LU-Tan,CHEN Hua-tao,ZHANG Wei,et al.Screening of Tolerant Soybean Varieties and Analysis of Differential Expressed Genes of Lee 68 Under Low-Potassium Stress[J].Soybean Science,2020,39(04):489-499.[doi:10.11861/j.issn.1000-9841.2020.04.0489]
耐低钾大豆品种筛选及低钾胁迫下Lee 68的差异表达基因分析
- Title:
- Screening of Tolerant Soybean Varieties and Analysis of Differential Expressed Genes of Lee 68 Under Low-Potassium Stress
- 文献标志码:
- A
- 摘要:
- 摘要：为了从分子水平上研究大豆幼苗对低钾胁迫的耐性机理，本研究首先依据生物量指标从25份大豆材料中筛选出耐低钾品种Lee 68，并对低钾胁迫下大豆Lee 68幼苗进行转录组测序和分析。通过对转录组Solexa/Illumina高通量测序数据的分析，共得到160 211 759个reads，将获得的数据与大豆Williams 82基因组序列比对，比对率达到92.83%以上。比较组LK_VS_CK中差异表达基因为3 521个，其中下调和上调基因分别为2 393和1 128个。GO功能聚类分析显示LK_VS_CK比较组的差异表达基因主要富集于植物的代谢过程、胁迫响应及信号转导；KEGG pathway 分析中，LK_VS_CK比较组有390个差异表达基因显著富集在19个pathway途径中，其中富集最为显著的是代谢途径，包括氨基酸代谢、脂肪酸和类脂代谢以及碳水化合物代谢等；COG分类统计结果表明LK_VS_CK比较组除649个差异表达基因具有一般性功能之外，377个基因被划分到转录因子功能类，343个基因被划分到信号转导机制功能中。结合差异表达基因的功能分析及茉莉酸信号转导调控机制，筛选到了茉莉酸信号途径上可能参与钾离子吸收转运过程的8个关键候选基因，分别是Glyma09g08290、Glyma09g33730、Glyma03g32890、Glyma04g39010、Glyma 08g09720、Glyma12g36310、Glyma16g32821、Glyma19g45260。研究结果对深入研究大豆钾胁迫下与钾离子高效吸收相关基因的调控及克隆研究具有重要的参考价值。
- Abstract:
- In order to study the tolerance mechanism of soybean seedlings to low potassium stress at the molecular level,this study selected the low potassium tolerant variety Lee 68 from 25 soybean materials according to the biomass index firstly, and used Lee 68 as test materials in transcriptome sequencing under low potassium stress.Through the analysis of Solexa/Illumina sequencing data, 160 211 759 reads were obtained. The alignment rate reached more than 92.83% compared with the genome sequence of Williams 82.The total differential expressed genes of LK_VS_CK were 3 521, of which down/up-regulated genes were 2 393/1 128 respectively.The GO functional clustering analysis showed that the differential expressed genes in the LK_VS_CK group were mainly enriched in plant metabolic processes, stress response, and signal transduction. The KEGG pathway analysis showed that there were 390 differential expressed genes in LK_VS_CK group and enriched in 19 pathway approach, especially in the metabolic pathways, including amino acids, fatty acid and lipid metabolism, and carbohydrate metabolism. COG classification statistics showed that in the LK_VS_CK comparison group, beside the 649 differentially expressed genes with general function, 377 genes were classified into the function of transcription, and 343 genes were classified into the function of signal transduction mechanism. Combination the function analysis of differential expressed genes with jasmonic acid signal transduction regulation mechanism, eight key candidate genes were screened as follow: Glyma09g08290, Glyma09g33730, Glyma03g32890, Glyma04g39010, Glyma08g09720, Glyma12g36310, Glyma16g32821, and Glyma19g45260, which may participate in the uptake of potassium ion transport process in jasmonic acid signaling pathway. These results provide an important reference for further study on the regulation and cloning of genes related to potassium efficient absorption in soybean under potassium stress.
参考文献/References:
［1］姜存仓, 王运华, 鲁剑巍, 等. 植物钾效率基因型差异机理的研究进展［J］. 华中农业大学学报, 2004, 23 (4):483-487. (Jiang C C, Wang Y H, Lu J W, et al. Advances of study on the K-efficiency indifferent plant genotypes ［J］ .Journal of Huazhong Agricultural University, 2004, 23(4) :483-487.)［2］黄初女, 金东淳, 董艺兰, 等．浅谈大豆蛋白质品质改良［J］. 吉林农业科学, 2006, 31(1) : 37-40．(Huang C N, Jin D C, Dong Y L, et al．Talking about the improvement of soybean protein quality［J］. Journal of Jilin Agricultural Sciences, 2006, 31(1): 37-40.)［3］李兴涛, 佟晓楠, 于海秋, 等. 不同低钾耐性大豆品种钾素效率的差异［J］. 大豆科学, 2014, 33(3): 385-388. (LI X T, Tong X N, Yu H Q, et al. Potassium efficiency of different low K tolerant soybean varieties［J］. Soybean Science, 2014, 33(3): 385-388.)［4］王利, 陈防, 万开元．植物钾效率及其评价的研究进展与展望［J］．土壤, 2010, 42 (2):164 -170.(Wang L, Cheng F, Wang K Y. Progress and expectation of the research on plant K efficiency and its evaluation［J］. Soils, 2010, 42(2):164-170.)［5］Ahmad I,Maathuis F J. Cellular and tissue distribution of potassium: Physiological relevance, mechanisms and regulation［J］. Journal of Plant Physiology, 2014, 171(9): 708-714.［6］Wang Y, Wu W H. Regulation of potassium transport and signaling in plants［J］. Current Opinion in Plant Biology, 2017, 39(10): 123-128.［7］Marschnert H, Kirkby E A, Engels C. Importance of cycling and recycling of mineral nutrients within plants for growth and development［J］. Plant Biology, 2015, 110(4): 265-273.［8］Bari R, Jones J D. Role of plant hormones in plant defense responses［J］. Plant Molecular Biology, 2009, 69: 473-488.［9］Croucher N J, Fookes M C, Perkins T T, et al. A simple method for directional transcriptome sequencing using Illumina technology［J］. Nucleic Acids Research, 2009, 37(22):e148.［10］〖JP4〗Lopez-maestre H, Brinza L, Marchet C, et al. SNP calling from RNA-seq data without a reference genome: Identification, quantification, differential analysis and impact on the protein sequence［J］. Nucleic Acids Research, 2016, 44(19): 1-13.［11］李妍, 徐兴祥.高通量测序技术的研究进展［J］.中国医学工程, 2019, 27(3):32-37.(Li Y, Xu X X. Research progress of high-throughput sequencing technology［J］. China Medical Engineering, 2019, 27(3):32-37.)［12］刘永杰, 王渊, 付强, 等. 高通量测序技术在病原生物学方面的研究进展［J］. 口岸卫生控制, 2019, 24(1):6-9.(Liu Y J, Wang Y, Fu Q, et al. Advances in high-throughput sequencing technology in the field of pathogen biology［J］. Port Health Control, 2019, 24(1):6-9.)［13］Park S T, Kim J. Trends in next-generation sequencing and a new era for whole genome sequencing［J］. International Neurourology Journal, 2016, 20(Supplement 2): 76-83.［14］Boycott K M, Vanstone M R, Bulman D E, et al. Rare-disease genetics in the era of next-generation sequencing: Discovery to translation［J］. Nature Review Genetic, 2013, 14(10): 681-691.［15］Müllauer L. Next generation sequencing: Clinical applications in solid tumours［J］. Magazine of European Medical Oncology, 2017, 10(4): 244-247.［16］岳桂东, 高强, 罗龙海, 等. 高通量测序技术在动植物研究领域中的应用［J］. 中国科学: 生命科学, 2012, 42(2):107-124. (Yue K D, Gao Q, Luo L H, et al.The application of High-throughput sequencing technology in plant and animal research ［J］.Scientia Sinica Vitae, 2012, 42(2):107-124.)［17］曹盈. 高通量测序技术在植物转录组研究中的应用［J］. 北京农业, 2013(6):6-7.(Cao Y. The application of high-throughput sequencing technology in plant transcriptome research［J］. Beijing Agriculture,2013(6):6-7.)［18］范秀朵. 基于高通量Illumina测序技术的干旱胁迫下大豆根和叶mRNA表达谱研究［D］. 吉林:吉林农业大学, 2011: 10-39. (Fan X D. Investigation of gene expression profiles of soybean leaves and roots under drought stress by high-throughput Illumina sequencing ［D］. Jilin: Jinlin Agricultural University, 2011:10-39.)［19］吴冰月, 沈良, 宋普文, 等. 大豆RNA依赖的RNA聚合酶基因GmRDR1的克隆与表达特性分析［J］. 大豆科学, 2015,34(1):19-25. (Wu B Y, Shen L, Song P W, et al. Cloning and expression pattern analysis of a RNA-dependant RNA polymerase gene GmRDR1 in soybean［J］. Soybean Science, 2015,34(1):19-25.)［20］吴冰月, 宋普文, 陈华涛, 等. 2个大豆 RNA 依赖的 RNA 聚合酶基因GmRDR6a和GmRDR6b的克隆与分析［J］. 南京农业大学学报, 2014, 37(3) : 27-34. (Wu B Y, Song P W, Chen H T, et al. Cloning and expression pattern analysis of GmRDR6a and GmRDR6b in soybean［J］. Journal of Nanjing Agricultural University, 2014, 37(3): 27-34.)［21］Wang C, Chen H,Hao Q, et al. Transcript profile of the response of two soybean genotypes to potassium deficiency［J］. PLoS One, 2012, 7(7): e39856.［22］Cole T, Lior P, Steven L, et al. TopHat: Discovering splice junctions with RNA-Seq［J］. Bioinformatics, 2009, 25(9):1105-1111.［23］Wang Y H, Garvin D F, Kochian L V. Rapid induction of regulatory and transporter genes in response to phosphorus,potassium,and iron deficiencies in tomato roots. Evidence for cross talk and root/rhizosphere-mediated signals［J］. Plant Physiology, 2002, 130(3): 1361-1370.［24］Van Kleeff P J M, Gao J, Mol S, et al. The Arabidopsis GORK K+-channel is phosphorylated by calcium-dependent protein kinase 21(CPK21), which in turn is activated by 14-3-3 proteins［J］. Plant Physiology and Biochemistry, 2018, 125: 219-231.［25］Chini A, Fonseca S,Chico J M, et al. The ZIM domain mediates-homo-and heteromeric interactions between Arabidopsis JAZ proteins［J］. The Plant Journal, 2009, 59(1): 77-87.［26］Adams E, Turner J. Illuminating COI1: A component of the Arabidopsis jasomonate receptor complex also interacts with ethylene signaling［J］. Plant Signaling and Behavior, 2010, 5(12): 1682-1684.［27］王秀燕, 孙莉萍, 张建锋, 等. F-box蛋白家族及其功能［J］. 生命科学, 2008, 20(5): 807-811. (Wang X Y, Sun L P, Zhang J F, et al. F-box protein families and their functions［J］. Life Science, 2008, 20(5): 807-811.)［28］Staswick P E. JAZing up jasmonate signaling［J］. Trends in Plant Science, 2008, 13(2): 66-71.［29］Valenzuela-Riffo F, Garrido-Bigotes A, Figueroa P M, et al. Structural analysis of the woodland strawberry COI1-JAZ1 co-receptor for the plant hormone jasmonoyl-isoleucine［J］. Journal of Molecular Graphics and Modelling, 2018, 85: 250-261.［30］王克晶, 李向华．国家基因库野生大豆(Glycine soja)资源最近十年考察与研究［J］．植物遗传资源学报, 2012(4): 507-514．(Wang K J, Li X H．Exploration and studies of wild soybean germplasm resources in the China genebank during recent decade［J］. Journal of Plant Genetic Resources, 2012(4): 507-514.)［31］徐晓燕, 唐迪. 耐盐性不同的大豆品种幼苗的蛋白质组学比较研究［J］. 江西农业大学学报, 2013, 35(1): 38-41. (Xu X Y, Tang D. Comparative analysis of proteomics in soybean cultivar seedlings with different salt resistance［J］. Acta Agriculturae Universitatis Jiangxiensis, 2013, 35(1): 38-41.)［32］Luo Q, Yu B, Liu Y. Differential sensitivity to chloride and sodium ions in seedlings of Glycine max and G. soja under NaCl stress ［J］. Journal of Plant Physiology, 2005, 162(9):1003-1012.［33］Chen X Q, Yu B J, Liu Y L. Relationship between chloride tolerance and polyamine accumulation in Glycine max, Glycine soja, and their hybrid seedlings［J］. Journal of Plant Physiology and Molecular Biology, 2007, 33(1):46-52.［34］Ma H, Song L, Shu Y, et al. Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes ［J］. Journal of Proteomics, 2012, 75(5):1529-1546.［35］Very A A, Nieves-Cordones M, Daly M, et al. Molecular biology of K+ transport across the plant cell membrane: What do we learn from comparison between plant species?［J］. Journal of Plant Physiology, 2014, 171(9): 748-769.［36］Chen G, Hu Q, Luo L, et al. Rice potassium transporter OsHAK1 is essential for maintaining potassium-mediated growth and functions in salt tolerance over low and high potassium concentration ranges［J］. Plant, Cell and Environment, 2015, 38(12):2747-2765.［37］Chen H T, He H, Yu D Y. Overexpression of a novel soybean gene modulating Na+ and K+ transport enhances salt tolerance in transgenic tobacco plants［J］. Physiologia Plantrum, 2011, 141(1): 11-18.［38］Zhao S, Zhang M L, Ma T L, et al. Phosphorylation of ARF2 relieves its repression of transcription of the K+ transporter gene HAK5 in response to low potassium stress［J］. Plant Cell, 2016, 28(12):3005-3019.［39］Chen X, Li C, Wang H, et al. WRKY transcription factors: Evolution, binding, and action［J］. Phytopathology Research, 2019(1):1-13.［40］Huang H, Gao H, Liu B, et al. bHLH13 regulates jasmonate-mediated defense responses and growth［J］. Evolutionary Bioinformatics, 2018, 14: 1-8.
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