Genome-wide association mapping of zinc and iron concentration in barley landraces from Ethiopia and Eritrea

Mamo, B.E., Barber, B., Steffenson, B.J., 2014. Genome- wide association mapping of zinc and iron concentration in barley landraces from Ethiopia and Eritrea. J. Cereal Sci. XX, XX-XX.Barley is one of the oldest cultivated crop plants and is a major part of a staple diet in some developing countries. The objectives of this study were to characterize genetic variation in grain zinc and iron concentration and kernel weight, and identify quantitative trait loci (QTL) associated with these traits in barley landraces from Ethiopia/Eritrea using a genome-wide association study (GWAS). Barley landraces were grown under greenhouse and field conditions, characterized for micronutrient concentration and kernel weight, and then genotyped with 7842 single nucleotide polymorphism (SNP) markers. The germplasm exhibited a wide range of variation for these traits with some accessions having high levels of zinc and iron. Heritability values of 0.65 and 0.59, respectively, were obtained for zinc and iron concentrations in grain samples harvested from field trials. One QTL associated with grain zinc concentration was identified in a unique genomic location on the long arm of chromosome 6H. For kernel weight, a known QTL region on the long arm of chromosome 2H was detected. This study demonstrates the existence of high genetic variation for grain zinc and iron concentration in Ethiopian/Eritrean barley landraces and also the utility of GWAS for identifying and mapping QTL underlying micronutrient accumulation

Effect of incubation time and temperature on the phenotypic expression of rpg4 to Puccinia graminis f. sp. tritici in barley

Canadian Journal of Plant Pathology website: http://www.tandfonline.com/loi/tcjp20To study the effect of incubation time and temperature on the phenotypic expression of rpg4, five barley genotypes with this resistance gene were infected with pathotype QCCJ of Puccinia graminis f. sp. tritici at the seedling stage, then subjected to various times of incubation at either 18-19°C or 27~28°C. Genotypes with rpg4 exhibited low (0, 0;, and 1), mesothetic (e.g. 3-210;, 120;3), and high (3,3) infection types at 18-19°C after initial incubation at 27-28°C for 0-28, 40-76, and 88 or more hours, respectively. A period of 88 or more hours of initial incubation at high temperature rendered the rpg4 resistance completely ineffective against this pathotype of P. g. f. sp. tritici. In contrast, high, mesothetic, and low infection types were found for the same genotypes at 27-28°C after initial incubation at 18-19°C for 0-40, 52-100, and 112 or more hours, respectively. The resistant infection types conferred by rpg4 are apparently established within the first 112 hours after the end of the infection period since subsequent shifts to higher temperature did not result in marked changes in the resistance response. These data indicate the critical importance of maintaining precise temperature control when assessing the infection phenotypes of barley genotypes carrying the stem rust resistance gene rpg4

Receptivity of barley to Puccinia graminis f. sp. tritici

Canadian Journal of Plant Pathology website: http://www.tandfonline.com/loi/tcjp20The receptivity of barley genotypes {Hordeum vulgare) was studied in seedlings and adult plants in the greenhouse and in adult plants in the field to races I13-RTQ and 151-QSH of Puccinia graminis f. sp. tritici. In the greenhouse, significant differences in number of uredia/cm2 of leaf were detected due to the effects of races, host genotypes, and their interaction. The cultivar Hiproly was most receptive (had the most uredia) and 80-TT-29 was least receptive (had the fewest uredia) to both races at both growth stages. With race 151-QSH, genotypes with the T-gene, 80-TT-29 and Manker had low weighted infection types (seedling stage), moderately resistant host responses (adult stage), and lower receptivity (both growth stages) than cultivars lacking this gene. With race 113-RTQ, the T-gene was associated with low receptivity only in 80-TT-29. The data suggest that gene(s) other than the T-gene may confer receptivity to P. graminis f. sp. tritici. The ranking of genotypes and the relative differences in receptivity were similar in seedling and adult plants. In the field, genotypes with the T-gene had mostly moderately resistant reactions and fewer uredia than those without the gene. The significant race x host genotype interaction in this study suggests that receptivity in barley varies due to the specific host-parasite combination

Identification of Cochliobolus sativus isolates expressing differential virulence on two-rowed barley genotypes from North Dakota

Canadian Journal of Plant Pathology website: http://www.tandfonline.com/loi/tcjp20Severe spot blotch infection was observed in 1990 on several two-row barley breeding lines previously regarded as resistant to Cochliobolus sativus. Studies were conducted to compare the virulence pattern of a C. sativus isolate (ND90Pr) obtained from this two-row breeding nursery with one (ND85F) used in previous disease screening evaluations. Greenhouse and field experiments were performed in 1991 and 1992 at Fargo, ND, using a split plot design with isolate as the main effect. Isolates ND90Pr and ND85F exhibited distinct differential virulence patterns on barley genotypes ND 5883, ND 12437, ND 12720, ND 12721, and Bowman. Isolate ND90Pr displayed high virulence on ND 12720, ND 12721, and Bowman, and low virulence on ND 5883 and ND 12437. In contrast, isolate ND85F was highly virulent on ND 5883 and ND 12437 and weakly virulent on ND 12720, ND 12721, and Bowman. Both isolates expressed low virulence on genotype ND Bl 12, the primary source of resistance to C. sativus in commercial six-row barley germplasm. To incorporate adequate levels of resistance into future two-row barley cultivars, disease evaluations should be made with C. sativus isolates that express the full spectrum of virulence found in North Dakota

Puccinia coronata var. hordei var. nov. morphology and pathogenicity

A new variety of Puccinia coronata causing a disease on barley and other gramineous species is described. The fungus is different from other reported forms of P coronata in both morphology and pathogenicity. Its most prominent characters are the elongated teliospore appendages with dichotomous branching and wide pathogenicity on species in the tribe Triticeae, particularly the genus Hordeum. The name of P coronata var. hordei is proposed for the rust fungus. The common name 'crown rust of barley' is proposed for the disease of barley caused by this rust fungus. Results of inoculation indicated that P coronata var. hordei is pathogenic on species of Aegilops, Agropyron, Elymus, Elytrigia, Leymus, Pascopyrum, Psathyrostachys, Secale, and Triticum in the tribe Triticeae, and some species of Brachypodium, Bromus, Festuca, and Lolium in the tribe Poeae, and Phalaris in the tribe Aveneae. In the northern Great Plains of the USA, the following native and introduced gramineous species were found naturally infected by P coronata var. hordei: Bromus tectorum, Elymus canadensis, E. trachycaulus, E. virginicus, Elytrigia intermedia, E. repens, Hordeum jubatum, H. vulgare, Leymus angustus, L. cinerius, L. dahuricus, L. racemosus, Pascopyrum smithii, Psathyrostachys juncea, and Secale cer- eale

Genome-wide association mapping of fusarium head blight resistance and agromorphological traits in barley landraces from Ethiopia and Eritrea

Fusarium head blight (FHB), caused primarily by Fusarium graminearum, is an important disease of barley (Hordeum vulgare L.), and other cereals. In barley, the genetic basis of FHB resistance has been intensively studied through linkage mapping that identified several quantitative trait loci (QTL). However, our understanding and application of these QTL in breeding is still limited due to the complex nature and low-to-moderate heritability of FHB resistance. Previous studies used either breeding lines, unimproved varieties, or germplasm selections. Here, we used association mapping in barley landraces to identify QTL associated with FHB severity, deoxynivalenol (DON) concentration and correlated agromorphological traits. Diverse barley landraces (n = 298) from Ethiopia and Eritrea were evaluated for the traits under field conditions for 2 yr (2011–2012) in Crookston, MN, and genotyped with 7842 single nucleotide polymorphism (SNP) markers. Association mapping analysis using a mixed model corrected for pairwise relatedness between individuals identified one common resistance QTL on barley chromosome 2HL significantly associated with both FHB severity and DON concentration and another one on 4HL associated with DON concentration. The QTL identified on 2HL is associated with the row-type locus Vrs1. Both of these QTL were not significantly associated with heading date or plant height unlike other QTL reported in previous studies. Thus, the resistant accessions carrying these QTL may be used in breeding programs without the confounding effects from these agromorphological traits. Importantly, these QTL could be new alleles preserved in this unique germplasm, and the linked SNP markers found may be useful in marker-assisted introgression of resistance

Genetic Characterization of Resistance to Wheat Stem Rust Race TTKSK in Landrace and Wild Barley Accessions Identifies the rpg4/Rpg5 Locus.

Race TTKSK of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) threatens the production of wheat and barley worldwide because of its broad-spectrum virulence on many widely grown cultivars. Sources of resistance against race TTKSK were recently identified in several barley landraces (Hordeum vulgare subsp. vulgare) and wild barley accessions (H. vulgare subsp. spontaneum). The objectives of this study were to characterize the inheritance of resistance to wheat stem rust race TTKSK in four barley landraces (Hv501, Hv545, Hv602, and Hv612) and two wild barley (WBDC213 and WBDC345) accessions, map the resistance genes, and determine the allelic relationships among the genes in these accessions and the previously described rpg4/Rpg5 locus. Resistant accessions were crossed with the susceptible cv. Steptoe and resulting F3 populations were evaluated for resistance to race TTKSK at the seedling stage. Segregation of F3 families in populations involving the resistance sources of Hv501, Hv545, Hv612, WBDC213, and WBDC345 fit a 1:2:1 ratio for homozygous resistant (HR)/segregating (SEG)/homozygous susceptible (HS) progenies (with χ2=2.27 to 5.87 and P=0.053 to 0.321), indicating that a single gene confers resistance to race TTKSK. Segregation of F3 families in cross Steptoe/Hv602 did not fit a 1:2:1 ratio (HR/SEG/HS of 20:47:43 with χ2=11.95 and P=0.003), indicating that more than one gene is involved in imparting resistance to race TTKSK. Bulked segregant analysis using >1,500 single-nucleotide polymorphism markers positioned a resistance locus in all six populations on chromosome 5HL in very close proximity to the known location of the rpg4/Rpg5 complex locus. Allelism tests were conducted by making crosses among resistant accessions Hv501, Hv545, and Hv612 and also Q21861 with the rpg4/Rpg5 complex. No segregation was observed in F2 families inoculated with race TTKSK, demonstrating that all Hv lines carry the same allele for resistance and that it resides at or very near the rpg4/Rpg5 locus. Phenotype evaluations of the six barley accessions with wheat stem rust race QCCJ revealed resistant infection types (ITs) at a low incubation temperature and susceptible ITs at a high incubation temperature, similar to Q21861, which carries the temperature-sensitive gene rpg4. The accessions also exhibited low ITs against the rye stem rust isolate 92-MN-90, suggesting that they also carry Rpg5. This result was confirmed through molecular analysis, which revealed that all six barley accessions contain the serine threonine protein kinase domain that confers Rpg5 resistance. These results indicate that cultivated barley is extremely vulnerable to African stem rust races such as TTKSK because even these diverse selections of landrace and wild barley accessions carry only one locus for resistance

The rpg4/Rpg5 stem rust resistance locus in barley; resistance genes and cytoskeleton dynamics

Two closely linked resistance genes, rpg4 and Rpg5, conferring resistance to several races of Puccinia graminis, were cloned and characterized. The Rpg5 gene confers resistance to an isolate of Puccinia graminis f. sp. secalis (Pgs), while rpg4 confers resistance to Puccinia graminis f. sp. tritici (Pgt). Rpg5 is a novel gene containing nucleotide binding site-leucine rich repeat domains in combination with a serine threonine protein kinase domain. High-resolution mapping plus allele and recombinant sequencing identified the rpg4 gene, which encodes an actin depolymerizing factor-like protein (ADF2). Resistance against the Pgt races QCCJ, MCCF, TTKSK (aka Ug99) and RCRS requires both Rpg5 and rpg4, while Rpg5 alone confers resistance to Pgs isolate 92-MN-90. The dependency on the actin modifying protein ADF2 indicates cytoskeleton reorganization or redirection plays a role in pathogen-host interactions. Rpg5 may interact with ADF2 to activate or deactivate its function in the resistance response. Alternatively, Rpg5 could initiate signal transduction leading to resistance in response to detecting ADF2 protein modification. Pgt may redirect the actin cytoskeleton by inducing modifications of ADF2. The redirection of actin could possibly enable the pathogen to develop a haustoria-plant cell cytoskeleton interface for acquisition of nutrients

Agronomic Characteristics, Malt Quality, and Disease Resistance of Barley Germplasm Lines with Partial Fusarium Head Blight Resistance

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe, has caused devastating losses in both yield and quality of barley (Hordeum vulgare L.) produced in the northern Great Plains from 1993 to 2003. Thirty-five barley germplasmlines with partial resistance to FHB have been identified in exotic and unadapted germplasm lines. Little is known about their agronomic characteristics, malt quality, and reaction to other diseases as compared to adapted cultivars. This information is needed so barley breeders can make informed decisions when planning crosses involving the resistant germplasm lines. The objective of this study was to compare the agronomic performance, malt quality, and disease reaction of barley germplasm lines with partial FHB resistance to cultivars grown in the northern Great Plains. Agronomic and malting data were collected on the 35 germplasm lines and five check cultivars grown in five environments in North Dakota from 1998 to 2000. Data for FHB severity and deoxynivalenol (DON, a mycotoxin produced by F. graminearum) accumulation were obtained for the same 40 entries grown in FHB-epidemic nurseries in North Dakota from 1997 to 1999. Seedling responses to foliar pathogens common in the northern Great Plains were determined in the greenhouse during fall 1997. None of the FHB-resistant barley germplasm lines had acceptable malt quality for all traits. Kernel plumpness, grain protein concentration, and malt extract were the traits impacted most severely. The FHB-resistant barley germplasm lines headed significantly later than the adapted barley cultivars. Most FHB-resistant germplasm lines were susceptible to the common foliar diseases of the northern Great Plains. At least four cycles of breeding will probably be necessary to develop FHB-resistant germplasm lines acceptable to producers and the malting and brewing industry

Predicting agronomic performance of barley using canopy reflectance data

The ability to accurately and rapidly predetermine agronomic performance would be desirable in most plant breeding programs. Remote sensing of canopy reflectance is a quick and nondestructive method that may be useful in the estimation of agronomic performance. Studies were conducted at Fargo and Langdon, North Dakota, to determine the effectiveness of a multispectral radiometer in estimating yield, kernel plumpness (KP), and 1000-kernel weight (TKW) in barley. Canopy reflectance was measured in eight (500–850 nm) discrete narrow-wavelength bands. Three types of reflectance models were evaluated: simple models using one to four wavelengths, simple ratio and normalized difference vegetation indices (NDVI) using green, red, and near-infrared wavelengths, and soil-adjusted vegetation indices (SAVI). The relationship between canopy reflectance and agronomic performance was significantly influenced by environment, growth stage, and plant genotype. Grain yield was best estimated near GS73 (0.84 < R2 < 0.92) at Fargo and at GS83 (0.55 < R2 < 0.81) at Langdon. In contrast, KP and TKW could be estimated at both late (GS83; 0.68 < R2 < 0.93) and early (GS24–GS47; 0.72 < R2 < 0.91) growth stages. The 550-nm and 800-nm wavelengths are critical for development of predictive models. A simple model using 550-nm, 600-nm, and 800-nm from GS47-GS73 gave significant (0.45 < R2 < 0.64) estimation of agronomic performance across all environments. In contrast, simple ratio, NDVI, and SAVI were less effective (0.05 < R2 < 0.77) in predicting agronomic performance. Remote sensing using canopy reflectance is a potential tool to estimate agronomic performance of barley, but genotypic and crop stage factors affect this method. Further studies are needed to improve the usefulness of multispectral radiometry in predicting agronomic performance