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Njuguna JN, Clark LV, Lipka AE, Anzoua KG, Bagmet L, Chebukin P, Dwiyanti MS, Dzyubenko E, Dzyubenko N, Ghimire BK, Jin X, Johnson DA, Kjeldsen JB, Nagano H, de Bem Oliveira I, Peng J, Petersen KK, Sabitov A, Seong ES, Yamada T, Yoo JH, Yu CY, Zhao H, Munoz P, Long SP, Sacks EJ. Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids. Plant Genome 2023; 16:e20401. [PMID: 37903749 DOI: 10.1002/tpg2.20401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/17/2023] [Accepted: 09/23/2023] [Indexed: 11/01/2023]
Abstract
Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed Bayesian statistical methods implemented in available software packages, polyRAD, EBG, and updog, incorporate error rates and population parameters to accurately estimate allelic dosage across any ploidy. We used empirical and simulated data to evaluate the three Bayesian algorithms and demonstrated their impact on the power of genome-wide association study (GWAS) analysis and the accuracy of genomic prediction. We further incorporated uncertainty in allelic dosage estimation by testing continuous genotype calls and comparing their performance to discrete genotypes in GWAS and genomic prediction. We tested the genotype-calling methods using data from two autotetraploid species, Miscanthus sacchariflorus and Vaccinium corymbosum, and performed GWAS and genomic prediction. In the empirical study, the tested Bayesian genotype-calling algorithms differed in their downstream effects on GWAS and genomic prediction, with some showing advantages over others. Through subsequent simulation studies, we observed that at low read depth, polyRAD was advantageous in its effect on GWAS power and limit of false positives. Additionally, we found that continuous genotypes increased the accuracy of genomic prediction, by reducing genotyping error, particularly at low sequencing depth. Our results indicate that by using the Bayesian algorithm implemented in polyRAD and continuous genotypes, we can accurately and cost-efficiently implement GWAS and genomic prediction in polyploid crops.
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Affiliation(s)
- Joyce N Njuguna
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lindsay V Clark
- Research Scientific Computing, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kossonou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Pavel Chebukin
- FSBSI "FSC of Agricultural Biotechnology of the Far East named after A.K. Chaiki", Ussuriysk, Russian Federation
| | - Maria S Dwiyanti
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Nicolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Bimal Kumar Ghimire
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul, South Korea
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Douglas A Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, Utah, USA
| | | | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | | | - Junhua Peng
- Spring Valley Agriscience Co. Ltd., Jinan, China
| | | | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, Russian Federation
| | - Eun Soo Seong
- Division of Bioresource Sciences, Kangwon National University, Chuncheon, South Korea
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Ji Hye Yoo
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Chang Yeon Yu
- Bioherb Research Institute, Kangwon National University, Chuncheon, South Korea
| | - Hua Zhao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Patricio Munoz
- Horticultural Science Department, University of Florida, Gainesville, Florida, USA
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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Bard AM, Clark LV, Cosgun E, Aldinger KA, Timms A, Quina LA, Lavista Ferres JM, Jardine D, Haas EA, Becker TM, Pagan CM, Santani A, Martinez D, Barua S, McNutt Z, Nesbitt A, Mitchell EA, Ramirez JM. Known pathogenic gene variants and new candidates detected in Sudden Unexpected Infant Death using Whole Genome Sequencing. medRxiv 2023:2023.09.11.23295207. [PMID: 37745463 PMCID: PMC10516094 DOI: 10.1101/2023.09.11.23295207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Purpose To gain insights into potential genetic factors contributing to the infant's vulnerability to Sudden Unexpected Infant Death (SUID). Methods Whole Genome Sequencing (WGS) was performed on 145 infants that succumbed to SUID, and 576 healthy adults. Variants were filtered by gnomAD allele frequencies and predictions of functional consequences. Results Variants of interest were identified in 86 genes, 63.4% of our cohort. Seventy-one of these have been previously associated with SIDS/SUID/SUDP. Forty-three can be characterized as cardiac genes and are related to cardiomyopathies, arrhythmias, and other conditions. Variants in 22 genes were associated with neurologic functions. Variants were also found in 13 genes reported to be pathogenic for various systemic disorders. Variants in eight genes are implicated in the response to hypoxia and the regulation of reactive oxygen species (ROS) and have not been previously described in SIDS/SUID/SUDP. Seventy-two infants met the triple risk hypothesis criteria (Figure 1). Conclusion Our study confirms and further expands the list of genetic variants associated with SUID. The abundance of genes associated with heart disease and the discovery of variants associated with the redox metabolism have important mechanistic implications for the pathophysiology of SUID.
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Labroo MR, Clark LV, Zhang S, Hu F, Tao D, Hamilton RS, Sacks EJ. Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa. Front Plant Sci 2023; 14:1278196. [PMID: 38034553 PMCID: PMC10684938 DOI: 10.3389/fpls.2023.1278196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
The undomesticated rice relative Oryza longistaminata is a valuable genetic resource for the improvement of the domesticated Asian rice, Oryza sativa. To facilitate the conservation, management, and use of O. longistaminata germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between O. longistaminata and O. sativa. Though past plant breeding efforts to introgress genes from O. longistaminata have improved biotic stress resistance, ratooning ability, and yield in O. sativa, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of O. sativa and O. longistaminata (aka "Obake") obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of O. longistaminata had not been previously investigated. We studied 190 O. longistaminata accessions, primarily from the International Rice Research Institute genebank collection, along with 309 O. sativa, 25 Oryza barthii, and 83 Oryza glaberrima control outgroups, and 17 control interspecific O. sativa/O. longistaminata hybrids. We analyzed the materials using 178,651 single-nucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of O. longistaminata, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that O. longistaminata is, perhaps counterintuitively, more closely related to the Asian species, O. sativa, than the African species O. barthii and O. glaberrima. We identified 19 recent spontaneous interspecific hybrid individuals between O. sativa and O. longistaminata in the germplasm sampled. Notably, the recent introgression between O. sativa and O. longistaminata has been bidirectional. Moreover, low levels of O. sativa alleles admixed in many predominantly O. longistaminata accessions suggest that introgression also occurred in the distant past, but only in Southern Africa.
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Affiliation(s)
- Marlee R. Labroo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Shilai Zhang
- School of Agriculture, Research Center for Perennial Rice Engineering and Technology in Yunnan, Yunnan University, Kunming, China
| | - Fengyi Hu
- School of Agriculture, Research Center for Perennial Rice Engineering and Technology in Yunnan, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Seed Laboratory & Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Ruaraidh Sackville Hamilton
- T.T. Chang Genetic Resources Center, International Rice Research Institute (IRRI), Los Baños, Philippines
- CGIAR Genebank Initiative, Salisbury, United Kingdom
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Ji N, Liang D, Clark LV, Sacks EJ, Kent AD. Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome. Microbiome 2023; 11:216. [PMID: 37777794 PMCID: PMC10541700 DOI: 10.1186/s40168-023-01646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/09/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Microbiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes. RESULTS Our results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla. CONCLUSIONS We provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity. Video Abstract.
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Affiliation(s)
- Niuniu Ji
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Institute for Sustainability, Energy and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Di Liang
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Institute for Sustainability, Energy and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lindsay V Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Erik J Sacks
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Angela D Kent
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Institute for Sustainability, Energy and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Sakhale SA, Yadav S, Clark LV, Lipka AE, Kumar A, Sacks EJ. Genome-wide association analysis for emergence of deeply sown rice ( Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field. Front Plant Sci 2023; 14:1172816. [PMID: 37377815 PMCID: PMC10291202 DOI: 10.3389/fpls.2023.1172816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.
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Affiliation(s)
- Sandeep A. Sakhale
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Shailesh Yadav
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Africa Rice Center (AfricaRice), Abidjan, Côte d’Ivoire
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Seattle Children’s Research Institute, Seattle, WA, United States
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Arvind Kumar
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
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Bingen JM, Clark LV, Band MR, Munzir I, Carrithers MD. Differential DNA methylation associated with multiple sclerosis and disease modifying treatments in an underrepresented minority population. Front Genet 2023; 13:1058817. [PMID: 36685876 PMCID: PMC9845287 DOI: 10.3389/fgene.2022.1058817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Black and Hispanic American patients frequently develop earlier onset of multiple sclerosis (MS) and a more severe disease course that can be resistant to disease modifying treatments. The objectives were to identify differential methylation of genomic DNA (gDNA) associated with disease susceptibility and treatment responses in a cohort of MS patients from underrepresented minority populations. Patients with MS and controls with non-inflammatory neurologic conditions were consented and enrolled under an IRB-approved protocol. Approximately 64% of donors identified as Black or African American and 30% as White, Hispanic-Latino. Infinium MethylationEPIC bead arrays were utilized to measure epigenome-wide gDNA methylation of whole blood. Data were analyzed in the presence and absence of adjustments for unknown covariates in the dataset, some of which corresponded to disease modifying treatments. Global patterns of differential methylation associated with MS were strongest for those probes that showed relative demethylation of loci with lower M values. Pathway analysis revealed unexpected associations with shigellosis and amoebiasis. Enrichment analysis revealed an over-representation of probes in enhancer regions and an under-representation in promoters. In the presence of adjustments for covariates that included disease modifying treatments, analysis revealed 10 differentially methylated regions (DMR's) with an FDR <1E-77. Five of these genes (ARID5B, BAZ2B, RABGAP1, SFRP2, WBP1L) are associated with cancer risk and cellular differentiation and have not been previously identified in MS studies. Hierarchical cluster and multi-dimensional scaling analysis of differential DNA methylation at 147 loci within those DMR's was sufficient to differentiate MS donors from controls. In the absence of corrections for disease modifying treatments, differential methylation in patients treated with dimethyl fumarate was associated with immune regulatory pathways that regulate cytokine and chemokine signaling, axon guidance, and adherens junctions. These results demonstrate possible associations of gastrointestinal pathogens and regulation of cellular differentiation with MS susceptibility in our patient cohort. This work further suggests that analyses can be performed in the presence and absence of corrections for immune therapies. Because of their high representation in our patient cohort, these results may be of specific relevance in the regulation of disease susceptibility and treatment responses in Black and Hispanic Americans.
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Affiliation(s)
- Jeremy M. Bingen
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States,Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States
| | - Lindsay V. Clark
- High Performance Biological Computing, and Roy J Carver Biotechnology Center, University of Illinois, Champaign, IL, United States
| | - Mark R. Band
- High Performance Biological Computing, and Roy J Carver Biotechnology Center, University of Illinois, Champaign, IL, United States
| | - Ilyas Munzir
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Michael D. Carrithers
- Neurology, University of Illinois College of Medicine, Chicago, IL, United States,Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States,Neurology, Jesse Brown Veterans Administration Hospital, Chicago, IL, United States,*Correspondence: Michael D. Carrithers,
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Lim CK, McCallister TX, Saporito-Magriña C, McPheron GD, Krishnan R, Zeballos C MA, Powell JE, Clark LV, Perez-Pinera P, Gaj T. CRISPR base editing of cis-regulatory elements enables the perturbation of neurodegeneration-linked genes. Mol Ther 2022; 30:3619-3631. [PMID: 35965414 PMCID: PMC9734028 DOI: 10.1016/j.ymthe.2022.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/25/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022] Open
Abstract
CRISPR technology has demonstrated broad utility for controlling target gene expression; however, there remains a need for strategies capable of modulating expression via the precise editing of non-coding regulatory elements. Here, we demonstrate that CRISPR base editors, a class of gene-modifying proteins capable of creating single-base substitutions in DNA, can be used to perturb gene expression via their targeted mutagenesis of cis-acting sequences. Using the promoter region of the human huntingtin (HTT) gene as an initial target, we show that editing of the binding site for the transcription factor NF-κB led to a marked reduction in HTT gene expression in base-edited cell populations. We found that these gene perturbations were persistent and specific, as a transcriptome-wide RNA analysis revealed minimal off-target effects resulting from the action of the base editor protein. We further demonstrate that this base-editing platform could influence gene expression in vivo as its delivery to a mouse model of Huntington's disease led to a potent decrease in HTT mRNA in striatal neurons. Finally, to illustrate the applicability of this concept, we target the amyloid precursor protein, showing that multiplex editing of its promoter region significantly perturbed its expression. These findings demonstrate the potential for base editors to regulate target gene expression.
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Affiliation(s)
- Colin K.W. Lim
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | - Ramya Krishnan
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | | | - Jackson E. Powell
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA
| | - Lindsay V. Clark
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL 61801, USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA,Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, University of Illinois, Urbana, IL 61801, USA,Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA,Corresponding author: Pablo Perez-Pinera, Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA.
| | - Thomas Gaj
- Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA,Corresponding author: Thomas Gaj, Department of Bioengineering, University of Illinois, Urbana, IL 61801, USA.
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Geary EL, Oba PM, Applegate CC, Clark LV, Fields CJ, Swanson KS. Effects of a mildly cooked human-grade dog diet on gene expression, skin and coat health measures, and fecal microbiota of healthy adult dogs. J Anim Sci 2022; 100:skac265. [PMID: 35965387 PMCID: PMC9527297 DOI: 10.1093/jas/skac265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Purported benefits of human-grade pet foods include reduced inflammation, enhanced coat quality, and improved gut health, but research is scarce. Therefore, we compared gene expression, skin and coat health measures, and the fecal microbiome of dogs consuming a mildly cooked human-grade or extruded kibble diet. Twenty beagles (BW = 10.25 ± 0.82 kg; age = 3.85 ± 1.84 yr) were used in a completely randomized design. Test diets included: 1) chicken and brown rice recipe [feed-grade; extruded; blue buffalo (BB)]; and 2) chicken and white rice [human-grade; mildly cooked; Just Food for Dogs (JFFD)]. The study consisted of a 4-week baseline when all dogs ate BB, and a 12-week treatment phase when dogs were randomized to either diet (n = 10/group). After the baseline and treatment phases, fresh fecal samples were scored and collected for pH, dry matter (DM), and microbiome analysis; blood samples were collected for gene expression analysis; hair samples were microscopically imaged; and skin was analyzed for delayed-type hypersensitivity (DTH), sebum concentration, hydration status, and transepidermal water loss (TEWL). Data were analyzed as a change from baseline (CFB) using the Mixed Models procedure of SAS (version 9.4). At baseline, fecal pH was higher (P < 0.05) and hair surface score, superoxide dismutase (SOD) expression, and tumor necrosis factor-α (TNF-α) expression was lower (P < 0.05) in dogs allotted to JFFD. The decrease in CFB fecal pH and DM was greater (P < 0.05) in dogs fed JFFD, but fecal scores were not different. The increase in CFB hair surface score was higher (P < 0.05) in dogs fed JFFD. The decrease in CFB TEWL (back region) was greater (P < 0.05) in dogs fed JFFD, but TEWL (inguinal and ear regions), hydration status, and sebum concentrations in all regions were not different. Hair cortex scores and DTH responses were not affected by diet. The increase in CFB gene expression of SOD, COX-2, and TNF-α was greater (P < 0.05) in dogs fed JFFD. PCoA plots based on Bray-Curtis distances of bacterial genera and species showed small shifts over time in dogs fed BB, but dramatic shifts in those fed JFFD. JFFD increased (adj. P < 0.05) relative abundances of 4 bacterial genera, 11 bacterial species, 68 KEGG pathways, and 167 MetaCyc pathways, and decreased (adj. P < 0.05) 16 genera, 25 species, 98 KEGG pathways, and 87 MetaCyc pathways. In conclusion, the JFFD diet dramatically shifted the fecal microbiome but had minor effects on skin and coat measures and gene expression.
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Affiliation(s)
- Elizabeth L Geary
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Patrícia M Oba
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Catherine C Applegate
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- The Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lindsay V Clark
- High Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Christopher J Fields
- High Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Finet S, He F, Clark LV, de Godoy MRC. Functional properties of miscanthus fiber and prebiotic blends in extruded canine diets. J Anim Sci 2022; 100:6547905. [PMID: 35279717 PMCID: PMC9047183 DOI: 10.1093/jas/skac078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Dietary fiber has become increasingly recognized as a key factor in maintaining gastrointestinal health. Dietary fiber sources are often comprised of several different fiber fractions, each with unique physicochemical properties. These properties can have varying physiological effects on the gastrointestinal tract that include modulation of microbiota, production of fermentation-derived metabolites, and laxation. The objectives of this study were 1) to determine the effects of a novel dietary fiber source, miscanthus grass fiber (MF), and prebiotic and fiber blends on gastrointestinal tolerance, apparent total tract digestibility, fecal metabolites, and fecal microbiota and 2) to evaluate the palatability of extruded diets containing MF in comparison to traditional dietary fiber sources. All animal procedures were approved by the University of Illinois Institutional Animal Care and Use Committee. Six dietary treatments were formulated to meet or exceed the AAFCO nutrient profile of 2018 and included either cellulose (CO), beet pulp (BP), MF, or a blend of MF and tomato pomace, MF and resistant starch, or MF and fructooligosaccharide. A total of 12 adult neutered female beagles (mean age 5.8 ± 1.1 yr; mean body weight 10.9 ± 1.0 kg; mean body condition score 5.7 ± 0.7) were randomly assigned to one of the six treatment diets in a replicated 6 × 6 Latin square design. Each dog was fed their assigned diet for a treatment period of 21 d with 17 d of diet adaptation followed by 4 d of total and fresh fecal collection. All diets were well accepted and digested by the dogs. Dogs fed BP had greater fecal total short-chain fatty acid concentration than the CO treatment (P < 0.05), while the dogs fed diets containing MF were intermediate. In a two-bowl palatability trial, no significant preference was observed between the extruded diets containing MF and CO (P > 0.05). However, a significant preference for the extruded diet containing BP over the diet containing only MF was observed (P < 0.05). The α-diversity of fecal microbial communities was not impacted by treatment (P > 0.05), but β-diversity indicated that dogs fed the BP diet differed from the other treatment groups (P < 0.05). The data from this study suggest that miscanthus grass can be successfully utilized in fiber blends in extruded diets for adult dogs, with modulatory effects similar to the traditional dietary fiber source, cellulose.
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Affiliation(s)
- Shannon Finet
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Fei He
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lindsay V Clark
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
| | - Maria Regina Cattai de Godoy
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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10
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Clark LV, Mays W, Lipka AE, Sacks EJ. A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes. BMC Bioinformatics 2022; 23:101. [PMID: 35317727 PMCID: PMC8939213 DOI: 10.1186/s12859-022-04635-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 03/10/2022] [Indexed: 12/02/2022] Open
Abstract
Background Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an effective tool for filtering loci but requires genotyping to be performed first at a high computational cost, whereas counting the number of sequence tags detected per genotype is computationally quick but very ineffective in inbred or polyploid populations. Therefore, new methods are needed for filtering paralogs. Results We introduce a novel statistic, Hind/HE, that uses the probability that two reads sampled from a genotype will belong to different alleles, instead of observed heterozygosity. The expected value of Hind/HE is the same across all loci in a dataset, regardless of read depth or allele frequency. In contrast to methods based on observed heterozygosity, it can be estimated and used for filtering loci prior to genotype calling. In addition to filtering paralogs, it can be used to filter loci with null alleles or high overdispersion, and identify individuals with unexpected ploidy and hybrid status. We demonstrate that the statistic is useful at read depths as low as five to 10, well below the depth needed for accurate genotype calling in polyploid and outcrossing species. Conclusions Our methodology for estimating Hind/HE across loci and individuals, as well as determining reasonable thresholds for filtering loci, is implemented in polyRAD v1.6, available at https://github.com/lvclark/polyRAD. In large sequencing datasets, we anticipate that the ability to filter markers and identify problematic individuals prior to genotype calling will save researchers considerable computational time. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04635-9.
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Affiliation(s)
- Lindsay V Clark
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Wittney Mays
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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11
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Chiu KK, Bashir ST, Abdel-Hamid AM, Clark LV, Laws MJ, Cann I, Nowak RA, Flaws JA. Isolation of DiNP-Degrading Microbes from the Mouse Colon and the Influence DiNP Exposure Has on the Microbiota, Intestinal Integrity, and Immune Status of the Colon. Toxics 2022; 10:toxics10020075. [PMID: 35202261 PMCID: PMC8877566 DOI: 10.3390/toxics10020075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/21/2022] [Accepted: 02/02/2022] [Indexed: 02/04/2023]
Abstract
Di-isononyl phthalate (DiNP) is a plasticizer used to impart flexibility or stability in a variety of products including polyvinyl chloride, cable coatings, artificial leather, and footwear. Previous studies have examined the impact of DiNP on gut integrity and the colonic immune microenvironment, but this study further expands the research by examining whether DiNP exposure alters the colonic microbiota and various immune markers. Previous studies have also revealed that environmental microbes degrade various phthalates, but no studies have examined whether anaerobic gut bacteria can degrade DiNP. Thus, this study tested the hypothesis that DiNP exposure alters the gut microbiota and immune-related factors, and that anaerobic bacteria in the gut can utilize DiNP as the sole carbon source. To test this hypothesis, adult female mice were orally dosed with corn oil or various doses of DiNP for 10–14 consecutive days. After the treatment period, mice were euthanized during diestrus. Colonic contents were collected for full-length 16S rRNA gene sequencing to identify the bacteria in the colon contents. Sanger sequencing of the 16S rRNA gene was used to identify bacteria that were able to grow in Bacteroides minimal media with DiNP as the sole carbon source. Colon tissues were collected for immunohistochemistry of immune(-related) factors. An environmentally relevant dose of DiNP (200 µg/kg) significantly increased a Lachnoclostridium taxon and decreased Blautia compared to the control. Collectively, minimal changes in the colonic microbiota were observed as indicated by non-significant beta-diversities between DiNP treatments and control. Furthermore, three strains of anaerobic bacteria derived from the colon were identified to use DiNP as the sole carbon source. Interestingly, DiNP exposure did not alter protein levels of interleukin-6, tumor necrosis factor alpha, claudin-1, and mucin-1 compared to the control. Collectively, these findings show that DiNP exposure alters the gut microbiota and that the gut contains DiNP-degrading microbes.
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Affiliation(s)
- Karen K. Chiu
- Division of Nutritional Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA;
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
| | - Shah Tauseef Bashir
- Department of Molecular and Integrative Physiology, College of Liberal Arts & Sciences, University of Illinois, Urbana, IL 61801, USA; (S.T.B.); (I.C.)
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA;
| | - Ahmed M. Abdel-Hamid
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA;
| | - Lindsay V. Clark
- High Performance Computing in Biology, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL 61801, USA;
| | - Mary J. Laws
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
| | - Isaac Cann
- Department of Molecular and Integrative Physiology, College of Liberal Arts & Sciences, University of Illinois, Urbana, IL 61801, USA; (S.T.B.); (I.C.)
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA;
| | - Romana A. Nowak
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA;
| | - Jodi A. Flaws
- Division of Nutritional Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois, Urbana, IL 61801, USA;
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA;
- Correspondence:
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12
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Finet SE, He F, Clark LV, de Godoy MR. 112 Modulating Effects of Miscanthus Grass and Prebiotic Blends on Canine Fecal Microbiota, Metabolites, and Digestibility. J Anim Sci 2021. [DOI: 10.1093/jas/skab235.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Dietary fiber plays an important role in gastrointestinal health as it modulates the gut environment and promotes microbiome homeostasis. However, dietary fiber sources vary in composition, physico-chemical properties, and physiological effects. The objective of this study was to evaluate the effects of miscanthus grass fiber and prebiotic fiber blends on fecal microbiota, fecal metabolites, and apparent total tract digestibility in comparison to traditional dietary fiber sources. Animal procedures were approved by the University of Illinois Institutional Animal Care and Use Committee. Six dietary treatments were formulated to meet or exceed AAFCO nutrient profile (2018) and included either cellulose, beet pulp, miscanthus fiber, or a blend of miscanthus fiber and tomato pomace, miscanthus fiber and resistant starch, or miscanthus fiber and fructooligosaccharide. Twelve female adult beagles were randomly assigned one of the six treatments in a replicated 6x6 Latin square design and fed for 21 d including 17 d of diet adaptation followed by 4 d of total and fresh fecal collection. All diets were well digested by the animals. Dogs fed beet pulp had greater fecal total short-chain fatty acid concentration than the cellulose treatment (P < 0.05), while the dogs fed diets containing miscanthus fiber were intermediate. No difference in the α-diversity of fecal microbial communities was observed among treatments (P >0.05), while β-diversity of dogs fed the beet pulp treatment differed from the other treatment groups. Miscanthus grass can be utilized successfully in diets for adult dogs with tomato pomace and resistant starch blends resulting in similar physiological effects to cellulose.
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Affiliation(s)
| | - Fei He
- University of Illinois at Urbana-Champaign
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13
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Gatta E, Saudagar V, Drnevich J, Forrest MP, Auta J, Clark LV, Sershen H, Smith RC, Grayson DR, Davis JM, Guidotti A. Concordance of Immune-Related Markers in Lymphocytes and Prefrontal Cortex in Schizophrenia. Schizophr Bull Open 2021; 2:sgab002. [PMID: 33585819 PMCID: PMC7865130 DOI: 10.1093/schizbullopen/sgab002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a severe neuropsychiatric disorder associated with a wide array of transcriptomic and neurobiochemical changes. Genome-wide transcriptomic profiling conducted in postmortem brain have provided novel insights into the pathophysiology of this disorder, and identified biological processes including immune/inflammatory-related responses, metabolic, endocrine, and synaptic function. However, few studies have investigated whether similar changes are present in peripheral tissue. Here, we used RNA-sequencing to characterize transcriptomic profiles of lymphocytes in 18 nonpsychotic controls and 19 individuals with schizophrenia. We identified 2819 differentially expressed transcripts (P nominal < .05) in the schizophrenia group when compared to controls. Bioinformatic analyses conducted on a subset of 293 genes (P nominal < .01 and |log2 FC| > 0.5) highlighted immune/inflammatory responses as key biological processes in our dataset. Differentially expressed genes in lymphocytes were highly enriched in gene expression profiles associated with cortex layer 5a and immune cells. Thus, we investigated whether the changes in transcripts levels observed in lymphocytes could also be detected in the prefrontal cortex (PFC, BA10) in a second replication cohort of schizophrenia subjects. Remarkably, mRNA levels detected in the PFC and lymphocytes were in strong agreement, and measurements obtained using RNA-sequencing positively correlated with data obtained by reverse transcriptase-quantitative polymerase chain reaction analysis. Collectively, our work supports a role for immune dysfunction in the pathogenesis of schizophrenia and suggests that peripheral markers can be used as accessible surrogates to investigate putative central nervous system disruptions.
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Affiliation(s)
- Eleonora Gatta
- Center for Alcohol Research in Epigenetics, Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Vikram Saudagar
- Center for Alcohol Research in Epigenetics, Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Jenny Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL
| | - Marc P Forrest
- Department of Physiology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - James Auta
- Center for Alcohol Research in Epigenetics, Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Lindsay V Clark
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois-Urbana Champaign, Urbana, IL
| | - Henry Sershen
- Nathan Kline Institute for Psychiatric Research, Orangeburg, NY
- Department of Psychiatry, NYU Langone Medical Center, New York, NY
| | - Robert C Smith
- Nathan Kline Institute for Psychiatric Research, Orangeburg, NY
- Department of Psychiatry, NYU Langone Medical Center, New York, NY
| | - Dennis R Grayson
- Center for Alcohol Research in Epigenetics, Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - John M Davis
- Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics, Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL
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14
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Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark LV, Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson JV, Liu S, Farrar K, Głowacka K, Jeżowski S, Barry K, Chae WB, Juvik JA, Gifford J, Oladeinde A, Yamada T, Grimwood J, Putnam NH, De Vega J, Barth S, Klaas M, Hodkinson T, Li L, Jin X, Peng J, Yu CY, Heo K, Yoo JH, Ghimire BK, Donnison IS, Schmutz J, Hudson ME, Sacks EJ, Moose SP, Swaminathan K, Rokhsar DS. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 2020; 11:5442. [PMID: 33116128 PMCID: PMC7595124 DOI: 10.1038/s41467-020-18923-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/19/2020] [Indexed: 02/05/2023] Open
Abstract
Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses. The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.
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Affiliation(s)
- Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Adam M Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Brandon T James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Guohong Albert Wu
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Mohammad B Belaffif
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Lindsay V Clark
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Hongxu Dong
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Adam Barling
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Jessica R Holmes
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Jessica E Mattick
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Siyao Liu
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Genetics, Curriculum of Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Kerrie Farrar
- Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Katarzyna Głowacka
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland.,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Stanisław Jeżowski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Won Byoung Chae
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Environmental Horticulture, Dankook University, Cheonan, 31116, Republic of Korea
| | - John A Juvik
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Justin Gifford
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Adebosola Oladeinde
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, 10-chōme-3 Kita 11 Jōnishi, Kita-ku, Sapporo, Hokkaido, 060-0811, Japan
| | - Jane Grimwood
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Nicholas H Putnam
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Jose De Vega
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, NR4 7UZ, UK
| | - Susanne Barth
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland
| | - Manfred Klaas
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland
| | - Trevor Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, D2, Dublin, Ireland
| | - Laigeng Li
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032, China
| | - Xiaoli Jin
- Department of Agronomy, Zhejiang University, Hangzhou, 310058, China
| | - Junhua Peng
- HuaZhi Rice Biotech Company, Changsha, 410125, Hunan, China
| | - Chang Yeon Yu
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Ji Hye Yoo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Bimal Kumar Ghimire
- Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea
| | - Iain S Donnison
- Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Matthew E Hudson
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Erik J Sacks
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Stephen P Moose
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA. .,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. .,DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA. .,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA. .,Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan. .,Chan-Zuckerberg BioHub, 499 Illinois St, San Francisco, CA, 94158, USA.
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15
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Olatoye MO, Clark LV, Labonte NR, Dong H, Dwiyanti MS, Anzoua KG, Brummer JE, Ghimire BK, Dzyubenko E, Dzyubenko N, Bagmet L, Sabitov A, Chebukin P, Głowacka K, Heo K, Jin X, Nagano H, Peng J, Yu CY, Yoo JH, Zhao H, Long SP, Yamada T, Sacks EJ, Lipka AE. Training Population Optimization for Genomic Selection in Miscanthus. G3 (Bethesda) 2020; 10:2465-2476. [PMID: 32457095 PMCID: PMC7341128 DOI: 10.1534/g3.120.401402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/20/2020] [Indexed: 01/08/2023]
Abstract
Miscanthus is a perennial grass with potential for lignocellulosic ethanol production. To ensure its utility for this purpose, breeding efforts should focus on increasing genetic diversity of the nothospecies Miscanthus × giganteus (M×g) beyond the single clone used in many programs. Germplasm from the corresponding parental species M. sinensis (Msi) and M. sacchariflorus (Msa) could theoretically be used as training sets for genomic prediction of M×g clones with optimal genomic estimated breeding values for biofuel traits. To this end, we first showed that subpopulation structure makes a substantial contribution to the genomic selection (GS) prediction accuracies within a 538-member diversity panel of predominately Msi individuals and a 598-member diversity panels of Msa individuals. We then assessed the ability of these two diversity panels to train GS models that predict breeding values in an interspecific diploid 216-member M×g F2 panel. Low and negative prediction accuracies were observed when various subsets of the two diversity panels were used to train these GS models. To overcome the drawback of having only one interspecific M×g F2 panel available, we also evaluated prediction accuracies for traits simulated in 50 simulated interspecific M×g F2 panels derived from different sets of Msi and diploid Msa parents. The results revealed that genetic architectures with common causal mutations across Msi and Msa yielded the highest prediction accuracies. Ultimately, these results suggest that the ideal training set should contain the same causal mutations segregating within interspecific M×g populations, and thus efforts should be undertaken to ensure that individuals in the training and validation sets are as closely related as possible.
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Affiliation(s)
| | | | | | - Hongxu Dong
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30605
| | - Maria S Dwiyanti
- Applied Plant Genome Laboratory, Research Faculty of Agriculture, Hokkaido University, Japan
| | - Kossonou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Joe E Brummer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523
| | - Bimal K Ghimire
- Department of Applied Bioscience, Konkuk University, Seoul 05029, South Korea
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42-44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Nikolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42-44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, 42-44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, 42-44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, 42-44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | | | - Kweon Heo
- Department of Applied Plant Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Xiaoli Jin
- Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junhua Peng
- China National Seed Group Co. Ltd, Wuhan, Hubei 430040, China
| | - Chang Y Yu
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Ji H Yoo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Stephen P Long
- Dept. of Crop Sciences, University of Illinois, Urbana, IL
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J Sacks
- Dept. of Crop Sciences, University of Illinois, Urbana, IL
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Clark LV, Jin X, Petersen KK, Anzoua KG, Bagmet L, Chebukin P, Deuter M, Dzyubenko E, Dzyubenko N, Heo K, Johnson DA, Jørgensen U, Kjeldsen JB, Nagano H, Peng J, Sabitov A, Yamada T, Yoo JH, Yu CY, Long SP, Sacks EJ. Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea. Ann Bot 2019; 124:731-748. [PMID: 30247525 PMCID: PMC6821896 DOI: 10.1093/aob/mcy161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/08/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.
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Affiliation(s)
- Lindsay V Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | | | - Kossanou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Larissa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | - Martin Deuter
- TINPLANT Biotechnik und Pflanzenvermehrung GmbH, Klein Wanzleben, Germany
- Present address: Rosmarienbergstrasse 3A, D-39164 Wanzleben-Börde, Germany
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | | | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Douglas A Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT, USA
- Present address: 1229 N. 1800 E., Logan, UT 84341, USA
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | | | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junhua Peng
- Life Science and Technology Center, China National Seed Group Co. Ltd, Wuhan, Hubei, China
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- For correspondence. E-mail
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17
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Clark LV, Jin X, Petersen KK, Anzoua KG, Bagmet L, Chebukin P, Deuter M, Dzyubenko E, Dzyubenko N, Heo K, Johnson DA, Jørgensen U, Kjeldsen JB, Nagano H, Peng J, Sabitov A, Yamada T, Yoo JH, Yu CY, Long SP, Sacks EJ. Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centred around the Yellow Sea. Ann Bot 2019. [PMID: 30247525 DOI: 10.1093/aob/mcy1161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. METHODS Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. KEY RESULTS Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was derived from the N China group, with a substantial bottleneck. Japanese and mainland tetraploids originated from independent polyploidization events. Hybrids between diploid M. sacchariflorus and M. sinensis were identified in Korea, but without introgression into either parent species. In contrast, tetraploid M. sacchariflorus in southern Japan and Korea exhibited substantial hybridization and introgression with local diploid M. sinensis. CONCLUSIONS Genetic data indicated that the land now under the Yellow Sea was a centre of diversity for M. sacchariflorus during the last glacial maximum, followed by a series of migrations as the climate became warmer and wetter. Overall, M. sacchariflorus has greater genetic diversity than M. sinensis, suggesting that breeding and selection within M. sacchariflorus will be important for the development of improved M. × giganteus. Ornamental M. sacchariflorus genotypes in Europe and North America represent a very narrow portion of the species' genetic diversity, and thus do not well represent the species as a whole.
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Affiliation(s)
- Lindsay V Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Research of Zhejiang Province, Zhejiang University, Hangzhou, China
| | | | - Kossanou G Anzoua
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Larissa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | - Martin Deuter
- TINPLANT Biotechnik und Pflanzenvermehrung GmbH, Klein Wanzleben, Germany
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | | | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Douglas A Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT, USA
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | | | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Junhua Peng
- Life Science and Technology Center, China National Seed Group Co. Ltd, Wuhan, Hubei, China
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, Russia
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon, South Korea
| | - Stephen P Long
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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18
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Clifton‐Brown J, Harfouche A, Casler MD, Dylan Jones H, Macalpine WJ, Murphy‐Bokern D, Smart LB, Adler A, Ashman C, Awty‐Carroll D, Bastien C, Bopper S, Botnari V, Brancourt‐Hulmel M, Chen Z, Clark LV, Cosentino S, Dalton S, Davey C, Dolstra O, Donnison I, Flavell R, Greef J, Hanley S, Hastings A, Hertzberg M, Hsu T, Huang LS, Iurato A, Jensen E, Jin X, Jørgensen U, Kiesel A, Kim D, Liu J, McCalmont JP, McMahon BG, Mos M, Robson P, Sacks EJ, Sandu A, Scalici G, Schwarz K, Scordia D, Shafiei R, Shield I, Slavov G, Stanton BJ, Swaminathan K, Taylor G, Torres AF, Trindade LM, Tschaplinski T, Tuskan GA, Yamada T, Yeon Yu C, Zalesny RS, Zong J, Lewandowski I. Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar. Glob Change Biol Bioenergy 2019; 11:118-151. [PMID: 30854028 PMCID: PMC6392185 DOI: 10.1111/gcbb.12566] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/18/2018] [Indexed: 05/07/2023]
Abstract
Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.
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Affiliation(s)
- John Clifton‐Brown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Antoine Harfouche
- Department for Innovation in Biological, Agrofood and Forest systemsUniversity of TusciaViterboItaly
| | | | - Huw Dylan Jones
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | | | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityGenevaNew York
| | - Anneli Adler
- SweTree Technologies ABUmeåSweden
- Institute of Crop Production EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Chris Ashman
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Danny Awty‐Carroll
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Sebastian Bopper
- Department of Seed Science and Technology, Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Vasile Botnari
- Institute of Genetics, Physiology and Plant Protection (IGFPP) of Academy of Sciences of MoldovaChisinauMoldova
| | | | - Zhiyong Chen
- Insitute of MiscanthusHunan Agricultural UniversityHunan ChangshaChina
| | - Lindsay V. Clark
- Department of Crop Sciences & Center for Advanced Bioenergy and Bioproducts Innovation, 279 Edward R Madigan LaboratoryUniversity of IllinoisUrbanaIllinois
| | - Salvatore Cosentino
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Sue Dalton
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Chris Davey
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Oene Dolstra
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Iain Donnison
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Joerg Greef
- Julius Kuhn‐Institut (JKI)Bundesforschungsinstitut fur KulturpflanzenBraunschweigGermany
| | | | - Astley Hastings
- Institute of Biological and Environmental ScienceUniversity of AberdeenAberdeenUK
| | | | - Tsai‐Wen Hsu
- Taiwan Endemic Species Research Institute (TESRI)Nantou CountyTaiwan
| | - Lin S. Huang
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Antonella Iurato
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Elaine Jensen
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Xiaoli Jin
- Department of Agronomy & The Key Laboratory of Crop Germplasm Resource of Zhejiang ProvinceZhejiang UniversityHangzhouChina
| | - Uffe Jørgensen
- Department of AgroecologyAarhus University Centre for Circular BioeconomyTjeleDenmark
| | - Andreas Kiesel
- Department of Biobased Products and Energy Crops, Institute of Crop ScienceUniversity of HohenheimStuttgartGermany
| | - Do‐Soon Kim
- Department of Plant Sciences, Research Institute of Agriculture & Life Sciences, CALSSeoul National UniversitySeoulKorea
| | - Jianxiu Liu
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Jon P. McCalmont
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Bernard G. McMahon
- Natural Resources Research InstituteUniversity of Minnesota – DuluthDuluthMinnesota
| | | | - Paul Robson
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Erik J. Sacks
- Department of Crop Sciences & Center for Advanced Bioenergy and Bioproducts Innovation, 279 Edward R Madigan LaboratoryUniversity of IllinoisUrbanaIllinois
| | - Anatolii Sandu
- Institute of Genetics, Physiology and Plant Protection (IGFPP) of Academy of Sciences of MoldovaChisinauMoldova
| | - Giovanni Scalici
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Kai Schwarz
- Julius Kuhn‐Institut (JKI)Bundesforschungsinstitut fur KulturpflanzenBraunschweigGermany
| | - Danilo Scordia
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Reza Shafiei
- James Hutton InstituteUniversity of DundeeDundeeUK
| | | | | | | | | | - Gail Taylor
- Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Andres F. Torres
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Luisa M. Trindade
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Timothy Tschaplinski
- The Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Gerald A. Tuskan
- The Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Toshihiko Yamada
- Field Science Centre for the Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chang Yeon Yu
- College of Agriculture and Life Sciences 2Kangwon National UniversityChuncheonSouth Korea
| | | | - Junqin Zong
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Iris Lewandowski
- Department of Biobased Products and Energy Crops, Institute of Crop ScienceUniversity of HohenheimStuttgartGermany
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Clark LV, Buckland M, Murphy G, Taylor N, Vleck V, Mein C, Wozniak E, Smuk M, White PD. Cytokine responses to exercise and activity in patients with chronic fatigue syndrome: case-control study. Clin Exp Immunol 2017; 190:360-371. [PMID: 28779554 DOI: 10.1111/cei.13023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Chronic fatigue syndrome (CFS) is characterized by fatigue after exertion. A systematic review suggested that transforming growth factor (TGF)-β concentrations are often elevated in cases of CFS when compared to healthy controls. This study attempted to replicate this finding and investigate whether post-exertional symptoms were associated with altered cytokine protein concentrations and their RNA in CFS patients. Twenty-four patients fulfilling Centers for Disease Control criteria for CFS, but with no comorbid psychiatric disorders, were recruited from two CFS clinics in London, UK. Twenty-one healthy, sedentary controls were matched by gender, age and other variables. Circulating proteins and RNA were measured for TGF-β, tumour necrosis factor (TNF), interleukin (IL)-8, IL-6 and IL-1β. We measured six further cytokine protein concentrations (IL-2, IL-4, IL-5, IL-10, IL-12p70, and interferon (IFN)-γ). Measures were taken at rest, and before and after both commuting and aerobic exercise. CFS cases had higher TGF-β protein levels compared to controls at rest (median (quartiles) = 43·9 (19·2, 61·8) versus 18·9 (16·1, 30·0) ng/ml) (P = 0·003), and consistently so over a 9-day period. However, this was a spurious finding due to variation between different assay batches. There were no differences between groups in changes to TGF-β protein concentrations after either commuting or exercise. All other cytokine protein and RNA levels were similar between cases and controls. Post-exertional symptoms and perceived effort were not associated with any increased cytokines. We were unable to replicate previously found elevations in circulating cytokine concentrations, suggesting that elevated circulating cytokines are not important in the pathophysiology of CFS.
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Affiliation(s)
- L V Clark
- Centre for Psychiatry, Wolfson Institute of Preventive Medicine, Queen Mary's School of Medicine and Dentistry, London, UK
| | - M Buckland
- UCL Centre for Immunodeficiency, Royal Free London NHS Foundation Trust, London, UK
| | - G Murphy
- UCL Centre for Immunodeficiency, Royal Free London NHS Foundation Trust, London, UK
| | - N Taylor
- UCL Centre for Immunodeficiency, Royal Free London NHS Foundation Trust, London, UK
| | - V Vleck
- CIPER, Faculty of Human Kinetics, University of Lisbon, Lisbon, Portugal
| | - C Mein
- Genome Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - E Wozniak
- Genome Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - M Smuk
- Centre for Psychiatry, Wolfson Institute of Preventive Medicine, Queen Mary's School of Medicine and Dentistry, London, UK
| | - P D White
- Centre for Psychiatry, Wolfson Institute of Preventive Medicine, Queen Mary's School of Medicine and Dentistry, London, UK
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Clark LV, Schreier AD. Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables. Mol Ecol Resour 2017; 17:1090-1103. [DOI: 10.1111/1755-0998.12639] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 11/06/2016] [Accepted: 11/16/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Lindsay V. Clark
- Department of Crop Sciences University of Illinois, Urbana‐Champaign 1201 W. Gregory Drive Urbana IL 61801 USA
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Clark LV, Dzyubenko E, Dzyubenko N, Bagmet L, Sabitov A, Chebukin P, Johnson DA, Kjeldsen JB, Petersen KK, Jørgensen U, Yoo JH, Heo K, Yu CY, Zhao H, Jin X, Peng J, Yamada T, Sacks EJ. Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. Ann Bot 2016; 118:941-955. [PMID: 27451985 PMCID: PMC5055818 DOI: 10.1093/aob/mcw137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/24/2016] [Indexed: 05/08/2023]
Abstract
Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.
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Affiliation(s)
- Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Nikolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Douglas A. Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT 84322-6300, USA
| | | | - Karen Koefoed Petersen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Årslev, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430040, China
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
- *For correspondence. E-mail
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Clark LV, Sacks EJ. TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source Code Biol Med 2016; 11:11. [PMID: 27408618 PMCID: PMC4940913 DOI: 10.1186/s13029-016-0057-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/06/2016] [Indexed: 01/24/2023]
Abstract
BACKGROUND In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. RESULTS We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user-supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. CONCLUSIONS TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.
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Affiliation(s)
- Lindsay V Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802 USA
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802 USA
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Clark LV, Stewart JR, Nishiwaki A, Toma Y, Kjeldsen JB, Jørgensen U, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Yamada T, Sacks EJ. Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression. J Exp Bot 2015; 66:4213-25. [PMID: 25618143 PMCID: PMC4493777 DOI: 10.1093/jxb/eru511] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Unilateral introgression from diploids to tetraploids has been hypothesized to be an important evolutionary mechanism in plants. However, few examples have been definitively identified, perhaps because data of sufficient depth and breadth were difficult to obtain before the advent of affordable high-density genotyping. Throughout Japan, tetraploid Miscanthus sacchariflorus and diploid Miscanthus sinensis are common, and occasionally hybridize. In this study, 667 M. sinensis and 78 M. sacchariflorus genotypes from Japan were characterized using 20 704 SNPs and ten plastid microsatellites. Similarity of SNP genotypes between diploid and tetraploid M. sacchariflorus indicated that the tetraploids originated through autopolyploidy. Structure analysis indicated a gradient of introgression from diploid M. sinensis into tetraploid M. sacchariflorus throughout Japan; most tetraploids had some M. sinensis DNA. Among phenotypically M. sacchariflorus tetraploids, M. sinensis ancestry averaged 7% and ranged from 1-39%, with introgression greatest in southern Japan. Unexpectedly, rare (~1%) diploid M. sinensis individuals from northern Japan were found with 6-27% M. sacchariflorus ancestry. Population structure of M. sinensis in Japan included three groups, and was driven primarily by distance, and secondarily by geographic barriers such as mountains and straits. Miscanthus speciation is a complex and dynamic process. In contrast to limited introgression between diploid M. sacchariflorus and M. sinensis in northern China, selection for adaptation to a moderate maritime climate probably favoured cross-ploidy introgressants in southern Japan. These results will help guide the selection of Miscanthus accessions for the breeding of biomass cultivars.
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Affiliation(s)
- Lindsay V Clark
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - J Ryan Stewart
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Aya Nishiwaki
- Field Science Center, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 889-2192, Japan
| | - Yo Toma
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | | | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Tjele DK-8830, Denmark
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430040, China
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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Nagano H, Clark LV, Zhao H, Peng J, Yoo JH, Heo K, Yu CY, Anzoua KG, Matsuo T, Sacks EJ, Yamada T. Contrasting allelic distribution of CO/Hd1 homologues in Miscanthus sinensis from the East Asian mainland and the Japanese archipelago. J Exp Bot 2015; 66:4227-4237. [PMID: 26089536 PMCID: PMC4493791 DOI: 10.1093/jxb/erv292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS (CO)/Heading date 1(Hd1) were cloned from Miscanthus sinensis and named MsiHd1. Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea. Two to five MsiHd1 alleles in each accession were identified, suggesting that MsiHd1 consists of at least three loci in the Miscanthus genome. Verifying the open reading frame in MsiHd1, they were classified as putative functional alleles without mutations or non-functional alleles caused by indels. The Neighbor-Joining tree indicated that one of the multiple MsiHd1 loci is a pseudogene locus without any functional alleles. The pseudogene locus was named MsiHd1b, and the other loci were considered to be part of the MsiHd1a multi-locus family. Interestingly, in most Japanese accessions 50% or more of the MsiHd1a alleles were non-functional, whereas accessions from the East Asian mainland harboured only functional alleles. Five novel miniature inverted transposable elements (MITEs) (MsiMITE1-MsiMITE5) were observed in MsiHd1a/b. MsiMITE1, detected in exon 1 of MsiHd1a, was only observed in Japanese accessions and its revertant alleles derived from retransposition were predominantly in Chinese accessions. These differences in MsiHd1a show that the dependency on functional MsiHd1a alleles is different between accessions from the East Asian mainland and Japan.
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Affiliation(s)
- Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Lindsay V Clark
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430206, China
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | | | - Tomoaki Matsuo
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J Sacks
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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Clark LV, Brummer JE, Głowacka K, Hall MC, Heo K, Peng J, Yamada T, Yoo JH, Yu CY, Zhao H, Long SP, Sacks EJ. A footprint of past climate change on the diversity and population structure of Miscanthus sinensis. Ann Bot 2014; 114:97-107. [PMID: 24918203 PMCID: PMC4071102 DOI: 10.1093/aob/mcu084] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Miscanthus is a perennial C4 grass that is a leading potential feedstock crop for the emerging bioenergy industry in North America, Europe and China. However, only a single, sterile genotype of M. × giganteus (M×g), a nothospecies derived from diploid M. sinensis (Msi) and tetraploid M. sacchariflorus (Msa), is currently available to farmers for biomass production. To facilitate breeding of Miscanthus, this study characterized genetic diversity and population structure of Msi in its native range of East Asia. METHODS A total of 767 accessions were studied, including 617 Msi from most of its native range in China, Japan and South Korea, and 77 ornamental cultivars and 43 naturalized individuals from the USA. Accessions were evaluated with 21 207 restriction site-associated DNA sequencing single nucleotide polymorphism (SNP) markers, 424 GoldenGate SNPs and ten plastid microsatellite markers. KEY RESULTS Six genetic clusters of Msi from geographically distinct regions in Asia were identified. Genetic data indicated that (1) south-eastern China was the origin of Msi populations found in temperate eastern Asia, which is consistent with this area probably having been a refugium during the last glacial maximum (LGM); (2) Msi migrated directly from south-eastern China to Japan before migrating to the same latitudes in China and Korea, which is consistent with the known sequence of warming post-LGM; (3) ornamental Msi cultivars were derived from the southern Japan population, and US naturalized populations were derived from a sub-set of the ornamental cultivars; and (4) many ornamental cultivars previously described as Msi have hybrid ancestry from Msa and Msi, whereas US naturalized populations of Msi do not. CONCLUSIONS Population structure of Msi was driven by patterns of warming since the LGM, and secondarily by geographical barriers. This study will facilitate germplasm conservation, association analyses and identification of potential heterotic groups for the improvement of Miscanthus as a bioenergy crop.
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Affiliation(s)
- Lindsay V Clark
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Joe E Brummer
- Colorado State University, Fort Collins, CO 80523, USA
| | - Katarzyna Głowacka
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland
| | | | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Junhua Peng
- Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | | | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Stephen P Long
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
| | - Erik J Sacks
- University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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Clark LV, Jasieniuk M. Spontaneous hybrids between native and exotic Rubus in the Western United States produce offspring both by apomixis and by sexual recombination. Heredity (Edinb) 2012; 109:320-8. [PMID: 22850699 DOI: 10.1038/hdy.2012.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Facultative asexual reproduction is a trait commonly found in invasive species. With a combination of sexual and asexual reproductive modes, such species may adapt to new environments via sexual recombination during range expansion, while at the same time having the benefits of asexuality such as the maintenance of fitness effects that depend upon heterozygosity. In the Western United States, native species of Rubus (Rosaceae) reproduce sexually whereas exotic naturalized Rubus species reproduce by pseudogamous apomixis. We hypothesized that new asexual lineages of Rubus could arise from hybridization in this range. To detect hybridization between native and exotic Rubus, we genotyped 579 individuals collected across California, Oregon and Washington with eight nuclear microsatellites and two chloroplast markers. Principal Coordinate Analysis and Bayesian clustering revealed a limited amount of hybridization of the native R. ursinus with the exotic R. armeniacus and R. pensilvanicus, as well as cultivated varieties. Genetic distances between these hybrids and their offspring indicated that both R. ursinus × R. armeniacus and R. ursinus × R. pensilvanicus produced a mix of apomictic and sexual seeds, with sexual seeds being more viable. Although neither of these hybrid types is currently considered invasive, they model the early stages of evolution of new invasive lineages, given the potential for fixed heterosis and the generation of novel genotypes. The hybrids also retain the ability to increase their fitness via sexual recombination and natural selection. Mixed reproductive systems such as those described here may be an important step in the evolution of asexual invasive species.
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Affiliation(s)
- L V Clark
- Department of Plant Sciences, University of California, Davis, CA, USA.
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Goldstein LH, Seed PT, Clark LV, Dowson AJ, Jenkins LM, Ridsdale L. Predictors of outcome in patients consulting their general practitioners for headache: a prospective study. Psychol Health 2011; 26:751-64. [PMID: 21432726 DOI: 10.1080/08870446.2010.493217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Headache is the most common neurological symptom presenting to general practitioners (GPs). Identifying factors predicting outcome in patients consulting their GPs for headache may help GPs with prognosis and choose management strategies which would improve patient care. We followed up a cohort of patients receiving standard medical care, recruited from 18 general practices in the South Thames region of England, approximately 9 months after their initial participation in the study. Of the baseline sample (N=255), 134 provided both full baseline and follow-up data on measures of interest. We determined associations between patients' follow-up scores on the Headache Impact Test-6 and baseline characteristics (including headache impact and frequency scores, mood, attributions about psychological/medical causes of their headaches, satisfaction with GP care and illness perceptions). Greater impact and stronger beliefs about the negative consequences of headaches at baseline were the strongest predictors of poor outcome at follow-up.
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Affiliation(s)
- L H Goldstein
- Department of Psychology, Institute of Psychiatry, King's College London, London, UK.
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White PD, Goldsmith KA, Johnson AL, Potts L, Walwyn R, DeCesare JC, Baber HL, Burgess M, Clark LV, Cox DL, Bavinton J, Angus BJ, Murphy G, Murphy M, O'Dowd H, Wilks D, McCrone P, Chalder T, Sharpe M. Comparison of adaptive pacing therapy, cognitive behaviour therapy, graded exercise therapy, and specialist medical care for chronic fatigue syndrome (PACE): a randomised trial. Lancet 2011; 377:823-36. [PMID: 21334061 PMCID: PMC3065633 DOI: 10.1016/s0140-6736(11)60096-2] [Citation(s) in RCA: 578] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Trial findings show cognitive behaviour therapy (CBT) and graded exercise therapy (GET) can be effective treatments for chronic fatigue syndrome, but patients' organisations have reported that these treatments can be harmful and favour pacing and specialist health care. We aimed to assess effectiveness and safety of all four treatments. METHODS In our parallel-group randomised trial, patients meeting Oxford criteria for chronic fatigue syndrome were recruited from six secondary-care clinics in the UK and randomly allocated by computer-generated sequence to receive specialist medical care (SMC) alone or with adaptive pacing therapy (APT), CBT, or GET. Primary outcomes were fatigue (measured by Chalder fatigue questionnaire score) and physical function (measured by short form-36 subscale score) up to 52 weeks after randomisation, and safety was assessed primarily by recording all serious adverse events, including serious adverse reactions to trial treatments. Primary outcomes were rated by participants, who were necessarily unmasked to treatment assignment; the statistician was masked to treatment assignment for the analysis of primary outcomes. We used longitudinal regression models to compare SMC alone with other treatments, APT with CBT, and APT with GET. The final analysis included all participants for whom we had data for primary outcomes. This trial is registered at http://isrctn.org, number ISRCTN54285094. FINDINGS We recruited 641 eligible patients, of whom 160 were assigned to the APT group, 161 to the CBT group, 160 to the GET group, and 160 to the SMC-alone group. Compared with SMC alone, mean fatigue scores at 52 weeks were 3·4 (95% CI 1·8 to 5·0) points lower for CBT (p = 0·0001) and 3·2 (1·7 to 4·8) points lower for GET (p = 0·0003), but did not differ for APT (0·7 [-0·9 to 2·3] points lower; p = 0·38). Compared with SMC alone, mean physical function scores were 7·1 (2·0 to 12·1) points higher for CBT (p = 0·0068) and 9·4 (4·4 to 14·4) points higher for GET (p = 0·0005), but did not differ for APT (3·4 [-1·6 to 8·4] points lower; p=0·18). Compared with APT, CBT and GET were associated with less fatigue (CBT p = 0·0027; GET p = 0·0059) and better physical function (CBT p=0·0002; GET p<0·0001). Subgroup analysis of 427 participants meeting international criteria for chronic fatigue syndrome and 329 participants meeting London criteria for myalgic encephalomyelitis yielded equivalent results. Serious adverse reactions were recorded in two (1%) of 159 participants in the APT group, three (2%) of 161 in the CBT group, two (1%) of 160 in the GET group, and two (1%) of 160 in the SMC-alone group. INTERPRETATION CBT and GET can safely be added to SMC to moderately improve outcomes for chronic fatigue syndrome, but APT is not an effective addition. FUNDING UK Medical Research Council, Department of Health for England, Scottish Chief Scientist Office, Department for Work and Pensions.
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Affiliation(s)
- P D White
- Wolfson Institute of Preventive Medicine, Barts and The London School of Medicine, Queen Mary University of London, UK.
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Ohlstein EH, Romanic AM, Clark LV, Kapadia RD, Sarkar SK, Gagnon R, Chandra S. Application of in vivo and ex vivo magnetic resonance imaging for evaluation of tranilast on neointima formation following balloon angioplasty of the rat carotid artery. Cardiovasc Res 2000; 47:759-68. [PMID: 10974224 DOI: 10.1016/s0008-6363(00)00120-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Recent studies suggest that tranilast inhibits a variety of agents implicated in neointimal growth and restenosis in experimental animal models and humans. We report here a study evaluating the efficacy of tranilast in the rat carotid artery balloon angioplasty model, a model that mimics many aspects of the percutaneous transluminal angioplasty procedure in humans. Efficacy was determined based on in vivo and ex vivo magnetic resonance imaging (MRI) as well as by histomorphometry. The utility of this study, using a reverse paradigm, is to investigate if agents successful in the clinic can demonstrate efficacy in this animal model primary screen as measured by MRI and histomorphometry. METHODS Tranilast (300 mg/kg/day, p.o.) was administered to Sprague-Dawley rats 3 days prior to balloon injury and continued for 14 days after injury. Three methods of measuring the vascular injury that occurs in this model were employed: (1) in vivo MRI, used to measure in vivo lumen volumes for the carotid artery once at baseline (pre-surgery) and again at 14 days post angioplasty; (2) ex vivo MRI (and histomorphometry), used to evaluate the total arterial wall thickness and the intima-to-media ratio; and (3) analysis of collagen density, used to evaluate the efficacy of tranilast to abrogate collagen synthesis and deposition following vascular injury. RESULTS Tranilast provided 33% protection (P<0.05) from angioplasty-induced lumen narrowing as measured by MRI in vivo. The results of the ex vivo MR analysis of total wall thickness showed a 14% protection of angioplasty-induced narrowing (P<0.05), and the mean intima-to-media ratio showed a 39% (P<0.006) protection for the tranilast-treated rats. Histological analysis of the mean intima-to-media ratio demonstrated that tranilast provided 36% (P<0. 01) protection in the intima-to-media ratio. Further, treatment with tranilast showed a 52% reduction in collagen density of the intimal layer and a 70% reduction in collagen density of the medial layer of the injured arteries. CONCLUSION The data obtained by in vivo MRI, ex vivo MRI, histology and collagen analysis demonstrate that tranilast provided significant beneficial effects in inhibiting neointimal formation in the rat carotid artery model. Also this study, to the best of our knowledge, is the first to harness complimentary information from various technologies, including lumen patency by in vivo MRI, neointimal formation by ex vivo MRI and conventional histomorphometry, and histological analysis for collagen density, to provide a comprehensive understanding of the pathology in this disease model.
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Affiliation(s)
- E H Ohlstein
- Department of Cardiovascular Pharmacology, SmithKline Beecham Pharmaceuticals, 709 Swedeland Road, P.O. Box 1539, King of Prussia, PA 19406-0939, USA.
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Chandra S, Clark LV, Coatney RW, Phan L, Sarkar SK, Ohlstein EH. Application of serial in vivo magnetic resonance imaging to evaluate the efficacy of endothelin receptor antagonist SB 217242 in the rat carotid artery model of neointima formation. Circulation 1998; 97:2252-8. [PMID: 9631875 DOI: 10.1161/01.cir.97.22.2252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Alleviating vascular restenosis after percutaneous transluminal angioplasty remains a formidable challenge. Although multiple factors have been implicated in the pathophysiology of this vascular remodeling disorder, only limited therapeutic success has been achieved. Endothelin (ET)-1 has recently been implicated in the pathogenesis of neointimal growth. We report the in vivo efficacy of SB 217242, a nonpeptide dual ET(A)/ET(B) receptor antagonist with high oral bioavailability, in the rat carotid artery balloon angioplasty model. METHODS AND RESULTS The lumen volumes of carotid arteries were estimated serially with magnetic resonance imaging (MRI) at baseline and at day 7 and day 14 after balloon catheter-induced denudation of the carotid arterial wall in the rat. Histomorphometric analysis was performed at day 14 after surgery to quantitate intimal hyperplasia. Statistical analysis was performed with ANOVA followed by post hoc Newman-Keuls multiple comparison test. In comparison to vehicle-treated animals, a 20% protection (P<0.05) from reduction was shown in the estimated lumen volume with long-term administration of SB 217242 (15 mg/kg BID p.o.). Histologic analyses indicated a 42% decrease (P<0.05) in neointimal growth. The MRI lumen volumes had a significant correlation with the corresponding histologic indices. CONCLUSIONS Serial MRI provides the opportunity to assess the progression of vascular lumen volume in vivo after balloon angioplasty. MRI measurements can, in conjunction with in vitro histologic measurements, contribute to the understanding of the actions of pharmacologic agents in experimental models of neointima formation. With the use of serial MRI and histologic measurements, it is demonstrated that protection from both lumen volume reduction and neointima formation is obtained in this model by use of a potent, nonpeptide dual ET(A)/ET(B) receptor antagonist, SB 217242. Furthermore, this study provides additional support to the implication of ET-1 in the pathophysiology of neointima formation.
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Affiliation(s)
- S Chandra
- Department of Physical and Structural Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.
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