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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Genetics and Genomics of Pathogen Resistance in Switchgrass (Final Report)

This project was funded by DOE under Grant no. DE-SC0016108. Originally approved for the 2016-2019 period, two no-cost extensions were solicited and approved, which prolonged the lifespan through July 2021. This final report informs on the results obtained so far from the research implemented. The research hinged on integrating genomics (genomic selection, RNAseq, virus-plant interactions) with classical genetics (conventional breeding) to incorporate durable resistance to fungal (rust) and viral (mosaic) diseases in switchgrass (Panicum virgatum) populations being bred for bioenergy. Higher biomass yield, higher quality (low lignin content), and durable disease resistance are key features to make lignocellulosic switchgrass feedstocks economically competitive and sustainable. Genomic selection is being applied on three generations of a switchgrass population derived from crossing two ecotypes (Kanlow as lowland female and Summer as upland male) with differential performance in terms of biomass yield and quality, disease resistance, and winter survivability. Target populations were screened for rust and mosaic in field and/or lab and phenotyped for biomass yield and quality traits. Genetic analyses were applied across generations to capture the joint inheritance of the targeted traits and predict breeding values for parents and progeny with greater accuracy. Parental and a panel of different switchgrass populations were genotyped with the DArTseq technology to develop SNP (0, 1, 2) and in-silico (presence/absence) DArT markers. Rust inoculations techniques were developed and applied successfully on switchgrass. The original populations (Kanlow and Summer) were sequenced with RNAseq to capture the gene expression profiles across sequential time-points and appraise the basis of greater resistance in the Kanlow vs the Summer ecotype. Constructs of PMV and sPMV mosaic virus were assembled and tested first on proso millet to find the best protocol to use later on switchgrass. Results from the preliminary analyses indicate that 1) ample additive genetic variation is available for selection and improving this inter-ecotypic population for yield, quality, and disease traits, 2) significant gains are to be expected with the genetic correlations being favorable between yield and lignin content and between yield and disease ratings, 3) substantial differences exist in the genetic regions controlling rust resistance in the two ecotypes, 4) co-infection with PMV isolates from Nebraska and its satellite from Kansas elicit severe mosaic symptoms, and 5) two different genetic systems are responsible for imparting resistance to rust and virus in switchgrass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Geographic_Distribution_of_Populus_trichocarpa_Genotypes_by_DBSCAN_Cluster

Aninteractive mapshowingPopulus trichocarpaGWAS sub-population structure identified by DBSCAN clustering, which were derived from a UMAP projection of the top 8 PCs of LD-pruned pangenome SNP data. Geographic origins are searchable by genotype or river system using the search bar.

09 BIOMASS FUELS↗
DOE OSTI2016

Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

Fillet yield (FY, %) is an economically-important trait in rainbow trout aquaculture that affects production efficiency. Despite that, FY has received little attention in breeding programs because it is difficult to measure on a large number of fish and cannot be directly measured on breeding candidates. The recent development of a high-density SNP array for rainbow trout has provided the needed tool for studying the underlying genetic architecture of this trait. A genome-wide association study (GWAS) was conducted for FY, body weight at 10 (BW10) and 13 (BW13) months post-hatching, head-off carcass weight (CAR), and fillet weight (FW) in a pedigreed rainbow trout population selectively bred for improved growth performance. The GWAS analysis was performed using the weighted single-step GBLUP method (wssGWAS). Phenotypic records of 1447 fish (1.5 kg at harvest) from 299 full-sib families in three successive generations, of which 875 fish from 196 full-sib families were genotyped, were used in the GWAS analysis. A total of 38,107 polymorphic SNPs were analyzed in a univariate model with hatch year and harvest group as fixed effects, harvest weight as a continuous covariate, and animal and common environment as random effects. A new linkage map was developed to create windows of 20 adjacent SNPs for use in the GWAS. The two windows with largest effect for FY and FW were located on chromosome Omy9 and explained only 1.0–1.5% of genetic variance, thus suggesting a polygenic architecture affected by multiple loci with small effects in this population. One window on Omy5 explained 1.4 and 1.0% of the genetic variance for BW10 and BW13, respectively. Three windows located on Omy27, Omy17, and Omy9 (same window detected for FY) explained 1.7, 1.7, and 1.0%, respectively, of genetic variance for CAR. Among the detected 100 SNPs, 55% were located directly in genes (intron and exons). Nucleotide sequences of intragenic SNPs were blasted to the Mus musculus genome to create a putative gene network. The network suggests that differences in the ability to maintain a proliferative and renewable population of myogenic precursor cells may affect variation in growth and fillet yield in rainbow trout.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Population Genetics of Sugar Kelp Throughout the Northeastern United States Using Genome-Wide Markers

An assessment of genetic diversity of marine populations is critical not only for the understanding and preserving natural biodiversity but also for its commercial potential. As commercial demand rises for marine resources, it is critical to generate baseline information for monitoring wild populations. Furthermore, anthropogenic stressors on the coastal environment, such as warming sea temperatures and overharvesting of wild populations, are leading to the destruction of keystone marine species such as kelps. In this study, we conducted a fine-scale genetic analysis using genome-wide high-density markers on Northwest Atlantic sugar kelp. The population structure for a total of 149 samples from the Gulf of Maine (GOM) and Southern New England (SNE) was investigated using AMOVA, FST, admixture, and PCoA. Genome-wide association analyses were conducted for six morphological traits, and the extended Lewontin and Krakauer (FLK) test was used to detect selection signatures. Our results indicate that the GOM region is more heterogeneous than SNE. These two regions have large genetic difference (between-location FST ranged from 0.21 to 0.32) and were separated by Cape Cod, which is known to be the biogeographic barrier for other taxa. We detected one significant SNP (P = 2.03 × 10 -7 ) associated with stipe length, and 248 SNPs with higher-than-neutral differentiation. The findings of this study provide baseline knowledge on sugar kelp population genetics for future monitoring, managing and potentially restoring wild populations, as well as assisting in selective breeding to improve desirable traits for future commercialization opportunities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Circulating levels of micronutrients and risk of osteomyelitis: a Mendelian randomization study

Background Few observational studies have investigated the effect of micronutrients on osteomyelitis, and these findings are limited by confounding and conflicting results. Therefore, we conducted Mendelian randomization (MR) analyses to evaluate the association between blood levels of eight micronutrients (copper, selenium, zinc, vitamin B12, vitamin C, and vitamin D, vitamin B6, vitamin E) and the risk of osteomyelitis. Methods We performed the two-sample and multivariable Mendelian randomization (MVMR) to investigate causation, where instrument variables for the predictor (micronutrients) were derived from the summary data of micronutrients from independent cohorts of European ancestry. The outcome instrumental variables were used from the summary data of European-ancestry individuals ( n = 486,484). The threshold of statistical significance was set at p < 0.00625. Results We found a significant causal association that elevated zinc heightens the risk of developing osteomyelitis in European ancestry individuals OR = 1.23 [95% confidence interval (CI) [1.07, 1.43]; p = 4.26E-03]. Similarly, vitamin B6 showed a similar significant causal effect on osteomyelitis as a risk factor OR = 2.78 (95% CI [1.34, 5.76]; p = 6.04E-03; in the secondary analysis). Post-hoc analysis suggested this result (vitamin B6). However, the multivariable Mendelian randomization (MVMR) provides evidence against the causal association between zinc and osteomyelitis OR = 0.98(95% CI [−0.11, 0.07]; p = 7.20E-1). After searching in PhenoScanner, no SNP with confounding factors was found in the analysis of vitamin B6. There was no evidence of a reverse causal impact of osteomyelitis on zinc and vitamin B6. Conclusion This study supported a strong causal association between vitamin B6 and osteomyelitis while reporting a dubious causal association between zinc and osteomyelitis.

Zhang, Xu↗
DOE OSTI2017

Characterization and Regulation of Aquaporin Genes of Sorghum [ Sorghum bicolor (L.) Moench] in Response to Waterlogging Stress

Waterlogging is a significant environmental constraint to crop production, and a better understanding of plant responses is critical for the improvement of crop tolerance to waterlogged soils. Aquaporins (AQPs) are a class of channel-forming proteins that play an important role in water transport in plants. Our study aimed to examine the regulation of AQP genes under waterlogging stress and to characterize the genetic variability of AQP genes in sorghum (Sorghum bicolor). Transcriptional profiling of AQP genes in response to waterlogging stress in nodal root tips and nodal root basal regions of two tolerant and two sensitive sorghum genotypes at 18 and 96 h after waterlogging stress imposition revealed significant gene-specific pattern with regard to genotype, root tissue sample, and time point. For some tissue sample and time point combinations, PIP2-6, PIP2-7, TIP2-2, TIP4-4, and TIP5-1 expression was differentially regulated in tolerant compared to sensitive genotypes. The differential response of these AQP genes suggests that they may play a tissue specific role in mitigating waterlogging stress. Genetic analysis of sorghum revealed that AQP genes were clustered into the same four subfamilies as in maize (Zea mays) and rice (Oryza sativa) and that residues determining the AQP channel specificity were largely conserved across species. Single nucleotide polymorphism (SNP) data from 50 sorghum accessions were used to build an AQP gene-based phylogeny of the haplotypes. Phylogenetic analysis based on single nucleotide polymorphisms of sorghum AQP genes placed the tolerant and sensitive genotypes used for the expression study in distinct groups. Expression analyses suggested that selected AQPs may play a pivotal role in sorghum tolerance to water logging stress. Furthermore experimentation is needed to verify their role and to leverage phylogenetic analyses and AQP expression data to improve water logging tolerance in sorghum.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Genetic Diversity and Resistance to Fusarium Head Blight in Synthetic Hexaploid Wheat Derived From Aegilops tauschii and Diverse Triticum turgidum Subspecies

Synthetic hexaploid wheat (SHW) can serve as a bridge for the transfer of useful genes from Aegilops tauschii and tetraploid wheat ( Triticum turgidum ) into common wheat ( T. aestivum ). The objective of this study was to evaluate 149 SHW lines and their 74 tetraploid parents for their genetic diversity, breeding values and inter-genomic interactions for resistance to Fusarium head blight (FHB). The genetic diversity analysis was performed based on the population structure established using 4,674 and 3,330 polymorphic SNP markers among the SHW lines and tetraploid parents, respectively. The results showed that all T. carthlicum and most T. dicoccum accessions formed different clusters and subpopulations, respectively, whereas all the T. durum , T. polonicum , T. turgidum , and T. turanicum accessions were clustered together, suggesting that T. durum was more closely related to T. polonicum , T. turgidum , and T. turanicum than to T. dicoccum . The genetic diversity of the SHW lines mainly reflected that of the tetraploid parents. The SHW lines and their tetraploid parents were evaluated for reactions to FHB in two greenhouse seasons and at two field nurseries for 2 years. As expected, most of the SHW lines were more resistant than their tetraploid parents in all environments. The FHB severities of the SHW lines varied greatly depending on the Ae. tauschii and tetraploid genotypes involved. Most of the SHW lines with a high level of FHB resistance were generally derived from the tetraploid accessions with a high level of FHB resistance. Among the 149 SHW lines, 140 were developed by using three Ae. tauschii accessions CIae 26, PI 268210, and RL 5286. These SHW lines showed FHB severities reduced by 21.7%, 17.3%, and 11.5%, respectively, with an average reduction of 18.3%, as compared to the tetraploid parents, suggesting that the D genome may play a major role in reducing disease severity in the SHW lines. Thirteen SHW lines consistently showed a high level of FHB resistance compared to the resistant check, Sumai 3, in each environment. These SHW lines will be useful for the development of FHB-resistant wheat germplasm and populations for discovery of novel FHB resistance genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana

Alternative splicing (AS) of pre-mRNAs contributes to transcriptome diversity and enables plants to generate different protein isoforms from a single gene and/or fine-tune gene expression during different development stages and environmental changes. Although AS is pervasive, the genetic basis for differential isoform usage in plants is still emerging. In this study, we performed genome-wide analysis in 666 geographically distributed diverse ecotypes of Arabidopsis thaliana to identify genomic regions [splicing quantitative trait loci (sQTLs)] that may regulate differential AS. These ecotypes belong to different microclimatic conditions and are part of the relict and non-relict populations. Although sQTLs were spread across the genome, we observed enrichment for trans-s QTL ( trans-s QTLs hotspots) on chromosome one. Furthermore, we identified several sQTL (911) that co-localized with trait-linked single nucleotide polymorphisms (SNP) identified in the Arabidopsis genome-wide association studies (AraGWAS). Many sQTLs were enriched among circadian clock, flowering, and stress-responsive genes, suggesting a role for differential isoform usage in regulating these important processes in diverse ecotypes of Arabidopsis. In conclusion, the current study provides a deep insight into SNPs affecting isoform ratios/genes and facilitates a better mechanistic understanding of trait-associated SNPs in GWAS studies. To the best of our knowledge, this is the first report of sQTL analysis in a large set of Arabidopsis ecotypes and can be used as a reference to perform sQTL analysis in the Brassicaceae family. Since whole genome and transcriptome datasets are available for these diverse ecotypes, it could serve as a powerful resource for the biological interpretation of trait-associated loci, splice isoform ratios, and their phenotypic consequences to help produce more resilient and high yield crop varieties.

Arabidopsis thaliana↗
DOE OSTI2022

Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes

High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted post hoc tests for genotype-by-environment interaction, using a mixed model ANOVA. We found that 8 of the 54 SNPs showed significant GxE. Candidate genes underlying variation in root pulling force included those involved in nutrient transport. Although they are often treated separately, variation in the ability of plant roots to sense and respond to variation in environmental resources including water and nutrients may be linked by the genes and pathways underlying this variation. While functional validation of the identified genes is needed, our results expand the current knowledge of root phenotypic plasticity at the whole plant and gene levels, and further elucidate the complex genetic architecture of maize root systems.

Woods, Patrick↗
DOE OSTI2022

Enhanced Salt Tolerance of Torreya grandis Genders Is Related to Nitric Oxide Level and Antioxidant Capacity

Nitric oxide (NO), a bioactive molecule, is often involved in the regulation of physiological and biochemical processes in stressed plants. However, the effects of NO donors on dioecious plants remain unclear. Using a pot experiment, female and male Torreya grandis were used to study the role of sex and NO in salt stress tolerance. In the present study, female and male T. grandis seedlings pretreated with an NO donor (sodium nitroprusside, SNP) were exposed to salt stress, and then leaf relative water content (RWC), photosynthetic pigments, chlorophyll fluorescence parameters, NO and glutathione levels, oxidative damage, and antioxidant enzyme activities were investigated. Female T. grandis plants had better tolerance to salinity, as they were characterized by significantly higher RWC, pigment content, and photochemical activities of photosystem II (PSII) and fewer negative effects associated with higher nitrate reductase (NR) activity and NO content. Pretreatment with an NO donor further increased the endogenous NO content and NR activity of both female and male T. grandis plants compared with salt treatment. Moreover, pretreatment with an NO donor alleviated salt-induced oxidative damage of T. grandis , especially in male plants, as indicated by reduced lipid peroxidation, through an enhanced antioxidant system, including proline and glutathione accumulation, and increased antioxidant enzyme activities. However, the ameliorating effect of the NO donor was not effective in the presence of the NO scavenger (Nω-nitro-L-arginine methyl ester, L-name). In conclusion, enhanced salt tolerance in T. grandis plants is related to nitric oxide levels and the supply of NO donors is an interesting strategy for alleviating the negative effect of salt on T. grandis . Our data provide new evidence to contribute to the current understanding of NO-induced salt stress tolerance.

Liu, Yang↗
DOE OSTI2023

Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel

Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum’s racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

bioenergy association panel↗
DOE OSTI2020

Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus Tomentosa

Cytokinins play important roles in the growth and development of plants. Physiological and photosynthetic characteristics are common indicators to measure the growth and development in plants. However, few reports have described the molecular mechanisms of physiological and photosynthetic changes in response to cytokinin, particularly in woody plants. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression in response to the external environment. In this study, we examined genome-wide DNA methylation variation and transcriptional variation in poplar (Populus tomentosa) after short-term treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 460 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 339 protein-coding genes, 262 long non-coding RNAs (lncRNAs), and 15,793 24-nt small interfering RNAs (siRNAs) were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa, and 102,819 allele-specific expression (ASE) loci in 19,200 genes were detected showing differences in ASE levels after 6-BA treatment. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 460 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa, and we identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Evidence of Asexual Overwintering of Melampsora paradoxa and Mapping of Stem Rust Host Resistance in Salix

Melampsora rust is a devastating disease of shrub willow in North America. Previous work has identified Melampsora paradoxa as one of two identified rust species in New York State that infect Salix purpurea and other important Salix host species, however little is known about the population of this rust species in this region. Genotyping-by-sequencing was used to identify single nucleotide polymorphisms (SNPs) and assess population diversity of M. paradoxa isolates collected from three Salix breeding populations in Geneva, NY between 2015 and 2020. Statistical analyses of SNP revealed that all isolates collected were clonally derived even though they were collected across years. In 2020, isolates were collected from stem infections where uredospore pustules were observed, and these isolates were also identical to M. paradoxa collected in previous seasons. These data suggest that M. paradoxa sampled across multiple years overwintered and reproduced asexually and that stem infection is a possible mechanism for overwintering, both of which are novel findings for this rust species. Additionally, field disease ratings were conducted on a S. purpurea × S. suchowensis F 1 breeding population with high disease severity, enabling the discovery of QTL for resistance on chromosomes 1 and 19. Lastly, Colletotrichum salicis was frequently associated with stem rust and may play a role in M. paradoxa stem infection. Together, this work is the first substantial exploration into M. paradoxa population biology, stem infection, and host resistance in Salix.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Retrospective Analysis Reveals That the 2021 Outbreaks of African Swine Fever Virus in Ghana Were Caused by Two Distinct Genotypes

African swine fever virus (ASFV) is the causative agent of African swine fever (ASF), a highly infectious and lethal disease of domesticated swine. Outbreaks of ASF have been mostly restricted to the continent of Africa. The outbreaks that have occurred outside of Africa were controlled by extensive depopulation of the domesticated pig population. However, in 2007, an outbreak occurred in the country of Georgia, where ASFV infected wild pigs and quickly spread across eastern Europe. Since the reintroduction of ASF into Europe, variants of the current pandemic strain, ASFV Georgia 2007/01 (ASFV-G), which is classified as Genotype 2 based on p72 sequencing, have been reported in countries within western Europe, Asia, and the island of Hispaniola. Additionally, isolates collected in 2020 confirmed the presence of variants of ASFV-G in Nigeria. Recently, we reported similar variants of ASFV-G collected from domestic pigs suspected of dying of ASF in Ghana in 2022. Here, we retroactively report, based on full-length sequencing, that similar variants were present in Ghana in 2021. The SNP analysis revealed derivatives of ASFV with distinct genetic markers. Furthermore, we identified three full-length ASFV genomes as Genotype 1, indicating that there were two genotypes circulating in proximity during the 2021 ASF outbreaks in Ghana.

Virology↗
DOE OSTI2018

Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F Population

Flowering is an important developmental event in switchgrass ( Panicum virgatum ), as the time to complete the life cycle affects overall biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) associated with flowering time. A pseudo-F population was created by crossing two siblings derived from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. Heading and anthesis dates were collected for 2 yr at two locations: DeKalb, IL and Lafayette, IN. Nine QTL for flowering time were detected, two of which were heading-associated, four anthesis-associated, and three associated with both heading and anthesis. One QTL on linkage group (LG) 2a was detected for heading and anthesis in each location and year when environments were analyzed separately, and in a combined analysis across both locations and years. The effect on heading and anthesis of the QTL on LG 2a ranged from 4 to 13 and 5 to 9 d, respectively, depending on environment. Our findings validate QTL for switchgrass flowering time from previous research and identified additional QTL. Based on the switchgrass reference genome version 1.1, flowering time gene homologs reside near the LG 2a QTL and include PSEUDO RESPONSE REGULATOR 5, SUPPRESSOR OF FRIGIDA 4, and APETALA 1, respectively involved in the circadian clock, vernalization, and floral meristem identity. Markers linked to the QTL can be used to improve the efficiency of breeding switchgrass for delayed flowering to increase biomass yield.

09 BIOMASS FUELS↗