Cool-season grasses are the most common forage types in livestock operations and amenities. Several of the cool-season grasses establish mutualistic associations with an endophytic fungus of the Epichloë genus. The grasses and endophytic fungi have evolved over a long period of time to form host-fungus specific relationships that confer protection for the grass against various stressors in exchange for housing and nutrients to the fungus. This review provides an overview of the mechanisms by which Epichloë endophytes and grasses interact, including molecular pathways for secondary metabolite production. It also outlines specific mechanisms by which the endophyte helps protect the plant from various abiotic and biotic stressors. Finally, the review provides information on how Epichloë infection of grass and stressors affect the rhizosphere environment of the plant.

Cool-season grasses are the most common forage types in livestock operations and amenities. Several of the cool-season grasses establish mutualistic associations with an endophytic fungus of the Epichloe genus. The grasses and endophytic fungi have evolved over a long period of time to form host-fungus specific relationships that confer protection for the grass against various stressors in exchange for housing and nutrients to the fungus. This review provides an overview of the mechanisms by which Epichloe endophytes and grasses interact, including molecular pathways for secondary metabolite production. It also outlines specific mechanisms by which the endophyte helps protect the plant from various abiotic and biotic stressors. Finally, the review provides information on how Epichloe infection of grass and stress affect the rhizosphere environment of the plant.

Accelerating crop improvement is critical to meeting food security demands in a changing climate. Long-read sequencing offers advantages over short-reads in resolving structural variations (SVs) and aligning to complex genomes, but its high cost has limited adoption in breeding programs. Here, we develop a high-throughput, scalable approach for long-read low-pass (LRLP) sequencing and variant analysis with PacBio HiFi reads, and apply it to trait mapping in a complex tetraploid peanut (Arachis hypogaea) genome multi-parent advanced generation intercross. We analyze LRLP using both a single reference genome and a pangraph, using both proprietary and open-source tools to analyze SVs and coverage. An increased number of variants are consistently called for LRLP data compared to short-read data. At 1.63x average depth, LRLP sequencing covered 55% of the genome and 58% of gene space, outperforming 1.68x depth short-read low-pass sequencing, which achieved only 17% and 11%, respectively. Enhanced data retention after filtering for probabilistic misalignment and an ~8.5x decrease in cost per value further demonstrated LRLPs efficacy. Our results highlight LRLP sequencing as a scalable, cost-effective tool for high-resolution trait mapping, with transformative potential for plant breeding and broader genomic applications.

The abiotic stresses associated with spring/fall freezes and extreme winter cold cause significant economic losses in blueberry production. These problems are exacerbated by climate change and increasingly erratic weather patterns. Developing freeze-tolerant blueberry cultivars with optimized cold hardiness, chilling requirement, and flowering and fruiting phenology holds promise for mitigating the risk of these weather-related damages. These weather-resilient cultivars will ensure the long-term productivity and sustainability of the blueberry industry. The focus of this review is to present the current understanding of the major components of genetic breeding for blueberry freeze tolerance, i.e., phenotyping, genotyping, genetic association analysis, and marker development. The advancement in gene regulation and corresponding proteomic changes upon cold acclimation, dormancy, de-acclamation, and flowering and fruiting aids in the understanding of the adaptive stress response in blueberries. A wide range of genetic diversity in freeze tolerance and phenological traits has been identified among cultivated and wild blueberry relatives. Significant efforts have been made to phenotype freeze tolerance, chilling requirement, and flower and fruit development in both field and controlled environmental conditions. Recent studies emphasize the need for high-throughput, image-based phenotyping of blueberry flower development to improve the precision and efficiency of selecting freeze-resilient genotypes. In addition, advancements in blueberry genomics and pangenome resources expanded the potential of variant calling and high-density linkage map construction. Genetic association studies have identified QTL regions linked to freeze tolerance in blueberries, providing valuable targets for selection. The implementation of these advanced genomic tools and high-throughput phenotyping methodology will accelerate the development of weather-resilient blueberry cultivars.

Background: Tall fescue (Festuca arundinacea [Schreb.], Lolium arundinaceum [Schreb.] Darbysh) and perennial ryegrass (Lolium perenne) are important cool‐season forage and amenity grasses that have a mutualistic association with an endophytic fungus. Endophytes confer insect and drought resistance to plants but can produce mammalian toxins. Novel endophytes that do not produce mammalian toxins have been introduced to elite cultivars for commercial production. Seed companies need to maintain adequate levels of novel endophytes within the elite forage cultivars. Endophyte detection is performed using immunochemical and molecular techniques because of their speed and reliability. Early detection in seedlings is essential to evaluate the viability of the endophyte within seed lots.Methods: This research aimed to identify the earliest growth stage in which immunochemical and molecular methods can detect viable endophyte in seedlings of tall fescue cultivars BarOptima (e34), Texoma MaxQII (584), and Jesup MaxQ (542), as well as the perennial ryegrass cultivar Remington (NEA2).Results: Immunochemical testing detected endophytes in seedlings 14 days after germination (DAG), but the detection rate increased until 42 DAG in some cultivars tested. The molecular marker Tef1exon detected endophytes at a lower rate than the immunochemical method at 28–42 DAG. However, there was insufficient DNA to detect endophytes in 14 DAG seedlings using markers.Conclusions: We conclude that the most accurate detection of viable endophytes in seedlings was 42 DAG, at which sufficient and consistent endophyte colonization occurred.