Improvement of asexual propagation and Anisogramma anomala detection protocols to facilitate applied breeding of new Corylus avellana and C. americana x C. avellana germplasm

Though hazelnut (Corylus L.) breeding has a long history, the discipline is still in the early stages of its development. Global hazelnut production continues to rely on wild selections and local cultivars in many countries. The lack of new cultivar development is a consequence of underutilization of the wide genetic diversity that exists within the genus and an exceptionally long breeding cycle. This cycle requires a minimum of eight years from seed to seed (generation time) and an additional nine years for selected individuals to proceed through replicated performance trials to cultivar release. At present, layering techniques are the primary method for asexual propagation of Corylus selections during the breeding cycle. While effective, that technique is relatively archaic and yields of successful cuttings are low. Propagation by cuttings provides an alternative with a higher production potential; however, variable root induction rates and bud abscission among traditional Corylus cultivars currently limit this approach. A recent study suggests use of ethylene-blocking compounds in combination with low auxin levels may help overcome these challenges. Presently, the efficacy of these treatments is known for only a narrow selection of C. avellana genotypes. In addition to working to overcome challenges associated with propagation, breeding efforts have expanded germplasm collections to increase sources of eastern filbert blight (EFB) resistance. Screening for EFB resistance greatly complicates breeding efforts because Anisogramma anomala (the causal pathogen of EFB) contains notable genetic and pathogenic variation. Screening U.S. collections for EFB resistance is largely done by phenotyping, which is problematic because A. anomala has a 12- to 16-month symptomless latent period that delays the culling of susceptible plants. Refinement of recently developed real-time polymerase chain reaction (PCR) protocols that provide early detection of EFB susceptible seedlings would greatly improve the capacity and pace of cultivar development. This thesis focuses on ways to increase breeding efficiency by improving: 1) protocols used to propagate stem cuttings and, 2) early detection of EFB susceptibility in seedling populations. A hybrid hazelnut (C. americana x C. avellana) progeny population was used in two experiments to observe adventitious rooting and bud abscission after treatment with low indole-3-butyric acid (IBA) (≥1000 ppm) and low IBA plus ethylene-inhibiting silver nitrate. Using subterminal softwood stem cuttings, adventitious root formation occurred at a rate of 62% or greater and bud abscission was not observed in either experiment. These results indicate adventitious rooting of softwood stems cuttings is a promising method for hybrid hazelnut breeders to use. To address the EFB screening bottleneck, a real-time PCR protocol for A. anomala detection in stem tissue was adapted by increasing the size of stem tissue sampled by 2-3 fold. This modification allowed for successful detection of anomala infection in symptomless seedlings 30 days after inoculation. Detection success was not improved by later (55 and 90 days) sampling. In addition to improving early diagnosis of A. anomala infection, this assay could be used to study A. anomala growth and development following infection

SNAPSHOT USA 2019 : a coordinated national camera trap survey of the United States

This article is protected by copyright. All rights reserved.With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August - 24 November of 2019). We sampled wildlife at 1509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the USA. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as well as future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.Publisher PDFPeer reviewe

Mammal responses to global changes in human activity vary by trophic group and landscape

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human–wildlife interactions along gradients of human influence.Peer reviewe

Towards the exploitation of the American hazelnut (Corylus americana)

In the Midwest U.S. landscape dominated by the corn-soybean rotation, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. While existing varieties and breeding selections of tree fruits and nuts provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. requires genetic improvement with respective to target environments. This dissertation begins by summarizing literature on the genetic improvement of underutilized temperate U.S. tree crops and their wild relatives, with emphasis on their strategic integration into the Midwest U.S. agricultural landscape. Subsequently, hazelnut is the focus of the three experimental chapters, with the theme of characterizing american hazelnut (Corylus american) germplasm for eastern filbert blight (EFB) resistance. EFB, caused by the fungus Anisogramma anomala, is a primary limitation to european hazelnut (Corylus avellana) cultivation in eastern North America. C. americana is the endemic host of A. anomala and, despite its tiny, thick-shelled nuts, is a potentially valuable source of EFB resistance and climatic adaptation. Interspecific hybrids (C. americana × C. avellana) have been explored for nearly a century as a means to combine EFB resistance with wider adaptability and larger nuts. While significant progress was made in the past, the genetic diversity of the starting material was limited, and additional improvements are needed for expansion of hazelnut production outside of Oregon, where 99% of the U.S. crop is currently produced. Towards this end, this Ph.D. research sought to expand the availability of characterized C. americana germplasm through: i) evaluating american and interspecific hybrid hazelnut (C. americana × C. avellana) germplasm for EFB resistance, ii) evaluating wild american hazelnut germplasm for genetic diversity and structure, and iii) mapping EFB resistance quantitative trait loci (QTL) in C. americana OSU 403.040. In the first study, to improve our understanding of C. americana as a donor of EFB resistance, 29 diverse EFB-resistant C. americana accessions were crossed with EFB-susceptible C. avellana selections (31 total progenies) to produce 2031 F1 plants. Additionally, new C. americana germplasm was procured from across the native range of the species – 1335 plants from 122 seed lots representing 72 counties and 22 states. The interspecific hybrid progenies and a subset of the american collection (616 trees from 62 seed lots) were field planted and evaluated for EFB response following inoculations and natural disease spread over seven growing seasons. EFB was rated on a scale of 0 (no EFB) to 5 (all stems containing cankers). Results showed that progeny means of the interspecific hybrids ranged from 0.96 to 4.72. Fourteen of the 31 progenies were comprised of at least one-third EFB-free or highly tolerant offspring (i.e., ratings 0 to 2), transmitting a significant level of resistance/tolerance. Several corresponding C. americana accessions that imparted a greater degree of resistance to their hybrid offsprings were also identified. In addition, results showed that 587 of the 616 (95.3%) C. americana plants evaluated remained completely free of EFB, confirming reports that the species rarely expresses signs or symptoms of the disease and should be further studied and used in breeding. In the second study, the genetic diversity and structure of new C. americana (272 individuals) collected from 33 seedlots across the species’ native range are reported. Two-thousand fifty-three SNPs were discovered using a genome-by-sequencing approach and support a heterozygous collection (HE = 0.276, HO = 0.280) with moderate differentiation (FST = 0.108) and low inbreeding (FIS = -0.136). Bayesian model-based and neighbor-joining (NJ) clustering corroborate an uppermost clustering level of K = 3. The NJ dendrogram depicts many small subgroups equally distant from common ancestry. Discriminant analysis of principal components reveals between-sub-group variation (K = 15) within the NJ dendrogram and allows the identification of 19 consensus subgroups. Fifty-one accessions were selected for inclusion within a core set based upon 95% representation of the observed allelic variation. Breeders can now exploit the breadth of genetic diversity held within this collection during development of interspecific hybrids. In the final study, a genetic linkage map was developed using a genome-by-sequencing approach and used to identify QTL associated with EFB resistance from the C. americana selection OSU 403.040 from Nebraska U.S. A bi-parental mapping population comprised of 121 seedling trees was evaluated for EFB under high disease pressure in New Jersey, where A. anomala is endemic and highly genetically diverse. With EFB response represented by the percent of diseased wood, a total of three QTLs were discovered on linkage groups (LG) 3, 6, and 11 that respectively represent 62.6%, 23.3%, and 11.1% of the phenotypic variation. EFB resistance from OSU 403.040 appears new based upon it being only the second mapped source from C. americana and due to it mapping to three loci – all other sources of EFB resistance in Corylus spp. are monogenic and map to a single locus. Additionally, OSU 403.040 likely exhibits resistance to a broad range of A. anomala given the genetically diverse A. anomala environment under which it was selected. Such durability is requisite for the development of a feasible commercial variety for the eastern U.S. and highlights a priority for its inclusion in gene pyramiding schemes with resistant C. avellana

Towards the exploitation of the American hazelnut (Corylus americana)

In the Midwest U.S. landscape dominated by the corn-soybean rotation, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. While existing varieties and breeding selections of tree fruits and nuts provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. requires genetic improvement with respective to target environments. This dissertation begins by summarizing literature on the genetic improvement of underutilized temperate U.S. tree crops and their wild relatives, with emphasis on their strategic integration into the Midwest U.S. agricultural landscape. Subsequently, hazelnut is the focus of the three experimental chapters, with the theme of characterizing american hazelnut (Corylus american) germplasm for eastern filbert blight (EFB) resistance. EFB, caused by the fungus Anisogramma anomala, is a primary limitation to european hazelnut (Corylus avellana) cultivation in eastern North America. C. americana is the endemic host of A. anomala and, despite its tiny, thick-shelled nuts, is a potentially valuable source of EFB resistance and climatic adaptation. Interspecific hybrids (C. americana × C. avellana) have been explored for nearly a century as a means to combine EFB resistance with wider adaptability and larger nuts. While significant progress was made in the past, the genetic diversity of the starting material was limited, and additional improvements are needed for expansion of hazelnut production outside of Oregon, where 99% of the U.S. crop is currently produced. Towards this end, this Ph.D. research sought to expand the availability of characterized C. americana germplasm through: i) evaluating american and interspecific hybrid hazelnut (C. americana × C. avellana) germplasm for EFB resistance, ii) evaluating wild american hazelnut germplasm for genetic diversity and structure, and iii) mapping EFB resistance quantitative trait loci (QTL) in C. americana OSU 403.040. In the first study, to improve our understanding of C. americana as a donor of EFB resistance, 29 diverse EFB-resistant C. americana accessions were crossed with EFB-susceptible C. avellana selections (31 total progenies) to produce 2031 F1 plants. Additionally, new C. americana germplasm was procured from across the native range of the species – 1335 plants from 122 seed lots representing 72 counties and 22 states. The interspecific hybrid progenies and a subset of the american collection (616 trees from 62 seed lots) were field planted and evaluated for EFB response following inoculations and natural disease spread over seven growing seasons. EFB was rated on a scale of 0 (no EFB) to 5 (all stems containing cankers). Results showed that progeny means of the interspecific hybrids ranged from 0.96 to 4.72. Fourteen of the 31 progenies were comprised of at least one-third EFB-free or highly tolerant offspring (i.e., ratings 0 to 2), transmitting a significant level of resistance/tolerance. Several corresponding C. americana accessions that imparted a greater degree of resistance to their hybrid offsprings were also identified. In addition, results showed that 587 of the 616 (95.3%) C. americana plants evaluated remained completely free of EFB, confirming reports that the species rarely expresses signs or symptoms of the disease and should be further studied and used in breeding. In the second study, the genetic diversity and structure of new C. americana (272 individuals) collected from 33 seedlots across the species’ native range are reported. Two-thousand fifty-three SNPs were discovered using a genome-by-sequencing approach and support a heterozygous collection (HE = 0.276, HO = 0.280) with moderate differentiation (FST = 0.108) and low inbreeding (FIS = -0.136). Bayesian model-based and neighbor-joining (NJ) clustering corroborate an uppermost clustering level of K = 3. The NJ dendrogram depicts many small subgroups equally distant from common ancestry. Discriminant analysis of principal components reveals between-sub-group variation (K = 15) within the NJ dendrogram and allows the identification of 19 consensus subgroups. Fifty-one accessions were selected for inclusion within a core set based upon 95% representation of the observed allelic variation. Breeders can now exploit the breadth of genetic diversity held within this collection during development of interspecific hybrids. In the final study, a genetic linkage map was developed using a genome-by-sequencing approach and used to identify QTL associated with EFB resistance from the C. americana selection OSU 403.040 from Nebraska U.S. A bi-parental mapping population comprised of 121 seedling trees was evaluated for EFB under high disease pressure in New Jersey, where A. anomala is endemic and highly genetically diverse. With EFB response represented by the percent of diseased wood, a total of three QTLs were discovered on linkage groups (LG) 3, 6, and 11 that respectively represent 62.6%, 23.3%, and 11.1% of the phenotypic variation. EFB resistance from OSU 403.040 appears new based upon it being only the second mapped source from C. americana and due to it mapping to three loci – all other sources of EFB resistance in Corylus spp. are monogenic and map to a single locus. Additionally, OSU 403.040 likely exhibits resistance to a broad range of A. anomala given the genetically diverse A. anomala environment under which it was selected. Such durability is requisite for the development of a feasible commercial variety for the eastern U.S. and highlights a priority for its inclusion in gene pyramiding schemes with resistant C. avellana

Germplasm Development of Underutilized Temperate U.S. Tree Crops

In the Midwest U.S. dominated corn-soybean landscape, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. Studies of the system-level integration of such approaches have proceeded by using the currently available cultivars and breeding selections of various tree nut and fruit species. While existing varieties and breeding selections provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. and its marginal land-types is unexplored. Thus, a second tier of research includes the genetic improvement and adaptation of tree crop selections to their respective target environments throughout the Midwest U.S. Fortunately, select tree crops of interest are amendable to systematic breeding and have wild relatives that are endemic across the region. In this paper, we discuss the value of these wild relatives for broadening the adaption of cultivated tree crop selections by using the hazelnut as an example species. We present a framework using geospatial tools to define and prioritize target environments for breeding and, in turn, exploiting wild relative germplasm

Temperate agroforestry research: considering multifunctional woody polycultures and the design of long-term field trials

The many benefits of agroforestry are well-documented, from ecological functions such as biodiversity conservation and water quality improvement, to cultural functions including aesthetic value. In North American agroforestry, however, little emphasis has been placed on production capacity of the woody plants themselves, taking into account their ability to transform portions of the landscape from annual monoculture systems to diversified perennial systems capable of producing fruits, nuts, and timber products. In this paper, we introduce the concept of multifunctional woody polycultures (MWPs) and consider the design of long-term experimental trials for supporting research on agroforestry emphasizing tree crops. Critical aspects of long-term agroforestry experiments are summarized, and two existing well-documented research sites are presented as case studies. A new long-term agroforestry trial at the University of Illinois, “Agroforestry for Food,” is introduced as an experiment designed to test the performance of increasingly complex woody plant combinations in an alley cropping system with productive tree crops. This trial intends to address important themes of food security, climate change, multifunctionality, and applied solutions. The challenges of establishing, maintaining, and funding long-term agroforestry research trials are discussed