The objectives of this study were to evaluate each assessment method's ability to map a major gene from cv. Ogle and potential quantitative trait loci (QTL) contributed by Ogle and TAM O-301. All three assessment methods identified the major gene in Ogle, which was mapped to linkage group OT6. The resolution produced by q-PCR, however, enabled more precise mapping of the major gene. Quantitative analysis indicated that 64% of the phenotypic variation was accounted for using q-PCR, whereas 41 and 52% were accounted for using visual and digital assessments, respectively. Data generated by q-PCR permitted identification of QTL on linkage groups OT32, accounting for 6% of the phenotypic variation, and OT2, accounting for 4% of the variation. QTL on both OT32 and OT2 were conferred by TAM O-301, one of which (OT2) was indiscernible using data from the visual and digital assessments. The new method of precisely phenotyping crown rust resistance provided a more accurate and thorough means of dissecting resistance in the OT mapping population. Similar methods could be developed and applied to other important cereal rust diseases.

Crown rust of cultivated oat (Avena sativa L.) caused byPuccinia coronata Corda f. sp.avenae Eriks, causes yield loss, reduction in test weight, and increased lodging. Genetic resistance is the most desirable method to control the disease. ‘TAM O‐301’, a cultivar released by the Texas A&M oat‐breeding program in 1973, has crown rust resistance, subsequently namedPc58. The main objectives of this study were to characterizePc58 in TAM O‐301 using an F6:7 recombinant inbred (RI) population of the ‘Ogle’ × TAM O‐301 cross and to map thePc58 resistance. Six crown rust isolates, avirulent on TAM O‐301 and virulent on Ogle, were used to test the parents and RI population. Genetic analyses of the segregation data to each of the six isolates indicated that the resistance was conditioned by three genes within a 41.0‐cM region. The resistance genes were mapped to linkage groups OT32 and OT33 in the published molecular linkage map of Ogle × TAM O‐301. This research has provided new information on thePc58 resistance gene complex that should facilitate new marker and germplasm development.