Comparative Physiological and Transcriptome Analysis Reveals Potential Pathways and Specific Genes Involved in Waterlogging Tolerance in Apple Rootstocks

Apple (Malus × domestica Borkh.) is one of the most cultivated fruit crops in China. Apple trees frequently encounter waterlogging stress, mainly due to excess rainfall, soil compaction, or poor soil drainage, results in yellowing leaves and declined fruit quality and yield in some regions. However, the mechanism underlying the response to waterlogging has not been well elucidated. Therefore, we performed a physiological and transcriptomic analysis to examine the differential responses of two apple rootstocks (waterlogging-tolerant M. hupehensis and waterlogging-sensitive M. toringoides) to waterlogging stress. The results showed that M. toringoides displayed more severe leaf chlorosis during the waterlogging treatment than M. hupehensis. Compared with M. hupehensis, the more severe leaf chlorosis induced by waterlogging stress in M. toringoides was highly correlated with increased electrolyte leakage and superoxide radicals, hydrogen peroxide accumulation, and increased stomata closure. Interestingly, M. toringoides also conveyed a higher ethylene production under waterlogging stress. Furthermore, RNA-seq revealed that a total of 13,913 common differentially expressed genes (DEGs) were differentially regulated between M. hupehensis and M. toringoides under waterlogging stress, especially those DEGs involved in the biosynthesis of flavonoids and hormone signaling. This suggests a possible link of flavonoids and hormone signaling to waterlogging tolerance. Taken together, our data provide the targeted genes for further investigation of the functions, as well as for future molecular breeding of waterlogging-tolerant apple rootstocks.

[1]  M. Shahid,et al.  Physiological, biochemical, and molecular responses of fruit trees to root zone hypoxia , 2022, Environmental and Experimental Botany.

[2]  F. Ma,et al.  Activation of the ABA Signal Pathway Mediated by GABA Improves the Drought Resistance of Apple Seedlings , 2021, International journal of molecular sciences.

[3]  Xuehao Chen,et al.  Mechanisms of Waterlogging Tolerance in Plants: Research Progress and Prospects , 2021, Frontiers in Plant Science.

[4]  N. Bhusal,et al.  Photosynthetic traits and plant–water relations of two apple cultivars grown as bi-leader trees under long-term waterlogging conditions , 2020 .

[5]  N. Bhusal,et al.  Waterlogging tolerance in apple trees grafted on rootstocks from G, CG, and M series , 2020, Horticulture, Environment, and Biotechnology.

[6]  Chunyan Li,et al.  Effects of waterlogging on grain yield and associated traits of historic wheat cultivars in the middle and lower reaches of the Yangtze River, China , 2020 .

[7]  Peng Zhang,et al.  ROS production and scavenging in three cherry rootstocks under short-term waterlogging conditions , 2019, Scientia Horticulturae.

[8]  Richong Zhang,et al.  Changes in photosynthesis, chloroplast ultrastructure, and antioxidant metabolism in leaves of sorghum under waterlogging stress , 2019, Photosynthetica.

[9]  Manjun Cai,et al.  A group VII ethylene response factor gene, ZmEREB180, coordinates waterlogging tolerance in maize seedlings , 2019, Plant biotechnology journal.

[10]  Xiaotian Ma,et al.  Waterlogging-induced adventitious root formation in cucumber is regulated by ethylene and auxin through reactive oxygen species signalling. , 2019, Plant, cell & environment.

[11]  T. Fukao,et al.  Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects , 2019, Front. Plant Sci..

[12]  K. Bashar.  Hormone dependent survival mechanisms of plants during post-waterlogging stress , 2018, Plant signaling & behavior.

[13]  M. Pinto,et al.  Root respiratory components of Prunus spp. rootstocks under low oxygen: Regulation of growth, maintenance, and ion uptake respiration , 2018, Scientia Horticulturae.

[14]  K. Nishitani,et al.  Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding , 2018, Science.

[15]  Nan Zhao,et al.  Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions , 2018, International journal of molecular sciences.

[16]  Shi-jie Zhao,et al.  Vulnerability of photosynthesis and photosystem I in Jerusalem artichoke (Helianthus tuberosus L.) exposed to waterlogging. , 2018, Plant physiology and biochemistry : PPB.

[17]  D. Gupta,et al.  Antioxidants and Antioxidant Enzymes in Higher Plants , 2018, Springer International Publishing.

[18]  L. Voesenek,et al.  Signal Dynamics and Interactions during Flooding Stress1[OPEN] , 2017, Plant Physiology.

[19]  Ping Wang,et al.  Improvement of drought tolerance by overexpressing MdATG18a is mediated by modified antioxidant system and activated autophagy in transgenic apple , 2017, Plant biotechnology journal.

[20]  J. Gouzy,et al.  High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development , 2017, Nature Genetics.

[21]  T. Repo,et al.  Photosynthesis, nutrient accumulation and growth of two Betula species exposed to waterlogging in late dormancy and in the early growing season , 2017, Tree physiology.

[22]  F. Alves,et al.  Physiological and morphological responses to permanent and intermittent waterlogging in seedlings of four evergreen trees of temperate swamp forests , 2017, Tree physiology.

[23]  N. Wang,et al.  Melatonin Improves Waterlogging Tolerance of Malus baccata (Linn.) Borkh. Seedlings by Maintaining Aerobic Respiration, Photosynthesis and ROS Migration , 2017, Front. Plant Sci..

[24]  Xiaotian Ma,et al.  Comparative Proteomic Analysis Provides Insight into the Key Proteins Involved in Cucumber (Cucumis sativus L.) Adventitious Root Emergence under Waterlogging Stress , 2016, Front. Plant Sci..

[25]  F. Ma,et al.  Comprehensive evaluation of tolerance to alkali stress by 17 genotypes of apple rootstocks , 2016 .

[26]  O. Pedersen,et al.  Mechanisms of waterlogging tolerance in wheat--a review of root and shoot physiology. , 2016, Plant, cell & environment.

[27]  S. Komatsu,et al.  Jasmonic acid induced protein response to biophoton emissions and flooding stress in soybean. , 2016, Journal of proteomics.

[28]  H. Nguyen,et al.  Comparative analysis of endogenous hormones level in two soybean (Glycine max L.) lines differing in waterlogging tolerance , 2015, Front. Plant Sci..

[29]  L. Voesenek,et al.  Ethylene-Mediated Acclimations to Flooding Stress1 , 2015, Plant Physiology.

[30]  Wang Huihui,et al.  Waterlogging-induced increase in fermentation and related gene expression in the root of cucumber (Cucumis sativus L.) , 2014 .

[31]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[32]  H. Rennenberg,et al.  Molecular and physiological responses of trees to waterlogging stress. , 2014, Plant, cell & environment.

[33]  J. Bailey-Serres,et al.  Plant tolerance of flooding stress--recent advances. , 2014, Plant, cell & environment.

[34]  Wenqing Zhao,et al.  Waterlogging during flowering and boll forming stages affects sucrose metabolism in the leaves subtending the cotton boll and its relationship with boll weight. , 2014, Plant science : an international journal of experimental plant biology.

[35]  N. Suzuki,et al.  ROS as key players in plant stress signalling. , 2014, Journal of experimental botany.

[36]  K. Kazan.  Auxin and the integration of environmental signals into plant root development. , 2013, Annals of botany.

[37]  S. Kanae,et al.  Global flood risk under climate change , 2013 .

[38]  A. Vianello,et al.  Plant Flavonoids—Biosynthesis, Transport and Involvement in Stress Responses , 2013, International journal of molecular sciences.

[39]  J. Bailey-Serres,et al.  Waterproofing Crops: Effective Flooding Survival Strategies1 , 2012, Plant Physiology.

[40]  R. Gao,et al.  RAP2.6L overexpression delays waterlogging induced premature senescence by increasing stomatal closure more than antioxidant enzyme activity , 2012, Plant Molecular Biology.

[41]  Mohammad Pessarakli,et al.  Reactive Oxygen Species, Oxidative Damage, and Antioxidative Defense Mechanism in Plants under Stressful Conditions , 2012 .

[42]  P. Perata,et al.  Reactive Oxygen Species-Driven Transcription in Arabidopsis under Oxygen Deprivation1[W] , 2012, Plant Physiology.

[43]  D. Iglesias,et al.  Root signalling and modulation of stomatal closure in flooded citrus seedlings. , 2011, Plant physiology and biochemistry : PPB.

[44]  Cole Trapnell,et al.  Role of Rodent Secondary Motor Cortex in Value-based Action Selection Nih Public Access Author Manuscript , 2006 .

[45]  R. Schneider,et al.  Effects of submergence on photosynthesis and growth of Pterocarya stenoptera (Chinese wingnut) seedlings in the recently-created Three Gorges Reservoir region of China , 2010, Wetlands Ecology and Management.

[46]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[47]  Matthew D. Young,et al.  Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.

[48]  S. Munné-Bosch,et al.  How relevant are flavonoids as antioxidants in plants? , 2009, Trends in plant science.

[49]  R. Sairam,et al.  Physiology and biochemistry of waterlogging tolerance in plants , 2008, Biologia Plantarum.

[50]  Bernard R. Glick,et al.  Promotion of plant growth by ACC deaminase-producing soil bacteria , 2007, European Journal of Plant Pathology.

[51]  J. Bailey-Serres,et al.  Sensing and signalling in response to oxygen deprivation in plants and other organisms. , 2005, Annals of botany.

[52]  H. Sandermann.  Molecular Ecotoxicology of Plants , 2004, Ecological Studies.

[53]  Sergey Shabala,et al.  Screening methods for waterlogging tolerance in lucerne: comparative analysis of waterlogging effects on chlorophyll fluorescence, photosynthesis, biomass and chlorophyll content. , 2003, Functional plant biology : FPB.

[54]  B. Winkel-Shirley,et al.  Biosynthesis of flavonoids and effects of stress. , 2002, Current opinion in plant biology.

[55]  William Armstrong,et al.  Root Growth and Metabolism Under Oxygen Deficiency , 2002 .

[56]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[57]  M. Jackson,et al.  Rapid changes in cell wall pectic polysaccharides are closely associated with early stages of aerenchyma formation, a spatially localized form of programmed cell death in roots of maize ( Zea mays L.) promoted by ethylene , 2001 .

[58]  J. Fisher,et al.  Influence of Flooding on Net CO2Assimilation, Growth and Stem Anatomy of Annona Species , 1999 .

[59]  H. Greenway,et al.  Metabolic evidence for stelar anoxia in maize roots exposed to low o(2) concentrations. , 1991, Plant physiology.

[60]  W. Armstrong,et al.  Evidence for the involvement of ethene in aerenchyma formation in adventitious roots of rice (Oryza sativa L.) , 1991 .

[61]  K. Bradford,et al.  Xylem Transport of 1-Aminocyclopropane-1-carboxylic Acid, an Ethylene Precursor, in Waterlogged Tomato Plants. , 1980, Plant physiology.

[62]  M. Drew,et al.  EARLY EFFECTS OF FLOODING ON NITROGEN DEFICIENCY AND LEAF CHLOROSIS IN BARLEY , 1977 .

[63]  Xian-bo Zheng,et al.  Genome‑wide identification and expression analysis of the ASMT gene family reveals their role in abiotic stress tolerance in apple , 2022, Scientia Horticulturae.

[64]  Xuehao Chen,et al.  Involvement of auxin in growth and stress response of cucumber , 2022, Vegetable Research.

[65]  V. Baskar,et al.  Flavonoids (Antioxidants Systems) in Higher Plants and Their Response to Stresses , 2018 .

[66]  Ahmad,et al.  Environmental Adaptations and Stress Tolerance of Plants in the Era of Climate Change , 2012, Springer New York.

[67]  B. Glick,et al.  Ethylene and Abiotic Stress Tolerance in Plants , 2012 .

[68]  S. Shabala,et al.  Waterlogging signalling and tolerance in plants , 2010 .

[69]  L. Wegner,et al.  Oxygen Transport in Waterlogged Plants , 2010 .

[70]  W. Kun.  Physiological Responses and Analysis of Tolerance of Apple Rootstocks to Root-Zone Hypoxia Stress , 2008 .

[71]  P. Bakker,et al.  New Perspectives and Approaches in Plant Growth-Promoting Rhizobacteria Research , 2007 .

[72]  B. Glick,et al.  Increased Plant Fitness by Rhizobacteria , 2004 .

[73]  M. Nair,et al.  Modulation of liposomal membrane fluidity by flavonoids and isoflavonoids. , 2000, Archives of biochemistry and biophysics.

[74]  L. C. Purcell,et al.  Soybean Root Morphological and Anatomical Traits Associated with Acclimation to Flooding , 1999 .

[75]  H. Kende,et al.  Gas Composition in the Internal Air Spaces of Deepwater Rice in Relation to Growth Induced by Submergence , 1989 .

[76]  Thomas D. Schmittgen,et al.  Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .