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Contiliani DF, Nebó JFCDO, Ribeiro RV, Landell MGDA, Pereira TC, Ming R, Figueira A, Creste S. Drought-triggered leaf transcriptional responses disclose key molecular pathways underlying leaf water use efficiency in sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1182461. [PMID: 37223790 PMCID: PMC10200899 DOI: 10.3389/fpls.2023.1182461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/25/2023]
Abstract
Drought is a major constraint to sugarcane (Saccharum spp.) production and improving the water use efficiency (WUE) is a critical trait for the sustainability of this bioenergy crop. The molecular mechanism underlying WUE remains underexplored in sugarcane. Here, we investigated the drought-triggered physiological and transcriptional responses of two sugarcane cultivars contrasting for drought tolerance, 'IACSP97-7065' (sensitive) and 'IACSP94-2094' (tolerant). After 21 days without irrigation (DWI), only 'IACSP94-2094' exhibited superior WUE and instantaneous carboxylation efficiency, with the net CO2 assimilation being less impacted when compared with 'IACSP97-7065'. RNA-seq of sugarcane leaves at 21 DWI revealed a total of 1,585 differentially expressed genes (DEGs) for both genotypes, among which 'IACSP94-2094' showed 617 (38.9%) exclusive transcripts (212 up- and 405 down-regulated). Functional enrichment analyses of these unique DEGs revealed several relevant biological processes, such as photosynthesis, transcription factors, signal transduction, solute transport, and redox homeostasis. The better drought-responsiveness of 'IACSP94-2094' suggested signaling cascades that foster transcriptional regulation of genes implicated in the Calvin cycle and transport of water and carbon dioxide, which are expected to support the high WUE and carboxylation efficiency observed for this genotype under water deficit. Moreover, the robust antioxidant system of the drought-tolerant genotype might serve as a molecular shield against the drought-associated overproduction of reactive oxygen species. This study provides relevant data that may be used to develop novel strategies for sugarcane breeding programs and to understand the genetic basis of drought tolerance and WUE improvement of sugarcane.
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Affiliation(s)
- Danyel F. Contiliani
- Graduate Program in Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Sugarcane Center, Agronomic Institute (IAC), Ribeirão Preto, SP, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | | | - Tiago C. Pereira
- Graduate Program in Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Biology, Faculty of Philosophy, Sciences, and Letters of Ribeirão Preto, Universidade de São Paulo, Ribeirao Preto, SP, Brazil
| | - Ray Ming
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Silvana Creste
- Graduate Program in Genetics, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Sugarcane Center, Agronomic Institute (IAC), Ribeirão Preto, SP, Brazil
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Raman H, Raman R, Pirathiban R, McVittie B, Sharma N, Liu S, Qiu Y, Zhu A, Kilian A, Cullis B, Farquhar GD, Stuart‐Williams H, White R, Tabah D, Easton A, Zhang Y. Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola. PLANT, CELL & ENVIRONMENT 2022; 45:2019-2036. [PMID: 35445756 PMCID: PMC9325393 DOI: 10.1111/pce.14337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/06/2022] [Indexed: 05/29/2023]
Abstract
Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ13 C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ13 C QTL. QTL contributing to main and QTL × environment interaction effects for Δ13 C and yield were identified. One multiple-trait QTL for Δ13 C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ13 C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.
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Affiliation(s)
- Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Rosy Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Ramethaa Pirathiban
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research AustraliaUniversity of WollongongWollongongNew South WalesAustralia
| | - Brett McVittie
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Niharika Sharma
- NSW Department of Primary IndustriesOrange Agricultural InstituteOrangeNew South WalesAustralia
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRCOil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Yu Qiu
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNew South WalesAustralia
| | - Anyu Zhu
- Diversity Arrays Technology P/LUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Andrzej Kilian
- Diversity Arrays Technology P/LUniversity of CanberraCanberraAustralian Capital TerritoryAustralia
| | - Brian Cullis
- Centre for Biometrics and Data Science for Sustainable Primary Industries, National Institute for Applied Statistics Research AustraliaUniversity of WollongongWollongongNew South WalesAustralia
| | - Graham D. Farquhar
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Hilary Stuart‐Williams
- Research School of BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | | | - David Tabah
- Advanta Seeds Pty LtdToowoombaQueenslandAustralia
| | | | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of PRCOil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanHubeiChina
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Xiong R, Liu S, Considine MJ, Siddique KHM, Lam HM, Chen Y. Root system architecture, physiological and transcriptional traits of soybean (Glycine max L.) in response to water deficit: A review. PHYSIOLOGIA PLANTARUM 2021; 172:405-418. [PMID: 32880966 DOI: 10.1111/ppl.13201] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 05/24/2023]
Abstract
Drought stress is the main limiting factor for global soybean growth and production. Genetic improvement for water and nutrient uptake efficiency is critical to advance tolerance and enable more sustainable and resilient production, underpinning yield growth. The identification of quantitative traits and genes related to water and nutrient uptake will enhance our understanding of the mechanisms of drought tolerance in soybean. This review summarizes drought stress in the context of the physiological traits that enable effective acclimation, with a particular focus on roots. Genes controlling root system architecture play an important role in water and nutrient availability, and therefore important targets for breeding strategies to improve drought tolerance. This review highlights the candidate genes that have been identified as regulators of important root traits and responses to water stress. Progress in our understanding of the function of particular genes, including GmACX1, GmMS and GmPEPCK are discussed in the context of developing a system-based platform for genetic improvement of drought tolerance in soybean.
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Affiliation(s)
- Rentao Xiong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi, China
| | - Shuo Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi, China
| | - Michael J Considine
- School of Molecular Sciences, The University of Western Australia, LB 5005, Perth, Western Australia, 6001, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, and UWA School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, Western Australia, 6001, Australia
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yinglong Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, and Chinese Academy of Sciences, Yangling, Shaanxi, China
- The UWA Institute of Agriculture, and UWA School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, Western Australia, 6001, Australia
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Ribeiro IA, Voltolini TV, Simões WL, Ferreira MAJDF, Sobreira AM, Gois GC. Responses of forage watermelon genotypes submitted to different water supply. BIOL RHYTHM RES 2019. [DOI: 10.1080/09291016.2019.1594122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Isadora Almeida Ribeiro
- Postgraduate Program in Animal Sciences, Federal University of San Francisco valley, Petrolina, Brazil
| | | | - Welson Lima Simões
- Brazilian Agricultural Research Corporation, EMBRAPA Semiarid, Petrolina, Brazil
| | | | - Alysson Menezes Sobreira
- Postgraduate Program in Plant production, Federal University Rural of Pernambuco, Serra Talhada, Brazil
| | - Glayciane Costa Gois
- Postgraduate Program in Veterinary Sciences in the Semi-Arid, PNPD-CAPES, Federal University of San Francisco valley, Petrolina, Brazil
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Ahmed V, Verma MK, Gupta S, Mandhan V, Chauhan NS. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes. Front Microbiol 2018; 9:159. [PMID: 29472909 PMCID: PMC5809485 DOI: 10.3389/fmicb.2018.00159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022] Open
Abstract
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.
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Affiliation(s)
- Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Manoj K Verma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Shashank Gupta
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vibha Mandhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Nar S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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Fan Y, Wang Q, Kang L, Liu W, Xu Q, Xing S, Tao C, Song Z, Zhu C, Lin C, Yan J, Li J, Sang T. Transcriptome-wide characterization of candidate genes for improving the water use efficiency of energy crops grown on semiarid land. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6415-29. [PMID: 26175351 PMCID: PMC4588889 DOI: 10.1093/jxb/erv353] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Understanding the genetic basis of water use efficiency (WUE) and its roles in plant adaptation to a drought environment is essential for the production of second-generation energy crops in water-deficit marginal land. In this study, RNA-Seq and WUE measurements were performed for 78 individuals of Miscanthus lutarioriparius grown in two common gardens, one located in warm and wet Central China near the native habitats of the species and the other located in the semiarid Loess Plateau, the domestication site of the energy crop. The field measurements showed that WUE of M. lutarioriparius in the semiarid location was significantly higher than that in the wet location. A matrix correlation analysis was conducted between gene expression levels and WUE to identify candidate genes involved in the improvement of WUE from the native to the domestication site. A total of 48 candidate genes were identified and assigned to functional categories, including photosynthesis, stomatal regulation, protein metabolism, and abiotic stress responses. Of these genes, nearly 73% were up-regulated in the semiarid site. It was also found that the relatively high expression variation of the WUE-related genes was affected to a larger extent by environment than by genetic variation. The study demonstrates that transcriptome-wide correlation between physiological phenotypes and expression levels offers an effective means for identifying candidate genes involved in the adaptation to environmental changes.
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Affiliation(s)
- Yangyang Fan
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lifang Kang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qin Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Tao
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihong Song
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiyun Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong Lin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Juan Yan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Jianqiang Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Tao Sang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Sun S, Wang Y, Wang F, Liu J, Luan X, Li X, Zhou T, Wu P. Alleviating Pressure on Water Resources: A new approach could be attempted. Sci Rep 2015; 5:14006. [PMID: 26364756 PMCID: PMC4650578 DOI: 10.1038/srep14006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022] Open
Abstract
Water and food safety are two major challenges which the world faces today. Traditional water management focuses on the reduction of water use through improvements in water saving technologies. However, quantitative research is needed to evaluate the effects of changing food consumption patterns on water resources. Here we report the water saving effects of changing diet pattern of the major crops and animal products in mainland China. By using the concepts of water footprint (WF) per weight unit and per calorie unit, provided by 13 primary crop and animal products, the WFs of the 13 agricultural products in each province are compared, and their water/energy conversion efficiencies are analyzed. Then, impacts of different scenarios of changing diet pattern on water consumption were explored. Results show that there are obvious differences between the WF per weight and calorie unit provided by crop and animal products due to the nutritional properties of the agricultural products. Promoting water savings from the food consumption side could give a positive feedback on water consumption. Scenario analysis of adjustments to the diet pattern proves that it is potentially feasible to reach the objective of alleviating stress on water resources while guaranteeing nutritional value of the residents.
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Affiliation(s)
- Shikun Sun
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, 712100, China
- Institute of Water Saving Agriculture in Arid regions of China, Northwest A&F University, Yangling, 712100, China
- Key Laboratory of Agriculture al Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, 712100, China
| | - Yubao Wang
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, 712100, China
- Institute of Water Saving Agriculture in Arid regions of China, Northwest A&F University, Yangling, 712100, China
- Key Laboratory of Agriculture al Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, 712100, China
| | - Feifei Wang
- College of Economics and Management, Northwest A&F University, Yangling, 712100, China
| | - Jing Liu
- Institute of Soil and Water Conservation, Northwest A&F University, Yangling, 712100, China
| | - Xiaobo Luan
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China
| | - Xiaolei Li
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China
| | - Tianwa Zhou
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China
| | - Pute Wu
- Institute of Water Saving Agriculture in Arid regions of China, Northwest A&F University, Yangling, 712100, China
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China
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Pujar A, Menda N, Bombarely A, Edwards JD, Strickler SR, Mueller LA. From manual curation to visualization of gene families and networks across Solanaceae plant species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat028. [PMID: 23681907 PMCID: PMC3655285 DOI: 10.1093/database/bat028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants. Database URL:http://solgenomics.net/
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Affiliation(s)
- Anuradha Pujar
- Boyce Thompson Institute for Plant Research, 533, Tower Road, Ithaca, NY 14853, USA
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