Transcriptome-based analysis of salt-related genes during the sprout stage of common bean (Phaseolus vulgaris) under salt stress conditions

References

• Munns R, Tester M. Mechanisms of salinity tolerance. Annu Rev Plant Biol. 2008;59:651–681.
   PubMed Web of Science ®Google Scholar
• Mahajan S, Tuteja N. Cold, salinity and drought stresses: an overview. Arch Biochem Biophys. 2005;444(2):139–158.
   PubMed Web of Science ®Google Scholar
• Mäser P, Eckelman B, Vaidyanathan R, et al. Altered shoot/root Na + distribution and bifurcating salt sensitivity in Arabidopsis by genetic disruption of the Na + transporter AtHKT1. FEBS Lett. 2002;531(2):157–161.
   PubMed Web of Science ®Google Scholar
• Munns R. Physiological processes limiting plant growth in saline soils: some dogmas and hypotheses. Plant Cell Environ. 1993;16(1):15–24.
   Web of Science ®Google Scholar
• Royce TE, Rozowsky JS, Gerstein MB. Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification. Nucleic Acids Res. 2007;35(15):e99.
   PubMed Web of Science ®Google Scholar
• Evans MJ, Choi WG, Gilroy S, et al. A ROS-assisted calcium wave dependent on the AtRBOHD NADPH oxidase and TPC1 cation channel propagates the systemic response to salt stress. Plant Physiol. 2016;171(3):1771–1784.
   PubMed Web of Science ®Google Scholar
• Roxas VP, Lodhi SA, Garrett DK, et al. Stress tolerance in transgenic tobacco seedlings that overexpress glutathione S-transferase/glutathione peroxidase. Plant Cell Physiol. 2000;41(11):1229–1234.
   PubMed Web of Science ®Google Scholar
• Qi W, Zhang L, Xu H, et al. Physiological and molecular characterization of the enhanced salt tolerance induced by low-dose gamma irradiation in Arabidopsis seedlings. Biochem Biophys Res Commun. 2014;450(2):1010–1015.
   PubMed Web of Science ®Google Scholar
• Postnikova OA, Shao J, Nemchinov LG. Analysis of the alfalfa root transcriptome in response to salinity stress. Plant Cell Physiol. 2013;54(7):1041–1055.
   PubMed Web of Science ®Google Scholar
• Xu P, Liu Z, Fan X, et al. De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. Gene. 2013;525(1):26–34.
   PubMed Web of Science ®Google Scholar
• Parra-González LB, Aravena-Abarzúa GA, Navarro-Navarro CS, et al. Yellow lupin (Lupinus luteus L.) transcriptome sequencing: molecular marker development and comparative studies. BMC Genomics. 2012; 13:425.
   PubMed Web of Science ®Google Scholar
• Wu N, Matand K, Wu H, et al. De novo next-generation sequencing, assembling and annotation of Arachis hypogaea L. Spanish botanical type whole plant transcriptome. Theor Appl Genet. 2013;126(5):1145–1149.
   PubMed Web of Science ®Google Scholar
• Teshome A, Byrne SL, Didion T, et al. Transcriptome sequencing of Festulolium accessions under salt stress. BMC Res Notes. 2019;12(1):311.
   PubMedGoogle Scholar
• Zhao L, Cui J, Cai Y, et al. Comparative transcriptome analysis of two contrasting soybean varieties in response to aluminum toxicity. IJMS. 2020;21(12):4316.
   Google Scholar
• Li WY, Wang C, Shi HH, et al. Genome-wide analysis of ethylene-response factor family in adzuki bean and functional determination of VaERF3 under saline-alkaline stress. Plant Physiol Biochem. 2020;147:215–222.
   PubMed Web of Science ®Google Scholar
• López-Hernández F, Cortés AJ. Last-generation genome-environment associations reveal the genetic basis of heat tolerance in common bean (Phaseolus vulgaris L.). Front Genet. 2019; 10:954.
   PubMed Web of Science ®Google Scholar
• Schmutz J, McClean PE, Mamidi S, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet. 2014;46(7):707–713.
   PubMed Web of Science ®Google Scholar
• Blair MW, Soler A, Cortés AJ. Diversification and population structure in common beans (Phaseolus vulgaris L.). PloS One. 2012;7(11):e49488.
   PubMed Web of Science ®Google Scholar
• Cortés AJ, Skeen P, Blair MW, et al. Does the genomic landscape of species divergence in Phaseolus beans coerce parallel signatures of adaptation and domestication?Front Plant Sci. 2018; 9:1816.
   PubMed Web of Science ®Google Scholar
• Matney JE, Parker BC, Neck DW, et al. Evaluation of a commercial flatbed document scanner and radiographic film scanner for radiochromic EBT film dosimetry. J Appl Clin Med Phys. 2010;11(2):3165.
   PubMed Web of Science ®Google Scholar
• Zhang Q, Zhang WJ, Yin ZG, et al. Genome- and transcriptome-wide identification of C3Hs in common bean (Phaseolus vulgaris L.) and structural and expression-based analyses of their functions during the sprout stage under salt-stress conditions. Front Genet. 2020; 11:564607.
   PubMed Web of Science ®Google Scholar
• Desjardins P, Conklin D. NanoDrop microvolume quantitation of nucleic acids. JoVE. 2010;(45):2565.
   Google Scholar
• Kim D, Pertea G, Trapnell C, et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013a;14(4):R36.
   PubMed Web of Science ®Google Scholar
• Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–515.
   PubMed Web of Science ®Google Scholar
• Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11(10):R106.
   PubMed Web of Science ®Google Scholar
• Chen C, Chen H, Zhang Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–1202.
   PubMed Web of Science ®Google Scholar
• Conesa A, Götz S, García-Gómez JM, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005;21(18):3674–3676.
   PubMed Web of Science ®Google Scholar
• Ye J, Fang L, Zheng H, et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006;34(Web Server issue):W293–W297.
   PubMed Web of Science ®Google Scholar
• Borges A, Tsai SM, Caldas DG. Validation of reference genes for RT-qPCR normalization in common bean during biotic and abiotic stresses. Plant Cell Rep. 2012;31(5):827–838.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Cui Y, Huang S, et al. Genome-wide analysis of the glucose-6-phosphate dehydrogenase family in soybean and functional identification of GmG6PDH2 involvement in salt stress. Front Plant Sci. 2020;11:214.
   PubMed Web of Science ®Google Scholar
• Lopez-Molina L, Mongrand S, Chua NH. A postgermination developmental arrest checkpoint is mediated by abscisic acid and requires the ABI5 transcription factor in Arabidopsis. Proc Natl Acad Sci USA. 2001;98(8):4782–4787.
   PubMed Web of Science ®Google Scholar
• Li M, Zhang K, Sun Y, et al. Growth, physiology, and transcriptional analysis of two contrasting Carex rigescens genotypes under salt stress reveals salt-tolerance mechanisms. J Plant Physiol. 2018;229:77–88.
   PubMed Web of Science ®Google Scholar
• Mian MA, Hossain J. Nitrogen level and physiological basis of yield of mungbean at varying plant population in High Ganges River Flood Plain soil of Bangladesh. Pak J Biol Sci. 2014;17(7):925–930.
   PubMedGoogle Scholar
• Chan BKC. Data analysis using R programming. Adv Exp Med Bio. 2018;1082:47–122.
   Google Scholar
• Pereira WJ, Melo ATO, Coelho ASG, et al. Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean. Genet Mol Biol. 2020;43(1):e20180259.
   PubMed Web of Science ®Google Scholar
• Hiz MC, Canher B, Niron H, et al. Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PLoS One. 2014;9(3):e92598.
   PubMed Web of Science ®Google Scholar
• Badowiec A, Weidner S. Proteomic changes in the roots of germinating Phaseolus vulgaris seeds in response to chilling stress and post-stress recovery. J Plant Physiol. 2014;171(6):389–398.
   PubMed Web of Science ®Google Scholar
• Silva DAD, Tsai SM, Chiorato AF, et al. Analysis of the common bean (Phaseolus vulgaris L.) transcriptome regarding efficiency of phosphorus use. PLoS One. 2019;14(1):e0210428.
   PubMed Web of Science ®Google Scholar
• Cortés AJ, This D, Chavarro C, et al. Nucleotide diversity patterns at the drought-related DREB2 encoding genes in wild and cultivated common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2012;125(5):1069–1085.
   PubMed Web of Science ®Google Scholar
• Blair MW, Cortés AJ, This D. Identification of an ERECTA gene and its drought adaptation associations with wild and cultivated common bean. Plant Sci. 2016;242:250–259.
   PubMed Web of Science ®Google Scholar
• Yang H, Chen Y, Zhang F. Evaluation of comprehensive improvement for mild and moderate soil salinization in arid zone. PLoS One. 2019;14(11):e0224790.
   PubMed Web of Science ®Google Scholar
• Ibrahim EA. Seed priming to alleviate salinity stress in germinating seeds. J Plant Physiol. 2016;192:38–46.
   PubMed Web of Science ®Google Scholar
• Johnson DW, Smith SE, Dobrenz AK. Genetic and phenotypic relationships in response to NaCl at different developmental stages in alfalfa. Theor Appl Genet. 1992;83(6–7):833–838.
   PubMed Web of Science ®Google Scholar
• Zhang W, Xie Z, Wang L, et al. Silicon alleviates salt and drought stress of Glycyrrhiza uralensis seedling by altering antioxidant metabolism and osmotic adjustment. J Plant Res. 2017;130(3):611–624.
   PubMed Web of Science ®Google Scholar
• Tian S, Guo R, Zou X, et al. Priming with the green leaf volatile (Z)-3-hexeny-1-yl acetate enhances salinity stress tolerance in peanut (Arachis hypogaea L.) seedlings. Front Plant Sci. 2019; 10:785.
   PubMed Web of Science ®Google Scholar
• Arif MR, Islam MT, Robin AHK. Salinity stress alters root morphology and root hair traits in Brassica napus. Plants (Basel, Switzerland). 2019;8(7):192.
   PubMedGoogle Scholar
• Liu AL, Zou J, Liu CF, et al. Over-expression of OsHsfA7 enhanced salt and drought tolerance in transgenic rice. BMB Rep. 2013;46(1):31–36.
   PubMed Web of Science ®Google Scholar
• Rossi L, Borghi M, Francini A, et al. Salt stress induces differential regulation of the phenylpropanoid pathway in Olea europaea cultivars Frantoio (salt-tolerant) and Leccino (salt-sensitive). J Plant Physiol. 2016;204:8–15.
   PubMed Web of Science ®Google Scholar
• Kovinich N, Wang Y, Adegboye J, et al. Arabidopsis MATE45 antagonizes local abscisic acid signaling to mediate development and abiotic stress responses. Plant Direct. 2018;2(10):e00087.
   PubMedGoogle Scholar
• Liu C, Wang B, Li Z, et al. TsNAC1 is a key transcription factor in abiotic stress resistance and growth. Plant Physiol. 2018;176(1):742–756.
   PubMed Web of Science ®Google Scholar
• Cortés AJ, Chavarro MC, Blair MW. SNP marker diversity in common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2011;123(5):827–845.
   PubMed Web of Science ®Google Scholar
• Galeano CH, Cortés AJ, Fernández AC, et al. Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean. BMC Genet. 2012;13:48.
   PubMed Web of Science ®Google Scholar
• Blair MW, Cortés AJ, Penmetsa RV, et al. A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2013;126(2):535–548.
   PubMed Web of Science ®Google Scholar
• Blair MW, Cortés AJ, Farmer AD, et al. Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.). PLoS One. 2018;13(3):e0189597.
   PubMed Web of Science ®Google Scholar
• Pan L, Yu X, Shao J, et al. Transcriptomic profiling and analysis of differentially expressed genes in asparagus bean (Vigna unguiculata ssp. sesquipedalis) under salt stress. PLoS One. 2019;14(7):e0219799.
   PubMed Web of Science ®Google Scholar
• Yang F, Chen H, Liu C, et al. Transcriptome profile analysis of two Vicia faba cultivars with contrasting salinity tolerance during seed germination. Sci Rep. 2020;10(1):7250.
   PubMed Web of Science ®Google Scholar
• Yuan Y, Xing H, Zeng W, et al. Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage. BMC Plant Biol. 2019;19(1):394.
   PubMed Web of Science ®Google Scholar
• Shi P, Gu M. Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress. BMC Plant Biol. 2020;20(1):568.
   PubMed Web of Science ®Google Scholar
• Zhang W, Liu S, Li C, et al. Transcriptome sequencing of Antarctic moss under salt stress emphasizes the important roles of the ROS-scavenging system. Gene. 2019;696:122–134.
   PubMed Web of Science ®Google Scholar
• Li S, Fan C, Li Y, et al. Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq. BMC Genomics. 2016;17:200.
   PubMed Web of Science ®Google Scholar
• Diaz-Vivancos P, Faize M, Barba-Espin G, et al. Ectopic expression of cytosolic superoxide dismutase and ascorbate peroxidase leads to salt stress tolerance in transgenic plums. Plant Biotechnol J. 2013;11(8):976–985.
   PubMed Web of Science ®Google Scholar
• Arias-Moreno DM, Jiménez-Bremont JF, Maruri-López I, et al. Effects of catalase on chloroplast arrangement in Opuntia streptacantha chlorenchyma cells under salt stress. Sci Rep. 2017;7(1):8656.
   PubMedGoogle Scholar
• Hamooh BT, Sattar FA, Wellman G, et al. Metabolomic and biochemical analysis of two potato (Solanum tuberosum L.) cultivars exposed to in vitro osmotic and salt stresses. Plants (Basel, Switzerland). 2021;10(1):98.
   PubMedGoogle Scholar
• Guan L, Haider MS, Khan N, et al. Transcriptome sequence analysis elaborates a complex defensive mechanism of grapevine (Vitis vinifera L.) in response to salt stress. IJMS. 2018;19(12):4019.
   Google Scholar
• Wang HM, Xiao XR, Yang MY, et al. Effects of salt stress on antioxidant defense system in the root of Kandelia candel. Bot Stud. 2014;55(1):57.
   PubMedGoogle Scholar
• Wang M, Wang Y, Zhang Y, et al. Comparative transcriptome analysis of salt-sensitive and salt-tolerant maize reveals potential mechanisms to enhance salt resistance. Genes Genomics. 2019;41(7):781–801.
   PubMed Web of Science ®Google Scholar
• He L, Wu YH, Zhao Q, et al. Chrysanthemum DgWRKY2 gene enhances tolerance to salt stress in transgenic Chrysanthemum. IJMS. 2018;19(7):2062.
   Google Scholar
• Su P, Yan J, Li W, et al. A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress. BMC Plant Biol. 2020;20(1):392.
   PubMed Web of Science ®Google Scholar
• Wu J, Jiang Y, Liang Y, et al. Expression of the maize MYB transcription factor ZmMYB3R enhances drought and salt stress tolerance in transgenic plants. Plant Physiol Biochem. 2019; 137:179–188.
   PubMed Web of Science ®Google Scholar
• Funck D, Eckard S, Müller G. Non-redundant functions of two proline dehydrogenase isoforms in Arabidopsis. BMC Plant Biol. 2010; 10:70.
   PubMed Web of Science ®Google Scholar
• Amirbakhtiar N, Ismaili A, Ghaffari MR, et al. Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar. PLoS One. 2019;14(3):e0213305.
   PubMed Web of Science ®Google Scholar
• Kong Q, Mostafa HHA, Yang W, et al. Comparative transcriptome profiling reveals that brassinosteroid-mediated lignification plays an important role in garlic adaption to salt stress. Plant Physiol Biochem. 2021;158:34–42.
   PubMed Web of Science ®Google Scholar
• Crizel RL, Perin EC, Siebeneichler TJ, et al. Abscisic acid and stress induced by salt: effect on the phenylpropanoid, L-ascorbic acid and abscisic acid metabolism of strawberry fruits. Plant Physiol Biochem. 2020;152:211–220.
   PubMed Web of Science ®Google Scholar
• Yaish MW, Patankar HV, Assaha DVM, et al. Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity. BMC Genomics. 2017;18(1):246.
   PubMedGoogle Scholar
• Vanholme R, De Meester B, Ralph J, et al. Lignin biosynthesis and its integration into metabolism. Curr Opin Biotechnol. 2019;56:230–239.
   PubMed Web of Science ®Google Scholar
• Chun HJ, Baek D, Cho HM, et al. Lignin biosynthesis genes play critical roles in the adaptation of Arabidopsis plants to high-salt stress. Plant Signal Behav. 2019;14(8):1625697.
   PubMed Web of Science ®Google Scholar
• Chen K, Guo Y, Song M, et al. Dual role of MdSND1 in the biosynthesis of lignin and in signal transduction in response to salt and osmotic stress in apple. Hortic Res. 2020;7(1):204.
   PubMed Web of Science ®Google Scholar
• Duan AQ, Tao JP, Jia LL, et al. AgNAC1, a celery transcription factor, related to regulation on lignin biosynthesis and salt tolerance. Genomics. 2020;112(6):5254–5264.
   PubMed Web of Science ®Google Scholar
• Llorente F, López-Cobollo RM, Catalá R, et al. A novel cold-inducible gene from Arabidopsis, RCI3, encodes a peroxidase that constitutes a component for stress tolerance. Plant J. 2002;32(1):13–24.
   PubMed Web of Science ®Google Scholar
• Gaudet P, Livstone MS, Lewis SE, et al. Phylogenetic-based propagation of functional annotations within the gene ontology consortium. Brief Bioinform. 2011;12(5):449–462.
   PubMed Web of Science ®Google Scholar