J. Paul Murphy

Variation Among Isolates of Fusarium graminearum Associated with Fusarium Head Blight in North Carolina

ABSTRACT Fusarium head blight (FHB) can reduce yield of wheat and decrease the value of harvested grain by accumulation of detrimental toxins. Understanding the variability of the fungal population associated with infection could improve disease control strategies. Sixty-six isolates of Fusarium graminearum associated with FHB were collected in North Carolina and tested for in vitro growth rate, in vitro production of deoxynivalenol (DON) and zearalenone, and pathogenicity on three cultivars of soft red winter wheat. Significant differences among isolates were found for all three traits. Randomly Amplified Polymorphic DNA (RAPD) analysis revealed high levels of genotypic diversity among isolates. Isolates of F. graminearum, F. culmorum, and F. avenaceum acquired from the Pennsylvania State University Fusarium Center were included for comparison in all tests. In vivo levels of DON were measured for the five isolates associated with the highest levels of disease and the five isolates associated with the low...

CHANGES OVER TIME IN THE ALLELOCHEMICAL CONTENT OF TEN CULTIVARS OF RYE (Secale cereale L.)

Published studies focused on characterizing the allelopathy-based weed suppression by rye cover crop mulch have provided varying and inconsistent estimates of weed suppression. Studies were initiated to examine several factors that could influence the weed suppressiveness of rye: kill date, cultivar, and soil fertility. Ten cultivars of rye were planted with four rates of nitrogen fertilization, and tissue from each of these treatment combinations was harvested three times during the growing season. Concentrations of a known rye allelochemical DIBOA (2,4-dihydroxy-1,4-(2H)benzoxazine-3-one) were quantified from the harvested rye tissue using high performance liquid chromatography (HPLC). Phytotoxicity observed from aqueous extracts of the harvested rye tissue correlated with the levels of DIBOA recovered in harvested tissue. The amount of DIBOA in rye tissue varied depending on harvest date and rye cultivar, but was generally lower with all cultivars when rye was harvested later in the season. However, the late maturing variety ‘Wheeler’ retained greater concentrations of DIBOA in comparison to other rye cultivars when harvested later in the season. The decline in DIBOA concentrations as rye matures, and the fact that many rye cultivars mature at different rates may help explain why estimates of weed suppression from allelopathic agents in rye have varied so widely in the literature.

Virulence Structure of the Eastern U.S. Wheat Powdery Mildew Population

Little is known about the population structure of wheat powdery mildew in the eastern United States, and the most recent report on virulence in this population involved isolates collected in 1993-94. In the present study, wheat leaves naturally infected with powdery mildew were collected from 10 locations in the southeastern United States in 2003 and 2005 and a collection of 207 isolates was derived from single ascospores. Frequencies of virulence to 16 mildew resistance (Pm) genes were determined by inoculating the isolates individually on replicated plates of detached leaves of differential wheat lines. These virulence frequencies were used to infer local effectiveness of Pm genes, estimate virulence complexity, detect significant associations between pairs of pathogen avirulence loci, and assess whether phenotypic differences between pathogen subpopulations increased with geographic distance. In both years, virulence to Pm3a, Pm3c, Pm5a, and Pm7 was present in more than 90% of sampled isolates and virulence to Pm1a, Pm16, Pm17, and Pm25 was present in fewer than 10% of isolates. In each year, 71 to 88% of all sampled isolates possessed one of a few multilocus virulence phenotypes, although there were significant differences among locations in frequencies of virulence to individual Pm genes. Several significant associations were detected between alleles for avirulence to pairs of Pm genes. Genetic (phenotypic) distance between isolate subpopulations increased significantly (R2 = 0.40, P < 0.001) with increasing geographic separation; possible explanations include different commercial deployment of Pm genes and restricted gene flow in the pathogen population.

Molecular characterization of a new powdery mildew resistance gene Pm54 in soft red winter wheat

Key messageA new powdery mildew resistance genePm54was identified on chromosome 6BL in soft red winter wheat.AbstractPowdery mildew is causing increasing damage to wheat production in the southeastern USA. To combat the disease, a continuing need exists to discover new genes for powdery mildew resistance and to incorporate those genes into breeding programs. Pioneer® variety 26R61 (shortened as 26R61) and AGS 2000 have been used as checks in the Uniform Southern Soft Red Winter Wheat Nursery for a decade, and both have provided good resistance across regions during that time. In the present study, a genetic analysis of mildew resistance was conducted on a RIL population developed from a cross of 26R61 and AGS 2000. Phenotypic evaluation was conducted in the field at Plains, GA, and Raleigh, NC, in 2012 and 2013, a total of four environments. Three quantitative trait loci (QTL) with major effect were consistently detected on wheat chromosomes 2BL, 4A and 6BL. The 2BL QTL contributed by 26R61 was different from Pm6, a widely used gene in the southeastern USA. The other two QTL were identified from AGS 2000. The 6BL QTL was subsequently characterized as a simple Mendelian factor when the population was inoculated with a single Blumeria graminis f. sp. tritici (Bgt) isolate in controlled environments. Since there is no known powdery mildew resistance gene (Pm) on this particular location of common wheat, the gene was designated Pm54. The closely linked marker Xbarc134 was highly polymorphic in a set of mildew differentials, indicating that the marker should be useful for pyramiding Pm54 with other Pm genes by marker-assisted selection.

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

An AFLP-based survey of genetic diversity among accessions of sea oats (Uniola paniculata, Poaceae) from the southeastern Atlantic and Gulf coast states of the United States

Uniola paniculata, commonly known as sea oats, is a C4 perennial grass capable of stabilizing sand dunes. It is most abundant along the Gulf of Mexico and southeastern Atlantic coastal regions of the United States. The species exhibits low seed set and low rates of germination and seedling emergence, and so extensive clonal reproduction is achieved through production of rhizomes, which may contribute to a decline in genetic diversity. To date, there has been no systematic assessment of genetic variability and population structure in naturally occurring stands in the USA. This study was conducted to assess the genetic relationship and diversity among nineteen U. paniculata accessions representing eight states: Texas, Louisiana, Mississippi, Alabama, Florida, South Carolina, North Carolina, and Virginia, using amplified fragment length polymorphism (AFLP). Twelve AFLP EcoRI+MseI primer combinations generated a wide range of polymorphisms (42–81%) with a mean of 59%. Overall, the sea oats plants exhibited a low range of genetic similarity. Florida accessions, FL-33 and FL-39, were most genetically diverse and the accessions from both Carolinas and Virginia (NC-1, NC-11, SC-15, and VA-53) harbored less genetic variability. Cluster analysis using the UPGMA approach separated U. paniculata plants into four major clusters which were also confirmed by principal coordinate analysis (PCO). Further examination of the different components of genetic variation by analysis of molecular variance (AMOVA) indicated the largest proportion of variability at the state level (47.8%) followed by the variation due to the differences among the genotypes within an accession (34.4%), and the differences among the accessions within a state (17.8%). The relationship between genetic diversity and geographic source of sea oats populations of the United States as revealed through this comprehensive study will be helpful to resource managers and commercial nurseries in identifying suitable plant materials for restoration of new areas without compromising the adaptation and genetic diversity.

Population Structure, Linkage Disequilibrium, and Genetic Diversity in Soft Winter Wheat Enriched for Fusarium Head Blight Resistance

The occurrence of epidemics of Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, in U.S. winter wheat (Triticum aestivum L.) during the past two decades led to significant emphasis on development of resistant cultivars. Understanding the genetic diversity, population structure (PS), and linkage disequilibrium (LD) in winter wheat in the eastern United States is important for marker‐assisted breeding and association analysis in this germplasm. Lines selected from collaborative FHB screening nurseries were genotyped with simple sequence repeat (SSR), sequence tagged site (STS), and Diversity Array Technology (DArT) markers to assess LD, genetic diversity, and PS. The genomewide average of LD decay to r2 < 0.2 was 9.9 cM and moderate levels of LD (r2 > 0.2) were generally constrained to markers less than 5 cM apart. Although the lines evaluated were targeted to distinct production zones of the eastern winter wheat region, cluster and principal component analyses did not detect separation of lines into subpopulations. The short, intense breeding history for scab resistance may have localized effects on LD. Lack of subgroups within our population could be due to intercrossing among common resistant parents and indicate frequent admixture and germplasm exchange among U.S. winter wheat programs focused on development of FHB resistant cultivars.

Population Genomics Related to Adaptation in Elite Oat Germplasm

An oat association‐mapping panel contributed by active breeding programs worldwide. Characterized population structure and found subdivisions related to adaptation Characterized genome‐wide and chromosome‐specific linkage disequilibrium Performed association‐mapping and post hoc modeling of heading date Found several consistently associated QTL

A Comparison of Methods for Evaluating the Suppressive Ability of Winter Wheat Cultivars against Italian Ryegrass (Lolium perenne)

Abstract Infestations of Italian ryegrass are problematic in both conventional and organic wheat production systems. The development of wheat cultivars with superior competitive ability against Italian ryegrass could play a role in maintaining acceptable yields and suppressing weed populations. Research was conducted in North Carolina to identify indirect methods of selection for Italian ryegrass suppressive ability (hereafter referred to as weed suppressive ability) of winter wheat cultivars that correlate well with Italian ryegrass-to-wheat biomass ratios. Two winter wheat cultivars (Dyna-Gro Baldwin and Dyna-Gro Dominion) and one experimental wheat line (NC05-19684) with differing morphological traits were overseeded with varying densities of Italian ryegrass. Wheat height measured throughout the growing season in weed-free plots was strongly associated with weed suppressive ability, but high wheat tillering capacity had no significant effect on weed suppressive ability in the lines tested in this study. Italian ryegrass seed head density during grain fill was strongly correlated (r  =  0.94) with Italian ryegrass-to-wheat biomass ratio, the generally accepted measure of weed suppressive ability. Visual estimates of percent Italian ryegrass biomass relative to the plot with the highest level of Italian ryegrass infestation in each replicate were also strongly correlated with weed suppressive ability at all growth stages, especially during heading (r  =  0.87) (Zadoks growth stage [GS] 55). Measurements from nonimaging spectrophotometers and overhead photographs taken from tillering (Zadoks 23 to 25) to early dough development (Zadoks 80) were unreliable estimates of end-of-season Italian ryegrass-to-wheat biomass ratios because they failed to account for wheat cultivar differences in biomass, color, and growth habit. Italian ryegrass seed head density and visual estimates of Italian ryegrass biomass during grain fill are appropriate indirect methods of selection for weed suppressive ability in breeding programs. Nomenclature: Italian ryegrass, Lolium perenne L. ssp. multiflorum (Lam.) Husnot LOLMU; wheat, Triticum aestivum L.

Selection For Resistance and Tolerance to Oat Mosaic Virus and Oat Golden Stripe Virus in Hexaploid Oats

Coker 716, a hexaploid oat cultivar resistant to both oat mosaic virus (OMV) and oat golden stripe virus (OGSV) was crossed to three susceptible cultivars (Brooks, Madison, and Tech) to form three individual populations. Individual breeding lines were derived from each cross in the F2 generation and tested in plots consisting of equally spaced individual hills in OMV- and OGSV-infested soils and non-infested soils to evaluate resistance and yield loss of individual lines. Foliar symptoms, harvest index, and yield loss were examined as selection criteria for resistant genotypes. The study was conducted over 2 years at two North Carolina locations that differed in soil type and climate. Multiple regression models describing yield loss in each cross due to rating, year, and location were calculated. Coefficients of multiple determination in these models ranged from 0.39 to 0.51. Yield loss ranged from 39 to 60% among different crosses. Infection by OMV and OGSV accounted for the majority of yield loss in two of the populations. Disease severity varied widely over years and locations. The results suggest that selection of lines with symptomatic tissue of 10% or less, or selection of tolerant lines, is needed for breeding progress.