1
|
Ding Z, Fu L, Tie W, Yan Y, Wu C, Dai J, Zhang J, Hu W. Highly dynamic, coordinated, and stage-specific profiles are revealed by a multi-omics integrative analysis during tuberous root development in cassava. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7003-7017. [PMID: 32777039 DOI: 10.1093/jxb/eraa369] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/01/2020] [Indexed: 05/23/2023]
Abstract
Cassava (Manihot esculenta) is an important starchy root crop that provides food for millions of people worldwide, but little is known about the regulation of the development of its tuberous root at the multi-omics level. In this study, the transcriptome, proteome, and metabolome were examined in parallel at seven time-points during the development of the tuberous root from the early to late stages of its growth. Overall, highly dynamic and stage-specific changes in the expression of genes/proteins were observed during development. Cell wall and auxin genes, which were regulated exclusively at the transcriptomic level, mainly functioned during the early stages. Starch biosynthesis, which was controlled at both the transcriptomic and proteomic levels, was mainly activated in the early stages and was greatly restricted during the late stages. Two main branches of lignin biosynthesis, coniferyl alcohol and sinapyl alcohol, also functioned during the early stages of development at both the transcriptomic and proteomic levels. Metabolomic analysis further supported the stage-specific roles of particular genes/proteins. Metabolites related to lignin and flavonoid biosynthesis showed high abundance during the early stages, those related to lipids exhibited high abundance at both the early and middle stages, while those related to amino acids were highly accumulated during the late stages. Our findings provide a comprehensive resource for broadening our understanding of tuberous root development and will facilitate future genetic improvement of cassava.
Collapse
Affiliation(s)
- Zehong Ding
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lili Fu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Weiwei Tie
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Yan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chunlai Wu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Jing Dai
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Jiaming Zhang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Key Laboratory for Protection and Utilization of Tropical Bioresources, Hainan Institute for Tropical Agricultural Resources, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| |
Collapse
|
2
|
Zeng N, Yang Z, Zhang Z, Hu L, Chen L. Comparative Transcriptome Combined with Proteome Analyses Revealed Key Factors Involved in Alfalfa ( Medicago sativa) Response to Waterlogging Stress. Int J Mol Sci 2019; 20:ijms20061359. [PMID: 30889856 PMCID: PMC6471898 DOI: 10.3390/ijms20061359] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 12/26/2022] Open
Abstract
Alfalfa (Medicago sativa) is the most widely grown and most important forage crop in the world. However, alfalfa is susceptible to waterlogging stress, which is the major constraint for its cultivation area and crop production. So far, the molecular mechanism of alfalfa response to the waterlogging is largely unknown. Here, comparative transcriptome combined with proteomic analyses of two cultivars (M12, tolerant; M25, sensitive) of alfalfa showing contrasting tolerance to waterlogging were performed to understand the mechanism of alfalfa in response to waterlogging stress. Totally, 748 (581 up- and 167 down-regulated) genes were differentially expressed in leaves of waterlogging-stressed alfalfa compared with the control (M12_W vs. M12_CK), whereas 1193 (740 up- and 453 down-regulated) differentially abundant transcripts (DATs) were detected in the leaves of waterlogging-stressed plants in comparison with the control plants (M25_W vs. M25_CK). Furthermore, a total of 187 (122 up- and 65 down-regulated) and 190 (105 up- and 85 down-regulated) differentially abundant proteins (DAPs) were identified via isobaric tags for relative and absolute quantification (iTRAQ) method in M12_W vs. M12_CK and M25_W vs. M25_CK comparison, respectively. Compared dataset analysis of proteomics and transcriptomics revealed that 27 and eight genes displayed jointly up-regulated or down-regulated expression profiles at both mRNA and protein levels in M12_W vs. M12_CK comparison, whereas 30 and 27 genes were found to be co-up-regulated or co-down-regulated in M25_W vs. M25_CK comparison, respectively. The strongly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for co-up-regulated genes at mRNA and protein levels in M12_W vs. M12_CK comparison were 'Amino sugar and nucleotide sugar metabolism', 'Arginine and proline metabolism' and 'Starch and sucrose metabolism', whereas co-up-regulated protein-related pathways including 'Arginine and proline metabolism' and 'Valine, leucine and isoleucine degradation' were largely enriched in M25_W vs. M25_CK comparison. Importantly, the identified genes related to beta-amylase, Ethylene response Factor (ERF), Calcineurin B-like (CBL) interacting protein kinases (CIPKs), Glutathione peroxidase (GPX), and Glutathione-S-transferase (GST) may play key roles in conferring alfalfa tolerance to waterlogging stress. The present study may contribute to our understanding the molecular mechanism underlying the responses of alfalfa to waterlogging stress, and also provide important clues for further study and in-depth characterization of waterlogging-resistance breeding candidate genes in alfalfa.
Collapse
Affiliation(s)
- Ningbo Zeng
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Zhijian Yang
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Zhifei Zhang
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Longxing Hu
- Department of Pratacultural Sciences, College of Agriculture, Hunan Agricultural University, Changsha 410128, China.
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Science, Wuhan 430074, China.
| |
Collapse
|
3
|
Ren CG, Kong CC, Yan K, Zhang H, Luo YM, Xie ZH. Elucidation of the molecular responses to waterlogging in Sesbania cannabina roots by transcriptome profiling. Sci Rep 2017; 7:9256. [PMID: 28835646 PMCID: PMC5569044 DOI: 10.1038/s41598-017-07740-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 07/04/2017] [Indexed: 01/22/2023] Open
Abstract
Sesbania cannabina, a multipurpose leguminous crop, is highly resistant to waterlogging stress. However, the scant genomic resources in the genus Sesbania have greatly hindered further exploration of the mechanisms underlying its waterlogging tolerance. Here, the genetic basis of flooding tolerance in S. cannabina was examined by transcriptome-wide gene expression changes using RNA-Seq in seedlings exposed to short-term (3 h) and long-term (27 h) waterlogging. After de- novo assembly, 213990 unigenes were identified, of which 145162 (79.6%) were annotated. Gene Ontology and pathway enrichment analyses revealed that the glycolysis and fermentation pathways were stimulated to produce ATP under hypoxic stress conditions. Energy-consuming biosynthetic processes were dramatically repressed by short and long term waterlogging, while amino acid metabolism was greatly induced to maintain ATP levels. The expression pattern of 10 unigenes involved in phenylpropanoid biosynthesis, glycolysis, and amino acid metabolism revealed by qRT-PCR confirmed the RNA-Seq data. The present study is a large-scale assessment of genomic resources of Sesbania and provides guidelines for probing the molecular mechanisms underlying S. cannabina waterlogging tolerance.
Collapse
Affiliation(s)
- Cheng-Gang Ren
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Cun-Cui Kong
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Kun Yan
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Hua Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yong-Ming Luo
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhi-Hong Xie
- Key Laboratory of Biology and Utilization of Biological Resources of Coastal Zone, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.
| |
Collapse
|
4
|
Wang X, Jiang Y, Zhao X, Song X, Xiao X, Pei Z, Liu H. Association of Candidate Genes With Submergence Response in Perennial Ryegrass. FRONTIERS IN PLANT SCIENCE 2017; 8:791. [PMID: 28559908 PMCID: PMC5432546 DOI: 10.3389/fpls.2017.00791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
Perennial ryegrass is a popular cool-season grass species due to its high quality for forage and turf. The objective of this study was to identify associations of candidate genes with growth and physiological traits to submergence stress and recovery after de-submergence in a global collection of 94 perennial ryegrass accessions. Accessions varied largely in leaf color, plant height (HT), leaf fresh weight (LFW), leaf dry weight (LDW), and chlorophyll fluorescence (Fv/Fm) at 7 days of submergence and in HT, LFW and LDW at 7 days of recovery in two experiments. Among 26 candidate genes tested by various models, single nucleotide polymorphisms (SNPs) in 10 genes showed significant associations with traits including 16 associations for control, 10 for submergence, and 8 for recovery. Under submergence, Lp1-SST encoding sucrose:sucrose 1-fructosyltransferase and LpGA20ox encoding gibberellin 20-oxidase were associated with LFW and LDW, and LpACO1 encoding 1-aminocyclopropane-1-carboxylic acid oxidase was associated with LFW. Associations between Lp1-SST and HT, Lp6G-FFT encoding fructan:fructan 6G-fructosyltransferase and Fv/Fm, LpCAT encoding catalase and HT were also detected under submergence stress. Upon de-submergence, Lp1-SST, Lp6G-FFT, and LpPIP1 encoding plasma membrane intrinsic protein type 1 were associated with LFW or LDW, while LpCBF1b encoding C-repeat binding factor were associated with HT. Nine significant SNPs in Lp1-SST, Lp6G-FFT, LpCAT, and LpACO1 resulted in amino acid changes with five substitutions found in Lp1-SST under submergence or recovery. The results indicated that allelic diversity in genes involved in carbohydrate and antioxidant metabolism, ethylene and gibberellin biosynthesis, and transcript factor could contribute to growth variations in perennial ryegrass under submergence stress and recovery after de-submergence.
Collapse
Affiliation(s)
- Xicheng Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences and Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementNanjing, China
| | - Yiwei Jiang
- College of Agronomy and Resources and Environment, Tianjin Agricultural UniversityTianjin, China
- Department of Agronomy, Purdue University, West LafayetteIN, USA
| | - Xiongwei Zhao
- Department of Agronomy, Purdue University, West LafayetteIN, USA
- Department of Crop Genetics and Breeding, Sichuan Agricultural UniversityChengdu, China
| | - Xin Song
- College of Pastoral Agriculture Science and Technology, Lanzhou UniversityLanzhou, China
| | - Xiangye Xiao
- Department of Agronomy, Purdue University, West LafayetteIN, USA
| | - Zhongyou Pei
- College of Agronomy and Resources and Environment, Tianjin Agricultural UniversityTianjin, China
| | - Huifen Liu
- College of Agronomy and Resources and Environment, Tianjin Agricultural UniversityTianjin, China
| |
Collapse
|
5
|
Vaid N, Pandey P, Srivastava VK, Tuteja N. Pea lectin receptor-like kinase functions in salinity adaptation without yield penalty, by alleviating osmotic and ionic stresses and upregulating stress-responsive genes. PLANT MOLECULAR BIOLOGY 2015; 88:193-206. [PMID: 25863480 DOI: 10.1007/s11103-015-0319-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 04/04/2015] [Indexed: 05/29/2023]
Abstract
Lectin receptor-like kinases (LecRLKs) are members of RLK family composed of lectin-like extracellular recognition domain, transmembrane domain and cytoplasmic kinase domain. LecRLKs are plasma membrane proteins believed to be involved in signal transduction. However, most of the members of the protein family even in plants have not been functionally well characterized. Herein, we show that Pisum sativum LecRLK (PsLecRLK) localized in plasma membrane systems and/or other regions of the cell and its transcript upregulated under salinity stress. Overexpression of PsLecRLK in transgenic tobacco plants confers salinity stress tolerance by alleviating both the ionic as well the osmotic component of salinity stress. The transgenic plants show better tissue compartmentalization of Na(+) and higher ROS scavenging activity which probably results in lower membrane damage, improved growth and yield maintenance even under salinity stress. Also, expression of several genes involved in cellular homeostasis is perturbed by PsLecRLK overexpression. Alleviation of osmotic and ionic components of salinity stress along with reduced oxidative damage and upregulation of stress-responsive genes in transgenic plants under salinity stress conditions could be possible mechanism facilitating enhanced stress tolerance. This study presents PsLecRLK as a promising candidate for crop improvement and also opens up new avenue to investigate its signalling pathway.
Collapse
Affiliation(s)
- Neha Vaid
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | | | | |
Collapse
|
6
|
Tang Z, Zhang L, Xu C, Yuan S, Zhang F, Zheng Y, Zhao C. Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. PLANT PHYSIOLOGY 2012; 159:721-38. [PMID: 22508932 PMCID: PMC3375937 DOI: 10.1104/pp.112.196048] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/15/2012] [Indexed: 05/18/2023]
Abstract
The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNAs) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 78 unique miRNA sequences from 30 families and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. To identify smRNA targets in the wheat TGMS line, we applied the degradome sequencing method, which globally and directly identifies the remnants of smRNA-directed target cleavage. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing data sets and TaqMan quantitative polymerase chain reaction results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF [for Auxin-Responsive Factor]) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, the expression of cold stress-responsive smRNAs integrated in the auxin-signaling pathway and their target genes was largely noncorrelated. We investigated the tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress.
Collapse
MESH Headings
- Adaptation, Physiological
- Cold Temperature
- Computational Biology
- Flowers/genetics
- Flowers/physiology
- Gene Expression Profiling
- Gene Expression Regulation, Plant
- Genes, Plant
- Indoleacetic Acids/metabolism
- MicroRNAs/metabolism
- Plant Infertility
- Plant Proteins/genetics
- Plant Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Real-Time Polymerase Chain Reaction
- Sequence Analysis, RNA/methods
- Signal Transduction
- Stress, Physiological
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Triticum/genetics
- Triticum/physiology
Collapse
|