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Nagle MF, Yuan J, Kaur D, Ma C, Peremyslova E, Jiang Y, Zahl B, Niño de Rivera A, Muchero W, Fuxin L, Strauss SH. GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa. HORTICULTURE RESEARCH 2023; 10:uhad125. [PMID: 37560019 PMCID: PMC10407606 DOI: 10.1093/hr/uhad125] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/05/2023] [Indexed: 08/11/2023]
Abstract
Adventitious rooting (AR) is critical to the propagation, breeding, and genetic engineering of trees. The capacity for plants to undergo this process is highly heritable and of a polygenic nature; however, the basis of its genetic variation is largely uncharacterized. To identify genetic regulators of AR, we performed a genome-wide association study (GWAS) using 1148 genotypes of Populus trichocarpa. GWASs are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale; to help overcome this limitation, we developed a computer vision system to measure an array of traits related to adventitious root development in poplar, including temporal measures of lateral and basal root length and area. GWAS was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical power. These analyses yielded a total of 277 unique associations, suggesting that genes that control rooting include regulators of hormone signaling, cell division and structure, reactive oxygen species signaling, and other processes with known roles in root development. Numerous genes with uncharacterized functions and/or cryptic roles were also identified. These candidates provide targets for functional analysis, including physiological and epistatic analyses, to better characterize the complex polygenic regulation of AR.
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Affiliation(s)
- Michael F Nagle
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Jialin Yuan
- Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
| | - Damanpreet Kaur
- Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
| | - Cathleen Ma
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Ekaterina Peremyslova
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Yuan Jiang
- Statistics Department, Oregon State University, 103 SW Memorial Place, Corvallis, OR, 97331, United States
| | - Bahiya Zahl
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Alexa Niño de Rivera
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, United States
- Bredesen Center for Interdisciplinary Research, University of Tennessee, 821 Volunteer Blvd., Knoxville, TN, 37996, United States
| | - Li Fuxin
- Department of Electrical Engineering and Computer Science, Oregon State University, 110 SW Park Terrace, Corvallis, OR, 97331, United States
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, 3180 SW Jefferson Way, Corvallis, OR, 97331, United States
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Fang S, Xia Q, Zhang L, Zhan P, Qing Y, Wu Z, Wang H, Shao L, Liu N, He J, Liu J. Differentiated Fractionation of Various Biomass Resources by p-Toluenesulfonic Acid at Mild Conditions. ACS OMEGA 2023; 8:24247-24255. [PMID: 37457452 PMCID: PMC10339397 DOI: 10.1021/acsomega.3c00927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Biomass is the ideal substitute for petrochemical resources because of its renewable and abundant sources. p-Toluenesulfonic acid (p-TsOH) can effectively separate lignin from biomass under mild conditions, so it is highly expected in biomass fractionation to improve the utilization efficiency. In this study, we investigated the effect of p-TsOH differentiated fractionation of poplar sawdust, eucalyptus sawdust, and rice straw below 100 °C. According to the experimental results, upon pretreatment by p-TsOH of the three kinds of raw biomass, most of the lignin and hemicellulose of poplar sawdust and eucalyptus sawdust were removed, whereas the cellulose was retained, but most of the hemicellulose and cellulose of rice straw were kept, whereas the lignin was removed at similar conditions. The structures and compositions of pretreatment residues, lignin, and hemicellulose extracted from raw biomass were characterized by XRD, FTIR, HSQC-NMR, XPS, and SEM. The differentiated fractionation mechanism of biomass was analyzed. A better recognition and understanding of the factors affecting biomatrix opening and fractionation will allow for the identification of new pretreatment strategies that improve biomass utilization and permit the rational enzymatic hydrolysis of cellulose.
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Affiliation(s)
- Shaohua Fang
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Qiuli Xia
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lin Zhang
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Peng Zhan
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yan Qing
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhiping Wu
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Hui Wang
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Lishu Shao
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Na Liu
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jiaying He
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jin Liu
- College
of Materials Science and Engineering, Central
South University of Forestry and Technology, Changsha 410004, China
- Ministry
of Forestry Bioethanol Research Center, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan
International Joint Laboratory of Woody Biomass Conversion, Central South University of Forestry and Technology, Changsha 410004, China
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Kyaw TY, Siegert CM, Dash P, Poudel KP, Pitts JJ, Renninger HJ. Using hyperspectral leaf reflectance to estimate photosynthetic capacity and nitrogen content across eastern cottonwood and hybrid poplar taxa. PLoS One 2022; 17:e0264780. [PMID: 35271605 PMCID: PMC8912144 DOI: 10.1371/journal.pone.0264780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Eastern cottonwood (Populus deltoides W. Bartram ex Marshall) and hybrid poplars are well-known bioenergy crops. With advances in tree breeding, it is increasingly necessary to find economical ways to identify high-performing Populus genotypes that can be planted under different environmental conditions. Photosynthesis and leaf nitrogen content are critical parameters for plant growth, however, measuring them is an expensive and time-consuming process. Instead, these parameters can be quickly estimated from hyperspectral leaf reflectance if robust statistical models can be developed. To this end, we measured photosynthetic capacity parameters (Rubisco-limited carboxylation rate (Vcmax), electron transport-limited carboxylation rate (Jmax), and triose phosphate utilization-limited carboxylation rate (TPU)), nitrogen per unit leaf area (Narea), and leaf reflectance of seven taxa and 62 genotypes of Populus from two study plantations in Mississippi. For statistical modeling, we used least absolute shrinkage and selection operator (LASSO) and principal component analysis (PCA). Our results showed that the predictive ability of LASSO and PCA models was comparable, except for Narea in which LASSO was superior. In terms of model interpretability, LASSO outperformed PCA because the LASSO models needed 2 to 4 spectral reflectance wavelengths to estimate parameters. The LASSO models used reflectance values at 758 and 935 nm for estimating Vcmax (R2 = 0.51 and RMSPE = 31%) and Jmax (R2 = 0.54 and RMSPE = 32%); 687, 746, and 757 nm for estimating TPU (R2 = 0.56 and RMSPE = 31%); and 304, 712, 921, and 1021 nm for estimating Narea (R2 = 0.29 and RMSPE = 21%). The PCA model also identified 935 nm as a significant wavelength for estimating Vcmax and Jmax. Therefore, our results suggest that hyperspectral leaf reflectance modeling can be used as a cost-effective means for field phenotyping and rapid screening of Populus genotypes because of its capacity to estimate these physicochemical parameters.
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Affiliation(s)
- Thu Ya Kyaw
- Department of Forestry, Forest and Wildlife Research Center, Mississippi State University, Starkville, Mississippi, United States of America
- * E-mail:
| | - Courtney M. Siegert
- Department of Forestry, Forest and Wildlife Research Center, Mississippi State University, Starkville, Mississippi, United States of America
| | - Padmanava Dash
- Department of Geosciences, Mississippi State University, Starkville, Mississippi, United States of America
| | - Krishna P. Poudel
- Department of Forestry, Forest and Wildlife Research Center, Mississippi State University, Starkville, Mississippi, United States of America
| | - Justin J. Pitts
- Department of Forestry, Forest and Wildlife Research Center, Mississippi State University, Starkville, Mississippi, United States of America
| | - Heidi J. Renninger
- Department of Forestry, Forest and Wildlife Research Center, Mississippi State University, Starkville, Mississippi, United States of America
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Differences in Environmental and Hormonal Regulation of Growth Responses in Two Highly Productive Hybrid Populus Genotypes. FORESTS 2022. [DOI: 10.3390/f13020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phenotypic plasticity, in response to adverse conditions, determines plant productivity and survival. The aim of this study was to test if two highly productive Populus genotypes, characterised by different in vitro etiolation patterns, differ also in their responses to hormones gibberellin (GA) and abscisic acid (ABA), and to a GA biosynthesis inhibitor paclobutrazol (PBZ). The experiments on shoot cultures of ‘Hybrida 275′ (abbr. H275; Populus maximowiczii × P. trichocarpa) and IBL 91/78 (Populus tremula × P. alba) were conducted by either modulating the physical in vitro environment or by adding specific chemicals to the nutrient medium. Our results revealed two main sets of differences between the studied genotypes in environmental and hormonal regulation of growth responses. First, the genotype H275 responded to darkness with PBZ-inhibitable shoot elongation; in contrast, the elongation of IBL 91/78 shoots was not affected either by darkness or PBZ treatment. Secondly, the explants of H275 were unable to recover their growth if it was inhibited with ABA; in contrast, those of IBL 91/78 recovered so well after the temporal inhibition by ABA that, when rooted subsequently, they developed longer shoots and roots than without a previous ABA treatment. Our results indicate that GA catabolism and repressive signalling provide an important pathway to control growth and physiological adaptation in response to immediate or impending adverse conditions. These observations can help breeders define robust criteria for identifying genotypes with high resistance and productivity and highlight where genotypes exhibit susceptibility to stress.
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Coppiced Biochars as Partial Replacement of Carbon Black Filler in Polybutadiene/Natural Rubber Composites. JOURNAL OF COMPOSITES SCIENCE 2020. [DOI: 10.3390/jcs4040147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although carbon black has been the dominant filler material for rubber composites for over a century, it is a finite, fossil fuel-based product that is sensitive to geopolitical issues and economics. Renewable sources of carbon need to be developed to replace carbon black in order to reduce dependence on petroleum. Biochar is the solid material left over after the anaerobic treatment of biomass at high temperature. In this work, two biochars made from coppiced hardwoods, Paulownia elongata and Populus tremuloides were used to partially replace carbon black in rubber composites using a 50/50 blend of butadiene rubber and natural rubber. Rubber composite samples using these biochars were able to replace 30% of the carbon black with virtually no loss in tensile strength, and improved elongation and toughness compared to the reference sample containing 100% carbon black.
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Techno-Economic Analysis of Producing Glacial Acetic Acid from Poplar Biomass via Bioconversion. Molecules 2020; 25:molecules25184328. [PMID: 32967253 PMCID: PMC7571159 DOI: 10.3390/molecules25184328] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022] Open
Abstract
Most of the current commercial production of glacial acetic acid (GAA) is by petrochemical routes, primarily methanol carbonylation. GAA is an intermediate in the production of plastics, textiles, dyes, and paints. GAA production from biomass might be an economically viable and sustainable alternative to petroleum-derived routes. Separation of acetic acid from water is a major expense and requires considerable energy. This study evaluates and compares the technical and economic feasibility of GAA production via bioconversion using either ethyl acetate or alamine in diisobutylkerosene (DIBK) as organic solvents for purification. Models of a GAA biorefinery with a production of 120,650 tons/year were simulated in Aspen software. This biorefinery follows the path of pretreatment, enzymatic hydrolysis, acetogen fermentation, and acid purification. Estimated capital costs for different scenarios ranged from USD 186 to 245 million. Recovery of GGA using alamine/DIBK was a more economical process and consumed 64% less energy, due to lower steam demand in the recovery distillation columns. The estimated average minimum selling prices of GGA were USD 756 and 877/ton for alamine/DIBK and ethyl acetate scenarios, respectively. This work establishes a feasible and sustainable approach to produce GGA from poplar biomass via fermentation.
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