Economic and Sustainability Impacts of Yield and Composition Variation in Bioenergy Crops: Switchgrass (Panicum virgatum L.)

Economically viable production of biobased products and fuels requires high-yielding, high-quality, sustainable process-advantaged crops, developed using bioengineering or advanced breeding approaches. Understanding which crop phenotypic traits have the largest impact on biofuel economics and sustainability outcomes is important for the targeted feedstock crop development. Here, we evaluated biomass yield and cell-wall composition traits across a large natural variant population of switchgrass (Panicum virgatum L.) grown across three common garden sites. Samples from 331 switchgrass genotypes were collected and analyzed for carbohydrate and lignin components. Considering plant survival and biomass after multiple years of growth, we found that 84 of the genotypes analyzed may be suited for commercial production in the southeastern U.S. These genotypes show a range of growth and compositional traits across the population that are apparently independent of each other. We used these data to conduct techno-economic analyses and life cycle assessments evaluating the performance of each switchgrass genotype under a standard cellulosic ethanol process model with pretreatment, added enzymes, and fermentation. We find that switchgrass yield per area is the largest economic driver of the minimum fuel selling price (MSFP), ethanol yield per hectare, global warming potential (GWP), and cumulative energy demand (CED). At any yield, the carbohydrate content is significant but of secondary importance. Water use follows similar trends but has more variability due to an increased dependence on the biorefinery model. Analyses presented here highlight the primary importance of plant yield and the secondary importance of carbohydrate content when selecting a feedstock that is both economical and sustainable.

Host Genetic Background Effect on Vertical Seed Transmission of Epichloë Endophyte Strains in Tall Fescue

Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass widely grown for forage and turf. Tall fescue lives in association with a fungal endophyte that helps the grass overcome abiotic and biotic stressors. The endophyte is asexual and transmits vertically from the tall fescue plant to the next generation through the seed. Producers of endophyte-infected tall fescue must have endophyte infection in at least 70% of their seed. Therefore, endophyte seed transmission is vital in breeding and seed production. Transfer of endophytes from their native host to different backgrounds of elite tall fescue cultivars can lead to a low seed transmission of the endophyte to the seed. This study screened 23 previously uncharacterized endophyte strains for transmissibility when artificially inoculated into continental and Mediterranean-type host tall fescue. We found no correlation between the rate of successful inoculation and the seed transmission rate of the endophyte in the new host. Nor did the seed transmission rate of the endophyte strains in their native host correlate with the seed transmission rate of the endophyte in the new host. Five strains exhibited seed transmission above 70% in both Mediterranean and Continental host backgrounds and will be characterized further for potential use in cultivar development.

Interaction between Grasses and Epichloë Endophytes and Its Significance to Biotic and Abiotic Stress Tolerance and the Rhizosphere

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.

Interaction between Grasses and Epichloë Endophytes and Its Significance to Biotic and Abiotic Stress Tolerance and the Rhizosphere

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.

Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes

Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F₂ mapping populations were developed by crossing two different F₁ sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.

Genome-Wide Association Mapping for Yield and Related Traits Under Drought Stressed and Non-stressed Environments in Wheat

Understanding the genetics of drought tolerance in hard red spring wheat (HRSW) in northern USA is a prerequisite for developing drought-tolerant cultivars for this region. An association mapping (AM) study for drought tolerance in spring wheat in northern USA was undertaken using 361 wheat genotypes and Infinium 90K single-nucleotide polymorphism (SNP) assay. The genotypes were evaluated in nine different locations of North Dakota (ND) for plant height (PH), days to heading (DH), yield (YLD), test weight (TW), and thousand kernel weight (TKW) under rain-fed conditions. Rainfall data and soil type of the locations were used to assess drought conditions. A mixed linear model (MLM), which accounts for population structure and kinship (PC+K), was used for marker–trait association. A total of 69 consistent QTL involved with drought tolerance-related traits were identified, with p ≤ 0.001. Chromosomes 1A, 3A, 3B, 4B, 4D, 5B, 6A, and 6B were identified to harbor major QTL for drought tolerance. Six potential novel QTL were identified on chromosomes 3D, 4A, 5B, 7A, and 7B. The novel QTL were identified for DH, PH, and TKW. The findings of this study can be used in marker-assisted selection (MAS) for drought-tolerance breeding in spring wheat.

Identification of Main-Effect and Environmental Interaction QTL and Their Candidate Genes for Drought Tolerance in a Wheat RIL Population Between Two Elite Spring Cultivars

Understanding the genetics of drought tolerance can expedite the development of drought-tolerant cultivars in wheat. In this study, we dissected the genetics of drought tolerance in spring wheat using a recombinant inbred line (RIL) population derived from a cross between a drought-tolerant cultivar, ‘Reeder’ (PI613586), and a high-yielding but drought-susceptible cultivar, ‘Albany.’ The RIL population was evaluated for grain yield (YLD), grain volume weight (GVW), thousand kernel weight (TKW), plant height (PH), and days to heading (DH) at nine different environments. The Infinium 90 k-based high-density genetic map was generated using 10,657 polymorphic SNP markers representing 2,057 unique loci. Quantitative trait loci (QTL) analysis detected a total of 11 consistent QTL for drought tolerance-related traits. Of these, six QTL were exclusively identified in drought-prone environments, and five were constitutive QTL (identified under both drought and normal conditions). One major QTL on chromosome 7B was identified exclusively under drought environments and explained 13.6% of the phenotypic variation (PV) for YLD. Two other major QTL were detected, one each on chromosomes 7B and 2B under drought-prone environments, and explained 14.86 and 13.94% of phenotypic variation for GVW and YLD, respectively. One novel QTL for drought tolerance was identified on chromosome 2D. In silico expression analysis of candidate genes underlaying the exclusive QTLs associated with drought stress identified the enrichment of ribosomal and chloroplast photosynthesis-associated proteins showing the most expression variability, thus possibly contributing to stress response by modulating the glycosyltransferase (TraesCS6A01G116400) and hexosyltransferase (TraesCS7B01G013300) unique genes present in QTL 21 and 24, respectively. While both parents contributed favorable alleles to these QTL, unexpectedly, the high-yielding and less drought-tolerant parent contributed desirable alleles for drought tolerance at four out of six loci. Regardless of the origin, all QTL with significant drought tolerance could assist significantly in the development of drought-tolerant wheat cultivars, using genomics-assisted breeding approaches.

QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland

BACKGROUND

Switchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies.

RESULTS

We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21-23.27% for FRH, 4.47-24.06% for NDVI, 4.35-32.77% for SE, and 4.61-29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55-0.64 H²) and NDVI (0.30-0.61 H²) implies the possibility of using the traits for indirect selection for biomass yield.

CONCLUSION

Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.

67 2018 Alfalfa in the South Workshop Series: A review of regional Extension efforts

Alfalfa research in the Southeast has steadily increased over the past ten years. Researchers have a renewed interest in this perennial legume as new varieties have been released that are better suited to the challenging climate and use in the Southeast. Extensive effort has been put forth in establishing programs promoting the use of alfalfa as a viable high-quality forage option in the south. In 2018, the “Alfalfa in the South” workshop series was designed to provide in-depth extension education, circulate new research findings, and engage in discussions with producers as related to the use of alfalfa in the southeast. The series consisted of 4 one-day workshops, organized by University of Georgia Extension in conjunction with America’s Alfalfa, and included Extension specialists, faculty, and graduate students from both the University of Georgia and Auburn University. Topics were broken into five classroom learning modules: 1) site selection and establishment, 2) improving animal performance with alfalfa, 3) managing alfalfa for persistence, 4) alfalfa breeding programs, and 5) graduate student research updates. Each workshop concluded with an on-farm demonstration where attendees engaged in discussion with producers utilizing alfalfa in their operation. Postworkshop evaluation results determined that, on a scale of 1 to 5, where “1” was “no change” and “5” indicated “greatly improved,” producers rated their change in interest using alfalfa as a 4.73 and their confidence in using alfalfa management skills as 4.36. Additionally, the producer discussion and field tour section rated the highest, 4.67 (1 being “poor” and 5 being “excellent”); however, all topics rated 4.12 or higher, indicating that attendees found this workshop to be very good to excellent. Of the 60 participants, 68% indicated that they would make some major changes and 32% plan to try to make minor management changes following the workshops.

Tuberculosis of the sternoclavicular joint. Report of two cases

The sternoclavicular joint accounts for only 1 to 2% of all cases of peripheral tuberculous arthritis and is more often infected by pyogenic organisms than by the tubercle bacillus. We report two cases of sternoclavicular joint tuberculosis, in a 38-year-old man and a 46-year-old woman without risk factors for immune deficiency. Swelling of the joint was the presenting manifestation. Laboratory tests indicated inflammation in only one of the patients. The intradermal tuberculin test was strongly positive in both patients, whereas smears and cultures of sputum and urine samples were negative for the tubercle bacillus. Serologic tests for the human immunodeficiency virus were negative. Erosions of the affected joint were seen by computed tomography. Histological studies of a surgical biopsy specimen confirmed the diagnosis. Cultures of the biopsy specimens were negative. The outcome was favorable after treatment with rifampin, isoniazid and pyrazinamide for six months in the man and nine in the woman. Follow-ups were eight and six months, respectively, at the time of this writing. Tuberculosis of the sternoclavicular joint is extraordinarily rare and can raise diagnostic problems. The diagnosis should be considered in every patient with arthritis in a sternoclavicular joint or unexplained pain in a shoulder. Possible complications include compression or erosion of the large blood vessels at the base of the neck and migration of tuberculous abscesses to the mediastinum.