American chestnut ( Castanea dentata ) is a deciduous tree species of eastern North America that was decimated by the introduction of the chestnut blight fungus ( Cryphonectria parasitica ) in the early 20th century. Although millions of American chestnuts survive as root collar sprouts, these trees rarely reproduce. Thus, the species is considered functionally extinct. American chestnuts with improved blight resistance have been developed through interspecific hybridization followed by conspecific backcrossing, and by genetic engineering. Incorporating adaptive genomic diversity into these backcross families and transgenic lines is important for restoring the species across broad climatic gradients. To develop sampling recommendations for ex situ conservation of wild adaptive genetic variation, we coupled whole-genome resequencing of 384 stump sprouts with genotype–environment association analyses and found that the species range can be subdivided into three seed zones characterized by relatively homogeneous adaptive allele frequencies. We estimated that 21 to 29 trees per seed zone will need to be conserved to capture most extant adaptive diversity. We also resequenced the genomes of 269 backcross trees to understand the extent to which the breeding program has already captured wild adaptive diversity, and to estimate optimal reintroduction sites for specific families on the basis of their adaptive portfolio and future climate projections. Taken together, these results inform the development of an ex situ germplasm conservation and breeding plan to target blight-resistant breeding populations to specific environments and provides a blueprint for developing restoration plans for other imperiled tree species.

Understanding temporal variation of threats that cause species endangerment is a key to understand conservation strategies needed to improve species recovery. We assessed temporal variation in the threats to species listed under the United States Endangered Species Act (ESA) as identified by the United States Fish and Wildlife Service (USFWS) and National Marine Fisheries Service (NMFS). Based on initial review of ESA listing decisions and literature, we identified six overarching threat categories: habitat modification, overutilization, pollution, species–species interaction, demographic stochasticity, and environmental stochasticity. We screened listing decision documents to determine threat occurrence (i.e., presence/absence of a given threat in a listing decision) for each threat category for all species listed between 1975 and 2017. We evaluated how the number of threats and specific threat occurrences changed over the past four decades. We found that the number of threats per listing decision increased more than twofold from an average of 1.5 (95% CI: 1.3–1.7) threats in 1975 to 3.7 (95% CI: 3.4–4.0) threats in 2017. Threat occurrence increased for habitat modification, environmental stochasticity and species–species interaction, while it decreased for overutilization since 1975 and for demographic stochasticity and pollution since the mid‐2000s. The documented increase in number of threats at time of listing may be due to a growing human population exerting increased pressure on species persistence, improved scientific advancement in understanding factors influencing species endangerment, or prolonged time taken for more recent species to be listed under the ESA. We believe that key federal and state governmental regulations have resulted in a documented decrease in overutilization, demographic stochasticity, and pollution, and we recommend large‐scale strategies combined with local planning efforts to address the growing threats of habitat loss, environmental stochasticity, and species–species interaction.

Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato (Ipomoea batatas [L.] Lam) genome for molecular-marker-assisted breeding and genomic prediction. The creation of this marker panel has the potential to bring cost-effective and rapid genotyping capabilities to sweetpotato breeding programs worldwide. The open access provided by this platform will allow the genetic datasets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of sweetpotato.

Alfalfa ( Medicago sativa L.) is a globally vital forage crop valued for its perennial growth and multiple annual harvests. A breeding effort is underway to improve the crop for productivity and persistence against biotic and abiotic stresses using “creeping rootedness,” a trait where plants exhibit horizontal root growth, similar to rhizomes, with increased vegetative ground surface area. In this study, we genotyped a breeding population of 648 alfalfa lines segregating for creeping rootedness using the 3K DArTag marker panel to identify trait‐associated genomic loci and evaluate the feasibility of genomic prediction to accelerate breeding cycles. Using genome‐wide association studies (GWAS), we identified three quantitative trait loci (QTLs), with one major QTL located on chromosome 6.1 associated with this trait. Genomic prediction showed moderate predictive ability ( r = 0.68) for creeping rootedness. A significant advancement in this study was the development and utilization of the Breeding Insight Genomics Application (BIGapp), an R Shiny application designed to streamline the processing of genomic data through an intuitive interface. This tool makes integrating genomics into existing breeding programs accessible, regardless of species ploidy or the researcher's coding proficiency. The identified QTL will be essential in future efforts to develop new alfalfa cultivars with the creeping rootedness trait and accelerate the breeding cycle, with BIGapp playing a pivotal role in these advancements.

More than a century after two introduced pathogens killed billions of American chestnut trees, introgression of resistance alleles from Chinese chestnuts has contributed to the recovery of self-sustaining populations. However, progress has been slow because of the complex genetic architecture of resistance. To better understand blight resistance, we compared reference genomes, gene expression responses, and stem metabolite profiles of the resistant Chinese and susceptible American chestnut species. To accelerate resistance breeding, we conducted large-scale phenotyping and genotyping in hybrids of these species. Simulation and inoculation experiments suggest that significant resistance gains are possible through selectively breeding trees with an average of 70 to 85% American chestnut ancestry. The resources developed in this work are foundational for breeding to create diverse restoration populations with sufficient disease resistance and competitive growth.