1
|
Jiang Y, Dong L, Li H, Liu Y, Wang X, Liu G. Genetic linkage map construction and QTL analysis for plant height in proso millet (Panicum miliaceum L.). Theor Appl Genet 2024; 137:78. [PMID: 38466414 DOI: 10.1007/s00122-024-04576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024]
Abstract
KEY MESSAGE A genetic linkage map representing proso millet genome was constructed with SSR markers, and a major QTL corresponding to plant height was mapped on chromosome 14 of this map. Proso millet (Panicum miliaceum L.) has the lowest water requirements of all cultivated cereal crops. However, the lack of a genetic map and the paucity of genomic resources for this species have limited the utility of proso millet for detailed genetic studies and hampered genetic improvement programs. In this study, 97,317 simple sequence repeat (SSR) markers were developed based on the genome sequence of the proso millet landrace Longmi 4. Using some of these markers in conjunction with previously identified SSRs, an SSR-based linkage map for proso millet was successfully constructed using a large mapping population (316 F2 offspring). In total, 186 SSR markers were assigned to 18 linkage groups corresponding to the haploid chromosomes. The constructed map had a total length of 3033.42 centimorgan (cM) covering 78.17% of the assembled reference genome. The length of the 18 linkage groups ranged from 88.89 cM (Chr. 15) to 274.82 cM (Chr. 16), with an average size of 168.17 cM. To our knowledge, this is the first genetic linkage map for proso millet based on SSR markers. Plant height is one of the most important traits in crop improvement. A major QTL was repeatedly detected in different environments, explaining 8.70-24.50% of the plant height variations. A candidate gene affecting auxin biosynthesis and transport, and ROS homeostasis regulation was predicted. Thus, the linkage map and QTL analysis provided herein will promote the development of gene mining and molecular breeding in proso millet.
Collapse
Affiliation(s)
- Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Li Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Xindong Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China.
| |
Collapse
|
2
|
Han X, Tang S, Ma X, Liu W, Yang R, Zhang S, Wang N, Song X, Fu C, Yang R, Cao X. Blocking miR528 function promotes tillering and regrowth in switchgrass. Plant Biotechnol J 2024; 22:712-721. [PMID: 37929781 PMCID: PMC10893936 DOI: 10.1111/pbi.14218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/28/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
MiRNAs have been reported to be the key regulators involving a wide range of biological processes in diverse plant species, but their functions in switchgrass, an important biofuel and forage crop, are largely unknown. Here, we reported the novel function of miR528, which has expanded to four copies in switchgrass, in controlling biomass trait of tillering number and regrowth rate after mowing. Blocking miR528 activity by expressing short tandem target mimic (STTM) increased tiller number and regrowth rate after mowing. The quadruple pvmir528 mutant lines derived from genome editing also showed such improved traits. Degradome and RNA-seq analysis, combined with in situ hybridization assay revealed that up-regulation of two miR528 targets coding for Cu/Zn-SOD enzymes, might be responsible for the improved traits of tillering and regrowth in pvmir528 mutant. Additionally, natural variations in the miR528-SOD interaction exist in C3 and C4 monocot species, implying the distinct regulatory strength of the miR528-SOD module during monocot evolution. Overall, our data illuminated a novel role of miR528 in controlling biomass traits and provided a new target for genetic manipulation-mediated crop improvement.
Collapse
Affiliation(s)
- Xiangyan Han
- Department of Plant Biology and Ecology, Tianjin Key Laboratory of Protein Sciences, College of Life SciencesNankai UniversityTianjinChina
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Shanjie Tang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| | - Xuan Ma
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant ResistanceTianjin Normal UniversityTianjinChina
| | - Wenwen Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Ruijuan Yang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Shuaibin Zhang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Ningning Wang
- Department of Plant Biology and Ecology, Tianjin Key Laboratory of Protein Sciences, College of Life SciencesNankai UniversityTianjinChina
| | - Xianwei Song
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Chunxiang Fu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Rongxin Yang
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life ScienceNanchang UniversityJiangxiChina
| | - Xiaofeng Cao
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of the Chinese Academy of SciencesBeijingChina
| |
Collapse
|
3
|
Guan C, Li W, Wang G, Yang R, Zhang J, Zhang J, Wu B, Gao R, Jia C. Transcriptomic analysis of ncRNAs and mRNAs interactions during drought stress in switchgrass. Plant Sci 2024; 339:111930. [PMID: 38007196 DOI: 10.1016/j.plantsci.2023.111930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
Switchgrass (Panicum virgatum L.) plays a pivotal role as a bioenergy feedstock in the production of cellulosic ethanol and contributes significantly to enhancing ecological grasslands and soil quality. The utilization of non-coding RNAs (ncRNAs) has gained momentum in deciphering the intricate genetic responses to abiotic stress in various plant species. Nevertheless, the current research landscape lacks a comprehensive exploration of the responses of diverse ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), to drought stress in switchgrass. In this study, we employed whole transcriptome sequencing to comprehensively characterize the expression profiles of both mRNA and ncRNAs during episodes of drought stress in switchgrass. Our analysis identified a total of 12,511 mRNAs, 59 miRNAs, 38 circRNAs, and 368 lncRNAs that exhibited significant differential expression between normal and drought-treated switchgrass leaves. Notably, the majority of up-regulated mRNAs displayed pronounced enrichment within the starch and sucrose metabolism pathway, as validated through KEGG analysis. Co-expression analysis illuminated that differentially expressed (DE) lncRNAs conceivably regulated 1308 protein-coding genes in trans and 7110 protein-coding genes in cis. Furthermore, both cis- and trans-target mRNAs of DE lncRNAs exhibited enrichment in four common KEGG pathways. The intricate interplay between lncRNAs and circRNAs with miRNAs via miRNA response elements was explored within the competitive endogenous RNA (ceRNA) network framework. As a result, we constructed elaborate regulatory networks, including lncRNA-novel_miRNA480-mRNA, lncRNA-novel_miRNA304-mRNA, lncRNA/circRNA-novel_miRNA122-PvSS4, and lncRNA/circRNA-novel_miRNA14-PvSS4, and subsequently validated the functionality of the target gene, starch synthase 4 (PvSS4). Furthermore, through the overexpression of PvSS4, we ascertained its capacity to enhance drought tolerance in yeast. However, it is noteworthy that PvSS4 did not exhibit any discernible impact under salt stress conditions. These findings, as presented herein, not only contribute substantively to our understanding of ceRNA networks but also offer a basis for further investigations into their potential functions in response to drought stress in switchgrass.
Collapse
Affiliation(s)
- Cong Guan
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Wei Li
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Guoliang Wang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Ruimei Yang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Jinglei Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Jinhong Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Bo Wu
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Run Gao
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Chunlin Jia
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China.
| |
Collapse
|
4
|
Wang H, Zhang H, Liu J, Ma Q, Wu E, Gao J, Yang Q, Feng B. Transcriptome analysis reveals the mechanism of nitrogen fertilizers in starch synthesis and quality in waxy and non-waxy proso millet. Carbohydr Polym 2024; 323:121372. [PMID: 37940241 DOI: 10.1016/j.carbpol.2023.121372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 11/10/2023]
Abstract
Recent findings suggest that optimal application of nitrogen fertilizers can effectively improve the quality of proso millet (PM). Here, we aimed to investigate the pathways associated with starch synthesis and metabolism to elucidate the effect and molecular mechanisms of nitrogen fertilization in starch synthesis and properties in waxy and non-waxy PM varieties using transcriptomic techniques. Co-expression network analysis revealed that the regulation of starch synthesis and quality in PM by nitrogen fertilizer mainly occurred in the S2 and S3 stages during grain filling. Nitrogen fertilization inhibited glycolysis/gluconeogenesis and starch biosynthesis in grains, but increased starch degradation to maltose and dextrin and then to glucose. Moreover, nitrogen fertilization increased starch accumulation by upregulating the expression of SuS and malZ genes, thereby increasing the total starch content in grains. In contrast, nitrogen fertilization suppressed the expression of GBSS gene and decreased amylose content in PM grains, resulting in a relatively higher crystallinity, light transmittance, and breakdown viscosity in the two PM varieties. Overall, these results provided transcriptomics insights into the molecular mechanisms by which nitrogen fertilization regulates starch quality in PM, identified key genes that associated with the starch properties, and provided new insights into the quality cultivation of PM.
Collapse
Affiliation(s)
- Honglu Wang
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Hui Zhang
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Jiajia Liu
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Qian Ma
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Enguo Wu
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Jinfeng Gao
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Qinghua Yang
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China
| | - Baili Feng
- Northwest A&F University, College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Yangling 712100, Shaanxi Province, China.
| |
Collapse
|
5
|
Chen J, Liu Y, Liu M, Guo W, Wang Y, He Q, Chen W, Liao Y, Zhang W, Gao Y, Dong K, Ren R, Yang T, Zhang L, Qi M, Li Z, Zhao M, Wang H, Wang J, Qiao Z, Li H, Jiang Y, Liu G, Song X, Deng Y, Li H, Yan F, Dong Y, Li Q, Li T, Yang W, Cui J, Wang H, Zhou Y, Zhang X, Jia G, Lu P, Zhi H, Tang S, Diao X. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet. Nat Genet 2023; 55:2243-2254. [PMID: 38036791 PMCID: PMC10703678 DOI: 10.1038/s41588-023-01571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet.
Collapse
Affiliation(s)
- Jinfeng Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Minxuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiyao Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Liyuan Zhang
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Mingyu Qi
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Zhiguang Li
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Min Zhao
- Chifeng Academy of Agricultural and Animal Husbandry Sciences, Chifeng, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Junjie Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Xiaoqiang Song
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Yarui Deng
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Hai Li
- High Latitude Crops Institute to Shanxi Academy, Shanxi Agricultural University (Shanxi Academy of Agricultural Sciences), Datong, China
| | - Feng Yan
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yang Dong
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Qingquan Li
- Qiqihar Sub-academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Tao Li
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenyao Yang
- Institute of Crop Sciences, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Jianghui Cui
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hongru Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| |
Collapse
|
6
|
Choi S, Prabhakar PK, Chowdhury R, Pendergast TH, Urbanowicz BR, Maranas C, Devos KM. A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass. J Exp Bot 2023; 74:5532-5546. [PMID: 37402629 PMCID: PMC10540729 DOI: 10.1093/jxb/erad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023]
Abstract
Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.
Collapse
Affiliation(s)
- Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Pradeep K Prabhakar
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ratul Chowdhury
- Chemical Engineering, Penn State University, State College, PA 16801, USA
| | - Thomas H Pendergast
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Costas Maranas
- Chemical Engineering, Penn State University, State College, PA 16801, USA
| | - Katrien M Devos
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
7
|
Palmer NA, Alvarez S, Naldrett MJ, Muhle A, Sarath G, Edmé SJ, Tatineni S, Mitchell RB, Yuen G. Dynamic Reconfiguration of Switchgrass Proteomes in Response to Rust ( Puccinia novopanici) Infection. Int J Mol Sci 2023; 24:14630. [PMID: 37834079 PMCID: PMC10572835 DOI: 10.3390/ijms241914630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) can be infected by the rust pathogen (Puccinia novopanici) and results in lowering biomass yields and quality. Label-free quantitative proteomics was conducted on leaf extracts harvested from non-infected and infected plants from a susceptible cultivar (Summer) at 7, 11, and 18 days after inoculation (DAI) to follow the progression of disease and evaluate any plant compensatory mechanisms to infection. Some pustules were evident at 7 DAI, and their numbers increased with time. However, fungal DNA loads did not appreciably change over the course of this experiment in the infected plants. In total, 3830 proteins were identified at 1% false discovery rate, with 3632 mapped to the switchgrass proteome and 198 proteins mapped to different Puccinia proteomes. Across all comparisons, 1825 differentially accumulated switchgrass proteins were identified and subjected to a STRING analysis using Arabidopsis (A. thaliana L.) orthologs to deduce switchgrass cellular pathways impacted by rust infection. Proteins associated with plastid functions and primary metabolism were diminished in infected Summer plants at all harvest dates, whereas proteins associated with immunity, chaperone functions, and phenylpropanoid biosynthesis were significantly enriched. At 18 DAI, 1105 and 151 proteins were significantly enriched or diminished, respectively. Many of the enriched proteins were associated with mitigation of cellular stress and defense.
Collapse
Affiliation(s)
- Nathan A. Palmer
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Sophie Alvarez
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Michael J. Naldrett
- Proteomics and Metabolomics Core Facility, Center for Biotechnology, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA; (S.A.); (M.J.N.)
| | - Anthony Muhle
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Serge J. Edmé
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Satyanarayana Tatineni
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
| | - Robert B. Mitchell
- Wheat, Sorghum, and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583-0937, USA; (N.A.P.); (A.M.); (S.J.E.); (S.T.); (R.B.M.)
| | - Gary Yuen
- Department of Plant Pathology, University of Nebraska at Lincoln, Lincoln, NE 68583-0722, USA;
| |
Collapse
|
8
|
Shrestha SL, Tobias CM, Bhandari HS, Bragg J, Nayak S, Goddard K, Allen F. Mapping quantitative trait loci for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) multiple populations. G3 (Bethesda) 2023; 13:jkad061. [PMID: 36947434 PMCID: PMC10151402 DOI: 10.1093/g3journal/jkad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/15/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
Switchgrass can be used as an alternative source for bioenergy production. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Quantitative trait loci (QTL) mapping can help to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped 7 hybrid populations and one combined of 2 hybrid populations (30-96 F1s) derived from Alamo and Kanlow genotypes. The populations were evaluated for biomass yield, plant height, and crown size in a simulated-sward plot with 2 replications at 2 locations in Tennessee from 2019 to 2021. The populations showed significant genetic variation for the evaluated traits and exhibited transgressive segregation. The 17,251 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) were used to construct a linkage map using a fast algorithm for multiple outbred families. The linkage map spanned 1,941 cM with an average interval of 0.11 cM between SNPs. The QTL analysis was performed on evaluated traits for each and across environments (year and location) that identified 5 QTL for biomass yield (logarithm of the odds, LOD 3.12-4.34), 4 QTL for plant height (LOD 3.01-5.64), and 7 QTL for crown size (LOD 3.0-4.46) (P ≤ 0.05). The major QTL for biomass yield, plant height, and crown size resided on chromosomes 8N, 6N, and 8K explained phenotypic variations of 5.6, 5.1, and 6.6%, respectively. SNPs linked to QTL could be incorporated into marker-assisted breeding to maximize the selection gain in switchgrass breeding.
Collapse
Affiliation(s)
- Surya L Shrestha
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Christian M Tobias
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Plant Systems-Production, USDA National Institute of Food and Agriculture (NIFA), Beacon Complex, USA
| | - Hem S Bhandari
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Jennifer Bragg
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Santosh Nayak
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
- USDA ARS, Crop Improvement and Protection Research Unit, 1636 E Alisal Street, Salinas, CA 93905, USA
| | - Ken Goddard
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Fred Allen
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| |
Collapse
|
9
|
Guan C, Wu B, Ma S, Zhang J, Liu X, Wang H, Zhang J, Gao R, Jiang H, Jia C. Genome-wide characterization of LBD transcription factors in switchgrass (Panicum virgatum L.) and the involvement of PvLBD12 in salt tolerance. Plant Cell Rep 2023; 42:735-748. [PMID: 36806743 DOI: 10.1007/s00299-023-02989-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
PvLBD12 enhanced the salt tolerance by increasing proline accumulation, improving K+ accumulation, and decreasing reactive oxygen species level in switchgrass. Abiotic stresses are the serious factors which limit plant development and productivity and restrict the agricultural economy. It is important, therefore, to understand the mechanism of abiotic tolerance in plants. Lateral organ boundaries domain (LBD) proteins as plant-specific transcription factors play important function in plant lateral organ development, plant regeneration, and abiotic stress. In our study, we identify 69 LBD members from switchgrass genome-wide sequences and classify them based on their homology with LBD proteins in Arabidopsis. RT-qPCR showed that PvLBD genes had different expression patterns under abiotic stress conditions, indicating that they play important roles in various stress. PvLBD12 was selected as a candidate gene for further functional analysis because it had the highest expression level under salt stress. Overexpression of PvLBD12 enhanced salt tolerance by altering a wide range of physiological responses (like increased proline accumulation, reduced malondialdehyde production, improved K+ accumulation, and reduced Na+ absorption) in switchgrass. Some stress response genes such as proline biosynthesis gene PvP5CS1, vacuolar Na+(K+)/H+ antiporter gene PvNHX1, two key ROS-scavenging enzyme genes PvCAT and PvSOD were all upregulated in PvLBD12 overexpression lines. Taken together, PvLBD12 plays a pivotal role in response to salt stress by increasing proline accumulation, improving K+ accumulation, reducing Na+ absorption, and decreasing reactive oxygen species level. It will be better to understand the potential biological functions of LBD genes in other plants.
Collapse
Affiliation(s)
- Cong Guan
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China
- Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan, 250100, China
- Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan, 250100, China
| | - Bo Wu
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China
- Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan, 250100, China
- Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan, 250100, China
| | - Shu Ma
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Jinhong Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China
- Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan, 250100, China
- Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan, 250100, China
| | - Xuesi Liu
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Jinglei Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China
- Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan, 250100, China
- Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan, 250100, China
| | - Run Gao
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China
- Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan, 250100, China
- Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan, 250100, China
| | - Huixin Jiang
- Shandong Provincial Animal Husbandry General Station, Jinan, China.
| | - Chunlin Jia
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan, 250100, China.
- Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan, 250100, China.
- Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan, 250100, China.
| |
Collapse
|
10
|
Song G, Zhang J, Wang Y, Ji Y, Fang Z, Cai Q, Xu B. Overexpression of PvBiP2 improved biomass yield and cadmium tolerance in switchgrass (Panicum virgatum L.). J Hazard Mater 2023; 446:130648. [PMID: 36580780 DOI: 10.1016/j.jhazmat.2022.130648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Switchgrass (Panicum virgatum L.), the prime bioenergy feedstock crop, is one ideal candidate for phytoremediation of cadmium (Cd). The absorption of Cd imposes severe endoplasmic reticulum (ER)-stress in plants. ER chaperone binding proteins (BiPs) are important modulators in ER-stress responses. The objective of this study was to characterize one Cd-responsive BiP gene, PvBiP2, in switchgrass for its roles in Cd tolerance and plant growth. PvBiP2 was up-regulated by Cd and the ER-stress inducer, dithiothreitol (DTT) and could be trans-activated by one Cd-responsive heat shock transcription factor PvHsfA4. Overexpression of PvBiP2 in switchgrass significantly increased its plant growth with higher height, stem diameter, leaf width, internode length, and tiller numbers than those of the wildtype (WT) plants under non-stress conditions. After 30 days of Cd treatment, the PvBiP2 over-expression transgenic lines showed 40-45% higher dry biomass accumulation with net photosynthesis rate (Pn), but lower electrolyte leakage (EL), malondialdehyde (MDA), and glutathione (GSH) levels than WT. Moreover, over-expressing PvBiP2 led to ∼90-140% Cd accumulation in plants but 46-57% lower Cd translocation rates to shoots. Together, the PvHSFA4-PvBiP2 module acted as positive regulators in plant Cd tolerance, and over-expressing PvBiP2 promoted plant vegetative growth as well as Cd tolerance making it an ideal molecular target for genetic improvement in switchgrass in the future.
Collapse
Affiliation(s)
- Gang Song
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Vocational College of Agriculture and Forestry, Jvrong 212400, China.
| | - Jing Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yulong Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yanling Ji
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhigang Fang
- College of Life and Geographic Sciences, Kashi University, Kashi 844006, China.
| | - Qingsheng Cai
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
11
|
Sun Y, Liu Y, Shi J, Wang L, Liang C, Yang J, Chen J, Chen M. Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome. Plant J 2023; 113:787-801. [PMID: 36575912 DOI: 10.1111/tpj.16085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/07/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome-scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at ~4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about ~0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element-rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels.
Collapse
Affiliation(s)
- Yanling Sun
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jinfeng Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Lun Wang
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, 030031, Taiyuan, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 201602, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Jinfeng Chen
- University of Chinese Academy of Sciences, 100039, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| |
Collapse
|
12
|
Heckman RW, Rueda A, Bonnette JE, Aspinwall MJ, Khasanova A, Hawkes CV, Juenger TE, Fay PA. Legacies of precipitation influence primary production in Panicum virgatum. Oecologia 2023; 201:269-278. [PMID: 36372830 DOI: 10.1007/s00442-022-05281-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 10/31/2022] [Indexed: 11/15/2022]
Abstract
Precipitation is a key driver of primary production worldwide, but primary production does not always track year-to-year variation in precipitation linearly. Instead, plant responses to changes in precipitation may exhibit time lags, or legacies of past precipitation. Legacies can be driven by multiple mechanisms, including persistent changes in plant physiological and morphological traits and changes to the physical environment, such as plant access to soil water. We used three precipitation manipulation experiments in central Texas, USA to evaluate the magnitude, duration, and potential mechanisms driving precipitation legacies on aboveground primary production of the perennial C4 grass, Panicum virgatum. Specifically, we performed a rainout shelter study, where eight genotypes grew under different precipitation regimes; a transplant study, where plants that had previously grown in a rainout shelter under different precipitation regimes were moved to a common environment; and a mesocosm study, where the effect of swapping precipitation regime was examined with a single genotype. Across these experiments, plants previously grown under wet conditions generally performed better than expected when exposed to drought. Panicum virgatum exhibited stronger productivity legacies of past wet years on current-year responses to drought than of past dry years on current-year responses to wet conditions. Additionally, previous year tiller counts, a proxy for meristem availability, were important in determining legacy effects on aboveground production. As climate changes and precipitation extremes-both dry and wet-become more common, these results suggest that populations of P. virgatum may become less resilient.
Collapse
Affiliation(s)
- Robert W Heckman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- USDA Forest Service, Rocky Mountain Research Station, Cedar City, UT, 84721, USA.
| | - Austin Rueda
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- PathogenDx, Tucson, AZ, 85714, USA
| | - Jason E Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Michael J Aspinwall
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- College of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Albina Khasanova
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 74720, USA
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Philip A Fay
- Grassland Soil and Water Research Lab, USDA-ARS, Temple, TX, 76502, USA
| |
Collapse
|
13
|
Willick IR, Lowry DB. Cold acclimation threshold induction temperatures of switchgrass ecotypes grown under a long and short photoperiod. Physiol Plant 2022; 174:e13812. [PMID: 36326192 PMCID: PMC9828680 DOI: 10.1111/ppl.13812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 05/04/2023]
Abstract
Plants can cold acclimate to enhance their freezing tolerance by sensing declining temperature and photoperiod cues. However, the factors influencing genotypic variation in the induction of cold acclimation are poorly understood among perennial grasses. We hypothesized that the more northern upland switchgrass (Panicum virgatum L.) ecotype develops a higher degree of freezing tolerance by initiating cold acclimation at higher temperatures as compared with the coastal and southern lowland ecotypes. First, we determined the optimal method for assessing freezing tolerance and the length of exposure to 8/4°C required to induce the maximum level of freezing tolerance in the most northern upland and most southern lowland genotypes. We characterized the maximum freezing tolerance of eight uplands, three coastal and five lowland genotypes grown for 21 days at 8/4°C and a 10 or 16 h photoperiod. Next, we identified the temperature required to induce cold acclimation by exposing the 16 genotypes for 7 days at 20-6°C constant temperatures under a 10 or 16 h photoperiod. Cold acclimation initiated at temperatures 5 and 7°C higher in upland than in coastal and lowland genotypes. Among upland genotypes the shorter photoperiod induced cold acclimation at a 1°C higher temperature. Genotypes originating from a more northern latitude initiate cold acclimation at higher temperatures and develop higher maximum freezing tolerances. An earlier response to declining temperatures may provide the upland ecotype with additional time to prepare for winter and provide an advantage when plants are subjected to the rapid changes in fall temperature associated with injurious frosts.
Collapse
Affiliation(s)
- Ian R. Willick
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- Plant Resilience InstituteMichigan State UniversityEast LansingMichiganUSA
- Kentville Research and Development CentreAgriculture and Agri‐Food CanadaKentvilleNSCanada
| | - David B. Lowry
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
- Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMichiganUSA
- Plant Resilience InstituteMichigan State UniversityEast LansingMichiganUSA
- Department of Ecology, Evolutionary Biology, and BehaviorMichigan State UniversityEast LansingMichiganUSA
| |
Collapse
|
14
|
Xie Z, Yu G, Lei S, Wang H, Xu B. STRONG STAYGREEN inhibits DNA binding of PvNAP transcription factors during leaf senescence in switchgrass. Plant Physiol 2022; 190:2045-2058. [PMID: 36005925 PMCID: PMC9614497 DOI: 10.1093/plphys/kiac397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Fine tuning the progression of leaf senescence is important for plant fitness in nature, while the "staygreen" phenotype with delayed leaf senescence has been considered a valuable agronomic trait in crop genetic improvement. In this study, a switchgrass (Panicum virgatum L.) CCCH-type Zinc finger gene, Strong Staygreen (PvSSG), was characterized as a suppressor of leaf senescence as overexpression or suppression of the gene led to delayed or accelerated leaf senescence, respectively. Transcriptomic analysis marked that chlorophyll (Chl) catabolic pathway genes were involved in the PvSSG-regulated leaf senescence. PvSSG was identified as a nucleus-localized protein with no transcriptional activity. By yeast two-hybrid screening, we identified its interacting proteins, including a pair of paralogous transcription factors, PvNAP1/2 (NAC-LIKE, ACTIVATED BY AP3/PI). Overexpression of PvNAPs led to precocious leaf senescence at least partially by directly targeting and transactivating Chl catabolic genes to promote Chl degradation. PvSSG, through protein-protein interaction, repressed the DNA-binding efficiency of PvNAPs and alleviated its transactivating effect on downstream genes, thereby functioning as a "brake" in the progression of leaf senescence. Moreover, overexpression of PvSSG resulted in up to 47% higher biomass yield and improved biomass feedstock quality, reiterating the importance of leaf senescence regulation in the genetic improvement of switchgrass and other feedstock crops.
Collapse
Affiliation(s)
- Zheni Xie
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guohui Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Lei
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bin Xu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
15
|
Karasov TL, Lundberg DS. The changing influence of host genetics on the leaf fungal microbiome throughout plant development. PLoS Biol 2022; 20:e3001748. [PMID: 35960709 PMCID: PMC9374218 DOI: 10.1371/journal.pbio.3001748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Talia L. Karasov
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| | | |
Collapse
|
16
|
Zhang L, MacQueen A, Weng X, Behrman KD, Bonnette J, Reilley JL, Rouquette FM, Fay PA, Wu Y, Fritschi FB, Mitchell RB, Lowry DB, Boe AR, Juenger TE. The genetic basis for panicle trait variation in switchgrass (Panicum virgatum). Theor Appl Genet 2022; 135:2577-2592. [PMID: 35780149 PMCID: PMC9325832 DOI: 10.1007/s00122-022-04096-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
We investigate the genetic basis of panicle architecture in switchgrass in two mapping populations across a latitudinal gradient, and find many stable, repeatable genetic effects and limited genetic interactions with the environment. Grass species exhibit large diversity in panicle architecture influenced by genes, the environment, and their interaction. The genetic study of panicle architecture in perennial grasses is limited. In this study, we evaluate the genetic basis of panicle architecture including panicle length, primary branching number, and secondary branching number in an outcrossed switchgrass QTL population grown across ten field sites in the central USA through multi-environment mixed QTL analysis. We also evaluate genetic effects in a diversity panel of switchgrass grown at three of the ten field sites using genome-wide association (GWAS) and multivariate adaptive shrinkage. Furthermore, we search for candidate genes underlying panicle traits in both of these independent mapping populations. Overall, 18 QTL were detected in the QTL mapping population for the three panicle traits, and 146 unlinked genomic regions in the diversity panel affected one or more panicle trait. Twelve of the QTL exhibited consistent effects (i.e., no QTL by environment interactions or no QTL × E), and most (four of six) of the effects with QTL × E exhibited site-specific effects. Most (59.3%) significant partially linked diversity panel SNPs had significant effects in all panicle traits and all field sites and showed pervasive pleiotropy and limited environment interactions. Panicle QTL co-localized with significant SNPs found using GWAS, providing additional power to distinguish between true and false associations in the diversity panel.
Collapse
Affiliation(s)
- Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kathrine D Behrman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - John L Reilley
- Kika de la Garza Plant Materials Center, National Resources Conservation Service, US Department of Agriculture, Kingsville, TX, 78363, USA
| | - Francis M Rouquette
- Texas A&M AgriLife Research and Extension Center, Texas A&M University, Overton, TX, 75684, USA
| | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, Agricultural Research Service, US Department of Agriculture, Temple, TX, 76502, USA
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Robert B Mitchell
- Wheat, Sorghum, and Forage Research Unit, Agricultural Research Service, US Department of Agriculture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - David B Lowry
- Department of Plant Biology and DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Arvid R Boe
- Departmentof Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
17
|
Li Y, Xiong W, He F, Qi T, Sun Z, Liu Y, Bai S, Wang H, Wu Z, Fu C. Down-regulation of PvSAMS impairs S-adenosyl-L-methionine and lignin biosynthesis, and improves cell wall digestibility in switchgrass. J Exp Bot 2022; 73:4157-4169. [PMID: 35383829 DOI: 10.1093/jxb/erac147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
S-adenosyl- l-methionine (SAM) is the methyl donor involved in the biosynthesis of guaiacyl (G) and syringyl (S) lignins in vascular plants. SAM is synthesized from methionine through the catalysis of the enzyme S-adenosylmethionine synthase (SAMS). However, the detailed function of SAMS in lignin biosynthesis has not been widely investigated in plants, particularly in monocot species. In this study, we identified PvSAMS genes from switchgrass (Panicum virgatum L.), an important dual-purpose fodder and biofuel crop, and generated numerous transgenic switchgrass lines through PvSAMS RNA interference technology. Down-regulation of PvSAMS reduced the contents of SAM, G-lignins, and S-lignins in the transgenic switchgrass. The methionine and glucoside derivatives of caffeoyl alcohol were found to accumulate in the transgenic plants. Moreover, down-regulation of PvSAMS in switchgrass resulted in brownish stems associated with reduced lignin content and improved cell wall digestibility. Furthermore, transcriptomic analysis revealed that most sulfur deficiency-responsive genes were differentially expressed in the transgenic switchgrass, leading to a significant increase in total sulfur content; thus implying an important role of SAMS in the methionine cycle, lignin biosynthesis, and sulfur assimilation. Taken together, our results suggest that SAMS is a valuable target in lignin manipulation, and that manipulation of PvSAMS can simultaneously regulate the biosynthesis of SAM and methylated monolignols in switchgrass.
Collapse
Affiliation(s)
- Yu Li
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wangdan Xiong
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Feng He
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Tianxiong Qi
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Zhen Sun
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuchen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, 611731, China
| | - Honglun Wang
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| |
Collapse
|
18
|
An P, Li X, Liu T, Shui Z, Chen M, Gao X, Wang Z. The Identification of Broomcorn Millet bZIP Transcription Factors, Which Regulate Growth and Development to Enhance Stress Tolerance and Seed Germination. Int J Mol Sci 2022; 23:ijms23126448. [PMID: 35742892 PMCID: PMC9224411 DOI: 10.3390/ijms23126448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 05/31/2022] [Accepted: 06/07/2022] [Indexed: 12/04/2022] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) is a water-efficient and highly salt-tolerant plant. In this study, the salt tolerance of 17 local species of broomcorn millet was evaluated through testing based on the analysis of the whitening time and the germination rate of their seeds. Transcriptome sequencing revealed that PmbZIP131, PmbZIP125, PmbZIP33, PmABI5, PmbZIP118, and PmbZIP97 are involved in seed germination under salt stress. Seedling stage expression analysis indicates that PmABI5 expression was induced by treatments of high salt (200 mM NaCl), drought (20% W/V PEG6000), and low temperature (4 °C) in seedlings of the salt-tolerant variety Y9. The overexpression of PmABI5 significantly increases the germination rate and root traits of Arabidopsis thaliana transgenic lines, with root growth and grain traits significantly enhanced compared to the wild type (Nipponbare). BiFC showed that PmABI5 undergoes homologous dimerization in addition to forming a heterodimer with either PmbZIP33 or PmbZIP131. Further yeast one-hybrid experiments showed that PmABI5 and PmbZIP131 regulate the expression of PmNAC1 by binding to the G-box in the promoter. These results indicate that PmABI5 can directly regulate seed germination and seedling growth and indirectly improve the salt tolerance of plants by regulating the expression of the PmNAC1 gene through the formation of heterodimers with PmbZIP131.
Collapse
Affiliation(s)
| | | | | | | | | | - Xin Gao
- Correspondence: (X.G.); (Z.W.)
| | | |
Collapse
|
19
|
Liu J, Zhang D, Zhang Y, Zhou H, Chen P, Yuan Y, Yang Q, Zhao L, Feng B. Dynamic and Comparative Transcriptome Analyses Reveal Key Factors Contributing to Cadmium Tolerance in Broomcorn Millet. Int J Mol Sci 2022; 23:ijms23116148. [PMID: 35682827 PMCID: PMC9181813 DOI: 10.3390/ijms23116148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) has great potential in Cd phytoextraction, but its mechanisms are largely unknown. Two contrasting broomcorn millet varieties, 'Ningmi6' (Cd-sensitive variety) and '4452' (Cd-tolerant variety), were investigated through morphological, physiological, and transcriptomic analyses to determine the factors responsible for their differential Cd tolerance and translocation. The Cd-tolerant variety can accumulate more Cd, and its cell wall and vacuole component Cd proportions were higher compared with the Cd-sensitive variety. Under Cd stress, the glutathione content and peroxidase activity of the Cd-tolerant variety were significantly higher than those of the Cd-sensitive variety. Additionally, weighted gene co-expression network analysis (WGCNA) revealed hub modules that were associated with Cd stress and/or variety. Notably, genes involved in these hub modules were significantly enriched for roles in glutathione metabolism, phenylpropanoid biosynthesis, ABC transport, and metal ion transport process. These results suggested that regulation of genes associated with cell wall precipitation and vacuole compartmentalization may increase Cd tolerance and reduce Cd translocation in the Cd-tolerant variety, although it can absorb more Cd. This study provides a foundation for exploring molecular mechanisms of Cd tolerance and transport in broomcorn millet and new insights into improving Cd phytoremediation with this crop through genetic engineering.
Collapse
Affiliation(s)
- Jiajia Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Dazhong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Yuanbo Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Hao Zhou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Pengliang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Yuhao Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Qinghua Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
| | - Lin Zhao
- Shaanxi Provincial Research Academy of Environmental Sciences, Xi’an 710061, China
- Correspondence: (L.Z.); (B.F.)
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A & F University, Xianyang 712100, China; (J.L.); (D.Z.); (Y.Z.); (H.Z.); (P.C.); (Y.Y.); (Q.Y.)
- Correspondence: (L.Z.); (B.F.)
| |
Collapse
|
20
|
Xie K, Wang Y, Bai X, Ye Z, Zhang C, Sun F, Zhang C, Xi Y. Overexpression of PvSTK1 gene from Switchgrass (Panicum virgatum L.) affects flowering time and development of floral organ in transgenic Arabidopsis thaliana. Plant Physiol Biochem 2022; 178:93-104. [PMID: 35276599 DOI: 10.1016/j.plaphy.2022.02.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Flowering means that the plant enters the reproductive growth stage, which is a crucial stage in the plant life cycle. Delaying flowering time to prolong vegetative growth is an important method to increase biomass yield and saccharification efficiency in switchgrass, It is of great significance to study the molecular mechanism of plant flowering and regulate the process of plant flowering in the process of biomass production. In this study, we identified 55 serine/threonine-protein kinase genes related to flower development from the switchgrass transcriptome database. Simultaneously, we cloned one of them, PvSTK1, whose expression level and differential fold were significantly higher than other members. PvSTK1 is located on chromosome 8N and its protein was in the cell membrane, cytoplasm, and nucleus. The spatio-temporal expression analysis of the PvSTK1 in switchgrass displayed that the PvSTK1 is crucial in vegetative period, however, not in the transition to reproductive period. Overexpression of PvSTK1 in Arabidopsis resulted in down-regulation of flower-promoting genes and up-regulation of flower-suppressing genes, thereby delaying flowering. In addition, PvSTK1 caused atrophy of the ovules of the florets at the base of the inflorescence, leading to sterility of the florets. The function of PvSTK1 is to inhibit the development of floral organs, and its overexpression can prolong its vegetative period. In the future, overexpression of the PvSTK1 gene in switchgrass will change the flowering time and increase yield and utilization efficiency of biomass.
Collapse
Affiliation(s)
- Kunliang Xie
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
| | - Yongfeng Wang
- School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Xinchen Bai
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
| | - Zi Ye
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
| | - Chuqiu Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
| | - Fengli Sun
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
| | - Chao Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China
| | - Yajun Xi
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
21
|
Hayford RK, Serba DD, Xie S, Ayyappan V, Thimmapuram J, Saha MC, Wu CH, Kalavacharla VK. Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses. BMC Plant Biol 2022; 22:107. [PMID: 35260072 PMCID: PMC8903725 DOI: 10.1186/s12870-022-03477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Sustainable production of high-quality feedstock has been of great interest in bioenergy research. Despite the economic importance, high temperatures and water deficit are limiting factors for the successful cultivation of switchgrass in semi-arid areas. There are limited reports on the molecular basis of combined abiotic stress tolerance in switchgrass, particularly the combination of drought and heat stress. We used transcriptomic approaches to elucidate the changes in the response of switchgrass to drought and high temperature simultaneously. RESULTS We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Out of a total of 32,190 genes, we identified 3912, as drought (DT) responsive genes, 2339 and 4635 as, heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively. Gene ontology annotation identified the metabolic process as the significant term enriched in DTHT genes. Other biological processes identified in DTHT responsive genes included: response to water, photosynthesis, oxidation-reduction processes, and response to stress. KEGG pathway enrichment analysis on DT and DTHT responsive genes revealed that TFs and genes controlling phenylpropanoid pathways were important for individual as well as combined stress response. For example, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) from the phenylpropanoid pathway was induced by single DT and combinations of DTHT stress. CONCLUSION Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.
Collapse
Affiliation(s)
- Rita K Hayford
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology, Delaware State University, Dover, DE, USA
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA
| | - Desalegn D Serba
- USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN, USA
| | - Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology, Delaware State University, Dover, DE, USA
| | | | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, OK, USA.
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA
| | - Venu Kal Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology, Delaware State University, Dover, DE, USA.
- Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE, USA.
| |
Collapse
|
22
|
Ma Q, Yuan Y, Wu E, Wang H, Dang K, Feng Y, Ivanistau A, Feng B. Endogenous bioactive gibberellin/abscisic acids and enzyme activity synergistically promote the phytoremediation of alkaline soil by broomcorn millet (Panicum miliaceum L.). J Environ Manage 2022; 305:114362. [PMID: 34965501 DOI: 10.1016/j.jenvman.2021.114362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.), an important food crop, grows in arid and semi-arid areas that face soil saline-alkalization. To date, no studies have investigated the mechanisms by which broomcorn millet seeds respond to and tolerate alkali stress. In this study, six broomcorn millet genotypes (B102, B220, B269, B279, B289, and B297) were selected to explore the physiological and molecular mechanisms of alkali stress at the germination stage. The results showed that alkali stress delayed the germination of broomcorn millet, and α-amylase activity was positively correlated with the germination rate. After alkali stress, the genotypes with lower alkali damage rates exhibited stronger antioxidant defenses. Real-time polymerase chain reaction analysis showed that alkali stress downregulated gibberellic acid (GA) synthesis genes but upregulated GA inactivation and abscisic acid (ABA) synthesis genes. Similarly, seeds displayed lower GA concentrations and higher ABA concentrations after alkali stress. Therefore, the ratios of various GAs/ABA decreased within the range of 35.77% to approximately 96.45%. Additionally, genotypes associated with lower alkali damage rates had higher GA/ABA ratios. These findings indicate that the alkali tolerance of broomcorn millet at the germination stage may be attributed to higher GA/ABA ratios, higher α-amylase activity, and stronger antioxidant defense, which synergistically resist alkali stress. This study will contribute to molecular breeding aiming to enhance alkali-tolerance and restoration of alkaline soils.
Collapse
Affiliation(s)
- Qian Ma
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China
| | - Yuhao Yuan
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China
| | - Enguo Wu
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China
| | - Honglu Wang
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China
| | - Ke Dang
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China
| | - Yu Feng
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China
| | | | - Baili Feng
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A & F University, Yangling, 712100, Shaanxi, PR China.
| |
Collapse
|
23
|
Huang Y, Zheng Z, Bi X, Guo K, Liu S, Huo X, Tian D, Liu H, Wang L, Zhang Y. Integrated morphological, physiological and omics analyses reveal the arylalkylamine N-acetyltransferase (AANAT) gene contributing to growth, flowering and defence in switchgrass (Panicum virgatum L.). Plant Sci 2022; 316:111165. [PMID: 35151442 DOI: 10.1016/j.plantsci.2021.111165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/07/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Arylalkylamine N-acetyltransferase (AANAT) catalyses the acetylation of serotonin, a rate-limiting process in melatonin biosynthesis. To obtain better insight into the underlying mechanism of AANAT's actions in switchgrass growth, flowering and defence, we performed integrated morphological, physiological and omics analyses between overexpressed oAANAT transgenic lines in wild-type and transgenic control (expressing only the empty vector) plants. We showed that oAANAT played pivotal roles in modulating plant growth through its regulation of cell elongation, and regulating flowering through photoperiod and GA pathways. In relation to photosynthesis, oAANAT promoted photosynthetic efficiency primarily through regulating leaf anatomical structures, stomatal development and chlorophyll metabolism. Moreover, oAANAT overexpression can trigger a number of defence responses or strategies, including antioxidant enzymatic properties, non-enzymatic capacity, significantly activated phenylpropanoid biosynthesis, and adaptive morphological characteristics. This study unveils the possible molecular mechanisms underlying oAANAT dependent melatonin functions in switchgrass, providing an important starting point for further analyses.
Collapse
Affiliation(s)
- Yanhua Huang
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, China.
| | - Zehui Zheng
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, China.
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
| | - Kai Guo
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, China.
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Xuexue Huo
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong, China.
| | - Danyang Tian
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
| | - Huayue Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
| | - Lei Wang
- Forestry College, Inner Mongolia Agricultural University, Hohhot, China.
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
24
|
Griffiths M, Wang X, Dhakal K, Guo H, Seethepalli A, Kang Y, York LM. Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.). J Exp Bot 2022; 73:967-979. [PMID: 34604906 PMCID: PMC8793874 DOI: 10.1093/jxb/erab437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The response of plant growth and development to nutrient and water availability is an important adaptation for abiotic stress tolerance. Roots need to intercept both passing nutrients and water while foraging into new soil layers for further resources. Substantial amounts of nitrate can be lost in the field when leaching into groundwater, yet very little is known about how deep rooting affects this process. Here, we phenotyped root system traits and deep 15N nitrate capture across 1.5 m vertical profiles of solid media using tall mesocosms in switchgrass (Panicum virgatum L.), a promising cellulosic bioenergy feedstock. Root and shoot biomass traits, photosynthesis and respiration measures, and nutrient uptake and accumulation traits were quantified in response to a water and nitrate stress factorial experiment for switchgrass upland (VS16) and lowland (AP13) ecotypes. The two switchgrass ecotypes shared common plastic abiotic responses to nitrogen (N) and water availability, and yet had substantial genotypic variation for root and shoot traits. A significant interaction between N and water stress combination treatments for axial and lateral root traits represents a complex and shared root development strategy for stress mitigation. Deep root growth and 15N capture were found to be closely linked to aboveground growth. Together, these results represent the wide genetic pool of switchgrass and show that deep rooting promotes nitrate capture, plant productivity, and sustainability.
Collapse
Affiliation(s)
- Marcus Griffiths
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Xueyan Wang
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Kundan Dhakal
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Haichao Guo
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Anand Seethepalli
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Yun Kang
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Larry M York
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| |
Collapse
|
25
|
Prías-Blanco M, Chappell TM, Freed EF, Illa-Berenguer E, Eckert CA, Parrott WA. An Agrobacterium strain auxotrophic for methionine is useful for switchgrass transformation. Transgenic Res 2022; 31:661-676. [PMID: 36239844 PMCID: PMC9747830 DOI: 10.1007/s11248-022-00328-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 09/26/2022] [Indexed: 01/20/2023]
Abstract
Auxotrophic strains of Agrobacterium tumefaciens can contribute to the development of more efficient transformation systems, especially for crops historically considered recalcitrant. Homologous recombination was used to derive methionine auxotrophs of two common A. tumefaciens strains, LBA4404 and EHA105. The EHA105 strains were more efficient for switchgrass transformation, while both the EHA105 and LBA4404 strains worked equally well for the rice control. Event quality, as measured by transgene copy number, was not affected by auxotrophy, but was higher for the LBA4404 strains than the EHA105 strains. Ultimately, the use of auxotrophs reduced bacterial overgrowth during co-cultivation and decreased the need for antibiotics.
Collapse
Affiliation(s)
- Mónica Prías-Blanco
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Timothy M Chappell
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Emily F Freed
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA
| | | | - Carrie A Eckert
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, CO, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Wayne A Parrott
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA.
| |
Collapse
|
26
|
Barre P, Asp T, Byrne S, Casler M, Faville M, Rognli OA, Roldan-Ruiz I, Skøt L, Ghesquière M. Genomic Prediction of Complex Traits in Forage Plants Species: Perennial Grasses Case. Methods Mol Biol 2022; 2467:521-541. [PMID: 35451789 DOI: 10.1007/978-1-0716-2205-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The majority of forage grass species are obligate outbreeders. Their breeding classically consists of an initial selection on spaced plants for highly heritable traits such as disease resistances and heading date, followed by familial selection on swards for forage yield and quality traits. The high level of diversity and heterozygosity, and associated decay of linkage disequilibrium (LD) over very short genomic distances, has hampered the implementation of genomic selection (GS) in these species. However, next generation sequencing technologies in combination with the development of genomic resources have recently facilitated implementation of GS in forage grass species such as perennial ryegrass (Lolium perenne L.), switchgrass (Panicum virgatum L.), and timothy (Phleum pratense L.). Experimental work and simulations have shown that GS can increase significantly the genetic gain per unit of time for traits with different levels of heritability. The main reasons are (1) the possibility to select single plants based on their genomic estimated breeding values (GEBV) for traits measured at sward level, (2) a reduction in the duration of selection cycles, and less importantly (3) an increase in the selection intensity associated with an increase in the genetic variance used for selection. Nevertheless, several factors should be taken into account for the successful implementation of GS in forage grasses. For example, it has been shown that the level of relatedness between the training and the selection population is particularly critical when working with highly structured meta-populations consisting of several genetic groups. A sufficient number of markers should be used to estimate properly the kinship between individuals and to reflect the variability of major QTLs. It is also important that the prediction models are trained for relevant environments when dealing with traits with high genotype × environment interaction (G × E). Finally, in these outbreeding species, measures to reduce inbreeding should be used to counterbalance the high selection intensity that can be achieved in GS.
Collapse
Affiliation(s)
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus University, Slagelse, Denmark
| | - Stephen Byrne
- Teagasc, Crop Science Department, Oak Park, Carlow, Ireland
| | - Michael Casler
- U.S. Dairy Forage Research Center, USDA-ARS, Madison, WI, USA
| | - Marty Faville
- AgResearch Ltd , Grasslands Research Centre, Palmerston North, New Zealand
| | - Odd Arne Rognli
- Department of Plant Sciences, Faculty of Biosciences, Norwegian, University of Life Sciences (NMBU), Ås, Norway
| | - Isabel Roldan-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO)-Plant Sciences Unit, Melle, Belgium
| | - Leif Skøt
- IBERS, Aberystwyth University, Ceredigion, UK
| | | |
Collapse
|
27
|
Qiao Z, Yates TB, Shrestha HK, Engle NL, Flanagan A, Morrell‐Falvey JL, Sun Y, Tschaplinski TJ, Abraham PE, Labbé J, Wang Z, Hettich RL, Tuskan GA, Muchero W, Chen J. Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor-like kinase. Plant Biotechnol J 2021; 19:2454-2468. [PMID: 34272801 PMCID: PMC8633507 DOI: 10.1111/pbi.13671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 06/24/2021] [Accepted: 07/09/2021] [Indexed: 05/22/2023]
Abstract
Soil-borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole-genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor-like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor-root colonization by the ectomycorrhizal fungus Laccaria bicolor. By introducing PtLecRLK1 into a perennial grass known to be a non-host of L. bicolor, switchgrass (Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro-PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non-host to a host of L. bicolor. Furthermore, transcriptomic and proteomic analyses on inoculated-transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down-regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N-containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non-host to enhance plant productivity and fitness on marginal lands.
Collapse
Affiliation(s)
- Zhenzhen Qiao
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Timothy B. Yates
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTNUSA
| | - Him K. Shrestha
- Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Nancy L. Engle
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Yali Sun
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Paul E. Abraham
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jessy Labbé
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | - Robert L. Hettich
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
- Chemical Science DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | | | | | - Jin‐Gui Chen
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| |
Collapse
|
28
|
Tilhou NW, Casler MD. Subsampling and DNA pooling can increase gains through genomic selection in switchgrass. Plant Genome 2021; 14:e20149. [PMID: 34626166 DOI: 10.1002/tpg2.20149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross-validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence-based GS when sequencing resources were restricted (2,000 DNA samples per 5-yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5-yr cycle). This study highlights multiple routes for reduced sequencing costs in GS.
Collapse
Affiliation(s)
- Neal Wepking Tilhou
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI, 53706, USA
| | - Michael D Casler
- U.S. Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr, Madison, WI, 53706-1108, USA
| |
Collapse
|
29
|
Muchlinski A, Jia M, Tiedge K, Fell JS, Pelot KA, Chew L, Davisson D, Chen Y, Siegel J, Lovell JT, Zerbe P. Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.). Plant J 2021; 108:1053-1068. [PMID: 34514645 PMCID: PMC9292899 DOI: 10.1111/tpj.15492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 05/02/2023]
Abstract
Specialized diterpenoid metabolites are important mediators of plant-environment interactions in monocot crops. To understand metabolite functions in plant environmental adaptation that ultimately can enable crop improvement strategies, a deeper knowledge of the underlying species-specific biosynthetic pathways is required. Here, we report the genomics-enabled discovery of five cytochrome P450 monooxygenases (CYP71Z25-CYP71Z29) that form previously unknown furanoditerpenoids in the monocot bioenergy crop Panicum virgatum (switchgrass). Combinatorial pathway reconstruction showed that CYP71Z25-CYP71Z29 catalyze furan ring addition directly to primary diterpene alcohol intermediates derived from distinct class II diterpene synthase products. Transcriptional co-expression patterns and the presence of select diterpenoids in switchgrass roots support the occurrence of P450-derived furanoditerpenoids in planta. Integrating molecular dynamics, structural analysis and targeted mutagenesis identified active site determinants that contribute to the distinct catalytic specificities underlying the broad substrate promiscuity of CYP71Z25-CYP71Z29 for native and non-native diterpenoids.
Collapse
Affiliation(s)
- Andrew Muchlinski
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
- Present address:
Firmenich Inc.4767 Nexus Center Dr.San DiegoCalifornia9212USA
| | - Meirong Jia
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
- Present address:
State Key Laboratory of Bioactive Substance and Function of Natural Medicines & NHC Key Laboratory of Biosynthesis of Natural ProductsInstitute of Materia MedicaChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100050China
| | - Kira Tiedge
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Jason S. Fell
- Genome CenterUniversity of California – DavisDavisCalifornia95616USA
| | - Kyle A. Pelot
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Lisl Chew
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Danielle Davisson
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Yuxuan Chen
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| | - Justin Siegel
- Genome CenterUniversity of California – DavisDavisCalifornia95616USA
- Department of ChemistryUniversity of California – DavisDavisCalifornia95616USA
- Department of Biochemistry & Molecular MedicineUniversity of California – DavisDavisCalifornia95616USA
| | - John T. Lovell
- Genome Sequencing CenterHudson Alpha Institute for BiotechnologyHuntsvilleAlabama35806USA
| | - Philipp Zerbe
- Department of Plant BiologyUniversity of California – DavisDavisCalifornia95616USA
| |
Collapse
|
30
|
Poudel HP, Tilhou NW, Sanciangco MD, Vaillancourt B, Kaeppler SM, Buell CR, Casler MD. Genetic loci associated with winter survivorship in diverse lowland switchgrass populations. Plant Genome 2021; 14:e20159. [PMID: 34661986 DOI: 10.1002/tpg2.20159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
High winter mortality limits biomass yield of lowland switchgrass (Panicum virgatum L.) planted in the northern latitudes of North America. Breeding of cold tolerant switchgrass cultivars requires many years due to its perennial growth habit and the unpredictable winter selection pressure that is required to identify winter-hardy individuals. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 populations with differential winter survivorship were used for BSA. A maximum of 10% of the individuals (8-20) were bulked to create survivor and nonsurvivor DNA pools from each population and location. The DNA pools were evaluated using exome capture sequencing, and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine quatitative trait loci (QTL) from tetraploid populations and seven QTL from octoploid populations. Many QTL were population-specific, but some were identified in multiple populations that originated across a broad geographic landscape. Four QTL (at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N) were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.
Collapse
Affiliation(s)
- Hari P Poudel
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Neal W Tilhou
- Dep. of Agronomy, Univ. of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - C Robin Buell
- Dep. of Plant Biology, Michigan State Univ., East Lansing, MI, USA
| | | |
Collapse
|
31
|
Ray P, Guo Y, Chi MH, Krom N, Boschiero C, Watson B, Huhman D, Zhao P, Singan VR, Lindquist EA, Yan J, Adam C, Craven KD. Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship. Mol Plant Microbe Interact 2021; 34:1128-1142. [PMID: 34260261 DOI: 10.1094/mpmi-04-21-0084-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yingqing Guo
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Bonnie Watson
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - David Huhman
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Patrick Zhao
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Vasanth R Singan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Erika A Lindquist
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Juying Yan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Catherine Adam
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | | |
Collapse
|
32
|
Li G, Zhang L, Xue P. Codon usage pattern and genetic diversity in chloroplast genomes of Panicum species. Gene 2021; 802:145866. [PMID: 34352297 DOI: 10.1016/j.gene.2021.145866] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022]
Abstract
Exploring the molecular identities and the genetic diversity of a plant species is crucial in figuring out the evolutionary pressure of genes as well as in molecular breeding application. Nineteen chloroplast genomes of Panicum species in the National Center for Biotechnology Information database were downloaded and analyzed. The base composition, the effective number of codons, the relative synonymous codon usage, the codon bias index and the codon adaptation index of all genes in all chloroplast genomes, as well as the correlation coefficient among them, were calculated and discussed. The correspondence analysis and the clustering characteristics among nineteen genomes base on the relative synonymous codon usage values of nineteen chloroplast genomes were calculated and analyzed. In order to figuring out the evolutionary diversity of certain genes, the codon usage pattern of forty-one typical genes were separately counted and compared. Summations of their standard deviations were considered to evaluate their genetic diversities. The results of codon usage pattern showed that all genes were obvious AU-rich ones in chloroplast genomes of Panicum species, revealing that the natural selection was the main factor that influenced their evolutionary process. The correspondence and clustering analysis among nineteen chloroplast genomes showed that the overall evolutionary differences among them were not significant. However, the analysis on the genetic diversity of tyical genes showed that the degrees of diversity are different, and that the shorter sequences are more prone to instability. These findings would improve our understanding on the evolution of chloroplast genomes of Panicum species and be useful for further study on their evolutionary phenomenon.
Collapse
Affiliation(s)
- Gun Li
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronics Information Engineering, Xi'An Technological University, Xi'An, China.
| | - Liang Zhang
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronics Information Engineering, Xi'An Technological University, Xi'An, China
| | - Pei Xue
- Laboratory for Biodiversity Science, Department of Biomedical Engineering, School of Electronics Information Engineering, Xi'An Technological University, Xi'An, China
| |
Collapse
|
33
|
Liu Y, Yan J, Wang K, Li D, Yang R, Luo H, Zhang W. MiR396-GRF module associates with switchgrass biomass yield and feedstock quality. Plant Biotechnol J 2021; 19:1523-1536. [PMID: 33567151 PMCID: PMC8384596 DOI: 10.1111/pbi.13567] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 05/10/2023]
Abstract
Improving plant biomass yield and/or feedstock quality for highly efficient lignocellulose conversion has been the main research focus in genetic modification of switchgrass (Panicum virgatum L.), a dedicated model plant for biofuel production. Here, we proved that overexpression of miR396 (OE-miR396) leads to reduced plant height and lignin content mainly by reducing G-lignin monomer content. We identified nineteen PvGRFs in switchgrass and proved thirteen of them were cleaved by miR396. MiR396-targeted PvGRF1, PvGRF9 and PvGRF3 showed significantly higher expression in stem. By separately overexpressing rPvGRF1, 3 and 9, in which synonymous mutations abolished the miR396 target sites, and suppression of PvGRF1/3/9 activity via PvGRF1/3/9-SRDX overexpression in switchgrass, we confirmed PvGRF1 and PvGRF9 played positive roles in improving plant height and G-lignin content. Overexpression of PvGRF9 was sufficient to complement the defective phenotype of OE-miR396 plants. MiR396-PvGRF9 modulates these traits partly by interfering GA and auxin biosynthesis and signalling transduction and cell wall lignin, glucose and xylan biosynthesis pathways. Moreover, by enzymatic hydrolysis analyses, we found that overexpression of rPvGRF9 significantly enhanced per plant sugar yield. Our results suggest that PvGRF9 can be utilized as a candidate molecular tool in modifying plant biomass yield and feedstock quality.
Collapse
Affiliation(s)
- Yanrong Liu
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
| | - Jianping Yan
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
| | - Kexin Wang
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
| | - Dayong Li
- College of Life SciencesShandong Normal UniversityJinanShandongChina
| | - Rui Yang
- Beijing Key Laboratory of New Technology in Agricultural ApplicationCollege of Plant Science and TechnologyBeijing University of AgricultureBeijingChina
| | - Hong Luo
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Wanjun Zhang
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
- Key Lab of Grassland Science in BeijingChina Agricultural UniversityBeijingChina
| |
Collapse
|
34
|
Boukail S, Macharia M, Miculan M, Masoni A, Calamai A, Palchetti E, Dell'Acqua M. Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.). BMC Plant Biol 2021; 21:330. [PMID: 34243721 PMCID: PMC8268170 DOI: 10.1186/s12870-021-03111-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/23/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND The climate crisis threatens sustainability of crop production worldwide. Crop diversification may enhance food security while reducing the negative impacts of climate change. Proso millet (Panicum milaceum L.) is a minor cereal crop which holds potential for diversification and adaptation to different environmental conditions. In this study, we assembled a world collection of proso millet consisting of 88 varieties and landraces to investigate its genomic and phenotypic diversity for seed traits, and to identify marker-trait associations (MTA). RESULTS Sequencing of restriction-site associated DNA fragments yielded 494 million reads and 2,412 high quality single nucleotide polymorphisms (SNPs). SNPs were used to study the diversity in the collection and perform a genome wide association study (GWAS). A genotypic diversity analysis separated accessions originating in Western Europe, Eastern Asia and Americas from accessions sampled in Southern Asia, Western Asia, and Africa. A Bayesian structure analysis reported four cryptic genetic groups, showing that landraces accessions had a significant level of admixture and that most of the improved proso millet materials clustered separately from landraces. The collection was highly diverse for seed traits, with color varying from white to dark brown and width spanning from 1.8 to 2.6 mm. A GWAS study for seed morphology traits identified 10 MTAs. In addition, we identified three MTAs for agronomic traits that were previously measured on the collection. CONCLUSION Using genomics and automated seed phenotyping, we elucidated phylogenetic relationships and seed diversity in a global millet collection. Overall, we identified 13 MTAs for key agronomic and seed traits indicating the presence of alleles with potential for application in proso breeding programs.
Collapse
Affiliation(s)
- Sameh Boukail
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Mercy Macharia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Mara Miculan
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Alberto Masoni
- School of Agriculture, University of Florence, Florence, Italy
| | | | | | - Matteo Dell'Acqua
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
| |
Collapse
|
35
|
Qi P, Pendergast TH, Johnson A, Bahri BA, Choi S, Missaoui A, Devos KM. Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes. Theor Appl Genet 2021; 134:1957-1975. [PMID: 33760937 PMCID: PMC8263549 DOI: 10.1007/s00122-021-03798-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/19/2021] [Indexed: 06/06/2023]
Abstract
Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F2 mapping populations were developed by crossing two different F1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.
Collapse
Affiliation(s)
- Peng Qi
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Thomas H Pendergast
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Alex Johnson
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Katrien M Devos
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
- Institute of Plant Breeding, Genetics and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
36
|
Wang Y, Dong W, Saha MC, Udvardi MK, Kang Y. Improved node culture methods for rapid vegetative propagation of switchgrass (Panicum virgatum L.). BMC Plant Biol 2021; 21:128. [PMID: 33663376 PMCID: PMC7931530 DOI: 10.1186/s12870-021-02903-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is an important bioenergy and forage crop. The outcrossing nature of switchgrass makes it infeasible to maintain a genotype through sexual propagation. Current asexual propagation protocols in switchgrass have various limitations. An easy and highly-efficient vegetative propagation method is needed to propagate large natural collections of switchgrass genotypes for genome-wide association studies (GWAS). RESULTS Micropropagation by node culture was found to be a rapid method for vegetative propagation of switchgrass. Bacterial and fungal contamination during node culture is a major cause for cultural failure. Adding the biocide, Plant Preservative Mixture (PPM, 0.2%), and the fungicide, Benomyl (5 mg/l), in the incubation solution after surface sterilization and in the culture medium significantly decreased bacterial and fungal contamination. In addition, "shoot trimming" before subculture had a positive effect on shoot multiplication for most genotypes tested. Using the optimized node culture procedure, we successfully propagated 330 genotypes from a switchgrass GWAS panel in three separate experiments. Large variations in shoot induction efficiency and shoot growth were observed among genotypes. Separately, we developed an in planta node culture method by stimulating the growth of aerial axillary buds into shoots directly on the parent plants, through which rooted plants can be generated within 6 weeks. By circumventing the tissue culture step and avoiding application of exterior hormones, the in planta node culture method is labor- and cost-efficient, easy to master, and has a high success rate. Plants generated by the in planta node culture method are similar to seedlings and can be used directly for various experiments. CONCLUSIONS In this study, we optimized a switchgrass node culture protocol by minimizing bacterial and fungal contamination and increasing shoot multiplication. With this improved protocol, we successfully propagated three quarters of the genotypes in a diverse switchgrass GWAS panel. Furthermore, we established a novel and high-throughput in planta node culture method. Together, these methods provide better options for researchers to accelerate vegetative propagation of switchgrass.
Collapse
Affiliation(s)
- Yongqin Wang
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Weihong Dong
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | | | - Yun Kang
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA.
| |
Collapse
|
37
|
Mahelka V, Krak K, Fehrer J, Caklová P, Nagy Nejedlá M, Čegan R, Kopecký D, Šafář J. A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes. Plant J 2021; 105:1141-1164. [PMID: 33484020 DOI: 10.1111/tpj.15167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Intra-specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeum bogdanii and 219 kb in the South American Hordeum pubiflorum, resides on a pair of nucleolar organizer region (NOR)-bearing chromosomes. Conserved synteny and micro-collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5-1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress-related protein-coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein-coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non-synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein-coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species.
Collapse
Affiliation(s)
- Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Karol Krak
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, 16500, Czech Republic
| | - Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | | | - Radim Čegan
- Institute of Biophysics, Czech Academy of Sciences, Brno, 61265, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| |
Collapse
|
38
|
Hao Z, Yogiswara S, Wei T, Benites VT, Sinha A, Wang G, Baidoo EEK, Ronald PC, Scheller HV, Loqué D, Eudes A. Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.). BMC Plant Biol 2021; 21:56. [PMID: 33478381 PMCID: PMC7819203 DOI: 10.1186/s12870-021-02842-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/13/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lignin deposited in plant cell walls negatively affects biomass conversion into advanced bioproducts. There is therefore a strong interest in developing bioenergy crops with reduced lignin content or altered lignin structures. Another desired trait for bioenergy crops is the ability to accumulate novel bioproducts, which would enhance the development of economically sustainable biorefineries. As previously demonstrated in the model plant Arabidopsis, expression of a 3-dehydroshikimate dehydratase in plants offers the potential for decreasing lignin content and overproducing a value-added metabolic coproduct (i.e., protocatechuate) suitable for biological upgrading. RESULTS The 3-dehydroshikimate dehydratase QsuB from Corynebacterium glutamicum was expressed in the bioenergy crop switchgrass (Panicum virgatum L.) using the stem-specific promoter of an O-methyltransferase gene (pShOMT) from sugarcane. The activity of pShOMT was validated in switchgrass after observation in-situ of beta-glucuronidase (GUS) activity in stem nodes of plants carrying a pShOMT::GUS fusion construct. Under controlled growth conditions, engineered switchgrass lines containing a pShOMT::QsuB construct showed reductions of lignin content, improvements of biomass saccharification efficiency, and accumulated higher amount of protocatechuate compared to control plants. Attempts to generate transgenic switchgrass lines carrying the QsuB gene under the control of the constitutive promoter pZmUbi-1 were unsuccessful, suggesting possible toxicity issues associated with ectopic QsuB expression during the plant regeneration process. CONCLUSION This study validates the transfer of the QsuB engineering approach from a model plant to switchgrass. We have demonstrated altered expression of two important traits: lignin content and accumulation of a co-product. We found that the choice of promoter to drive QsuB expression should be carefully considered when deploying this strategy to other bioenergy crops. Field-testing of engineered QsuB switchgrass are in progress to assess the performance of the introduced traits and agronomic performances of the transgenic plants.
Collapse
Affiliation(s)
- Zhangying Hao
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Tong Wei
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Present address: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518000 China
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Anagh Sinha
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - George Wang
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Pamela C. Ronald
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| |
Collapse
|
39
|
Guan C, Li X, Tian DY, Liu HY, Cen HF, Tadege M, Zhang YW. ADP-ribosylation factors improve biomass yield and salinity tolerance in transgenic switchgrass (Panicum virgatum L.). Plant Cell Rep 2020; 39:1623-1638. [PMID: 32885306 DOI: 10.1007/s00299-020-02589-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
PvArf regulate proline biosynthesis by physically interacting with PvP5CS1 to improve salt tolerance in switchgrass. The genetic factors that contribute to stress resiliency are yet to be determined. Here, we identified three ADP-ribosylation factors, PvArf1, PvArf-B1C, and PvArf-related, which contribute to salinity tolerance in transgenic switchgrass (Panicum virgatum L.). Switchgrass overexpressing each of these genes produced approximately twofold more biomass than wild type (WT) under normal growth conditions. Transgenic plants accumulated modestly higher levels of proline under normal conditions, but this level was significantly increased under salt stress providing better protection to transgenic plants compared to WT. We found that PvArf genes induce proline biosynthesis genes under salt stress to positively regulate proline accumulation, and further demonstrated that PvArf physically interact with PvP5CS1. Moreover, the transcript levels of two key ROS-scavenging enzyme genes were significantly increased in the transgenic plants compared to WT, leading to reduced H2O2 accumulation under salt stress conditions. PvArf genes also protect cells against stress-induced changes in Na+ and K+ ion concentrations. Our findings uncover that ADP-ribosylation factors are key determinants of biomass yield in switchgrass, and play pivotal roles in salinity tolerance by regulating genes involved in proline biosynthesis.
Collapse
Affiliation(s)
- Cong Guan
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
- Shandong institute of agricultural sustainable development, Jinan, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Dan-Yang Tian
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Hua-Yue Liu
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Hui-Fang Cen
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Bioscience, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Yun-Wei Zhang
- College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing, 100193, China.
- Beijing Key Laboratory for Grassland Science, China Agricultural University, Beijing, China.
- National Energy R&D Center for Biomass (NECB), Beijing, China.
- Beijing Sure Academy of Biosciences, Beijing, China.
| |
Collapse
|
40
|
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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
41
|
Bragg J, Tomasi P, Zhang L, Williams T, Wood D, Lovell JT, Healey A, Schmutz J, Bonnette JE, Cheng P, Chanbusarakum L, Juenger T, Tobias CM. Environmentally responsive QTL controlling surface wax load in switchgrass. Theor Appl Genet 2020; 133:3119-3137. [PMID: 32803378 DOI: 10.1007/s00122-020-03659-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE Quantitation of leaf surface wax on a population of switchgrass identified three significant QTL present across six environments that contribute to leaf glaucousness and wax composition and that show complex genetic × environmental (G × E) interactions. The C4 perennial grass Panicum virgatum (switchgrass) is a native species of the North American tallgrass prairie. This adaptable plant can be grown on marginal lands and is useful for soil and water conservation, biomass production, and as a forage. Two major switchgrass ecotypes, lowland and upland, differ in a range of desirable traits, and the responsible underlying loci can be localized efficiently in a pseudotestcross design. An outbred four-way cross (4WCR) mapping population of 750 F2 lines was used to examine the genetic basis of differences in leaf surface wax load between two lowland (AP13 and WBC) and two upland (DAC and VS16) tetraploid cultivars. The objective of our experiments was to identify wax compositional variation among the population founders and to map underlying loci responsible for surface wax variation across environments. GCMS analyses of surface wax extracted from 4WCR F0 founders and F1 hybrids reveal higher levels of wax in lowland genotypes and show quantitative differences of β-diketones, primary alcohols, and other wax constituents. The full mapping population was sampled over two seasons from four field sites with latitudes ranging from 30 to 42 °N, and leaf surface wax was measured. We identified three high-confidence QTL, of which two displayed significant G × E effects. Over 50 candidate genes underlying the QTL regions showed similarity to genes in either Arabidopsis or barley known to function in wax synthesis, modification, regulation, and transport.
Collapse
Affiliation(s)
- Jennifer Bragg
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Pernell Tomasi
- Arid-Land Agricultural Research Center, Plant Physiology and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Maricopa, AZ, USA
| | - Li Zhang
- Department of Integrative Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Tina Williams
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Delilah Wood
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jason E Bonnette
- Department of Integrative Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Prisca Cheng
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Lisa Chanbusarakum
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA
| | - Thomas Juenger
- Department of Integrative Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Christian M Tobias
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Albany, CA, USA.
| |
Collapse
|
42
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.)
| |
Collapse
|
43
|
Yazdizadeh M, Fahmideh L, Mohammadi-Nejad G, Solouki M, Nakhoda B. Association analysis between agronomic traits and AFLP markers in a wide germplasm of proso millet (Panicum miliaceum L.) under normal and salinity stress conditions. BMC Plant Biol 2020; 20:427. [PMID: 32933479 PMCID: PMC7493190 DOI: 10.1186/s12870-020-02639-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Proso millet is a highly nutritious cereal considered an essential component of processed foods. It is also recognized with high water-use efficiency as well as short growing seasons. This research was primarily aimed at investigating the genetic diversity among genotypes based on evaluating those important traits proposed in previous researches under both normal and salinity- stress conditions. Use of Amplified fragment length polymorphism (AFLP) molecular markers as well as evaluating the association between markers and the investigated traits under both conditions was also another purpose of this research. RESULTS According to the phenotypic correlation coefficients, the seed yield had the highest correlation with the forage and biological yields under both conditions. By disintegrating those traits investigated under normal and salinity-stress conditions into principal component analysis, it was found that the first four principal components justified more than 59.94 and 62.48% of the whole variance, respectively. The dendrogram obtained by cluster analysis displayed three groups of genotypes under both normal and salinity- stress conditions. Then, association analyses were conducted on 143 proso millet genotypes and 15 agronomic traits as well as 514 polymorphic AFLP markers (out of 866 created bands) generated by 11 primer combinations (out of the initial 20 primer combinations) EcoRI/MseI. The results obtained by mixed linear model (MLM) indicated that under normal conditions, the M14/E10-45 and M14/E10-60 markers had strong associations with seed yield. A similar trend was also observed for M14/E10-45 and M14/E11-44 markers in relation to forage yield. On the other hand, M14/E10-14, M14/E10-64 markers (for seed yield) and M14/E10-64 marker (for forage yield), had significant and stable association in all environments under salinity-stress conditions. Moreover, a number of markers showed considerable associations and stability under both normal and salinity stress conditions. CONCLUSIONS According to the analysis of phenotypic data, the wide germplasm of Iranian proso millet has significant variation in terms of measured traits. It can be concluded that markers showing strong associations with traits under salinity-stress conditions are suitable candidates to be used in future marker-assisted selection (MAS) studies to improve salinity-resistance genotypes of Panicum miliaceum in arid and semiarid areas.
Collapse
Affiliation(s)
- Mehdi Yazdizadeh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Sistan and Baluchestan province, Iran
| | - Leila Fahmideh
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Sistan and Baluchestan province, Iran.
| | - Ghasem Mohammadi-Nejad
- Department of Agronomy and Plant Breeding, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Sistan and Baluchestan province, Iran
| | - Babak Nakhoda
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Mahdasht Rd, Karaj, 31535-1897, Iran
| |
Collapse
|
44
|
VanWallendael A, Bonnette J, Juenger TE, Fritschi FB, Fay PA, Mitchell RB, Lloyd-Reilley J, Rouquette FM, Bergstrom GC, Lowry DB. Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum). New Phytol 2020; 227:1696-1708. [PMID: 32202657 DOI: 10.1111/nph.16555] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/06/2020] [Indexed: 05/28/2023]
Abstract
Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.
Collapse
Affiliation(s)
- Acer VanWallendael
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65201, USA
| | - Philip A Fay
- Soil and Water Research Laboratory, USDA-ARS Grassland, Temple, TX, 76508, USA
| | - Robert B Mitchell
- USDA-ARS Wheat, Sorghum, and Forage Research Unit, University of Nebraska, Lincoln, NE, 68588, USA
| | - John Lloyd-Reilley
- USDA-NRCS, Kika de la Garza Plant Materials Center, Kingsville, TX, 78572, USA
| | - Francis M Rouquette
- Texas A&M AgriLife Research, Texas A&M AgriLife Research and Extension Center, Overton, TX, 75684, USA
| | - Gary C Bergstrom
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|
45
|
Zhang T, Li K, Ding X, Sui Z, Yang QQ, Shah NP, Liu G, Corke H. Starch properties of high and low amylose proso millet (Panicum miliaceum L.) genotypes are differentially affected by varying salt and pH. Food Chem 2020; 337:127784. [PMID: 32795860 DOI: 10.1016/j.foodchem.2020.127784] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/23/2020] [Accepted: 08/03/2020] [Indexed: 11/17/2022]
Abstract
Variation in salt content and in pH are common in starch-based foods and can affect starch properties and final product texture. Fifteen accessions of proso millet starch with diverse amylose content were selected to investigate single factor and interaction effects of pH and NaCl on thermal, pasting, and textural properties. Pasting properties and gelatinization temperatures were markedly altered by salt addition. Changes in pH only had substantial effects on ΔH, but other properties were generally stable under different pH conditions. From two-way ANOVA, interactive effects of salt and pH were found to affect ΔH. The response of starch of different genotypes in terms of thermal and pasting properties differed under the same pH and salinity conditions. The reason is likely that ions in the starch-water system performed the roles of both reducing water activity and building of hydrogen bonds, which will have opposite effects on starch gelatinization.
Collapse
Affiliation(s)
- Tongze Zhang
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China; School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, People's Republic of China
| | - Kehu Li
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Xinghua Ding
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, People's Republic of China
| | - Zhongquan Sui
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Qiong-Qiong Yang
- Department of Food Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Nagendra P Shah
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region, People's Republic of China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Science, Shijiazhuang 050035, People's Republic of China.
| | - Harold Corke
- Biotechnology and Food Engineering Program, Guangdong Technion - Israel Institute of Technology, Shantou 515063, People's Republic of China; Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
46
|
Fan KH, Devos KM, Schliekelman P. Strategies for eQTL mapping in allopolyploid organisms. Theor Appl Genet 2020; 133:2477-2497. [PMID: 32462429 DOI: 10.1007/s00122-020-03612-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE This study uses simulations to explore statistical power and false-positive rates for eQTL mapping in allopolyploid organisms and provides guidelines to apply eQTL mapping in these organisms. In recent years, RNA-seq has become the dominant technology for eQTL studies. However, most work has been in diploid organisms. Many species of economic and environmental importance are polyploid, and approaches for eQTL mapping in polyploids are not well developed. High similarity between duplicated genes in polyploids will cause misassignment of sequence reads and may cause false-positive results and/or lack of power to detect eQTL. In this paper, we first explore the similarity of homoeologous transcripts in polyploid organisms. We find that 5-20% of genes (varying with organism) in important agricultural plants such as wheat, soybean, and switchgrass are not sufficiently diverged between duplicated genomes to allow unambiguous assignment of reads. Second, we examine the impact of misassigned reads on eQTL mapping and show that both false-positive and false-negative rates can be greatly inflated. Third, we compare four strategies for dealing with ambiguous reads: (1) dividing ambiguous reads evenly between homoeologous transcripts, (2) assigning them proportionally, (3) using all reads for all genes, and (4) discarding ambiguous reads. We find that the strategy of discarding ambiguous reads gives the best balance of false-positive and false-negative rates for most genes. However, for genes that are very similar between genomes, using all reads is the only choice. This leads to reduced power, but false-positive rates will be maintained. We also discuss QTL mapping in polyploids using allele-specific expression (ASE) and show how the proportion of ASE-informative reads varies according to the divergence between homoeologous genes.
Collapse
Affiliation(s)
- Kang-Hsien Fan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Katrien M Devos
- Department of Crop and Soil Sciences, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | | |
Collapse
|
47
|
Cheng Q, Xiao H, Xiong Q. Conserved exitrons of FLAGELLIN-SENSING 2 (FLS2) across dicot plants and their functions. Plant Sci 2020; 296:110507. [PMID: 32540022 DOI: 10.1016/j.plantsci.2020.110507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/20/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
The alternative splicing of pattern recognition receptor genes regulates immune signalling in mammals, but in plants its role is still unknown. Here, we detected alternatively spliced introns (exitrons) in the first annotated exons of FLAGELLIN-SENSING 2 (FLS2) genes in all the examined dicot plants across nine families. The 5' splice site (SS) regions were conserved and with rare synonymous substitutions. Point mutations and gene swaps indicated that the position and efficiency of exitron splicing primarily depended on the nucleotide sequences of FLS2 genes. Single-nucleotide mutations in the invariable codon carrying 5' SS dramatically altered the accumulation of poplar and tomato FLS2 transcripts, indicating the 5'-proximal exitrons of FLS2 function as stimulatory introns on gene expression. The 3' SSs of exitrons are diverse and can be changed by 1-2 nucleotide mutations in Salicaceae FLS2. The alternative transcripts (ATs) of poplar and tobacco FLS2, which encode small secreted proteins, were specifically induced by flg22, and one such AT from tobacco FLS2 suppressed flg22-induced response. Our results indicated that the exitrons of FLS2 genes regulate the accumulation of transcripts by an intron mediated enhancement (IME) mechanism and some ATs have the potential to encode suppressors for FLS2 pathway.
Collapse
Affiliation(s)
- Qiang Cheng
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Hongju Xiao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Qin Xiong
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| |
Collapse
|
48
|
Cen H, Liu Y, Li D, Wang K, Zhang Y, Zhang W. Heterologous expression of a chimeric gene, OsDST-SRDX, enhanced salt tolerance of transgenic switchgrass (Panicum virgatum L.). Plant Cell Rep 2020; 39:723-736. [PMID: 32130473 DOI: 10.1007/s00299-020-02526-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
Overexpression of OsDST-SRDX chimeric gene in switchgrass promotes plant growth and improves the salt tolerance of transgenic switchgrass by improving its antioxidative ability. Switchgrass (Panicum virgatum L.) is a forage and model feedstock plant. To avoid competing with crops in arable land utilization, improving salt tolerance of switchgrass is required to use marginal saline land for switchgrass production. To improve salt tolerance of switchgrass, a chimeric DROUGHT AND SALT TOLERANCE (DST) gene OsDST-SRDX was constructed using the Chimeric REpressor gene-Silencing Technology (CRES-T), and introduced into switchgrass genome by Agrobacterium-mediated transformation. Compared to wild-type (WT) plants, OsDST-SRDX transgenic (TG) switchgrass plants showed wider leaves and thicker stems. They performed better under salt stress, had higher relative leaf water content, lower electrolyte leakage and lower malondialdehyde (MDA) content, and accumulated less Na+ and more K+ than WT controls. The transgenic plants had also higher activities of antioxidant enzymes associated with suppressed expressing of genes in H2O2 homeostasis, including glutathione S-transferase (GST2, GST6), cytochrome P450, peroxidase 24 precursor, and induced expressing of CAT and SOD under salt stress to eliminate excess H2O2. Our results indicate that overexpression of the chimeric gene OsDST-SRDX improves salt tolerance of switchgrass, a C4 biofuel crop.
Collapse
Affiliation(s)
- Huifang Cen
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dayong Li
- College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Kexin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
- National Energy R&D Center for Biomass (NECB), China Agricultural University, Beijing, 100193, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
- National Energy R&D Center for Biomass (NECB), China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
49
|
Zhao J, Zhou M, Meng Y. Identification and Validation of Reference Genes for RT-qPCR Analysis in Switchgrass under Heavy Metal Stresses. Genes (Basel) 2020; 11:genes11050502. [PMID: 32375288 PMCID: PMC7291066 DOI: 10.3390/genes11050502] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 11/22/2022] Open
Abstract
Switchgrass (Panicum Virgatum L.) has been recognized as the new energy plant, which makes it ideal for the development of phytoremediation on heavy metal contamination in soils with great potential. This study aimed to screen the best internal reference genes for the real-time quantitative PCR (RT-qPCR) in leaves and roots of switchgrass for investigating its response to various heavy metals, such as cadmium (Cd), lead (Pb), mercury (Hg), chromium (Cr), and arsenic (As). The stability of fourteen candidate reference genes was evaluated by BestKeeper, GeNorm, NormFinder, and RefFinder software. Our results identified U2AF as the best reference gene in Cd, Hg, Cr, and As treated leaves as well as in Hg, Pb, As, and Cr stressed root tissues. In Pb treated leaf tissues, 18S rRNA was demonstrated to be the best reference gene. CYP5 was determined to be the optimal reference gene in Cd treated root tissues. The least stable reference gene was identified to be CYP2 in all tested samples except for root tissues stressed by Pb. To further validate the initial screening results, we used the different sets of combinatory internal reference genes to analyze the expression of two metal transport associated genes (PvZIP4 and PvPDB8) in young leaves and roots of switchgrass. Our results demonstrated that the relative expression of the target genes consistently changed during the treatment when CYP5/UBQ1, U2AF/ACT12, eEF1a/U2AF, or 18S rRNA/ACT12 were combined as the internal reference genes. However, the time-dependent change pattern of the target genes was significantly altered when CYP2 was used as the internal reference gene. Therefore, the selection of the internal reference genes appropriate for specific experimental conditions is critical to ensure the accuracy and reliability of RT-qPCR. Our findings established a solid foundation to further study the gene regulatory network of switchgrass in response to heavy metal stress.
Collapse
Affiliation(s)
- Junming Zhao
- Department of Grassland Science, Sichuan Agricultural University, Chengdu 611130, China;
| | - Man Zhou
- Zonation Fringe Technology Co., Metro Vancouver, BC V5C 2A0, Canada;
| | - Yu Meng
- College of Science and Technology, Wenzhou-Kean University, Wenzhou 325060, China
- Correspondence:
| |
Collapse
|
50
|
Guan C, Cen HF, Cui X, Tian DY, Tadesse D, Zhang YW. Proline improves switchgrass growth and development by reduced lignin biosynthesis. Sci Rep 2019; 9:20117. [PMID: 31882839 PMCID: PMC6934488 DOI: 10.1038/s41598-019-56575-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/08/2019] [Indexed: 01/08/2023] Open
Abstract
Transgenic switchgrass overexpressing Lolium perenne L. delta1-pyrroline 5-carboxylate synthase (LpP5CS) in group I (TG4 and TG6 line) and group II (TG1 and TG2 line) had significant P5CS and ProDH enzyme activities, with group I plants (TG4 and TG6) having higher P5CS and lower ProDH enzyme activity, while group II plants had higher ProDH and lower P5CS enzyme activity. We found group II transgenic plants showed stunted growth, and the changed proline content in overexpressing transgenic plants may influence the growth and development in switchgrass. RNA-seq analysis showed that KEGG enrichment included phenylpropanoid biosynthesis pathway among group I, group II and WT plants, and the expression levels of genes related to lignin biosynthesis were significantly up-regulated in group II. We also found that lignin content in group II transgenic plants was higher than that in group I and WT plants, suggesting that increased lignin content may suppress switchgrass growth and development. This study uncover that proline can appropriately reduce lignin biosynthesis to improve switchgrass growth and development. Therefore, appropriate reduction in lignin content and increase in biomass are important for bioenergy crop to lower processing costs for biomass fermentation-derived fuels.
Collapse
Affiliation(s)
- Cong Guan
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Hui-Fang Cen
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xin Cui
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Dan-Yang Tian
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Dimiru Tadesse
- Department of Plant and Soil Sciences, Institute for Agricultural Bioscience, Oklahoma State University, Oklahoma, OK, USA
| | - Yun-Wei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
- Beijing Key Laboratory for Grassland Science, China Agricultural University, Beijing, China.
- National Energy R&D Center for Biomass (NECB), Beijing, China.
- Beijing Sure Academy of Biosciences, Beijing, China.
| |
Collapse
|