Prevalence and Importance of the Necrotrophic Effector Gene ToxA in Bipolaris sorokiniana Populations Collected from Spring Wheat and Barley

Bipolaris sorokiniana is a necrotrophic fungal pathogen that causes foliar and root diseases on wheat and barley. These diseases are common in all wheat- and barley-growing regions, with more severe outbreaks occurring under warm and humid conditions. B. sorokiniana can also infect a wide range of grass species in the family Poaceae and secrete ToxA, an important necrotrophic effector also identified other wheat leaf spotting pathogens. In this study, the prevalence and virulence role of ToxA were investigated in a collection of 278 B. sorokiniana isolates collected from spring wheat and barley in the Upper Midwest of the United States or other places, including 169 from wheat leaves, 75 from wheat roots, 30 from barley leaves, and 4 from wild quack grass leaves. ToxA was present in the isolates from wheat leaves, wheat roots, and wild grass leaves but was absent from isolates collected from barley leaves. Prevalence of ToxA in wheat leaf isolates (34.3%) was much higher than that in wheat root isolates (16%). Sequencing analysis revealed the presence of two haplotypes, with the majority being BsH2. All ToxA+ isolates produced the functional effector in liquid cultures. Pathogenicity assays revealed that ToxA+ isolates caused significantly more disease on spring wheat lines harboring Tsn1 than their tsn1 mutants, suggesting that the ToxA-Tsn1 interaction plays an important role in spot blotch development. This work confirms the importance of ToxA in B. sorokiniana populations infecting wheat and, thus, the need to eliminate Tsn1 from spring wheat cultivars to reduce susceptibility to spot blotch.

Vulnerability of Barley to African Pathotypes of Puccinia graminis f. sp. tritici and Sources of Resistance

The emergence of widely virulent pathotypes (e.g., TTKSK in the Ug99 race group) of the stem rust pathogen (Puccinia graminis f. sp. tritici) in Africa threatens wheat production on a global scale. Although intensive research efforts have been advanced to address this threat in wheat, few studies have been conducted on barley, even though pathotypes such as TTKSK are known to attack the crop. The main objectives of this study were to assess the vulnerability of barley to pathotype TTKSK and identify possible sources of resistance. From seedling evaluations of more than 1,924 diverse cultivated barley accessions to pathotype TTKSK, more than 95% (1,844) were found susceptible. A similar high frequency (910 of 934 = 97.4%) of susceptibility was found for the wild progenitor (Hordeum vulgare subsp. spontaneum) of cultivated barley. Additionally, 55 barley lines with characterized or putative introgressions from various wild Hordeum spp. were also tested against pathotype TTKSK but none was found resistant. In total, more than 96% of the 2,913 Hordeum accessions tested were susceptible as seedlings, indicating the extreme vulnerability of the crop to the African pathotypes of P. graminis f. sp. tritici. In total, 32 (1.7% of accessions evaluated) and 13 (1.4%) cultivated and wild barley accessions, respectively, exhibited consistently highly resistant to moderately resistant reactions across all experiments. Molecular assays were conducted on these resistant accessions to determine whether they carried rpg4/Rpg5, the only gene complex known to be highly effective against pathotype TTKSK in barley. Twelve of the 32 (37.5%) resistant cultivated accessions and 11 of the 13 (84.6%) resistant wild barley accessions tested positive for a functional Rpg5 gene, highlighting the narrow genetic base of resistance in Hordeum spp. Other resistant accessions lacking the rpg4/Rpg5 complex were discovered in the evaluated germplasm and may possess useful resistance genes. Combining rpg4/Rpg5 with resistance genes from these other sources should provide more durable resistance against the array of different virulence types in the Ug99 race group.

Introgression of leaf rust and stripe rust resistance from Sharon goatgrass (Aegilops sharonensis Eig) into bread wheat (Triticum aestivum L.)

Leaf rust and stripe rust are devastating wheat diseases, causing significant yield losses in many regions of the world. The use of resistant varieties is the most efficient way to protect wheat crops from these diseases. Sharon goatgrass (Aegilops sharonensis or AES), which is a diploid wild relative of wheat, exhibits a high frequency of leaf and stripe rust resistance. We used the resistant AES accession TH548 and induced homoeologous recombination by the ph1b allele to obtain resistant wheat recombinant lines carrying AES chromosome segments in the genetic background of the spring wheat cultivar Galil. The gametocidal effect from AES was overcome by using an "anti-gametocidal" wheat mutant. These recombinant lines were found resistant to highly virulent races of the leaf and stripe rust pathogens in Israel and the United States. Molecular DArT analysis of the different recombinant lines revealed different lengths of AES segments on wheat chromosome 6B, which indicates the location of both resistance genes.

Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene

Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (S(sh)) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6S(sh)) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.

Identification and mapping of a leaf rust resistance gene in barley line Q21861

Barley line Q21861 possesses an incompletely dominant gene (RphQ) for resistance to leaf rust caused by Puccinia hordei. To investigate the allelic and linkage relations between RphQ and other known Rph genes, F2 populations from crosses between Q21861 and donors of Rph1 to Rph14 (except for Rph8) were evaluated for leaf rust reaction at the seedling stage. Results indicate that RphQ is either allelic with or closely linked to the Rph2 locus. A doubled haploid population derived from a cross between Q21861 and SM89010 (a leaf rust susceptible line) was used for molecular mapping of the resistance locus. Bulked segregant analysis was used to identify markers linked to RphQ, using random amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and sequence tagged sites (STSs). Of 600 decamer primers screened, amplified fragments generated by 9 primers were found to be linked to the RphQ locus; however, only 4 of them were within 10 cM of the target. The RphQ locus was mapped to the centromeric region of chromosome 7, with a linkage distance of 3.5 cM from the RFLP marker CDO749. Rrn2, an RFLP clone from the ribosomal RNA intergenic spacer region, was found to be very closely linked with RphQ, based on bulked segregant analysis. An STS marker, ITS1, derived from Rrn2, was also closely linked (1.6 cM) to RphQ.

Resistance to stem rust race TTKSK maps to the rpg4/Rpg5 complex of chromosome 5H of barley

Race TTKSK (Ug99) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) is a serious threat to both wheat and barley production worldwide because of its wide virulence on many cultivars and rapid spread from eastern Africa. Line Q21861 is one of the most resistant barleys known to this race. To elucidate the genetics of resistance in this line, we evaluated the Q21861/SM89010 (Q/SM) doubled-haploid population for reaction to race TTKSK at the seedling stage. Segregation for resistance:susceptibility in Q/SM doubled-haploid lines fit a 1:1 ratio (58:71 with chi2=1.31 and P=0.25), indicating that a single gene in Q21861 confers resistance to race TTKSK. In previous studies, a recessive gene (rpg4) and a partially dominant gene (Rpg5) were reported to control resistance to P. graminis f. sp. tritici race QCCJ and P. graminis f. sp. secalis isolate 92-MN-90, respectively, in Q21861. These resistance genes co-segregate with each other in the Q/SM population and were mapped to the long arm of chromosome 5H. Resistance to race TTKSK also co-segregated with resistance to both rusts, indicating that the gene conferring resistance to race TTKSK also lies at the rpg4/Rpg5 locus. This result was confirmed through the molecular analysis of recombinants previously used to characterize loci conferring resistance to race QCCJ and isolate 92-MN-90. The 70-kb region contains Rpg5 (a nucleotide-binding site leucine-rich repeat serine/threonine-protein kinase gene), rpg4 (an actin depolymerizing factor-like gene), and two other genes of unidentified function. Research is underway to resolve which of the genes are required for conferring resistance to race TTKSK. Regardless, the simple inheritance should make Q21861 a valuable source of TTKSK resistance in barley breeding programs.

Allele sequencing of the barley stem rust resistance gene Rpg1 identifies regions relevant to disease resistance

The stem rust resistance gene Rpg1 has protected North American barley cultivars from significant yield losses for over 65 years. The remarkable durability of this gene warrants further study as to its possible origin and allelic variation. Eight Swiss barley (Hordeum vulgare) landraces and eight wild barley (H. vulgare subsp. spontaneum) accessions from diverse geographic regions were analyzed to uncover new alleles of Rpg1 and learn about its possible origin. The two germplasm groups included accessions that were resistant and susceptible to Puccinia graminis f. sp. tritici pathotype MCCF. Allele-specific primers were utilized to amplify 1 kbp overlapping fragments spanning the Rpg1 gene and sequenced if a polymerase chain reaction (PCR) fragment was generated. Variation among the PCR products revealed significant polymorphisms among these Hordeum accessions. Landraces and wild barley accessions susceptible to pathotype MCCF exhibited the highest degree of Rpg1 polymorphism. One resistant landrace (Hv672) and one resistant wild barley accession (WBDC040) yielded all seven Rpg1-specific PCR fragments, but only landrace Hv672 coded for an apparently functional Rpg1 as determined by comparison to previously characterized resistant and susceptible alleles and also resistance to HKHJ, a stem rust pathotype that can specifically detect Rpg1 in the presence of other resistance genes. Accessions resistant to stem rust pathotype MCCF, but completely lacking Rpg1-specific PCR amplification and hybridization with an Rpg1-specific probe, suggested the presence of stem rust resistant gene(s) different from Rpg1 in the Hordeum germplasm pool. Some Rpg1 alleles that retained the ability to autophosphorylate did not confer resistance to Puccinia graminis f. sp. tritici pathotype MCCF, confirming our previous observations that autophosphorylation is essential, but not sufficient for disease resistance. Thus, the RPG1 protein plays a complex role in the stem rust disease resistance-signaling pathway.

Genetics of resistance to wheat leaf rust, stem rust, and powdery mildew in Aegilops sharonensis

Aegilops sharonensis (Sharon goatgrass) is a wild relative of wheat and a rich source of genetic diversity for disease resistance. The objectives of this study were to determine the genetic basis of leaf rust, stem rust, and powdery mildew resistance in A. sharonensis and also the allelic relationships between genes controlling resistance to each disease. Progeny from crosses between resistant and susceptible accessions were evaluated for their disease reaction at the seedling and/or adult plant stage to determine the number and action of genes conferring resistance. Two different genes conferring resistance to leaf rust races THBJ and BBBB were identified in accessions 1644 and 603. For stem rust, the same single gene was found to confer resistance to race TTTT in accessions 1644 and 2229. Resistance to stem rust race TPMK was conferred by two genes in accessions 1644 and 603. A contingency test revealed no association between genes conferring resistance to leaf rust race THBJ and stem rust race TTTT or between genes conferring resistance to stem rust race TTTT and powdery mildew isolate UM06-01, indicating that the respective resistance genes are not linked. Three accessions (1644, 2229, and 1193) were found to carry a single gene for resistance to powdery mildew. Allelism tests revealed that the resistance gene in accession 1644 is different from the respective single genes present in either 2229 or 1193. The simple inheritance of leaf rust, stem rust, and powdery mildew resistance in A. sharonensis should simplify the transfer of resistance to wheat in wide crosses.

Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross

Hordeum vulgare subsp. spontaneum is the progenitor of cultivated barley (Hordeum vulgare L.). Domestication combined with plant breeding has led to the morphological and agronomic characteristics of modern barley cultivars. The objective of this study was to map the genetic factors that morphologically and agronomically differentiate wild barley from modern barley cultivars. To address this objective, we identified quantitative trait loci (QTLs) associated with plant height, flag leaf width, spike length, spike width, glume length in relation to seed length, awn length, fragility of ear rachis, endosperm width and groove depth, heading date, flag leaf length, number of tillers per plant, and kernel color in a Harrington/OUH602 advanced backcross (BC2F8) population. This population was genotyped with 113 simple sequence repeat markers. Thirty QTLs were identified, of which 16 were newly identified in this study. One to 4 QTLs were identified for each of the traits except glume length, for which no QTL was detected. The portion of phenotypic variation accounted for by individual QTLs ranged from about 9% to 54%. For traits with more than one QTL, the phenotypic variation explained ranged from 25% to 71%. Taken together, our results reveal the genetic architecture of morphological and agronomic traits that differentiate wild from cultivated barley.

Resistance of Sharon Goatgrass (Aegilops sharonensis) to Fungal Diseases of Wheat

Sharon goatgrass (Aegilops sharonensis) is a wild relative of wheat that is native to Israel and Lebanon. The importance of A. sharonensis as a source of new resistance genes for wheat warrants additional research on the characterization of accessions for economically important genes. Thus, the objectives of this study were to evaluate a collection of A. sharonensis accessions for resistance to seven important fungal diseases of wheat and assess the phenotypic diversity of the germplasm for disease reaction. The frequency of resistance in A. sharonensis was highest to powdery mildew (79 to 83%) and leaf rust (60 to 77%). Resistance to stem rust also was common, although the percentage of resistant accessions varied markedly depending on the pathogen race-from 13% to race TTTT to 72% to race QCCJ. The frequency of resistance was intermediate to stripe rust (45%) and low to tan spot (15 to 29%) and spot blotch (0 to 34%). None of the A. sharonensis accessions was resistant to Fusarium head blight. Many of the accessions tested exhibited heterogeneous reactions (i.e., had both resistant and susceptible plants) to one or more of the diseases, suggesting that heterozygosity may be present at some resistance loci. Substantial variation was observed in the level of diversity to individual diseases because Shannon's Equitability index ranged from 0.116 (for Fusarium head blight) to 0.994 (for tan spot). A high level of diversity was found both between and within collection sites. Moreover, differences in the geographic distribution of resistant accessions were observed. For example, accessions from northern Israel generally were less diverse and less resistant to leaf rust and stripe rust than accessions from more southern locations. Four A. sharonensis accessions were highly resistant to most of the diseases evaluated and may provide a source of unique resistance genes for introgression into cultivated wheat.

Identification and chromosomal location of major genes for resistance to Pyrenophora teres in a doubled-haploid barley population

Net blotch, caused by Pyrenophora teres, is one of the most economically important diseases of barley worldwide. Here, we used a barley doubled-haploid population derived from the lines SM89010 and Q21861 to identify major quantitative trait loci (QTLs) associated with seedling resistance to P. teres f. teres (net-type net blotch (NTNB)) and P. teres f. maculata (spot-type net blotch (STNB)). A map consisting of simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers was used to identify chromosome locations of resistance loci. Major QTLs for NTNB and STNB resistance were located on chromosomes 6H and 4H, respectively. The 6H locus (NTNB) accounted for as much as 89% of the disease variation, whereas the 4H locus (STNB resistance) accounted for 64%. The markers closely linked to the resistance gene loci will be useful for marker-assisted selection.

Molecular mapping of Loci conferring resistance to different pathotypes of the spot blotch pathogen in barley

ABSTRACT Spot blotch, caused by Cochliobolus sativus, is an important disease of barley in many production areas and is best controlled through the deployment of resistant cultivars. Information on the genetics of resistance in various sources can be useful in developing effective breeding strategies. Parents of the doubled haploid mapping population Calicuchima-sib/ Bowman-BC (C/B) exhibit a differential reaction to pathotypes 1 and 2 of C. sativus. To elucidate the genetics of spot blotch resistance in this population, C/B progeny were evaluated with both pathotypes at the seedling stage in the greenhouse and at the adult plant stage in the field. At the seedling stage, progeny segregated 84 resistant to 26 susceptible based on the qualitative analysis of infection response (IR) data to pathotype 1. This fit best to a 3:1 ratio, indicating that two genes were involved in conferring resistance. Quantitative analysis of the raw IR data to pathotype 1 revealed a single quantitative trait locus (QTL) on chromosome 4(4H) explaining 14% of the phenotypic variance. Adult plant resistance to pathotype 1 was conferred by QTL on chromosome 2(2H) and chromosome 3(3H), explaining 21 and 32% of the phenotypic variation, respectively. Bowman contributed the resistance alleles on chromosome 3(3H) and chromosome 4(4H), whereas Calicuchima-sib contributed the resistance allele on chromosome 2(2H). Resistance to pathotype 2 was conferred by a single gene (designated Rcs6) on chromosome 5(1H) based on qualitative analysis of data. Rcs6 was effective at both the seedling and adult plant stages and was contributed by Calicuchima-sib. This result was corroborated in the quantitative analysis of raw IR (seedling stage) and disease severity (adult plant stage) data as a single major effect (r(2) = 0.93 and 0.88, respectively) QTL was identified on chromosome 5(1H). Progeny with resistance to both pathotypes were identified in the C/B population and may be useful in programs breeding for spot blotch resistance.

Comprehensive genetic analyses reveal differential expression of spot blotch resistance in four populations of barley

Spot blotch, caused by Cochliobolus sativus, is an important disease of barley in the Upper Midwest region of the United States. The resistance of six-rowed malting cultivars like Morex has remained effective for over 40 years and is considered durable. Previous research on Steptoe/Morex (S/M), a 6x6-rowed doubled haploid (DH) population, showed that seedling resistance is controlled by a single gene (Rcs5) on chromosome 1(7H) and adult plant resistance by two quantitative trait loci (QTL): one of the major effect on chromosome 5(1H) explaining 62% of the phenotypic variance and a second of minor effect on chromosome 1(7H) explaining 9% of the phenotypic variance. To corroborate these results in a 2x6-rowed DH population, composite interval mapping (CIM) was performed on Harrington/Morex (H/M). As in the S/M population, a single major gene (presumably Rcs5) on chromosome 1(7H) conferred resistance at the seedling stage. However, at the adult plant stage, the results were markedly different as no chromosome 5(1H) effect whatsoever was detected. Instead, a QTL at or near Rcs5 on chromosome 1(7H) explained nearly all of the phenotypic variance (75%) for disease severity. To determine whether this result might be due to the genetic background of the two-rowed susceptible parent Harrington, we analyzed another DH population that included the same resistance donor (Morex) and another six-rowed susceptible cultivar Dicktoo (D/M). Three QTL conferred seedling resistance in the D/M population: one near Rcs5 on chromosome 1(7H) explaining 30%, a second near the centromere of chromosome 1(7H) explaining 9%, and a third on the short arm of chromosome 3(3H) explaining 19% of the phenotypic variation. As in the H/M population, no chromosome 5(1H) QTL was detected for adult plant resistance in the D/M population. Instead, three QTL on other chromosomes explained most of the variation: one on the short arm of chromosome 3(3H) explaining 36%, a second on the long arm of chromosome 3(3H) explaining 11%, and a third at or near Rcs5 on chromosome 1(7H) explaining 20% of the phenotypic variation. These data demonstrate the complexity of expression of spot blotch resistance in different populations and have important implications in breeding for durable resistance.

High-resolution mapping of the barley leaf rust resistance gene Rph5 using barley expressed sequence tags (ESTs) and synteny with rice

The rapidly growing expressed sequence tag (EST) resources of species representing the Poacea family and availability of comprehensive sequence information for the rice (Oryza sativa) genome create an excellent opportunity for comparative genome analysis. Extensive synteny between rice chromosome 1 and barley (Hordeum vulgare L.) chromosome 3 has proven extremely useful for saturation mapping of chromosomal regions containing target genes of large-genome barley with conserved orthologous genes from the syntenic regions of the rice genome. Rph5 is a gene conferring resistance to the barley leaf rust pathogen Puccinia hordei. It was mapped to chromosome 3HS, which is syntenic with rice chromosome 1S. The objective of this study was to increase marker density within the sub-centimorgan region around Rph5, using sequence-tagged site (STS) markers that were developed based on barley ESTs syntenic to the phage (P1)-derived artificial chromosome (PAC) clones comprising the distal region of rice chromosome 1S. Five rice PAC clones were used as queries in a blastn search to screen 375,187 barley ESTs. Ninety-four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations. As a result, 9 barley EST-based STS markers were incorporated into the 'Bowman' x 'Magnif 102' high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, were found to co-segregate with Rph5. The results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley ESTs for marker saturation of targeted barley genomic regions.

Diversity and Sources of Multiple Disease Resistance in Hordeum spontaneum

Hordeum spontaneum, the progenitor of cultivated barley, is known to be a rich source of disease resistance genes. The objective of this study was to assess the diversity of H. spontaneum accessions from Israel and Jordan for their reaction to six fungal pathogens of importance to cultivated barley in the United States and Canada. Overall, a high level of macro-scale (across collection sites) and micro-scale (within a collection site) diversity for disease reaction was found in the 116 accessions of H. spontaneum evaluated at the seedling stage. Additionally, genetic heterozygosity for resistance loci was common in H. spontaneum. The frequency of resistance in accessions from Jordan and Israel was high for Septoria speckled leaf blotch (77 and 98%, respectively), leaf rust (70 and 90%), net blotch (72 and 68%), and powdery mildew (58 and 70%); intermediate for spot blotch (53 and 46%); and low for stem rust (2 and 26%). The level of disease resistance in H. spontaneum was not strongly correlated with any of the weather variables (temperature, precipitation, and humidity) monitored near the collection sites. However, in general, resistance was more often found in germ plasm from mesic (e.g., Mediterranean coast) than in xeric (e.g., Negev Desert) areas. Two H. spontaneum accessions (Shechem 12-32 and Damon 11-11) were resistant to all six pathogens and may be useful parents in programs breeding barley for multiple disease resistance. The high level of diversity and heterozygosity for disease reaction found in this study indicates that H. spontaneum is an extraordinarily rich and largely untapped source of unique disease resistance alleles for cultivated barley improvement.

Identification of QTLs associated with Fusarium head blight resistance in Zhedar 2 barley

Fusarium head blight (FHB) in barley and wheat, caused by Fusarium graminearum, is a continual problem worldwide. Primarily, FHB reduces yield and quality, and results in the production of the toxin deoxynivalenol (DON), which can affect food safety. Identification of QTLs for FHB severity, DON level and related traits heading-date (HD) and plant-height (HT) with consistent effects across a set of environments, would provide the basis for marker-assisted selection (MAS) and potentially increase the efficiency of selection for resistance. A segregating population of 75 double-haploid lines, developed from the three-way cross Zhedar 2/ND9712//Foster, was used for genome mapping and FHB severity evaluation. A linkage map of 214 RFLP, SSR and AFLP markers was constructed. Phenotypic data were collected in replicated field trials from five environments in two growing seasons. The data were analyzed using MQTL software to detect quantitative trait locus (QTL) x environment (E) interactions. Because of the presence of QTL x E, the MQM procedure in MAPQTL was applied to identify QTLs in single environments. We identified nine QTLs for FHB severity and five for low DON. Many of the disease-related QTLs identified were coincident with FHB QTLs identified in previous studies. Only two of the QTLs identified in this study were consistent across all five environments, and both were Zhedar 2 specific. Five of the FHB QTLs were associated with HD, and two were associated with HT. Regions that appear to be promising candidates for MAS and further genetic analysis include the two FHB QTLs on chromosome 2H and one on 6H, which were also associated with low DON and later heading-date in multiple environments. This study provides a starting point for manipulating Zhedar 2-derived resistance by MAS in barley to develop cultivars that will show effective resistance under disease pressure.

Sources and genetics of crown rust resistance in barley

ABSTRACT Crown rust, caused by Puccinia coronata var. hordei, is a new disease threat to barley in the Great Plains region of the United States. Deployment of resistant cultivars is the only economically viable option for the control of this disease. Thus, the objective of this study was to investigate the sources and genetics of crown rust resistance in barley. A geographically diverse sample of barley germ plasm collected around the world (526 accessions total) was evaluated at the seedling stage to P. coronata var. hordei, and only 10 accessions (1.9% of the total) were found resistant. These 10 accessions were also resistant at the adult plant stage in a greenhouse test. Three F(2) populations (Bowman x Hor2596, MR x Hor2596, and MD x Hor2596) were developed to study the inheritance of crown rust resistance in the resistant line Hor2596 (CIho 1243). A close fit to a 3:1 ratio of resistant/susceptible plants was observed in all three populations and is consistent with the segregation of a single resistance gene. F(1) plants from the Bowman x Hor2596 population exhibited slightly higher infection types than the resistant parent, indicating incomplete dominance. The locus symbol Rpc1 and allele symbol Rpc1.a were recommended for the crown rust resistance gene in Hor2596. An attempt was made to associate the Rpc1 locus with one of the seven barley chromosomes by analyzing linkage data with previously mapped morphological markers in crosses with multiple recessive (MR) and multiple dominant (MD) morphological marker stocks. However, no close linkages were detected between Rpc1 and the 20 morphological markers present in the marker stocks. The resistant accessions identified in this study should be useful to breeders for developing barley germ plasm with crown rust resistance.

Virulence and Molecular Diversity in Cochliobolus sativus

ABSTRACT Spot blotch, caused by the fungal pathogen Cochliobolus sativus, is an important disease of barley in many production areas of the world. To assess genetic diversity in this pathogen, a worldwide collection of C. sativus isolates was evaluated for virulence on barley and DNA polymorphism. Three pathotypes (0, 1, and 2) were identified among the 22 isolates tested in this study and the 36 isolates characterized previously on three barley differentials (ND5883, Bowman, and NDB112) that differ in their resistance to C. sativus. Pathotype 2, which exhibits high virulence on cv. Bowman, was only found in North Dakota, whereas the other two pathotypes occurred in many other regions of the world. Genetic diversity of the 58 C. sativus isolates, together with isolates of three related pathogenic Cochliobolus spp. (C. heterostrophus, C. carbonum, and C. victoriae) was analyzed using amplified fragment length polymorphism (AFLP) markers. A total of 577 polymorphic AFLP markers were recorded among the 70 isolates of the four Cochliobolus spp. using eight primer combinations. Cluster analysis revealed distinct groups corresponding to the four different species, except in one case where race 0 of C. carbonum was placed in an outgroup that may belong to a different species. In C. sativus, 95 polymorphic AFLP markers were detected with the eight primer pairs used, and each isolate exhibited a unique AFLP pattern. Allelic diversity in the pathotype 2 group was lower (0.10) than in the pathotype 0 (0.23) and pathotype 1 (0.15) groups, indicating that pathotype 2 may have arisen more recently. Cluster analysis did not reveal a close correlation between pathotypes and AFLP groups, although two AFLP markers unique to pathotype 2 isolates were identified. This low correlation suggests that genetic exchange may have occurred through parasexual recombination in the fungal population. Some isolates collected from different regions of the world were clustered into the same AFLP group, suggesting that migration of the fungal pathogen around these regions has occurred.

Mapping of quantitative trait Loci for fusarium head blight resistance in barley

ABSTRACT Fusarium head blight (FHB) is a devastating disease that causes significant reductions in yield and quality in wheat and barley. Barley grains infected with deoxynivalenol (DON), a vomitoxin produced by Fusarium graminearum, are rejected for malting and brewing. Among six-rowed barley cultivars tested thus far, only cv. Chevron exhibited resistance. This study was conducted to map genes and to identify DNA markers for marker-assisted breeding for FHB resistance in cv. Chevron with restriction fragment length polymorphism (RFLP) markers. A doubled haploid (DH) population was created from a cross between cv. Chevron and susceptible cv. Stander. Seven field experiments were conducted in four different locations in 2 years. A RFLP map containing 211 loci and covering over 1,000 centimorgans (cM) of the genome was used to map quantitative trait loci (QTL) associated with relatively low FHB severity and DON concentration. Morphological traits differing between the parents were also measured: heading date, plant height, spike angle, number of nodes per cm of rachis in the spike, and kernel plumpness. Many of the QTL for FHB and DON coincided with QTLs for these morphological traits. The "fix-QTL" algorithm in Mapmaker QTL was used to remove the part of the variance for FHB resistance that may be explained by heading date or plant height. Results from this study suggest that QTLs with major effects for FHB resistance probably do not exist in cv. Chevron. Three QTL intervals, Xcmwg706-Xbcd441 on chromosome 1H, Xbcd307b-Xcdo684b on chromosome 2H, and Xcdo959b-Xabg472 on chromosome 4H, that are not associated with late heading or height may be useful for marker-assisted selection.

Genes Governing Resistance to Puccinia hordei in Thirteen Spring Barley Accessions

ABSTRACT Leaf rust, caused by Puccinia hordei, is an important disease of barley in many parts of the world. In the eastern United States, this disease was effectively controlled for over 20 years through the deployment of cultivars carrying the resistance gene Rph7. Isolates of P. hordei with virulence for Rph7 appeared in this region in the early 1990s rendering barley cultivars with this gene vulnerable to leaf rust infection. From a preliminary evaluation test, 13 accessions from diverse geographic locations possessed resistance to P. hordei isolate VA90-34, which has virulence for genes Rph1, 2, 4, 6, 7, 8, and 11. Each of these 13 accessions was crossed with susceptible cvs. Moore or Larker to characterize gene number and gene action for resistance to P. hordei. Additionally, the 13 accessions were intercrossed and crossed to host differential lines possessing genes Rph3, Rph5, and Rph9 to determine allelic relationships of resistance genes. Seedlings of F(1), F(2), and BC(1)F(1) populations were evaluated in the greenhouse for their reaction to P. hordei isolate VA90-34. Leaf rust resistance in six of the accessions including Collo sib, CR270.3.2, Deir Alla 105, Giza 119, Gloria, and Lenka is governed by a single dominant gene located at or near the Rph3 locus. All accessions for which the gene Rph3 was postulated to govern leaf rust resistance, except for Deir Alla 105, likely possess an allele different than Rph3.c found in Estate based on the differential reaction to isolates of P. hordei. The resistance gene in Grit and Donan is located at or near the Rph9 locus. Alleles at both the Rph3 and Rph9 loci confer resistance in Femina and Dorina. In addition to Rph3, Caroline and CR366.13.2 likely possess a second unknown recessive gene for leaf rust resistance. Resistance in Carre 180 is governed by a recessive gene that is different from all other genes considered in this study. Identification of both known and unique genes conferring leaf rust resistance in the barley germplasm included in this study provides breeding programs with the knowledge and opportunity to assess currently used sources of leaf rust resistance and to incorporate new sources of resistance into their programs.

Fusarium Species Pathogenic to Barley and Their Associated Mycotoxins

Epidemics of Fusarium head blight (FHB) occurred on barley in Minnesota, North Dakota, and South Dakota from 1993 to 1998. The Red River Valley region was most severely impacted by the disease based on assessments of FHB severity in grain samples harvested from commercial fields. Fusarium graminearum was the primary pathogen causing these FHB epidemics. It comprised from 62 to 64% of all Fusarium species isolated from infected kernels from 1994 to 1996. Fusarium poae (range of isolation 13 to 20%),F. sporotrichioides (10 to 17%), and F. avenaceum (6 to 10%) also were isolated from barley kernels and were likely involved in causing some FHB infection, but to a very limited extent. All four Fusarium species were pathogenic on barley in inoculation tests conducted in both the greenhouse and the field. Mycotoxin screens were performed on barley spikes inoculated with the respective species in the greenhouse. Spikes infected with F. graminearum contained deoxynivalenol and 15-acetyldeoxyni-valenol; those infected with F. sporotrichioides contained T-2 toxin, HT-2 toxin, and T-2 tetraol; and those infected with F. poae contained nivalenol. Some isolates of F. poae also produced 15-acetoxyscirpenol and scirpentriol. Although F. graminearum and DON are recognized as the primary FHB pathogen and mycotoxin, respectively, in barley, the possible presence of other Fusarium species and mycotoxins should not be overlooked.

Identification of Molecular Genetic Markers in Pyrenophora teres f. teres Associated with Low Virulence on 'Harbin' Barley

ABSTRACT Two isolates of the barley net blotch pathogen (Pyrenophora teres f. teres), one possessing high virulence (0-1) and the other possessing low virulence (15A) on the barley cultivar Harbin, were crossed and the progeny of the mating were isolated. Conidia from cultures of the parent and progeny isolates were used as inoculum to determine the inheritance of virulence in the pathogen. Of the 82 progeny tested, 42 exhibited high virulence and 40 exhibited low virulence on 'Harbin' barley. The data support a model in which a single, major gene controls virulence in P. teres f. teres on this barley cultivar (1:1 ratio; chi(2) = 0.05, P = 0.83). Preparations of DNA were made from parental and progeny isolates, and the DNA was subjected to the random amplified polymorphic DNA (RAPD) technique in a search for molecular genetic markers associated with the virulence phenotype. Five RAPD markers were obtained that were associated in coupling with low virulence. The data indicate that the RAPD technique can be used to tag genetic determinants for virulence in P. teres f. teres.

Chromosomal location and genetic relationship of leaf rust resistance genes rph9 and rph12 in barley

ABSTRACT Barley lines Hor 2596 and Triumph are the sources of leaf rust resistance genes Rph9 and Rph12, respectively. An allelism test was performed with F(2) progeny of the cross Triumph/Hor 2596 inoculated with Puccinia hordei. No recombinants were found in a population of 3,858 progeny, indicating Rph9 and Rph12 are alleles. Molecular and morphological markers were used to identify the chromosomal location of these genes in the crosses Bowman/Hor 2596 and Triumph/I91-533-va. A linkage was detected between Rph9 and the flanking sequence-tagged site (STS) markers ABC155 and ABG3 on chromosome 7(5H) at a distance of 20.6 and 20.1 centimorgans (cM), respectively, and to the microsatellite marker dehydrin-9 (HVDHN9) at a distance of 10.2 cM in the Bowman/ Hor 2596 cross. Analysis of isozymes in bulks of the same population showed that Rph9 may be closely linked to the Est9 locus on chromosome 7(5H). The Rph12 locus was linked to the morphological trait locus va (controlling variegated leaf color) on chromosome 7(5H) at a distance of 22.6 cM in the Triumph/I91-533-va cross. Rph12 also was linked with STS marker ABC155 (24.4 cM) and RAPD marker OPA19 (1.5) (17.8 cM). These data indicate that Hor 2596 and Triumph carry a leaf rust resistance gene at the same locus on the long arm of chromosome 7(5H) of barley.

Genetics of Virulence in Cochliobolus sativus and Resistance in Barley

ABSTRACT Spot blotch, caused by Cochliobolus sativus, is one of the most common foliar diseases of barley in the upper midwest region of the United States. To examine the genetics of host-specific virulence in C. sativus, a cross was made between isolate ND90Pr (which exhibits high virulence on barley genotype Bowman and low virulence on genotype ND 5883) and ND93-1 (which exhibits low virulence on both genotypes). Ascospore progeny segregated 48:55 for low virulence/high virulence on Bowman, indicating the presence of a single virulence gene in isolate ND90Pr. To complement the study of host-specific virulence in the pathogen, an experiment also was conducted on the genetics of specific resistance in the host. Progeny from a Bowman/ND 5883 cross were evaluated for their infection responses (IRs) to isolate ND90Pr at the seedling stage. The F(2) population segregated 1:3 for low IRs (resistant)/high IRs (susceptible), indicating the presence of a single resistance gene in genotype ND 5883. This result was confirmed in the F(3) generation, as a 1:2:1 ratio was found for homozygous resistant, segregating, and homozygous susceptible families, respectively. The data from this study demonstrate that both virulence in the pathogen and resistance in the host are under monogenic control in this specific host genotype/fungal isolate combination.

Pathotypes of Cochliobolus sativus on Barley in North Dakota

Spot blotch, caused by Cochliobolus sativus, has become an important disease on two-rowed barley cultivars in North Dakota. Information on the variability of virulence in C. sativus is essential for the development of spot blotch-resistant barley germ plasm. To establish the number and distribution of C. sativus virulence types in North Dakota, 22 isolates from the state were evaluated for their virulence on three differential barley genotypes: ND 5883, Bowman, and ND B112. Eleven additional isolates from Minnesota, South Dakota, Nebraska, Colorado, Japan, and China were included for comparison. Three pathotypes were identified from the thirty-three isolates tested based on the infection responses of the three host genotypes. These pathotypes were designated 0, 1, and 2 according to the coded triplet system of nomenclature. In North Dakota, pathotype 0 (exhibits low virulence on all three differentials) comprised 65%, pathotype 2 (exhibits high virulence on Bowman and low virulence on ND 5883 and ND B112) comprised 25%, and pathotype 1 (exhibits high virulence on ND 5883 and low virulence on Bowman and ND B112) comprised 10% of the total number of barley isolates examined. Within North Dakota, pathotype 1 was found in the east-central and northeastern region only, whereas pathotypes 2 and 0 were distributed throughout the state where samples were taken. Isolates with the pathotype 1 virulence pattern were identified in Colorado, Nebraska, Japan, and China. The remaining isolates collected outside North Dakota were pathotype 0. The information obtained from this study will facilitate the deployment of effective resistance to C. sativus in barley.

Genetics of seedling and adult plant resistance to net blotch (Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) in barley

Net blotch (caused by Pyrenophora teres f. teres) and spot blotch (Cochliobolus sativus) are important foliar diseases of barley in the midwestern region of the USA. To determine the number and chromosomal location of Mendelian and quantitative trait loci (QTL) controlling resistance to these diseases, a doubled haploid population ('Steptoe'/'Morex') was evaluated to the pathogens at the seedling stage in the greenhouse and at the adult plant stage in the field. Alleles at two or three unlinked loci were found to confer resistance to the net blotch pathogen at the seedling stage depending on how progeny exhibiting an intermediate infection response were classified. This result was corroborated in the quantitative analysis of the raw infection response data as 2 major QTL were identified on chromosomes 4 and 6M. A third QTL was also identified on chromosome 6P. Seven QTL were identified for net blotch resistance at the adult plant stage and mapped to chromosomes 1P, 2P, 3P, 3M, 4, 6P, and 7P. The 7 QTL collectively accounted for 67.6% of the phenotypic variance under a multiple QTL model. Resistance to the spot blotch pathogen was conferred by a single gene at the seedling stage. This gene was mapped to the distal region of chromosome 1P on the basis of both qualitative and quantitative data analyses. Two QTL were identified for spot blotch resistance at the adult plant stage: the largest QTL effect mapped to chromosome 5P and the other mapped to chromosome 1P near the seedling resistance locus. Together, the 2 QTL explained 70.1% of the phenotypic variance under a multiple QTL model. On the basis of the chromosomal locations of resistance alleles detected in this study, it should be feasible to combine high levels of resistance to both P. teres f. teres and C. sativus in barley cultivars.

RFLP markers linked to the durable stem rust resistance gene Rpg1 in barley

The gene, Rpg1, conferring stable resistance in barley to the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) was mapped using two doubled haploid populations. Rpg1 mapped to the extreme subteleomeric region of barley chromosome 1P 0.3 and 1.1 cM proximal from the molecular markers ABG704 and plastocyanin (Plc), respectively, and 2.2 cM distal from MWG036B. The closest marker, ABG704, was sequenced and PCR-based markers were developed.

A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome

A map of the barley genome consisting of 295 loci was constructed. These loci include 152 cDNA restriction fragment length polymorphism (RFLP), 114 genomic DNA RFLP, 14 random amplified polymorphic DNA (RAPD), five isozyme, two morphological, one disease resistance and seven specific amplicon polymorphism (SAP) markers. The RFLP-identified loci include 63 that were detected using cloned known function genes as probes. The map covers 1,250 centiMorgans (cM) with a 4.2 cM average distance between markers. The genetic lengths of the chromosomes range from 124 to 223 cM and are in approximate agreement with their physical lengths. The centromeres were localized to within a few markers on all of the barley chromosomes except chromosome 5. Telomeric regions were mapped for the short (plus) arms of chromosomes 1, 2 and 3 and the long (minus) arm of chromosomes 7.