Appalachian Fruit Research Laboratory

Powdery mildew, caused by the fungus Erysiphe necator, is one of the primary causes of grape yield loss across the globe. Although numerous resistance loci have been identified in various grapevine species, the genetic determinants of susceptibility to E. necator remain largely unexplored. Understanding the genetics of susceptibility for pathogenesis is equally important for developing durable resistance grapevines against this pathogen. To identify these factors in Vitis interspecific hybrid 'Chambourcin,' a controlled leaf disc assay was conducted for 2 years using an automated microscopy phenotyping system with 273 F1 genotypes from a cross of 'Chambourcin' and V. vinifera 'Cabernet Sauvignon.' Additionally, a high-resolution linkage map using the same number of 'Chambourcin'-derived hybrids was constructed with 355 simple sequence repeats and 1,394 RNaseH2-dependent amplicon sequencing-derived haplotype markers that clustered into 19 linkage groups. A quantitative trait locus analysis identified a susceptibility locus (here named Sen2) on linkage group 7 explaining 8.90 to 12.57% of the total phenotypic variance. The markers associated with this susceptibility locus were used to identify 78 accessions in the U.S. Department of Agriculture Agricultural Research Service cold-hardy Vitis collection at Geneva, NY, that carry Sen2 and can be used to selectively exclude susceptible progenies. Additionally, six accessions carry the alternative haplotype encoding recessive resistance and can be used for resistance breeding. The identification of powdery mildew susceptibility loci is crucial for identifying genes that could be targeted for gene knockout, gene editing, RNA interference, or selection among breeding genotypes to enhance sustainable protection against pathogens.

Management of the brown marmorated stink bug, Halyomorpha halys (Stål), using attract-and-kill (AK) strategies in orchard crops has resulted in reduced pesticide inputs and the reestablishment of integrated pest management programs but also increased labor inputs and damage in pheromone-baited AK trees. Here, we re-tool previously developed AK practices for H. halys management using long-lasting insecticide netting (LLIN) as a low-input, effective killing agent. Simple LLIN AK stations were evaluated for efficacy compared with grower standard practices when hung directly on orchard perimeter fruit trees, hung on posts near, but not touching perimeter trees, and placed outside the orchard perimeter in commercial Mid-Atlantic apple orchards from 2017 to 2019. Treatments in which LLIN stations were attached to or hung near perimeter trees were equivalent to grower standards in terms of H. halys injury. In commercial pear orchards in Washington State in 2018 to 2020, efficacies of several LLIN station designs were evaluated as supplements to grower standard practices. A novel LLIN station design, referred to as the poncho trap, consistently caught nearly 3-fold more H. halys compared to a simple post-deployed "ghost trap" design when installed outside orchard perimeters. However, only LLIN stations mounted directly to perimeter trees provided statistically significant reductions in fruit damage. Our overall findings underscore the importance of positioning the pheromone lure, host plant (fruit tree), and LLIN in close proximity for successful AK H. halys management. Results also indicate that poncho trap LLIN fabric flaps could be integrated into near-mounted LLIN stations to further increase efficacy.

Huanglongbing (HLB) is a devastating citrus disease that threatens the citrus industry worldwide. HLB is associated with the bacteria Candidatus Liberibacter asiaticus (CLas) and as of today, there are no tools for economically viable disease management. Several wild Australian limes have been identified to be HLB resistant and their resistance is hypothesized to be conferred by resistance genes (R-genes), which mediate pathogen-specific defense responses. The aim of this study was to gain insight into the genomic features of R-genes in Australian limes, in comparison to susceptible citrus cultivars. In this study, we used five citrus genomes, including three Australian limes (Citrus australasica, C. glauca and C. inodora) and two cultivated citrus species (C. clementina and C. sinensis). Our results indicate up to 70% of the R-genes were identified in the unannotated regions in the original genome annotation of each species, owing to the use of a R-gene specific pipeline. Surprisingly, the two cultivated species harbored 15.8 to 104% more R-genes than the Australian limes. In all species, over 75% of the R-genes occurred in clusters and nearly 80% were concentrated in three chromosomes (Chr3, 5 and 7). The syntenic R-gene based phylogenic classification grouped the five species according to their HLB-resistance levels, reflecting the association between these R-genes and their distinct Australian origins. Domain structure analysis revealed substantial similarities in the R-genes between wild Australian limes and cultivated citrus. Investigation of chromosomal sites underlying Australian specific R genes revealed diversifying selection signatures on several chromosomal regions. The findings in this study will aid in the development of tools for genome-assisted breeding for HLB-resistant varieties.

Since its debut in 1982, The Land has embodied Walt Disney's vision, capturing the attention of millions of EPCOT guests with venues focusing on agriculture and environmental stewardship and sustainability. The Land pavilion spans more than 8 acres in the World Nature section of EPCOT at the Walt Disney World Resort in Lake Buena Vista, Florida. The pavilion houses three attractions, namely Soarin' Around the World, Awesome Planet, and the Living with the Land boat ride, complemented by a greenhouse walking tour entitled Behind the Seeds and two restaurants. Each attraction derives inspiration from nature and challenges mankind to be responsible stewards of planet earth. This feature article focuses on the Living with the Land boat ride attraction, which traverses greenhouses showcasing agricultural technologies and crops from around the world. The sections below describe both how various show elements are designed to engage guests and how the show is made possible by applying relevant science and technology.

Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.

Plants can adapt their growth to optimize light capture in competitive environments, with branch angle being a crucial factor influencing plant phenotype and physiology. Decreased branch angles in cereal crops have been shown to enhance productivity in high-density plantings. The Tiller Angle Control (TAC1) gene, known for regulating tiller inclination in rice and corn, has been found to control branch angle in eudicots. Manipulating TAC1 in field crops like cotton offers the potential for improving crop productivity. Using a homolog-based methodology, we examined the distribution of TAC1-related genes in cotton compared to other angiosperms. Furthermore, tissue-specific qPCR analysis unveiled distinct expression patterns of TAC1 genes in various cotton tissues. To silence highly expressed specific TAC1 homeologs in the stem, we applied CRISPR-Cas9 gene editing and Agrobacterium-mediated transformation, followed by genotyping and subsequent phenotypic validation of the mutants. Gene duplication events of TAC1 specific to the Gossypium lineage were identified, with 3 copies in diploid progenitors and 6 copies in allotetraploid cottons. Sequence analysis of the TAC1 homeologs in Gossypium hirsutum revealed divergence from other angiosperms with 1-2 copies, suggesting possible neo- or sub-functionalization for the duplicated copies. These TAC1 homeologs exhibited distinct gene expression patterns in various tissues over developmental time, with elevated expression of A11G109300 and D11G112200, specifically in flowers and stems, respectively. CRISPR-mediated loss of these TAC1 homeologous genes resulted in a reduction in branch angle and altered petiole angles, and a 5 to 10-fold reduction in TAC1 expression in the mutants, confirming their role in controlling branch and petiole angles. This research provides a promising strategy for genetically engineering branch and petiole angles in commercial cotton varieties, potentially leading to increased productivity.

Native apple maggot fly, Rhagoletis pomonella, and invasive spotted-wing drosophila, Drosophila suzukii, are key pests of apple and small fruit, respectively, in the United States. Both species are typically managed with standard insecticide applications. However, interest in alternative strategies that result in insecticide reductions has led to evaluations of nonnutritive sugars as toxicants for Drosophila species and development of attracticidal spheres for both species. Here, we evaluated the survivorship of R. pomonella and D. suzukii when provided with standard diets that substituted saccharin, sucralose, aspartame, erythritol, dextrose, or mannitol for the sucrose component and compared them with standard diets and water-only controls for up to 15 days. Presence of erythritol and mannitol significantly decreased survivorship of R. pomonella and erythritol significantly decreased the survivorship of D. suzukii. However, mobility trials following a 2 h exposure to aqueous solutions of each sugar treatment resulted in no strong impact on either species. Survivorship after 30 min exposure to erythritol or mannitol alone, or in combination with varying concentrations of sucrose (serving as a phagostimulant) at 30 min and 24 h were evaluated for both species. Only D. suzukii survivorship was affected with decreased survivorship on erythritol:sucrose solutions of 20:0% and 15:5% for 24 h. Based on all results, erythritol appeared most promising, and was integrated into attracticidal spheres as a toxicant but even at the highest concentration, survivorship remained unaffected for either species, thus making this nonnutritive sugar impractical and ineffective as a toxicant substitute in attracticidal spheres.

IGT/LAZY proteins play a central role in determining gravitropic set point angle and orientation of lateral organs across plant species. Recent work in model systems has demonstrated that interactions between IGT/LAZY proteins and BREVIS RADIX (BRX)-domain containing proteins, such as PH, RCC1, AND FYVE/RCC1-LIKE DOMAIN (PRAF/RLD), and BREVIS RADIX LIKE (BRXL) family members, are mechanistically important for setting gravitropic set point angle. Here, we identified peach PRAF/RLD proteins as interactors of the peach IGT/LAZY proteins PpeLAZY1 and DEEPER ROOTING 1 (PpeDRO1) from a yeast-two-hybrid screen. We also show that the BRX domains of these interacting proteins have high sequence similarity with PRAF/RLD and BRX family proteins from rice and Arabidopsis. Further, PpeLAZY1 and the peach PRAF/RLD interactors are all expressed at relatively high levels in leaf, meristem, and shoot tip tissues. Together, this evidence supports the importance and conservation of IGT/LAZY-BRX-domain interactions, which underlie setting gravitropic set point angle across angiosperms.

Abstract Apple (Malus×domesticaBorkh.) production faces many challenges stemming from abiotic and biotic stresses. Abiotic stressors, such as extreme temperatures, droughts, and spring frosts, can lead to diminished yields and tree loss, while biotic stresses like fire blight and pest infestations further reduce tree health and fruit quality. To lessen the threat of these challenges, plant breeders aim to introduce resistance and resilience genes into cultivated varieties. However, high-relatedness among cultivated varieties and breeding lines, coupled with the long juvenility and generation times in apples, hinder the breeding process. The introduction of resistance traits from wild relatives is also constrained by these factors, as well as the lack of genomic resources that could assist in accelerating the introgression process. Herein, we report the assembly and annotation ofMalus angustifolia, the Southern Crabapple, one of Eastern North America’s native species. Using a combination of Pacific Biosciences High Fidelity reads, Next-generation short read sequencing, as well as chromatin conformation capture sequencing, we achieve an extremely contiguous haplotype-resolved assembly. We perform comparative haplotypic analyses to identify SNPs and large structural variants, shedding light on the genomic landscape ofM. angustifolia. Finally, we explore the phylogenetic and syntenic relationships between EurasianMalusprogenitors and the recently sequenced North American species, contributing valuable insights to the broader understanding of apple evolution and potential breeding strategies.

Lycorma delicatula White (Hemiptera: Fulgoridae) is an invasive phloem feeder with a broad host range that includes both hardwood trees and cultivated temperate fruit crops. Here, we evaluated acceptability of wild hosts, A. altissima and Juglans nigra L. (Fagales: Juglandaceae) and cultivated hosts Vitis vinifera, Malus domestica (Rosales: Rosaceae), and Prunus persica L. Batsch (Rosales: Rosaceae) to L. delicatula under field conditions. Fluorescent-marked early instar nymphs, late instar nymphs, or adult L. delicatula were released at the base of single potted host plants and the number of individuals retained was recorded over 24 h. Paired choice trials with A. altissima and another host plant were conducted. Individuals retained on or moving between plants were recorded over 24 h. Sentinel A. altissima, J. nigra, V. vinifera, M. domestica, and P. persica potted plants were deployed at 5 sites and the number of L. delicatula present on each plant was recorded weekly. In single and paired host trials, early instars and adults were generally retained in higher numbers on A. altissima and V. vinifera, and late instars were retained on A. altissima and J. nigra. Significantly more L. delicatula were present on sentinel A. altissima compared with other host plants, except J. nigra during the period when late instars were the most prevalent lifestage in the field. These results indicate that wild hosts such as A. altissima and J. nigra are likely supporting establishment of L. delicatula populations, and that presence of cultivated V. vinifera may contribute to population establishment and growth.