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Zhang B, Lewis JA, Kovacs F, Sattler SE, Sarath G, Kang C. Activity of Cytosolic Ascorbate Peroxidase (APX) from Panicum virgatum against Ascorbate and Phenylpropanoids. Int J Mol Sci 2023; 24:1778. [PMID: 36675291 PMCID: PMC9864165 DOI: 10.3390/ijms24021778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
APX is a key antioxidant enzyme in higher plants, scavenging H2O2 with ascorbate in several cellular compartments. Here, we report the crystal structures of cytosolic ascorbate peroxidase from switchgrass (Panicum virgatum L., Pvi), a strategic feedstock plant with several end uses. The overall structure of PviAPX was similar to the structures of other APX family members, with a bound ascorbate molecule at the ɣ-heme edge pocket as in other APXs. Our results indicated that the H2O2-dependent oxidation of ascorbate displayed positive cooperativity. Significantly, our study suggested that PviAPX can oxidize a broad range of phenylpropanoids with δ-meso site in a rather similar efficiency, which reflects its role in the fortification of cell walls in response to insect feeding. Based on detailed structural and kinetic analyses and molecular docking, as well as that of closely related APX enzymes, the critical residues in each substrate-binding site of PviAPX are proposed. Taken together, these observations shed new light on the function and catalysis of PviAPX, and potentially benefit efforts improve plant health and biomass quality in bioenergy and forage crops.
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Affiliation(s)
- Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Frank Kovacs
- Chemistry Department, University of Nebraska-Kearney, Kearney, NE 68849, USA
| | - Scott E. Sattler
- Wheat, Sorghum and Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA
| | - Gautam Sarath
- Wheat, Sorghum and Forage Research Unit, U.S. Department of Agriculture—Agricultural Research Service, Lincoln, NE 68583, USA
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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Chapman EA, Thomsen HC, Tulloch S, Correia PMP, Luo G, Najafi J, DeHaan LR, Crews TE, Olsson L, Lundquist PO, Westerbergh A, Pedas PR, Knudsen S, Palmgren M. Perennials as Future Grain Crops: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2022; 13:898769. [PMID: 35968139 PMCID: PMC9372509 DOI: 10.3389/fpls.2022.898769] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Perennial grain crops could make a valuable addition to sustainable agriculture, potentially even as an alternative to their annual counterparts. The ability of perennials to grow year after year significantly reduces the number of agricultural inputs required, in terms of both planting and weed control, while reduced tillage improves soil health and on-farm biodiversity. Presently, perennial grain crops are not grown at large scale, mainly due to their early stages of domestication and current low yields. Narrowing the yield gap between perennial and annual grain crops will depend on characterizing differences in their life cycles, resource allocation, and reproductive strategies and understanding the trade-offs between annualism, perennialism, and yield. The genetic and biochemical pathways controlling plant growth, physiology, and senescence should be analyzed in perennial crop plants. This information could then be used to facilitate tailored genetic improvement of selected perennial grain crops to improve agronomic traits and enhance yield, while maintaining the benefits associated with perennialism.
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Affiliation(s)
| | | | - Sophia Tulloch
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Pedro M. P. Correia
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Javad Najafi
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Lennart Olsson
- Lund University Centre for Sustainability Studies, Lund, Sweden
| | - Per-Olof Lundquist
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna Westerbergh
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology in Uppsala, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pai Rosager Pedas
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Søren Knudsen
- Department of Raw Materials, Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
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Razar RM, Qi P, Devos KM, Missaoui AM. Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F 1 Populations (Lowland x Coastal and Coastal x Upland). FRONTIERS IN PLANT SCIENCE 2022; 13:739133. [PMID: 35665173 PMCID: PMC9162799 DOI: 10.3389/fpls.2022.739133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of genetic diversity in switchgrass germplasm can be exploited to capture favorable alleles that increase its range of adaptation and biomass yield. The objectives of the study were to analyze the extent of polymorphism and patterns of segregation distortion in two F1 populations and use the linkage maps to locate QTL for biomass yield. We conducted genotyping-by-sequencing on two populations derived from crosses between the allotetraploid lowland genotype AP13 (a selection from "Alamo") and coastal genotype B6 (a selection from PI 422001) with 285 progeny (AB population) and between B6 and the allotetraploid upland VS16 (a selection from "Summer") with 227 progeny (BV population). As predictable from the Euclidean distance between the parents, a higher number of raw variants was discovered in the coastal × upland BV cross (6 M) compared to the lowland × coastal AB cross (2.5 M). The final number of mapped markers was 3,107 on the BV map and 2,410 on the AB map. More segregation distortion of alleles was seen in the AB population, with 75% distorted loci compared to 11% distorted loci in the BV population. The distortion in the AB population was seen across all chromosomes in both the AP13 and B6 maps and likely resulted from zygotic or post-zygotic selection for increased levels of heterozygosity. Our results suggest lower genetic compatibility between the lowland AP13 and the coastal B6 ecotype than between B6 and the upland ecotype VS16. Four biomass QTLs were mapped in the AB population (LG 2N, 6K, 6N, and 8N) and six QTLs in the BV population [LG 1N (2), 8N (2), 9K, and 9N]. The QTL, with the largest and most consistent effect across years, explaining between 8.4 and 11.5% of the variation, was identified on 6N in the AP13 map. The cumulative effect of all the QTLs explained a sizeable portion of the phenotypic variation in both AB and BV populations and the markers associated with them may potentially be used for the marker-assisted improvement of biomass yield. Since switchgrass improvement is based on increasing favorable allele frequencies through recurrent selection, the transmission bias within individuals and loci needs to be considered as this may affect the genetic gain if the favorable alleles are distorted.
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Affiliation(s)
- Rasyidah M. Razar
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Genetic Resources and Improvement Unit, RRIM Research Station, Malaysian Rubber Board, Selangor, Malaysia
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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Effah Z, Li L, Xie J, Karikari B, Liu C, Xu A, Zeng M. Transcriptome profiling reveals major structural genes, transcription factors and biosynthetic pathways involved in leaf senescence and nitrogen remobilization in rainfed spring wheat under different nitrogen fertilization rates. Genomics 2022; 114:110271. [DOI: 10.1016/j.ygeno.2022.110271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/01/2021] [Accepted: 01/16/2022] [Indexed: 11/24/2022]
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Mehla S, Kumar U, Kapoor P, Singh Y, Sihag P, Sagwal V, Balyan P, Kumar A, Ahalawat N, Lakra N, Singh KP, Pesic V, Djalovic I, Mir RR, Dhankher OP. Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat ( Triticum aestivum L.). Front Genet 2022; 13:933560. [PMID: 36092892 PMCID: PMC9449350 DOI: 10.3389/fgene.2022.933560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/04/2022] [Indexed: 02/05/2023] Open
Abstract
Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.
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Affiliation(s)
- Sheetal Mehla
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Prexha Kapoor
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Yogita Singh
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Pooja Sihag
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Vijeta Sagwal
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P. G. College, CCS University, Meerut, India
| | - Anuj Kumar
- Shantou University Medical College, Shantou, China
- Dalhousie University, Halifax, NS, Canada
| | - Navjeet Ahalawat
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Nita Lakra
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences and Humanities, GB Pant University of Agriculture and Technology, Pantnagar, India
- Vice-Chancellor’s Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, India
| | - Vladan Pesic
- Department of Genetics and Plant Breeding, Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Ivica Djalovic
- Institute of Field and Vegetable Crops, National Institute of the Republic of Serbia, Maxim Gorki 30, Novi Sad, Serbia
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Srinagar, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA, United States
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Tejera-Nieves M, Abraha M, Chen J, Hamilton SK, Robertson GP, Walker James B. Seasonal decline in leaf photosynthesis in perennial switchgrass explained by sink limitations and water deficit. FRONTIERS IN PLANT SCIENCE 2022; 13:1023571. [PMID: 36684783 PMCID: PMC9846045 DOI: 10.3389/fpls.2022.1023571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/07/2022] [Indexed: 05/05/2023]
Abstract
Leaf photosynthesis of perennial grasses usually decreases markedly from early to late summer, even when the canopy remains green and environmental conditions are favorable for photosynthesis. Understanding the physiological basis of this photosynthetic decline reveals the potential for yield improvement. We tested the association of seasonal photosynthetic decline in switchgrass (Panicum virgatum L.) with water availability by comparing plants experiencing ambient rainfall with plants in a rainfall exclusion experiment in Michigan, USA. For switchgrass exposed to ambient rainfall, daily net CO2 assimilation ( A n e t ' ) declined from 0.9 mol CO2 m-2 day-1 in early summer to 0.43 mol CO2 m-2 day-1 in late summer (53% reduction; P<0.0001). Under rainfall exclusion shelters, soil water content was 73% lower and A n e t ' was 12% and 26% lower in July and September, respectively, compared to those of the rainfed plants. Despite these differences, the seasonal photosynthetic decline was similar in the season-long rainfall exclusion compared to the rainfed plants; A n e t ' in switchgrass under the shelters declined from 0.85 mol CO2 m-2 day-1 in early summer to 0.39 mol CO2 m-2 day-1 (54% reduction; P<0.0001) in late summer. These results suggest that while water deficit limited A n e t ' late in the season, abundant late-season rainfalls were not enough to restore A n e t ' in the rainfed plants to early-summer values suggesting water deficit was not the sole driver of the decline. Alongside change in photosynthesis, starch in the rhizomes increased 4-fold (P<0.0001) and stabilized when leaf photosynthesis reached constant low values. Additionally, water limitation under shelters had no negative effects on the timing of rhizome starch accumulation, and rhizome starch content increased ~ 6-fold. These results showed that rhizomes also affect leaf photosynthesis during the growing season. Towards the end of the growing season, when vegetative growth is completed and rhizome reserves are filled, diminishing rhizome sink activity likely explained the observed photosynthetic declines in plants under both ambient and reduced water availability.
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Affiliation(s)
- Mauricio Tejera-Nieves
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
| | - Michael Abraha
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Center for Global Change and Earth Observations, Michigan State University, East Lansing, MI, United States
| | - Jiquan Chen
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- Center for Global Change and Earth Observations, Michigan State University, East Lansing, MI, United States
- Department of Geography, Environment, and Spatial Sciences, Michigan State University, East Lansing, MI, United States
| | - Stephen K. Hamilton
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States
| | - G. Philip Robertson
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- W. K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Berkley Walker James
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- *Correspondence: Berkley Walker James,
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Xu N, Kang M, Zobrist JD, Wang K, Fei SZ. Genetic Transformation of Recalcitrant Upland Switchgrass Using Morphogenic Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:781565. [PMID: 35211127 PMCID: PMC8861204 DOI: 10.3389/fpls.2021.781565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/29/2021] [Indexed: 05/11/2023]
Abstract
Switchgrass (Panicum virgatum) is an excellent feedstock for biofuel production. While genetic transformation is routinely done in lowland switchgrass, upland cultivars remain recalcitrant to genetic transformation. Here we report the establishment of an efficient and reproducible transformation protocol for two upland cultivars, 'Summer' and 'Blackwell', by ectopic overexpression of morphogenic genes, Baby boom (Bbm) and Wuschel2 (Wus2). Two auxotrophic Agrobacterium strains, LBA4404Thy- and EHA105Thy-, each harboring the same construct containing ZmBbm, ZmWus2, and a green fluorescence protein (GFP) gene, ZsGreen1, were used to infect immature leaf segments derived from in vitro grown seedlings. The Agrobacterium strains also contain a transformation helper plasmid that carry additional copies of Agrobacterium virulence genes. GFP-expressing calli were identified and selected for regeneration. The highest transformation efficiency of 6% was obtained for the tetraploid cultivar Summer when LBA4404Thy- was used for infection, which is twice of that for the octoploid cultivar Blackwell. LBA4404Thy- consistently outperformed EHA105Thy- on transformation frequency across the two cultivars. Fifteen randomly selected putative transgenic plants of Summer and Blackwell, representing independent callus events, were confirmed as transgenic by the presence of the transgene, ZmAls, and the absence of AtuFtsZ, a chromosomal gene specific to the Agrobacterium strain LBA4404 using polymerase chain reaction. Transgene integration and expression was further confirmed by the detection of GFP in roots, and the resistance to herbicide injury to leaves of selected putative transgenic plants. The ZmBbm and ZmWus2 genes were successfully removed from 40 to 33.3% of the transgenic plants of Summer and Blackwell, respectively, via the Cre-Lox recombination system upon heat treatment of GFP-expressing embryogenic calli. Our successful transformation of recalcitrant upland switchgrass provides a method for gene function analysis and germplasm enhancement via biotechnology.
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Affiliation(s)
- Nuoya Xu
- Department of Horticulture, Iowa State University, Ames, IA, United States
- Crop Bioengineering Center, Iowa State University, Ames, IA, United States
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, United States
| | - Minjeong Kang
- Crop Bioengineering Center, Iowa State University, Ames, IA, United States
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Jacob D. Zobrist
- Crop Bioengineering Center, Iowa State University, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Interdepartmental Genetics and Genomics Major, Iowa State University, Ames, IA, United States
| | - Kan Wang
- Crop Bioengineering Center, Iowa State University, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Shui-zhang Fei
- Department of Horticulture, Iowa State University, Ames, IA, United States
- Crop Bioengineering Center, Iowa State University, Ames, IA, United States
- *Correspondence: Shui-zhang Fei,
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M Razar R, Missaoui A. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. BMC PLANT BIOLOGY 2020; 20:537. [PMID: 33256587 PMCID: PMC7708163 DOI: 10.1186/s12870-020-02714-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. RESULTS We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21-23.27% for FRH, 4.47-24.06% for NDVI, 4.35-32.77% for SE, and 4.61-29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55-0.64 H2) and NDVI (0.30-0.61 H2) implies the possibility of using the traits for indirect selection for biomass yield. CONCLUSION Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
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Affiliation(s)
- Rasyidah M Razar
- Institute of Plant Breeding Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, 30602, Athens, GA, USA
| | - Ali Missaoui
- Institute of Plant Breeding Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, 30602, Athens, GA, USA.
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Pingault L, Palmer NA, Koch KG, Heng-Moss T, Bradshaw JD, Seravalli J, Twigg P, Louis J, Sarath G. Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest. Int J Mol Sci 2020; 21:ijms21217966. [PMID: 33120946 PMCID: PMC7672581 DOI: 10.3390/ijms21217966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 02/01/2023] Open
Abstract
Yellow sugarcane aphid (YSA) (Sipha flava, Forbes) is a damaging pest on many grasses. Switchgrass (Panicum virgatum L.), a perennial C4 grass, has been selected as a bioenergy feedstock because of its perceived resilience to abiotic and biotic stresses. Aphid infestation on switchgrass has the potential to reduce the yields and biomass quantity. Here, the global defense response of switchgrass cultivars Summer and Kanlow to YSA feeding was analyzed by RNA-seq and metabolite analysis at 5, 10, and 15 days after infestation. Genes upregulated by infestation were more common in both cultivars compared to downregulated genes. In total, a higher number of differentially expressed genes (DEGs) were found in the YSA susceptible cultivar (Summer), and fewer DEGs were observed in the YSA resistant cultivar (Kanlow). Interestingly, no downregulated genes were found in common between each time point or between the two switchgrass cultivars. Gene co-expression analysis revealed upregulated genes in Kanlow were associated with functions such as flavonoid, oxidation-response to chemical, or wax composition. Downregulated genes for the cultivar Summer were found in co-expression modules with gene functions related to plant defense mechanisms or cell wall composition. Global analysis of defense networks of the two cultivars uncovered differential mechanisms associated with resistance or susceptibility of switchgrass in response to YSA infestation. Several gene co-expression modules and transcription factors correlated with these differential defense responses. Overall, the YSA-resistant Kanlow plants have an enhanced defense even under aphid uninfested conditions.
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Affiliation(s)
- Lise Pingault
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE 68583, USA;
| | - Kyle G. Koch
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Tiffany Heng-Moss
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Jeffrey D. Bradshaw
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
| | - Javier Seravalli
- Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Paul Twigg
- Biology Department, University of Nebraska-Kearney, Kearney, NE 68849, USA;
| | - Joe Louis
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Correspondence: (J.L.); (G.S.); Tel.: +1-402-472-8098 (J.L.); +1-402-472-4204 (G.S.)
| | - Gautam Sarath
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (L.P.); (K.G.K.); (T.H.-M.); (J.D.B.)
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE 68583, USA;
- Correspondence: (J.L.); (G.S.); Tel.: +1-402-472-8098 (J.L.); +1-402-472-4204 (G.S.)
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Koch KG, Palmer NA, Donze-Reiner T, Scully ED, Seravalli J, Amundsen K, Twigg P, Louis J, Bradshaw JD, Heng-Moss TM, Sarath G. Aphid-Responsive Defense Networks in Hybrid Switchgrass. FRONTIERS IN PLANT SCIENCE 2020; 11:1145. [PMID: 32849703 PMCID: PMC7412557 DOI: 10.3389/fpls.2020.01145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/14/2020] [Indexed: 05/30/2023]
Abstract
Aphid herbivory elicits plant defense-related networks that are influenced by host genetics. Plants of the upland switchgrass (Panicum virgatum) cultivar Summer can be a suitable host for greenbug aphids (Schizaphis graminum; GB), and yellow sugarcane aphids (Sipha flava, YSA), whereas the lowland cultivar Kanlow exhibited multi-species resistance that curtails aphid reproduction. However, stabilized hybrids of Summer (♀) x Kanlow (♂) (SxK) with improved agronomics can be damaged by both aphids. Here, hormone and metabolite analyses, coupled with RNA-Seq analysis of plant transcriptomes, were utilized to delineate defense networks induced by aphid feeding in SxK switchgrass and pinpoint plant transcription factors (TFs), such as WRKYs that potentially regulate these responses. Abscisic acid (ABA) levels were significantly higher in GB infested plants at 5 and 10 days after infestation (DAI). ABA levels were highest at 15DAI in YSA infested plants. Jasmonic acid levels were significantly elevated under GB infestation, while salicylic acid levels were signifi40cantly elevated only at 15 DAI in YSA infested plants. Similarly, levels of several metabolites were altered in common or specifically to each aphid. YSA infestation induced a significant enrichment of flavonoids consistent with an upregulation of many genes associated with flavonoid biosynthesis at 15DAI. Gene co-expression modules that responded singly to either aphid or in common to both aphids were differentiated and linked to specific TFs. Together, these data provide important clues into the interplay of metabolism and transcriptional remodeling accompanying defense responses to aphid herbivory in hybrid switchgrass.
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Affiliation(s)
- Kyle G. Koch
- Department of Entomology, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Teresa Donze-Reiner
- Biology Department, West Chester University of Pennsylvania, West Chester, PA, United States
| | - Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS, Manhattan, KS, United States
| | - Javier Seravalli
- Redox Biology Center, Department of Biochemistry, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Keenan Amundsen
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, United States
| | - Paul Twigg
- Biology Department, University of Nebraska at Kearney, Kearney, NE, United States
| | - Joe Louis
- Department of Entomology, University of Nebraska at Lincoln, Lincoln, NE, United States
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jeffrey D. Bradshaw
- Department of Entomology, University of Nebraska at Lincoln, Lincoln, NE, United States
| | | | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, United States
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, United States
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11
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Yuan J, Sun X, Guo T, Chao Y, Han L. Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves. PeerJ 2020; 8:e8426. [PMID: 32002335 PMCID: PMC6979412 DOI: 10.7717/peerj.8426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa.
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Affiliation(s)
- Jianbo Yuan
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Xinbo Sun
- College of Agronomy, Hebei Agricultural University, Key Laboratory of Crop Growth Regulation of Hebei Province, China
| | - Tao Guo
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Yuehui Chao
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Liebao Han
- College of Grassland Science, Beijing Forestry University, Beijing, China
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12
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Palmer NA, Chowda-Reddy RV, Muhle AA, Tatineni S, Yuen G, Edmé SJ, Mitchell RB, Sarath G. Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. PLoS One 2019; 14:e0222080. [PMID: 31513611 PMCID: PMC6742388 DOI: 10.1371/journal.pone.0222080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023] Open
Abstract
The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar 'Kanlow' and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown 'Kanlow', and 'Summer' plants. Three biological replicates of the 4th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.
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Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - R. V. Chowda-Reddy
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Anthony A. Muhle
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United states of America
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, Nebraska, United states of America
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13
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Ayyappan V, Sripathi VR, Kalavacharla V(K, Saha MC, Thimmapuram J, Bhide KP, Fiedler E. Genome-wide identification of histone methylation (H3K9 me2) and acetylation (H4K12 ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). BMC Genomics 2019; 20:667. [PMID: 31438854 PMCID: PMC6704705 DOI: 10.1186/s12864-019-6038-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/16/2019] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. RESULTS This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. CONCLUSIONS The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid-monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
| | - Venkateswara R. Sripathi
- Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL USA
| | - Venu ( Kal) Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE USA
| | | | | | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN USA
| | - Elizabeth Fiedler
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE USA
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Chowda-Reddy RV, Palmer N, Edme S, Sarath G, Kovacs F, Yuen G, Mitchell R, Tatineni S. A Two-Amino Acid Difference in the Coat Protein of Satellite panicum mosaic virus Isolates Is Responsible for Differential Synergistic Interactions with Panicum mosaic virus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:479-490. [PMID: 30379112 DOI: 10.1094/mpmi-09-18-0247-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Panicum mosaic virus (PMV) (genus Panicovirus, family Tombusviridae) and its molecular parasite, Satellite panicum mosaic virus (SPMV), synergistically interact in coinfected proso and pearl millet (Panicum miliaceum L.) plants resulting in a severe symptom phenotype. In this study, we examined synergistic interactions between the isolates of PMV and SPMV by using PMV-NE, PMV85, SPMV-KS, and SPMV-Type as interacting partner viruses in different combinations. Coinfection of proso millet plants by PMV-NE and SPMV-KS elicited severe mosaic, chlorosis, stunting, and eventual plant death compared with moderate mosaic, chlorotic streaks, and stunting by PMV85 and SPMV-Type. In reciprocal combinations, coinfection of proso millet by either isolate of PMV with SPMV-KS but not with SPMV-Type elicited severe disease synergism, suggesting that SPMV-KS was the main contributor for efficient synergistic interaction with PMV isolates. Coinfection of proso millet plants by either isolate of PMV and SPMV-KS or SPMV-Type caused increased accumulation of coat protein (CP) and genomic RNA copies of PMV, compared with infections by individual PMV isolates. Additionally, CP and genomic RNA copies of SPMV-KS accumulated at substantially higher levels, compared with SMPV-Type in coinfected proso millet plants with either isolate of PMV. Hybrid viruses between SPMV-KS and SPMV-Type revealed that SPMV isolates harboring a CP fragment with four differing amino acids at positions 18, 35, 59, and 98 were responsible for differential synergistic interactions with PMV in proso millet plants. Mutation of amino acid residues at these positions in different combinations in SPMV-KS, similar to those as in SPMV-Type or vice-versa, revealed that A35 and R98 in SPMV-KS CP play critical roles in enhanced synergistic interactions with PMV isolates. Taken together, these data suggest that the two distinct amino acids at positions 35 and 98 in the CP of SPMV-KS and SPMV-Type are involved in the differential synergistic interactions with the helper viruses.
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Affiliation(s)
- R V Chowda-Reddy
- 1 United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Nathan Palmer
- 1 United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Serge Edme
- 2 USDA-ARS and Department of Agronomy and Horticulture, University of Nebraska-Lincoln
| | - Gautam Sarath
- 2 USDA-ARS and Department of Agronomy and Horticulture, University of Nebraska-Lincoln
| | - Frank Kovacs
- 3 Department of Chemistry, University of Nebraska-Kearney, Kearney, NE 68849, U.S.A.; and
| | - Gary Yuen
- 4 Department of Plant Pathology, University of Nebraska-Lincoln
| | - Robert Mitchell
- 2 USDA-ARS and Department of Agronomy and Horticulture, University of Nebraska-Lincoln
| | - Satyanarayana Tatineni
- 1 United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
- 4 Department of Plant Pathology, University of Nebraska-Lincoln
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15
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Ramstein GP, Evans J, Nandety A, Saha MC, Brummer EC, Kaeppler SM, Buell CR, Casler MD. Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass ( Panicum virgatum L.) Identified by Genome-Wide Association Analyses. THE PLANT GENOME 2018; 11:180002. [PMID: 30512032 DOI: 10.3835/plantgenome2018.01.0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies.
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16
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Wang Y, Guo S, Wang L, Wang L, He X, Shu S, Sun J, Lu N. Identification of microRNAs associated with the exogenous spermidine-mediated improvement of high-temperature tolerance in cucumber seedlings (Cucumis sativus L.). BMC Genomics 2018; 19:285. [PMID: 29690862 PMCID: PMC5937831 DOI: 10.1186/s12864-018-4678-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-temperature stress inhibited the growth of cucumber seedlings. Foliar spraying of 1.0 mmol·L- 1 exogenous spermidine (Spd) to the sensitive cucumber cultivar 'Jinchun No. 2' grown at high-temperature (42 °C/32 °C) in an artificial climate box improved the high-temperature tolerance. Although there have been many reports on the response of microRNAs (miRNAs) to high-temperature stress, the mechanism by which exogenous Spd may mitigate the damage of high-temperature stress through miRNA-mediated regulation has not been studied. RESULTS To elucidate the regulation of miRNAs in response to exogenous Spd-mediated improvement of high-temperature tolerance, four small RNA libraries were constructed from cucumber leaves and sequenced: untreated-control (CW), Spd-treated (CS), high-temperature stress (HW), and Spd-treated and high-temperature stress (HS). As a result, 107 known miRNAs and 79 novel miRNAs were identified. Eight common differentially expressed miRNAs (miR156d-3p, miR170-5p, miR2275-5p, miR394a, miR479b, miR5077, miR5222 and miR6475) were observed in CS/CW, HW/CW, HS/CW and HS/HW comparison pairs, which were the first set of miRNAs that responded to not only high-temperature stress but also exogenous Spd in cucumber seedlings. Five of the eight miRNAs were predicted to target 107 potential genes. Gene function and pathway analyses highlighted the integral role that these miRNAs and target genes probably play in the improvement of the high-temperature tolerance of cucumber seedlings through exogenous Spd application. CONCLUSIONS Our study identified the first set of miRNAs associated with the exogenous Spd-mediated improvement of high-temperature tolerance in cucumber seedlings. The results could help to promote further studies on the complex molecular mechanisms underlying high-temperature tolerance in cucumber and provide a theoretical basis for the high-quality and efficient cultivation of cucumber with high-temperature resistance.
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Affiliation(s)
- Ying Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Shirong Guo
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Lei Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Liwei Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Xueying He
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Sheng Shu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China
| | - Jin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, Jiangsu, China.
| | - Na Lu
- Center for Environment, Health and Field Sciences, Chiba University, Kashiwa-no-ha 6-2-1, Kashiwa, Chiba, Japan
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17
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Niu J, Bi Q, Deng S, Chen H, Yu H, Wang L, Lin S. Identification of AUXIN RESPONSE FACTOR gene family from Prunus sibirica and its expression analysis during mesocarp and kernel development. BMC PLANT BIOLOGY 2018; 18:21. [PMID: 29368590 PMCID: PMC5784662 DOI: 10.1186/s12870-017-1220-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/20/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Auxin response factors (ARFs) in auxin signaling pathway are an important component that can regulate the transcription of auxin-responsive genes involved in almost all aspects of plant growth and development. To our knowledge, the comprehensive and systematic characterization of ARF genes has never been reported in Prunus sibirica, a novel woody biodiesel feedstock in China. RESULTS In this study, we identified 14 PsARF genes with a perfect open reading frame (ORF) in P. sibirica by using its previous transcriptomic data. Conserved motif analysis showed that all identified PsARF proteins had typical DNA-binding and ARF domain, but 5 members (PsARF3, 8 10, 16 and 17) lacked the dimerization domain. Phylogenetic analysis of the ARF proteins generated from various plant species indicated that ARFs could be categorized into 4 major groups (Class I, II, III and IV), in which all identified ARFs from P. sibirica showed a closest relationship with those from P. mume. Comparison of the expression profiles of 14 PsARF genes in different developmental stages of Siberian apricot mesocarp (SAM) and kernel (SAK) reflected distinct temporal or spatial expression patterns for PsARF genes. Additionally, based on the expressed data from fruit and seed development of multiple plant species, we identified 1514 ARF-correlated genes using weighted gene co-expression network analysis (WGCNA). And the major portion of ARF-correlated gene was characterized to be involved in protein, nucleic acid and carbohydrate metabolic, transport and regulatory processes. CONCLUSIONS In summary, we systematically and comprehensively analyzed the structure, expression pattern and co-expression network of ARF gene family in P. sibirica. All our findings provide theoretical foundation for the PsARF gene family and will pave the way for elucidating the precise role of PsARF genes in SAM and SAK development.
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Affiliation(s)
- Jun Niu
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228 China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Shuya Deng
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228 China
| | - Huiping Chen
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228 China
| | - Haiyan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Shanzhi Lin
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
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18
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Palmer NA, Saathoff AJ, Scully ED, Tobias CM, Twigg P, Madhavan S, Schmer M, Cahoon R, Sattler SE, Edmé SJ, Mitchell RB, Sarath G. Seasonal below-ground metabolism in switchgrass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1059-1075. [PMID: 29030891 DOI: 10.1111/tpj.13742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 05/25/2023]
Abstract
Switchgrass (Panicum virgatum), a perennial, polyploid, C4 warm-season grass is among the foremost herbaceous species being advanced as a source of biomass for biofuel end uses. At the end of every growing season, the aerial tissues senesce, and the below-ground rhizomes become dormant. Future growth is dependent on the successful over-wintering of the rhizomes. Although the importance of rhizome health to overall year-upon-year plant productivity has been long recognized, there is limited information on seasonal changes occurring during dormancy at both the transcriptome and metabolite levels. Here, global changes in transcriptomes and metabolites were investigated over two growing seasons in rhizomes harvested from field-grown plants. The objectives were: (a) synthesize information on cellular processes that lead to dormancy; and (b) provide models that could account for major metabolic pathways present in dormant switchgrass rhizomes. Overall, metabolism during dormancy appeared to involve discrete but interrelated events. One was a response to abscisic acid that resulted in dehydration, increases in osmolytes and upregulation of autophagic processes, likely through the target of rapamycin complex and sucrose non-fermentative-related kinase-based signaling cascades. Another was a recalibration of energy transduction through apparent reductions in mitochondrial oxidative phosphorylation, increases in substrate level generation of ATP and reducing equivalents, and recycling of N and possibly CO2 through refixation. Lastly, transcript abundances indicated that cold-related signaling was also occurring. Altogether, these data provide a detailed overview of rhizome metabolism, especially during dormancy, which can be exploited in the future to improve winter survival in switchgrass.
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Affiliation(s)
- Nathan A Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Aaron J Saathoff
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA-Agricultural Research Service Center for Grain and Animal Health, Manhattan, KS, 66502, USA
| | - Christian M Tobias
- Crop Improvement and Genetics Research, USDA-ARS, Albany, CA, 94710, USA
| | - Paul Twigg
- Biology Department, University of Nebraska at Kearney, Kearney, NE, 68849, USA
| | | | - Marty Schmer
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Rebecca Cahoon
- Department of Biochemistry, University of Nebraska at Lincoln, Lincoln, NE, 68588, USA
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Serge J Edmé
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Robert B Mitchell
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, Lincoln, NE, 68583, USA
- Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA
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Wu L, Li M, Tian L, Wang S, Wu L, Ku L, Zhang J, Song X, Liu H, Chen Y. Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention. PLoS One 2017; 12:e0185838. [PMID: 28973044 PMCID: PMC5626513 DOI: 10.1371/journal.pone.0185838] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/20/2017] [Indexed: 12/26/2022] Open
Abstract
In maize (Zea mays), leaf senescence acts as a nutrient recycling process involved in proteins, lipids, and nucleic acids degradation and transport to the developing sink. However, the molecular mechanisms of pre-maturation associated with pollination-prevention remain unclear in maize. To explore global gene expression changes during the onset and progression of senescence in maize, the inbred line 08LF, with severe early senescence caused by pollination prevention, was selected. Phenotypic observation showed that the onset of leaf senescence of 08LF plants occurred approximately 14 days after silking (DAS) by pollination prevention. Transcriptional profiling analysis of the leaf at six developmental stages during induced senescence revealed that a total of 5,432 differentially expressed genes (DEGs) were identified, including 2314 up-regulated genes and 1925 down-regulated genes. Functional annotation showed that the up-regulated genes were mainly enriched in multi-organism process and nitrogen compound transport, whereas down-regulated genes were involved in photosynthesis. Expression patterns and pathway enrichment analyses of early-senescence related genes indicated that these DEGs are involved in complex regulatory networks, especially in the jasmonic acid pathway. In addition, transcription factors from several families were detected, particularly the CO-like, NAC, ERF, GRAS, WRKY and ZF-HD families, suggesting that these transcription factors might play important roles in driving leaf senescence in maize as a result of pollination-prevention.
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Affiliation(s)
- Liancheng Wu
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Mingna Li
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Lei Tian
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Shunxi Wang
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Liuji Wu
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Lixia Ku
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Jun Zhang
- 3Cereal Institute, Henan Academy of Agricultural Sciences/Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xiaoheng Song
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
| | - Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Yanhui Chen
- College of Agronomy, Synergetic Innovation Centre of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China
- * E-mail:
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Havé M, Marmagne A, Chardon F, Masclaux-Daubresse C. Nitrogen remobilization during leaf senescence: lessons from Arabidopsis to crops. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2513-2529. [PMID: 27707774 DOI: 10.1093/jxb/erw365] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
As a result of climate changes, land use and agriculture have to adapt to new demands. Agriculture is responsible for a large part of the greenhouse gas (GHG) emissions that have to be urgently reduced in order to protect the environment. At the same time, agriculture has to cope with the challenges of sustainably feeding a growing world population. Reducing the use of the ammonia-nitrate fertilizers that are responsible for a large part of the GHGs released and that have a negative impact on carbon balance is one of the objectives of precision agriculture. One way to reduce N fertilizers without dramatically affecting grain yields is to improve the nitrogen recycling and remobilization performances of plants. Mechanisms involved in nitrogen recycling, such as autophagy, are essential for nutrient remobilization at the whole-plant level and for seed quality. Studies on leaf senescence and nutrient recycling provide new perspectives for improvement. The aim of this review is to give an overview of the mechanisms involved in nitrogen recycling and remobilization during leaf senescence and to present the different approaches undertaken to improve nitrogen remobilization efficiency using both model plants and crop species.
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Affiliation(s)
- Marien Havé
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Anne Marmagne
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Fabien Chardon
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
| | - Céline Masclaux-Daubresse
- INRA-AgroParisTech, Institut Jean-Pierre Bourgin, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, Versailles, France
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21
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Metabolite Profiling for Leaf Senescence in Barley Reveals Decreases in Amino Acids and Glycolysis Intermediates. AGRONOMY-BASEL 2017. [DOI: 10.3390/agronomy7010015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Donze-Reiner T, Palmer NA, Scully ED, Prochaska TJ, Koch KG, Heng-Moss T, Bradshaw JD, Twigg P, Amundsen K, Sattler SE, Sarath G. Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs. BMC PLANT BIOLOGY 2017; 17:46. [PMID: 28209137 PMCID: PMC5314684 DOI: 10.1186/s12870-017-0998-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/08/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND Aphid infestation of switchgrass (Panicum virgatum) has the potential to reduce yields and biomass quality. Although switchgrass-greenbug (Schizaphis graminum; GB) interactions have been studied at the whole plant level, little information is available on plant defense responses at the molecular level. RESULTS The global transcriptomic response of switchgrass cv Summer to GB was monitored by RNA-Seq in infested and control (uninfested) plants harvested at 5, 10, and 15 days after infestation (DAI). Differentially expressed genes (DEGs) in infested plants were analyzed relative to control uninfested plants at each time point. DEGs in GB-infested plants induced by 5-DAI included an upregulation of reactive burst oxidases and several cell wall receptors. Expression changes in genes linked to redox metabolism, cell wall structure, and hormone biosynthesis were also observed by 5-DAI. At 10-DAI, network analysis indicated a massive upregulation of defense-associated genes, including NAC, WRKY, and MYB classes of transcription factors and potential ancillary signaling molecules such as leucine aminopeptidases. Molecular evidence for loss of chloroplastic functions was also detected at this time point. Supporting these molecular changes, chlorophyll content was significantly decreased, and ROS levels were elevated in infested plants 10-DAI. Total peroxidase and laccase activities were elevated in infested plants at 10-DAI relative to control uninfested plants. The net result appeared to be a broad scale defensive response that led to an apparent reduction in C and N assimilation and a potential redirection of nutrients away from GB and towards the production of defensive compounds, such as pipecolic acid, chlorogenic acid, and trehalose by 10-DAI. By 15-DAI, evidence of recovery in primary metabolism was noted based on transcript abundances for genes associated with carbon, nitrogen, and nutrient assimilation. CONCLUSIONS Extensive remodeling of the plant transcriptome and the production of ROS and several defensive metabolites in an upland switchgrass cultivar were observed in response to GB feeding. The early loss and apparent recovery in primary metabolism by 15-DAI would suggest that these transcriptional changes in later stages of GB infestation could underlie the recovery response categorized for this switchgrass cultivar. These results can be exploited to develop switchgrass lines with more durable resistance to GB and potentially other aphids.
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Affiliation(s)
- Teresa Donze-Reiner
- Department of Biology, West Chester University of Pennsylvania, West Chester, PA 19383 USA
| | - Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, 251 Filley Hall, East Campus, UNL, Lincoln, NE 68583-0937 USA
| | - Erin D. Scully
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, 251 Filley Hall, East Campus, UNL, Lincoln, NE 68583-0937 USA
- Stored Product Insect and Engineering Research Unit, USDA-ARS, Manhattan, KS 66502 USA
| | - Travis J. Prochaska
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583-0816 USA
- Present address: North Central Research Extension Center, North Dakota State University, South Minot, ND 58701 USA
| | - Kyle G. Koch
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583-0816 USA
| | - Tiffany Heng-Moss
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583-0816 USA
| | - Jeffrey D. Bradshaw
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583-0816 USA
| | - Paul Twigg
- Biology Department, University of Nebraska-Kearney, Kearney, NE 68849 USA
| | - Keenan Amundsen
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583-0915 USA
| | - Scott E. Sattler
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, 251 Filley Hall, East Campus, UNL, Lincoln, NE 68583-0937 USA
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, USDA-ARS, 251 Filley Hall, East Campus, UNL, Lincoln, NE 68583-0937 USA
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Ayyappan V, Saha MC, Thimmapuram J, Sripathi VR, Bhide KP, Fiedler E, Hayford RK, Kalavacharla VK. Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass. PLANT CELL REPORTS 2017; 36:129-150. [PMID: 27812750 PMCID: PMC5206262 DOI: 10.1007/s00299-016-2065-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/18/2016] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE Transcriptomes of two switchgrass genotypes representing the upland and lowland ecotypes will be key tools in switchgrass genome annotation and biotic and abiotic stress functional genomics. Switchgrass (Panicum virgatum L.) is an important bioenergy feedstock for cellulosic ethanol production. We report genome-wide transcriptome profiling of two contrasting tetraploid switchgrass genotypes, VS16 and AP13, representing the upland and lowland ecotypes, respectively. A total of 268 million Illumina short reads (50 nt) were generated, of which, 133 million were obtained in AP13 and the rest 135 million in VS16. More than 90% of these reads were mapped to the switchgrass reference genome (V1.1). We identified 6619 and 5369 differentially expressed genes in VS16 and AP13, respectively. Gene ontology and KEGG pathway analysis identified key genes that regulate important pathways including C4 photosynthesis, photorespiration and phenylpropanoid metabolism. A series of genes (33) involved in photosynthetic pathway were up-regulated in AP13 but only two genes showed higher expression in VS16. We identified three dicarboxylate transporter homologs that were highly expressed in AP13. Additionally, genes that mediate drought, heat, and salinity tolerance were also identified. Vesicular transport proteins, syntaxin and signal recognition particles were seen to be up-regulated in VS16. Analyses of selected genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, membrane transporters, heat, drought and salinity stress responses confirmed significant variation in the relative expression reflected in RNA-Seq data between VS16 and AP13 genotypes. The phenylpropanoid pathway genes identified here are potential targets for biofuel conversion.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA
| | - Malay C Saha
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK, USA
| | | | - Venkateswara R Sripathi
- Plant Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN, USA
| | - Elizabeth Fiedler
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA
| | - Rita K Hayford
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA
| | - Venu Kal Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA.
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE, USA.
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Serba DD, Uppalapati SR, Krom N, Mukherjee S, Tang Y, Mysore KS, Saha MC. Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. BMC Genomics 2016; 17:1040. [PMID: 27986076 PMCID: PMC5162099 DOI: 10.1186/s12864-016-3377-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/05/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. RESULTS Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1.1) revealed that the lowland and upland ecotypes differ substantially in sets of genes transcribed as well as levels of expression. Differential gene expression analysis exhibited that transcripts related to photosynthesis efficiency and development and photosystem reaction center subunits were upregulated in lowlands compared to upland genotype. On the other hand, catalase isozymes, helix-loop-helix, late embryogenesis abundant group I, photosulfokinases, and S-adenosyl methionine synthase gene transcripts were upregulated in the upland compared to the lowlands. At ≥100x coverage and ≥5% minor allele frequency, a total of 25,894 and 16,979 single nucleotide polymorphism (SNP) markers were discovered for VS16 (upland ecotype) and K5 (lowland ecotype) against the reference genome. The allele combination of the SNPs revealed that the transition mutations are more prevalent than the transversion mutations. CONCLUSIONS The gene ontology (GO) analysis of the transcriptome indicated lowland ecotype had significantly higher representation for cellular components associated with photosynthesis machinery controlling carbon fixation. In addition, using the transcriptome data, SNP markers were detected, which were distributed throughout the genome. The differentially expressed genes and SNP markers detected in this study would be useful resources for traits mapping and gene transfer across ecotypes in switchgrass breeding for increased biomass yield for biofuel conversion.
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Affiliation(s)
- Desalegn D. Serba
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
- Present Address: Agricultural Research Center-Hays, Kansas State University, 1232 240th Avenue, Hays, KS 67601 USA
| | - Srinivasa Rao Uppalapati
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- Present Address: DuPont Crop Protection, Stine-Haskell Research Center, Newark, DE 19711 USA
| | - Nick Krom
- Computing Services, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Shreyartha Mukherjee
- Computing Services, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
- Present Address: Syngenta, Stanton, MN 55018 USA
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Kirankumar S. Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401 USA
| | - Malay C. Saha
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401 USA
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Frazier TP, Palmer NA, Xie F, Tobias CM, Donze-Reiner TJ, Bombarely A, Childs KL, Shu S, Jenkins JW, Schmutz J, Zhang B, Sarath G, Zhao B. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. BMC Genomics 2016; 17:892. [PMID: 27821048 PMCID: PMC5100175 DOI: 10.1186/s12864-016-3201-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. RESULTS In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated. CONCLUSIONS Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.
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Affiliation(s)
| | - Nathan A. Palmer
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583-0937 USA
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | | | - Teresa J. Donze-Reiner
- Department of Biology, West Chester University of Pennsylvania, Wester Chester, PA 19382 USA
| | | | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94595 USA
| | - Jerry W. Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94595 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583-0937 USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
- 407 Latham Hall, 220 Ag Quad Lane, Blacksburg, VA 24061 USA
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26
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Wu XY, Hu WJ, Luo H, Xia Y, Zhao Y, Wang LD, Zhang LM, Luo JC, Jing HC. Transcriptome profiling of developmental leaf senescence in sorghum (Sorghum bicolor). PLANT MOLECULAR BIOLOGY 2016; 92:555-580. [PMID: 27586543 DOI: 10.1007/s11103-016-0532-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/19/2016] [Indexed: 05/04/2023]
Abstract
This piece of the submission is being sent via mail. Leaf senescence is essential for the nutrient economy of crops and is executed by so-called senescence-associated genes (SAGs). Here we explored the monocot C4 model crop Sorghum bicolor for a holistic picture of SAG profiles by RNA-seq. Leaf samples were collected at four stages during developmental senescence, and in total, 3396 SAGs were identified, predominantly enriched in GO categories of metabolic processes and catalytic activities. These genes were enriched in 13 KEGG pathways, wherein flavonoid and phenylpropanoid biosynthesis and phenylalanine metabolism were overrepresented. Seven regions on Chromosomes 1, 4, 5 and 7 contained SAG 'hotspots' of duplicated genes or members of cupin superfamily involved in manganese ion binding and nutrient reservoir activity. Forty-eight expression clusters were identified, and the candidate orthologues of the known important senescence transcription factors such as ORE1, EIN3 and WRKY53 showed "SAG" expression patterns, implicating their possible roles in regulating sorghum leaf senescence. Comparison of developmental senescence with salt- and dark- induced senescence allowed for the identification of 507 common SAGs, 1996 developmental specific SAGs as well as 176 potential markers for monitoring senescence in sorghum. Taken together, these data provide valuable resources for comparative genomics analyses of leaf senescence and potential targets for the manipulation of genetic improvement of Sorghum bicolor.
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Affiliation(s)
- Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Wei-Juan Hu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Yan Xia
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Yi Zhao
- College of Life Sciences and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, People's Republic of China
| | - Li-Dong Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
| | - Jing-Chu Luo
- College of Life Sciences and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, People's Republic of China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
- Inner Mongolia Research Centre for Practaculture, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
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Yang J, Worley E, Ma Q, Li J, Torres‐Jerez I, Li G, Zhao PX, Xu Y, Tang Y, Udvardi M. Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum. THE NEW PHYTOLOGIST 2016; 211:75-89. [PMID: 26935010 PMCID: PMC6680227 DOI: 10.1111/nph.13898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/14/2016] [Indexed: 05/19/2023]
Abstract
Improving nitrogen (N) remobilization from aboveground to underground organs during yearly shoot senescence is an important goal for sustainable production of switchgrass (Panicum virgatum) as a biofuel crop. Little is known about the genetic control of senescence and N use efficiency in perennial grasses such as switchgrass, which limits our ability to improve the process. Switchgrass aboveground organs (leaves, stems and inflorescences) and underground organs (crowns and roots) were harvested every month over a 3-yr period. Transcriptome analysis was performed to identify genes differentially expressed in various organs during development. Total N content in aboveground organs increased from spring until the end of summer, then decreased concomitant with senescence, while N content in underground organs exhibited an increase roughly matching the decrease in shoot N during fall. Hundreds of senescence-associated genes were identified in leaves and stems. Functional grouping indicated that regulation of transcription and protein degradation play important roles in shoot senescence. Coexpression networks predict important roles for five switchgrass NAC (NAM, ATAF1,2, CUC2) transcription factors (TFs) and other TF family members in orchestrating metabolism of carbohydrates, N and lipids, protein modification/degradation, and transport processes during senescence. This study establishes a molecular basis for understanding and enhancing N remobilization and conservation in switchgrass.
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Affiliation(s)
- Jiading Yang
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
- BioEnergy Sciences Center (BESC)Oak Ridge National LaboratoryOak RidgeTN37831USA
| | - Eric Worley
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
- BioEnergy Sciences Center (BESC)Oak Ridge National LaboratoryOak RidgeTN37831USA
| | - Qin Ma
- Department of Plant ScienceSouth Dakota State UniversityBrookingsSD57007USA
| | - Jun Li
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
| | - Ivone Torres‐Jerez
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
| | - Gaoyang Li
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGA30602USA
| | - Patrick X. Zhao
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
| | - Ying Xu
- BioEnergy Sciences Center (BESC)Oak Ridge National LaboratoryOak RidgeTN37831USA
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGA30602USA
| | - Yuhong Tang
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
- BioEnergy Sciences Center (BESC)Oak Ridge National LaboratoryOak RidgeTN37831USA
| | - Michael Udvardi
- Plant Biology Divisionthe Samuel Roberts Noble FoundationArdmoreOK73401USA
- BioEnergy Sciences Center (BESC)Oak Ridge National LaboratoryOak RidgeTN37831USA
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28
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Paudel B, Das A, Tran M, Boe A, Palmer NA, Sarath G, Gonzalez-Hernandez JL, Rushton PJ, Rohila JS. Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. FRONTIERS IN PLANT SCIENCE 2016; 7:293. [PMID: 27014316 PMCID: PMC4789367 DOI: 10.3389/fpls.2016.00293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/24/2016] [Indexed: 05/03/2023]
Abstract
Senescence in biofuel grasses is a critical issue because early senescence decreases potential biomass production by limiting aerial growth and development. 2-Dimensional, differential in-gel electrophoresis (2D-DIGE) followed by mass spectrometry of selected protein spots was used to evaluate differences between leaf proteomes of early (ES)- and late- senescing (LS) genotypes of Prairie cordgrass (ES/LS PCG) and switchgrass (ES/LS SG), just before and after senescence was initiated. Analysis of the manually filtered and statistically evaluated data indicated that 69 proteins were significantly differentially abundant across all comparisons, and a majority (41%) were associated with photosynthetic processes as determined by gene ontology analysis. Ten proteins were found in common between PCG and SG, and nine and 18 proteins were unique to PCG and SG respectively. Five of the 10 differentially abundant spots common to both species were increased in abundance, and five were decreased in abundance. Leaf proteomes of the LS genotypes of both grasses analyzed before senescence contained significantly higher abundances of a 14-3-3 like protein and a glutathione-S-transferase protein when compared to the ES genotypes, suggesting differential cellular metabolism in the LS vs. the ES genotypes. The higher abundance of 14-3-3 like proteins may be one factor that impacts the senescence process in both LS PCG and LS SG. Aconitase dehydratase was found in greater abundance in all four genotypes after the onset of senescence, consistent with literature reports from genetic and transcriptomic studies. A Rab protein of the Ras family of G proteins and an s-adenosylmethionine synthase were more abundant in ES PCG when compared with the LS PCG. In contrast, several proteins associated with photosynthesis and carbon assimilation were detected in greater abundance in LS PCG when compared to ES PCG, suggesting that a loss of these proteins potentially contributed to the ES phenotype in PCG. Overall, this study provides important data that can be utilized toward delaying senescence in both PCG and SG, and sets a foundational base for future improvement of perennial grass germplasm for greater aerial biomass productivity.
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Affiliation(s)
- Bimal Paudel
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
| | - Aayudh Das
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
| | - Michaellong Tran
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
| | - Arvid Boe
- Department of Plant Science, South Dakota State UniversityBrookings, SD, USA
| | - Nathan A. Palmer
- Grain, Forage and Bioenergy Research Unit, United States Department of Agriculture - Agricultural Research ServiceLincoln, NE, USA
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, United States Department of Agriculture - Agricultural Research ServiceLincoln, NE, USA
| | | | | | - Jai S. Rohila
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, SD, USA
- Department of Plant Science, South Dakota State UniversityBrookings, SD, USA
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Rao X, Lu N, Li G, Nakashima J, Tang Y, Dixon RA. Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1649-62. [PMID: 26896851 PMCID: PMC4783356 DOI: 10.1093/jxb/erv553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Almost all C4 plants require the co-ordination of the adjacent and fully differentiated cell types, mesophyll (M) and bundle sheath (BS). The C4 photosynthetic pathway operates through two distinct subtypes based on how malate is decarboxylated in BS cells; through NAD-malic enzyme (NAD-ME) or NADP-malic enzyme (NADP-ME). The diverse or unique cell-specific molecular features of M and BS cells from separate C4 subtypes of independent lineages remain to be determined. We here provide an M/BS cell type-specific transcriptome data set from the monocot NAD-ME subtype switchgrass (Panicum virgatum). A comparative transcriptomics approach was then applied to compare the M/BS mRNA profiles of switchgrass, monocot NADP-ME subtype C4 plants maize and Setaria viridis, and dicot NAD-ME subtype Cleome gynandra. We evaluated the convergence in the transcript abundance of core components in C4 photosynthesis and transcription factors to establish Kranz anatomy, as well as gene distribution of biological functions, in these four independent C4 lineages. We also estimated the divergence between NAD-ME and NADP-ME subtypes of C4 photosynthesis in the two cell types within C4 species, including differences in genes encoding decarboxylating enzymes, aminotransferases, and metabolite transporters, and differences in the cell-specific functional enrichment of RNA regulation and protein biogenesis/homeostasis. We suggest that C4 plants of independent lineages in both monocots and dicots underwent convergent evolution to establish C4 photosynthesis, while distinct C4 subtypes also underwent divergent processes for the optimization of M and BS cell co-ordination. The comprehensive data sets in our study provide a basis for further research on evolution of C4 species.
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Affiliation(s)
- Xiaolan Rao
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA BioEnergy Science Center (BESC), US Department of Energy, Oak Ridge, TN 37831, USA
| | - Nan Lu
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Guifen Li
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Jin Nakashima
- Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Yuhong Tang
- BioEnergy Science Center (BESC), US Department of Energy, Oak Ridge, TN 37831, USA Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Richard A Dixon
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA BioEnergy Science Center (BESC), US Department of Energy, Oak Ridge, TN 37831, USA
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Yamaoka C, Suzuki Y, Makino A. Differential Expression of Genes of the Calvin-Benson Cycle and its Related Genes During Leaf Development in Rice. PLANT & CELL PHYSIOLOGY 2016; 57:115-124. [PMID: 26615032 DOI: 10.1093/pcp/pcv183] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/01/2015] [Indexed: 06/05/2023]
Abstract
To understand how the machinery for photosynthetic carbon assimilation is formed and maintained during leaf development, changes in the mRNA levels of the Calvin-Benson cycle enzymes, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase and two key enzymes for sucrose synthesis were determined in rice (Oryza sativa L.). According to the patterns of changes in the mRNA levels, these genes were categorized into three groups. Group 1 included most of the genes involved in the carboxylation and reduction phases of the Calvin-Benson cycle, as well as three genes in the regeneration phase. The mRNA levels increased and reached maxima during leaf expansion and then rapidly declined, although there were some variations in the residual mRNA levels in senescent leaves. Group 2 included a number of genes involved in the regeneration phase, one gene in the reduction phase of the Calvin-Benson cycle and one gene in sucrose synthesis. The mRNA levels increased and almost reached maxima before full expansion and then gradually declined. Group 3 included Rubisco activase, one gene involved in the regeneration phase and one gene in sucrose synthesis. The overall pattern was similar to that in group 2 genes except that the mRNA levels reached maxima after the stage of full expansion. Thus, genes of the Calvin-Benson cycle and its related genes were differentially expressed during leaf development in rice, suggesting that such differential gene expression is necessary for formation and maintenance of the machinery of photosynthetic carbon assimilation.
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Affiliation(s)
- Chihiro Yamaoka
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Yuji Suzuki
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan
| | - Amane Makino
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai, 981-8555 Japan CREST, JST, Gobancho, Chiyoda-ku, Tokyo, 102-0076 Japan
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Ichihashi Y, Tsukaya H. Behavior of Leaf Meristems and Their Modification. FRONTIERS IN PLANT SCIENCE 2015; 6:1060. [PMID: 26648955 PMCID: PMC4664833 DOI: 10.3389/fpls.2015.01060] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/13/2015] [Indexed: 05/06/2023]
Abstract
A major source of diversity in flowering plant form is the extensive variability of leaf shape and size. Leaf formation is initiated by recruitment of a handful of cells flanking the shoot apical meristem (SAM) to develop into a complex three-dimensional structure. Leaf organogenesis depends on activities of several distinct meristems that are established and spatiotemporally differentiated after the initiation of leaf primordia. Here, we review recent findings in the gene regulatory networks that orchestrate leaf meristem activities in a model plant Arabidopsis thaliana. We then discuss recent key studies investigating the natural variation in leaf morphology to understand how the gene regulatory networks modulate leaf meristems to yield a substantial diversity of leaf forms during the course of evolution.
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Affiliation(s)
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
- Bio-Next Project, Okazaki Institute for Integrative Bioscience, National Institutes of Natural SciencesOkazaki, Japan
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Rinerson CI, Scully ED, Palmer NA, Donze-Reiner T, Rabara RC, Tripathi P, Shen QJ, Sattler SE, Rohila JS, Sarath G, Rushton PJ. The WRKY transcription factor family and senescence in switchgrass. BMC Genomics 2015; 16:912. [PMID: 26552372 PMCID: PMC4640240 DOI: 10.1186/s12864-015-2057-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass yields. METHODS All potential WRKY genes present in the version 1.0 of the switchgrass genome were identified and curated using manual and bioinformatic methods. Expression profiles of WRKY genes in switchgrass flag leaf RNA-Seq datasets were analyzed using clustering and network analyses tools to identify both WRKY and WRKY-associated gene co-expression networks during leaf development and senescence onset. RESULTS We identified 240 switchgrass WRKY genes including members of the RW5 and RW6 families of resistance proteins. Weighted gene co-expression network analysis of the flag leaf transcriptomes across development readily separated clusters of co-expressed genes into thirteen modules. A visualization highlighted separation of modules associated with the early and senescence-onset phases of flag leaf growth. The senescence-associated module contained 3000 genes including 23 WRKYs. Putative promoter regions of senescence-associated WRKY genes contained several cis-element-like sequences suggestive of responsiveness to both senescence and stress signaling pathways. A phylogenetic comparison of senescence-associated WRKY genes from switchgrass flag leaf with senescence-associated WRKY genes from other plants revealed notable hotspots in Group I, IIb, and IIe of the phylogenetic tree. CONCLUSIONS We have identified and named 240 WRKY genes in the switchgrass genome. Twenty three of these genes show elevated mRNA levels during the onset of flag leaf senescence. Eleven of the WRKY genes were found in hotspots of related senescence-associated genes from multiple species and thus represent promising targets for future switchgrass genetic improvement. Overall, individual WRKY gene expression profiles could be readily linked to developmental stages of flag leaves.
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Affiliation(s)
- Charles I Rinerson
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
| | - Erin D Scully
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Nathan A Palmer
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Teresa Donze-Reiner
- Department of Biology, West Chester University of Pennsylvania, West Chester, PA, 19382, USA.
| | - Roel C Rabara
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
| | - Prateek Tripathi
- Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Qingxi J Shen
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Scott E Sattler
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Jai S Rohila
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA.
| | - Paul J Rushton
- Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA.
- Current address: 22nd Century Group Inc., Clarence, 14031, New York.
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Serba DD, Uppalapati SR, Mukherjee S, Krom N, Tang Y, Mysore KS, Saha MC. Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0075. [PMID: 33228298 DOI: 10.3835/plantgenome2014.10.0075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/23/2014] [Indexed: 06/11/2023]
Abstract
Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. To identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 × A4) × (AP13 × VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 × 100 bp) sequencing on the Illumina HiSeq2000 platform. Mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense-related genes, including the nucleotide binding site-leucine-rich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Furthermore, the rust-resistant genotypes and gene transcripts identified in this study can expedite rust-resistant cultivar development in switchgrass.
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Affiliation(s)
- Desalegn D Serba
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
| | - Srinivasa Rao Uppalapati
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Dupont Pioneer, Dupont Knowledge Center, Turakapally, Hyderabad, Telangana, India, 500 078
| | - Shreyartha Mukherjee
- Computing Services, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Nick Krom
- Computing Services, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
| | - Malay C Saha
- Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Pkwy., Ardmore, OK, 73401
- Department of Energy, BioEnergy Science Center, Oak Ridge National Lab., Oak Ridge, TN, 37831
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