Transcriptome analysis of differentially expressed genes in Reaumuria soongorica seeds germination under NaCl stress

doi:10.3969/j.issn.1000-2006.201811020

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2019, Vol. 62 ›› Issue (03): 28-36.doi: 10.3969/j.issn.1000-2006.201811020

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Transcriptome analysis of differentially expressed genes in Reaumuria soongorica seeds germination under NaCl stress

LIU Xiaowei¹,YANG Xiuyan¹,WU Haiwen¹,LIU Xiaoyan²,ZHU Jianfeng^1*,ZHANG Huaxin^1*

1.Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Beijing 100091, China; 2.College of Life Sciences of Henan Agricultural University, Zhengzhou 450000, China

Online:2019-05-15 Published:2019-05-15

Abstract

Abstract: 【Objective】Screen differentially expressed genes(DEG)at the germination stage of Reaumuria soongorica under NaCl stress and provide genetic resources for the breeding of salt-tolerant species.【Method】The R. soongorica seeds were treated with pre-fitting germination threshold concentration(273 mmol/L, marked as M), optimum germination concentration(43 mmol/L, marked as L)and distilled water(marked as C), and each treatment was repeated three times. The seeds were taken out when the radicle broke through the seed coat but not more than 2 mm, and the transcriptome sequencing was performed.【Result】There were 210, 2 273 and 2 888 DEG screened out in comparison group of L and C(LvsC), M and C(MvsC), M and L(MvsL), respectively, of which 116 were up-regulated and 94 were down-regulated in LvsC, 1 781 were up-regulated and 492 were down-regulated in MvsC, and 2 165 were up-regulated and 723 were down-regulated in MvsL. These up-regulated genes are mainly enriched in ribosome, carbon metabolism, cytochrome P450 metabolism, glutathione metabolism and other pathways in KEGG, down-regulated genes are mainly enriched in sucrose and starch metabolism, endoplasmic reticulum protein processing and other processes. 【Conclusion】Under stress conditions, the DEG induce related reactions synergistic responses, which ultimately lengthen the hypocotyl cells and break through the seed coat to complete germination.

CLC Number:

Q943.2

LIU Xiaowei,YANG Xiuyan,WU Haiwen,LIU Xiaoyan,ZHU Jianfeng,ZHANG Huaxin. Transcriptome analysis of differentially expressed genes in Reaumuria soongorica seeds germination under NaCl stress[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2019, 62(03): 28-36.

References

[1] 王遵亲, 祝寿泉, 俞仁培, 等. 中国盐渍土[M]. 北京:科学出版社, 1993:3.
WANG Z Q, ZHU S Q, YU R P, et al. Saline soil in China[M].Beijing: Science Press, 1993:3.
[2] KOVDA V A. Loss of productive land due to salinization[J]. Ambio,1983, 12(2):91-93. DOI: 10.1016/0167-8809(83)90034-8.
[3] 韩志平,张海霞,周凤. 盐胁迫对植物的影响及植物对盐胁迫的适应性[J]. 山西大同大学学报(自然科学版), 2015, 31(3): 59-62. DOI: 10.3969/j.issn.1674-0874.2015.03.019.
HAN Z P, ZHANG H X, ZHOU F. Effect of salinity on plant and adaptation of plant to salinity[J]. Journal of Shanxi Datong University(Natural Science),2015,31(3): 59-62.
[4] 张娟, 姜闯道, 平吉成. 盐胁迫对植物光合作用影响的研究进展[J]. 农业科学研究, 2008, 29(3):74-80. DOI:10.3969/j.issn.1673-0747.2008.03.020.
ZHANG J, JIANG C D, PING J C. Research advances about the effect of salt stress on photosynthesis of plant [J]. Journal of Agricultural Sciences, 2008,29(3): 74-80.
[5] ZHU J.Abiotic stress signaling and responses in plants[J]. Cell,2016, 167(2):313-324. DOI:10.1016/j.cell.2016.08.029.
[6] FLOEWRS T J. Physiology of halophytes[J]. Plant & Soil,1985, 89(1/3):41-56. DOI:10.1007/BF02182232.
[7] FLOWERS T J, COLMERTD.Salinity tolerance in halophytes [J].The New Phytologist, 2008:179(4):945-963. DOI: 10.1111/j.1469-8137.2008.02531.x.
[8] RODRIGUEZURIBE L, HIGBIE S M, STEWART J M, et al. Identification of salt responsive genes using comparative microarray analysis in upland cotton(Gossypium hirsutum L.)[J]. Plant Science,2011,180(3):461-469.DOI:10.1016/j.plantsci.2010.10.009.
[9] ZHU J K. Genetic analysis of plant salt tolerance using Arabidopsis[J]. Plant Physiology,2000, 124(3):941-948. DOI: 10.1104/pp.124.3.941.
[10] BEWLEY J D, BRADFORD K, HILHORST H, et al. Seeds: physiology of development, germination and dormancy[J]. Seed Science Research,2013, 23(4):289-289. DOI: 10.1017/S0960258513000287.
[11] ZHAO K F, FAN H, UNGAR I A.Survey of halophyte species in China[J]. Plant Science, 2002,163(3):491-498.DOI:10.1016/S0168-9452(02)00160-7.
[12] MA J Y, CHEN T, QIANG W Y, et al. Correlations between foliar stable carbon isotope composition and environmental factors in desert plant Reaumuria soongorica (Pall.)Maxim[J]. Journal of Integrative Plant Biology, 2005,47(9): 1065-1073.
[13] 白蕾, 单立山, 李毅, 等. 降雨格局变化对红砂幼苗根系生长和生物量分配的影响[J]. 西北植物学报, 2017, 37(1): 163-170. DOI: 10.7606/j.issn.1000-4025.2017.01.0163.
BAI L, SHAN L S, LI Y, et al. Effects of changing rainfall patterns on the root and biomass of Reaumuria soongorica seedlings[J]. Acta Botanica Boreali-Occidentalia Sinica,2017, 37(1): 163-170.
[14] 刘瑞香, 马迎梅, 刘冰, 等. 额济纳荒漠红砂(Reaumuria soongorica)根系分布与土壤环境关系的研究[J]. 干旱区资源与环境, 2018(6): 149-154.DOI:10.13448/j.cnki.jalre.2018.186.
LIU R X, MA Y M, LIU B, et al. Relationship between root distribution of Reaumuria soongorica and soil properties in Ejina Desert[J]. Journal of Arid Land Resources & Environment,2018(6): 149-154.
[15] 薛焱, 王迎春. 光照、温度和盐分对长叶红砂种子萌发的影响[J]. 植物生理学报, 2007, 43(4): 708-710.DOI:10.13592/j.cnki.ppj.2007.04.027.
XUE Y, WANG Y C.Influence of light, temperature and salinity on seed germination of Reaumuria trigyna Maxim[J]. Plant Physiology Communications, 2007, 43(4): 708-710.
[16] 曾彦军, 王彦荣, 张宝林, 等. 红砂和猫头刺种子萌发生态适应性的研究[J]. 草业学报, 2000,9(3):36-42.DOI:10.3321/j.issn:1004-5759.2000.03.006.
ZENG Y J, WANG Y R, ZHANG B L, et al. Eco-adaptability studies of seed germination in species of Reaumuria soongorica and Oxytropis aciphylla[J]. Acta Prataculturalence,2000, 9(3):36-42.
[17] 张勇, 薛林贵, 高天鹏, 等. 荒漠植物种子萌发研究进展[J]. 中国沙漠, 2005, 25(1): 106-112. DOI:10.3321/j.issn:1000-694X.2005.01.018.
ZHANG Y, XUE L G, GAO T P, et al. Research advance on seed germination of desert plants[J]. Journal of Desert Research, 2005, 25(1): 106-112.
[18] 王彦荣, 曾彦军, 张宝林,等. 不同退化红砂荒漠草地的水分分配格局[J].应用生态学报, 2002, 13(8):962-966.
WANG Y R, ZENG Y J, ZHANG B L, et al.Water distribution patterns in different degraded desert grasslands of Reaumuria soongorica[J]. Chinese Journalof Applied Ecology, 2002, 13(8):962-966.
[19] 陈金元, 陈学林, 满吉琳, 等. 混合盐碱胁迫对红砂种子萌发的影响[J]. 西北农林科技大学学报(自然科学版), 2016, 44(5): 113-119. DOI: 10.13207/j.cnki.jnwafu.2016.05.015.
CHEN J Y, CHEN X L, MAN J L, et al.Effects of mixed saline-alkali stress on germination of Reaumuria songarica seeds[J]. Journal of Northwest A & F University,2016, 44(5): 113-119.
[20] 高茜, 李毅, 苏世平, 等. 盐胁迫对红砂(Reaumuria soongorica)种子吸胀过程中生理特性的影响[J]. 中国沙漠, 2014, 34(1): 83-87. DOI: 10.7522/j.issn.1000-694X.2013.00288.
GAO Q, LI Y, SU S P, et al.Effects of salt stress on physiological characteristics of Reaumuria soongorica seeds during imbibition[J]. Journal of Desert Research, 2014, 34(1):83-87.
[21] 周航宇, 包爱科, 杜宝强, 等. 荒漠植物红砂响应高浓度NaCl的生理机制[J]. 草业科学, 2012, 29(1): 71-75.
ZHOU H Y, BAO A K, DU B Q,et al. The physiological mechanisms underlying how eremophyte Reaumuria soongorica responses to severe NaCl stress[J]. Pratacultural Science,2012, 29(1):71-75.
[22] DU C, ZHAO P P, ZHANG H R, et al. The Reaumuria trigyna transcription factor RtWRKY1 confers tolerance to salt stress in transgenic Arabidopsis[J].Journal of Plant Physiology, 2017,215:48-58.DOI:10.1016/j.jplph.2017.05.002.
[23] 刘丹, 刘玉冰, 张雯莉. 红砂(Reaumuria soongorica)响应干旱和UV-B辐射双重胁迫的基因转录表达[J]. 中国沙漠, 2017, 37(4): 705-713.DOI:10.7522/j.issn.1000-694X.2016.00167.
LIU D, LIU Y B, ZHANG W L. Gene transcriptional expression in Reaumuria soongorica under combined stress of drought and UV-B radiation[J]. Journal of Desert Research, 2017, 37(4): 705-713.
[24] LIU M L, LI X Y, LIU Y B, et al.Analysis of differentially expressed genes under UV-B radiation in the desert plant Reaumuria soongorica[J]. Gene,2015, 574(2):265-272. DOI: 10.1016/j.gene.2015.08.026.
[25] LIU Y B, LIU M Y, LI X L, et al.Identification of differentially expressed genes in leaf of Reaumuria soongorica under PEG-induced drought stress by digital gene expression profiling[J]. PLoS One, 2014, 9(4):e94277. DOI:10.1371/journal.pone.0094277.
[26] SHI Y, YAN X, ZHAO P S, et al. Transcriptomic analysis of a tertiary relict plant, extreme xerophyte Reaumuria soongorica to identify genes related to drought adaptation[J]. PloS One, 2013,8(5):e63993.DOI:10.1371/journal.pone.0063993.
[27] LIU Y B, LI X R, TAN H J, et al. Molecular characterization of RsMPK2, a C1 subgroup mitogen-activated protein kinase in the desert plant Reaumuria soongorica[J].Plant Physiology & Biochemistry,2010, 48(10-11):836-844. DOI: 10.1016/j.plaphy.2010.07.001.
[28] COCK P J A, FIELDS C J, GOTO N, et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants[J]. Nucleic Acids Research,2010, 38(6):1767-1771. DOI: 10.1093/nar/gkp1137.
[29] GRABHERR M G, HAAS B J, YASSOUR M, et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology,2011, 29(7):644. DOI: 10.1038/nbt.1883.
[30] FINN R D, TATE J, MISTRY J, et al.The PFAM protein families datubase[J]. Nudeic Acids Research, 2008, 36:281-288.DOI:10.1043/nar/gkm960.
[31] LI B, DEWEY C N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome[J]. Bmc Bioinformatics,2011,12(1):323-323.DOI:10.1186/1471-2105-12-323.
[32] ANDERS S, HUBER W. Differential expression analysis for sequence count data[J]. Genome Biology, 2010.11(10):R106.DOI:10.1186/gb-2010-11-10-r106.
[33] LOVE M I, HUBER W, ANDERS S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J]. Genome Biology, 2014,15(12):550.DOI:10.1186/s13059-014-0550-8.
[34] WANG L, FENG Z, WANG X, et al.DEGseq: an R package for identifying differentially expressed genes from RNA-seq data[J]. Bioinformatics,2010,26(1):136-138.DOI:10.1093/bioinformatics/btp612.
[35] KANEHISA M, ARAKI M, GOTO S, et al. KEGG for linking genomes to life and the environment[J]. Nucleic Acids Research, 2008, 36(Database issue):480-484.DOI:10.1093/nar/gkm882.
[36] MAO X, CAI T, OLYARCHUK J G, et al. Automated genome annotation and pathway identification using the KEGG Orthology(KO)as a controlled vocabulary[J]. Bioinformatics,2005, 21(19):3787-3793. DOI: 10.2307/1592215.
[37] YOUNG M D, WAKEFIELD M J, SMYTH G K, et al. Gene ontology analysis for RNA-seq: accounting for selection bias[J]. Genome Biology,2010,11(2):R14.DOI:10.1186/gb-2010-11-2-r14.
[38] GOTZ S, GARCIA-GOMEZ J M, TEROL J, et al. High-throughput functional annotation and data mining with the Blast2GO suite[J]. Nucleic Acids Research,2008, 36(10):3420-3435. DOI: 10.1093/nar/gkn176.
[39] TRAPNELL C, WILLIAMS B A, PERTEA G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation [J].Nature Biotechnology,2010, 28(5):511-515. DOI: 10.1038/nbt.1621.
[40] DANG Z H, ZHENG L L, WANG J, et al. Transcirptomic profiling of the salt-stress response in the wild recretohalophyte Reanmuria trigyna[J]. BMC Genomics, 2013, 14(1):24. DOI: 10.1186/1471-2164-10-29.
[41] XU P, LIU Z W, FAN X Q, et al. De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress[J]. Gene, 2013,525(1):26-34.DOI:10.1016/j.gene.2013.04.066.
[42] DEINLEIN U, STEPHAN A B, HORIE R, et al. Plant salt-tolerance mechanisms[J]. Trends in Plant Science, 2014, 19(6):371-379.DOI:10.1016/j.tplants.2014.02.001.
[43] 李翔宇, 王助乾, 孙春玉, 等.植物细胞色素P450s及其在植物新陈代谢中的作用[J].安徽农业科学,2016,44(13):129-134. DOI: 10.3969/j.issn.0517-6611.2016.13.043.
LI X Y, WANG Z Q, SUN C Y,et al. Cytochrome P450s and their function in plant metabolism[J]. Journal of Anhui Agricultural Sciences,2016, 44(13):129-134.
[44] 孙超, 黎家. 油菜素甾醇类激素的生物合成、代谢及信号转导[J]. 植物生理学报, 2017(3):291-307.DOI:10.13592/j.cnki.ppj.2017.1002.
SUN C, LI J.Biosynthesis,catabolism,and signal transduction of brassinosteroids[J]. Plant Physiology Journal, 2017(3):291-307.
[45] 赵剑, 杨文杰, 朱蔚华. 细胞色素P450与植物的次生代谢[J]. 生命科学, 1999(3):127-131.
ZHAO J, YANG W J, ZHU W H.Cytochrome P450 and plant secondary metabolism[J]. Chinese Bulletin of Life Sciences, 1999(3):127-131.
[46] 钟巍然,柴友荣,张凯,等.苯丙烷代谢途径中细胞色素P450的研究[J].安徽农业科学,2008, 36(13):5285-5289.DOI:10.3969/j.issn.0517-6611.2008.13.017.
ZHONG W R, CHAI Y R, ZHANG K, et al.Study on the cytochrome P450s in phenylpropanoid metabolic pathway[J]. Journal of Anhui Agricultural Sciences, 2008, 36(13):5285-5289.

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Transcriptome analysis of differentially expressed genes in Reaumuria soongorica seeds germination under NaCl stress

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