709
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Comparative transcriptome analysis of two varieties of common bean (Phaseolus vulgaris L.) to identify candidate drought resistance genes

, , , , , & show all
Article: 2238847 | Received 10 Feb 2023, Accepted 17 Jul 2023, Published online: 24 Jul 2023

References

  • Chen J, Zhang X, Jing R, et al. Cloning and genetic diversity analysis of a new P5CS gene from common bean (Phaseolus vulgaris L.). Theor Appl Genet. 2010;120(7):1–16. doi: 10.1007/s00122-010-1263-3.
  • Jones PG, Thornton PK. The potential impacts of climate change on maize production in Africa and Latin America in 2055. Global Environ Change. 2003;13(1):51–59. doi: 10.1016/S0959-3780(02)00090-0.
  • Cortés A, 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. doi: 10.1007/s00122-012-1896-5.
  • Sadeghipour O. Response of common bean (Phaseolus vulgaris L.) to exogenous application of salicylic acid (SA) under water stress conditions. Adv Environ Biol. 2012;6:1160–1168.
  • Wu L, Chang Y, Wang L, et al. The aquaporin gene PvXIP1;2 conferring drought resistance identified by GWAS at seedling stage in common bean. Theor Appl Genet. 2022;135(2):485–500. doi: 10.1007/s00122-021-03978-w.
  • Polania JA, Salazar-Chavarría V, Gonzalez-Lemes I, et al. Contrasting Phaseolus crop water use patterns and stomatal dynamics in response to terminal drought. Front Plant Sci. 2022;13:894657. doi: 10.3389/fpls.2022.894657.
  • Dong X, Zhu H, Hao X, et al. Genome-wide identification of common bean PvLTP family genes and expression profiling analysis in response to drought stress. Genes. 2022;13(12):2394. doi: 10.3390/genes13122394.
  • Shao HB, Chu LY, Jaleel CA, et al. Understanding water deficit stress-induced changes in the basic metabolism of higher plants-biotechnologically and sustainably improving agriculture and the ecoenvironment in arid regions of the globe. Crit Rev Biotechnol. 2009;29(2):131–151. doi: 10.1080/07388550902869792.
  • Singh SP. Broadening the genetic base of common bean cultivars. Crop Sci. 2001;41(6):1659–1675. doi: 10.2135/cropsci2001.1659.
  • Simsek M, Comlekcioglu N, Ozturk I. The effects of the regulated deficit irrigation on yield and some yield components of common bean (Phaseolus vulgaris L.) under semiarid conditions. African J Biotechnol. 2011;10:4057–4064.
  • Lizana C, Wentworth M, Martinez JP, et al. Differential adaptation of two varieties of common bean to abiotic stress I. Effects of drought on yield and photosynthesis. J Exp Bot. 2006;57(3):685–697. doi: 10.1093/jxb/erj062.
  • Papathanasiou F, Ninou E, Mylonas I, et al. The evaluation of common bean (Phaseolus vulgaris L.) genotypes under water stress based on physiological and agronomic parameters. Plants. 2022;11(18):2432. doi: 10.3390/plants11182432.
  • Davoudi M, Song M, Zhang M, et al. Long-distance control of the scion by the rootstock under drought stress as revealed by transcriptome sequencing and mobile mRNA identification. Hort Res. 2022;9:uhab033.
  • Sun M, Huang D, Zhang A, et al. Transcriptome analysis of heat stress and drought stress in pearl millet based on pacbio full-length transcriptome sequencing. BMC Plant Biol. 2020;20(1):323. doi: 10.1186/s12870-020-02530-0.
  • Ghodke P, Khandagale K, Thangasamy A, et al. Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress. PLoS One. 2020;15(8):e0237457. doi: 10.1371/journal.pone.0237457.
  • Zhou R, Yu X, Zhao T, et al. Physiological analysis and transcriptome sequencing reveal the effects of combined cold and drought on tomato leaf. BMC Plant Biol. 2019;19(1):377. doi: 10.1186/s12870-019-1982-9.
  • Zhou D, Xing GM, Zheng SW. Screening of drought-resistant varieties of common bean (Phaseolus vulgaris L.). J Shanxi Agricult Sci. 2020;48(1):15–22.
  • Yan W, Guohua MI, Amp CF, et al. Genotypic difference in nitrogen efficiency of five maize inbred lines as affected by nitrate levels. Chin J Appl Environ Biol. 2002;8:361–365.
  • van Delden SH, Nazarideljou MJ, Marcelis LFM. Nutrient solutions for Arabidopsis thaliana: a study on nutrient solution composition in hydroponics systems. Plant Methods. 2020;16:72. doi: 10.1186/s13007-020-00606-4.
  • Giannopolitis CN, Ries SK. Superoxide dismutases: i. Occurrence in higher plants. Plant Physiol. 1977;59(2):309–314. doi: 10.1104/pp.59.2.309.
  • Nickel KS, Cunningham B. Improved peroxidase assay method using leuco 2,3′,6-trichloroindophenol and application to comparative measurements of peroxidatic catalysis. Anal Biochem. 1969;27(2):292–299. doi: 10.1016/0003-2697(69)90035-9.
  • Aebi H. Catalase in vitro. Metho Enzym. 1984;105:121–126.
  • Metwally A, Finkemeier I, Georgi M, Georgi., et al. Salicylic acid alleviates the cadmium toxicity in barley seedlings. Plant Physiol. 2003;132(1):272–281., doi: 10.1104/pp.102.018457.
  • Snyder JC, Desborough SL. Rapid estimation of potato tuber total protein content with Coomassie brilliant blue G-250. Theor Appl Genet. 1978;52(3):135–139. doi: 10.1007/BF00264747.
  • Buysse JAN, Merckx R. An improved colorimetric method to quantify sugar content of plant tissue. J Exp Bot. 1993;44(10):1627–1629. doi: 10.1093/jxb/44.10.1627.
  • Bates LS, Waldren RP, Teare ID. Rapid determination of free proline for stress studies. Plant Soil. 1973;39(1):205–207. doi: 10.1007/BF00018060.
  • Li L, Zhang H, Liu Z, et al. Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development. BMC Plant Biol. 2016;16(1):223. doi: 10.1186/s12870-016-0866-5.
  • Wang J, Qin Q, Pan J, et al. Transcriptome analysis in roots and leaves of wheat seedlings in response to low-phosphorus stress. Sci Rep. 2019;9(1):19802. doi: 10.1038/s41598-019-56451-6.
  • Kanehisa M, Araki M, Goto S, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:D480–484. doi: 10.1093/nar/gkm882.
  • Mao X, Cai T, Olyarchuk JG, et al. Automated genome annotation and pathway identification using the KEGG orthology (KO) as a controlled vocabulary. Bioinformat. 2005;21(19):3787–3793. doi: 10.1093/bioinformatics/bti430.
  • Bu D, Luo H, Huo P, et al. KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis. Nucleic Acids Res. 2021;49(W1):W317–W325. doi: 10.1093/nar/gkab447.
  • Shamimuzzaman M, Vodkin L. Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. BMC Genomics. 2012;13:310. doi: 10.1186/1471-2164-13-310.
  • Guimares CM, Stone LF, Peloso M, et al. Common bean genotypes under water stress. Revista Brasileira De Engenharia Agrícola E Ambiental. 2011;15:649–656.
  • Wu J, Wang L, Li L, et al. De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes. PLoS One. 2014;9(10):e109262. doi: 10.1371/journal.pone.0109262.
  • Rama Reddy N, Ragimasalawada M, Sabbavarapu M, et al. Detection and validation of stay-green QTL in postrainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35. BMC Genomics. 2014;15(1):909. doi: 10.1186/1471-2164-15-909.
  • Mir MA, John R, Alyemeni MN, et al. Jasmonic acid ameliorates alkaline stress by improving growth performance, ascorbate glutathione cycle and glyoxylase system in maize seedlings. Sci Rep. 2018;8(1):2831. doi: 10.1038/s41598-018-21097-3.
  • Farnese FS, Oliveira JA, Paiva EAS, et al. The involvement of nitric oxide in integration of plant physiological and ultrastructural adjustments in response to arsenic. Front Plant Sci. 2017;8:516. doi: 10.3389/fpls.2017.00516.
  • Ma XF, Yu T, Wang LH, et al. Effects of water deficit at seedling stage on maize root development and anatomical structure. Chin J Appl Ecol. 2010;21:1731–1736.
  • Wang QM. Effects of drought stress on protective enzymes activities and membrane lipid peroxidation in leaves of soybean seedlings. J Agro-Environ Sci. 2006;25:918–921.
  • Khakwani AA, Dennett M, Khan NU, et al. Stomatal and chlorophyll limitations of wheat cultivars subjected to water stress at booting and anthesis stage. Pakistan J Bot. 2013;45:1925–1932.
  • Mafakheri A, Siosemardeh A, Bahramnejad B, et al. Effect of drought stress on yield, proline and chlorophyll contents in three chickpea cultivars. Australian J Crop Sci. 2010;4:580–585.
  • Cheng C, Yun KY, Ressom HW, et al. An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics. 2007;8(1):1–18. doi: 10.1186/1471-2164-8-175.
  • Jehle AK, Lipschis M, Albert M, et al. The receptor-like protein ReMAX of Arabidopsis detects the microbe-associated molecular pattern eMax from Xanthomonas. Plant Cell. 2013;25(6):2330–2340. doi: 10.1105/tpc.113.110833.
  • Lorena P, Meirav LM, Silvia S, et al. Tomato prenylated RAB acceptor protein 1 modulates trafficking and degradation of the pattern recognition receptor LeEIX2, affecting the innate immune response. Front Plant Sci. 2018;9:257–272.
  • Bar M, Sharfman M, Ron M, et al. BAK1 is required for the attenuation of ethylene-inducing xylanase (EIX)-induced defense responses by the decoy receptor LeEix1. Plant J. 2010;63(5):791–800. doi: 10.1111/j.1365-313X.2010.04282.x.
  • Ron M, Avni A. The receptor for the fungal elicitor ethylene-inducing xylanase is a member of a resistance-like gene family in tomato. Plant Cell. 2004;16(6):1604–1615. doi: 10.1105/tpc.022475.
  • Kaur S, Kumar A, Thakur S, et al. Antioxidant, antiproliferative and apoptosis-inducing efficacy of fractions from cassia fistula L. leaves. Antioxidants. 2020;9(2):173–181. doi: 10.3390/antiox9020173.
  • Wang G, Zhang C, Huang B. Transcriptome analysis and histopathological observations of Geloina erosa gills upon Cr (VI) exposure. Comp Biochem Physiol C Toxicol Pharmacol. 2020;231:108706. doi: 10.1016/j.cbpc.2020.108706.
  • Jia X, Zhu Y, Zhang R, et al. Ionomic and metabolomic analyses reveal the resistance response mechanism to saline-alkali stress in Malus halliana seedlings. Plant Physiol Biochem. 2020;147:77–90. doi: 10.1016/j.plaphy.2019.12.001.
  • Ras J, Van Ophem PW, Reijnders WN, et al. Isolation, sequencing, and mutagenesis of the gene encoding NAD-and gluthathione dependent. J Bacteriol. 1995;177(1):247–251. doi: 10.1128/jb.177.1.247-251.1995.
  • Barber RD, Rott MA, Donohue TJ. Characterization of a glutathione-dependent formaldehyde dehydrogenase from Rhodobacter sphaeroides. J Bacteriol. 1996;178(5):1386–1393. doi: 10.1128/jb.178.5.1386-1393.1996.
  • Gao T, Zhang Z, Liu X, et al. Physiological and transcriptome analyses of the effects of exogenous dopamine on drought tolerance in apple. Plant Physiol Biochem. 2020;148:260–272. doi: 10.1016/j.plaphy.2020.01.022.
  • Dubrovina AS, Aleynova OA, Ogneva ZV, et al. The effect of abiotic stress conditions on expression of calmodulin (CaM) and Calmodulin-Like (CML) genes in Wild-Growing grapevine Vitis amurensis. Plants. 2019;8(12):602–620. doi: 10.3390/plants8120602.
  • Dong Y, Guan M, Wang L, et al. Transcriptome analysis of low-temperature-induced breaking of garlic aerial bulb dormancy. Int J Genomics. 2019;2019:9140572. doi: 10.1155/2019/9140572.
  • Liu M, Wu F, Wang S, et al. Comparative transcriptome analysis reveals defense responses against soft rot in Chinese cabbage. Hortic Res. 2019;6:68. doi: 10.1038/s41438-019-0149-z.
  • Borrego-Benjumea A, Carter A, Tucker JR, et al. Genome-Wide analysis of gene expression provides new insights into waterlogging responses in barley (Hordeum vulgare L.). Plants. 2020;9(2):240–252. doi: 10.3390/plants9020240.
  • Zhou Y, Luo S, Hameed S, et al. Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita). BMC Genomics. 2020;21(1):117–135. doi: 10.1186/s12864-020-6492-5.
  • Tran AD, Cho K, Han O. Rice peroxygenase catalyzes lipoxygenase-dependent regiospecific epoxidation of lipid peroxides in the response to abiotic stressors. Bioorg Chem. 2023;131:106285. doi: 10.1016/j.bioorg.2022.106285.
  • Zhao D, Wang Y, Feng C, et al. Overexpression of MsGH3.5 inhibits shoot and root development through the auxin and cytokinin pathways in apple plants. Plant J. 2020;103(1):166–183. doi: 10.1111/tpj.14717.
  • Feng S, Yue R, Tao S, et al. Genome-wide identification, expression analysis of auxin-responsive GH3 family genes in maize (Zea mays L.) under abiotic stresses. J Integr Plant Biol. 2015;57(9):783–795. doi: 10.1111/jipb.12327.
  • Zou X, Long J, Zhao K, et al. Overexpressing GH3.1 and GH3.1L reduces susceptibility to Xanthomonas citri subsp. citri by repressing auxin signaling in citrus (citrus sinensis osbeck). PLoS One. 2019;14(12):e0220017. doi: 10.1371/journal.pone.0220017.
  • Hao Du NW, Fu J, Wang S, et al. A GH3 family member, OsGH3-2, modulates auxin and abscisic acid levels and differentially affects drought and cold tolerance in rice. J Exp Bot. 2012;63(18):6467–6480. doi: 10.1093/jxb/ers300.
  • Gan Z, Fei L, Shan N, et al. Identification and expression analysis of Gretchen hagen 3 (GH3) in kiwifruit (Actinidia chinensis) during postharvest process. Plants. 2019;8(11):473–486. doi: 10.3390/plants8110473.