Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (22): 3964-3975.doi: 10.3864/j.issn.0578-1752.2019.22.003

• MOLECULAR GENETICS • Previous Articles     Next Articles

Transcriptomics Analysis of NaCl Response in Foxtail Millet (Setaria italica L.) Seeds at Germination Stage

PAN JiaoWen1,LI Zhen1,WANG QingGuo1,GUAN YanAn2,3,LI XiaoBo1,4,DAI ShaoJun5,DING GuoHua4,LIU Wei1,3()   

  1. 1 Biotechnology Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan 250100
    2 Crop Research Institute, Shandong Academy of Agricultural Sciences/Shandong Engineering Laboratory for Featured Crops, Jinan 250100
    3 College of Life Sciences, Shandong Normal University, Jinan 250014
    4 School of Life Sciences and Technology, Harbin Normal University, Harbin 150025
    5 College of Life and Environmental Sciences, Shanghai Normal University/Development Center of Plant Germplasm Resources, Shanghai 200234
  • Received:2019-07-19 Accepted:2019-09-30 Online:2019-11-16 Published:2019-11-16
  • Contact: Wei LIU E-mail:wheiliu@163.com

RichHTML

53

PDF

547

Abstract:

【Objective】 Foxtail millet (Setaria italica L.) remarkably adapts to adverse ecologies, including drought, barren regions and high soil salinity. These characteristics promote it as a very promising model crop for exploring basic biology processes of plants. Unveil of mechanisms of foxtail millet under salinity is of immense significance. 【Method】 In this research, 14 millet varieties at germination stage were used for resistance screening under 150 mmol·L -1 NaCl. The germination rate, root and bud length of each variety were measured after been treated for 7 d, and the salt tolerance variety Yugu 2 and salt susceptible variety An 04 were obtained. These two varieties before and after salt treatment were used for transcriptomes analysis by RNA-seq sequencing. The functional and pathway enrichments of differentially expressed genes (DEGs) were also performed by GO and KEGG analysis. Fifteen DEGs were randomly selected for further qRT-PCR analysis to verify the RNA-seq data.【Result】 Totally 2 786 and 4 413 DEGs were identified in Yugu 2 and An 04, and there were 1 470 and 3 826 DEGs within each cultivar before and after salt treatment, respectively. GO and KEGG enrichment analysis suggested that DEGs were mainly clustered into signaling, antioxidant system, organic acid biosynthesis and transport, and secondary metabolism, and the DEGs participated in response to stress, ion transmembrane transport, redox homeostasis, secondary metabolism, organic acid, polyamine and phenylpropanoid biosynthetic process. The qRT-PCR results showed high correlation coefficient of 0.8817 with the data of RNA-seq. Especially the genes such as cation transporter (HKT8), peroxidase (POD), flavanone 3-dioxygenase (FL3H) and MYB transcription factors, which displayed higher vary degrees in Yugu2 under salinity may play key roles in salt response process of foxtail millet. 【Conclusion】There was difference in the response degree of salt tolerance variety and salt sensitive variety of millet under salinity. Moreover, the resistance trait formation and function to salt was mainly depends on the response degree instead of the number of DEGs under stress.

Key words: foxtail millet (Setaria italica L.), salt stress, seeds of germination stage, transcriptomics, molecular mechanisms

Fig. 1

The relative germination rate (A), relative root length (B) and relative seedling length (C) of 14 varieties of foxtail millet seeds under 150 mmol·L-1 NaCl"

Fig. 2

DEGs analysis of Yugu2 and An04 plantlets under salt stress A: The phenotypes of Yugu 2 and An 04 plantlets under 150 mmol·L-1 NaCl for 7 days; B: The DEGs in different comparison groups; C: Venn diagrams of DEGs among different comparisons"

Fig. 3

qRT-PCR verification of selected DEGs in Yugu2 and An04 under salt and correlation analysis with data of RNA-seq R value indicates the correlation coefficient between data of RNA-seq and qRT-PCR"

Fig. 4

Gene ontology (GO) analysis of DEGs"

Fig. 5

Scatterplot of top 20 KEGG pathways for the up-regulated DEG in Yugu2 and An04 after salt stress"

Fig. 6

The schematic presentation of salt-responsive mechanisms in seeds of foxtail millet at germination stage"

[1] DEINLEIN U, STEPHAN A B, HORIE T, LUO W, XU G, SCHROEDER J I . Plant salt-tolerance mechanisms. Trends in Plant Science, 2014,19(6):371-379.
[2] JULKOWSKA M M, TESTERINK C . Tuning plant signaling and growth to survive salt. Trends in Plant Science, 2015,20(9):586-594.
[3] PARIHAR P, SINGH S, SINGH R, SINGH V P, PRASAD S M . Effect of salinity stress on plants and its tolerance strategies: A review. Environmental Science and Pollution Research, 2015,22(6):4056-4075.
[4] ACOSTA-MOTOS J, ORTUÑO M, BERNAL-VICENTE A, DIAZ- VIVANCOS P, SANCHEZ-BLANCO M, HERNANDEZ J . Plant responses to salt stress: Adaptive mechanisms. Agronomy, 2017,7(1):18.
[5] ZHANG G, LIU X, QUAN Z, CHENG S, XU X, PAN S, XIE M, ZENG P, YUE Z, WANG W, TAO Y, BIAN C, HAN C, XIA Q, PENG X, CAO R, YANG X, ZHAN D, HU J, ZHANG Y, LI H, LI H, LI N, WANG J, WANG C, WANG R, GUO T, CAI Y, LIU C, XIANG H, SHI Q, HUANG P, CHEN Q, LI Y, WANG J, ZHAO Z, WANG J . Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnology, 2012,30(6):549-554.
[6] LATA C, GUPTA S, PRASAD M . Foxtail millet: A model crop for genetic and genomic studies in bioenergy grasses. Critical Reviews in Biotechnology, 2013,33(3):328-343.
[7] YANG Y, GUO Y . Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytologist, 2018,217(2):523-539.
[8] ZHU J K . Regulation of ion homeostasis under salt stress. Current Opinion in Plant Biology, 2003,6(5):441-445.
[9] LATA C, SAHU P P, PRASAD M . Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochemical and Biophysical Research Communications, 2010,393(4):720-727.
[10] PANDEY G, MISRA G, KUMARI K, GUPTA S, PARIDA S K, CHATTOPADHYAY D, PRASAD M . Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Research, 2013,20(2):197-207.
[11] QI X, XIE S, LIU Y, YI F, YU J . Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Molecular Biology, 2013,83(4-5):459-473.
[12] WANG Y, LI L, TANG S, LIU J, ZHANG H, ZHI H, JIA G Q, DIAO X M . Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet. BMC Genetics, 2016,17(1):57.
[13] TANG S, LI L, WANG Y, CHEN Q, ZHANG W, JIA G, ZHI H, ZHAO B, DIAO X M . Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses). Scientific Reports, 2017,7(1):10009.
[14] PAN J, LI Z, WANG Q, GARRELL A K, LIU M, GUAN Y, ZHOU W, LIU W . Comparative proteomic investigation of drought responses in foxtail millet. BMC Plant Biology, 2018,18(1):315.
[15] WANG J, ZHANG Q, CUI F, HOU L, ZHAO S, XIA H, QIU J, LI T, ZHANG Y, WANG X, ZHAO C . Genome-wide analysis of gene expression provides new insights into cold responses in Thellungiella salsuginea. Frontiers in Plant Science, 2017,8(1):713.
[16] XIONG H, GUO H, XIE Y, ZHAO L, GU J, ZHAO S, LI J, LIU L . RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant. Scientific Reports, 2017,7(1):2731.
[17] WANG F, XU Z, FAN X, ZHOU Q, CAO J, JI G, JING S, FENG B, WANG T . Transcriptome analysis reveals complex molecular mechanisms underlying UV tolerance of wheat (Triticum aestivum L.). Journal of Agricultural and Food Chemistry, 2019,67(2):563-577.
[18] ZHANG Y, WANG P, XIA H, ZHAO C, HOU L, LI C, GAO C, WANG X, ZHAO S . Comparative transcriptome analysis of basal and zygote-located tip regions of peanut ovaries provides insight into the mechanism of light regulation in peanut embryo and pod development. BMC Genomics, 2016,17(1):606.
[19] WANG A, LI R, REN L, GAO X, ZHANG Y, MA Z, MA D, LUO Y . A comparative metabolomics study of flavonoids in sweet potato with different flesh colors (Ipomoea batatas (L.) Lam). Food Chemistry , 2018,260:124-134.
[20] WU J, KIM S G, KANG K Y, KIM J G, PARK S R, GUPTA R, KIM Y H, WANG Y, KIM S T . Overexpression of a pathogenesis-related protein 10 enhances biotic and abiotic stress tolerance in rice. The Plant Pathology Journal, 2016,32(6):552-562.
[21] YAMAGUCHI S . Gibberellin metabolism and its regulation. Annual Review of Plant Biology, 2008,59:225-251.
[22] 张国伟, 路海玲, 张雷, 陈兵林, 周治国 . 棉花萌发期和苗期耐盐性评价及耐盐指标筛选. 应用生态学报, 2011,22(8):2045-2053.
ZHANG G W, LU H L, ZHANG L, CHEN B L, ZHOU Z G . Salt tolerance evaluation of cotton (Gossypium hirsutum) at its germinating and seedling stages and selection of related indices. Chinese Journal of Applied Ecology, 2011,22(8):2045-2053. (in Chinese)
[23] 於丽华, 王宇光, 孙菲, 杨瑞瑞, 王秋红, 耿贵 . 甜菜萌发—幼苗期不同阶段耐盐能力的研究. 中国农学通报, 2017,33(19):22-28.
YU L H, WANG Y G, SUN F, YANG R R, WANG Q H, GENG G . Salt tolerance of sugarbeet: From germination to seedling stage. Chinese Agricultural Science Bulletin, 2017,33(19):22-28. (in Chinese)
[24] GONG Q, LI P, MA S, INDU RUPASSARA S, BOHNERT H J . Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant Journal, 2005,44(5):826-839.
[25] ARBONA V, ARGAMASILLA R, GOMEZ-CADENAS A . Common and divergent physiological, hormonal and metabolic responses of Arabidopsis thaliana and Thellungiella halophila to water and salt stress. Journal of Plant Physiology, 2010,167(16):1342-1350.
[26] IGAMBERDIEV A U, EPRINTSEV A T . Organic acids: The pools of fixed carbon involved in redox regulation and energy balance in higher plants. Frontiers in Plant Science, 2016,7:1042.
[27] TAKENAKA Y, NAKANO S, TAMOI M, SAKUDA S, FUKAMIZO T . Chitinase gene expression in response to environmental stresses in Arabidopsis thaliana: Chitinase inhibitor allosamidin enhances stress tolerance. Bioscience Biotechnology and Biochemistry, 2009,73(5):1066-1071.
[28] YEH S, MOFFATT B A, GRIFFITH M, XIONG F, YANG D S, WISEMAN S B, SARHAN F, DANYLUK J, XUE Y Q, HEW C L, DOHERTY-KIRBY A, LAJOIE G . Chitinase genes responsive to cold encode antifreeze proteins in winter cereals. Plant Physiology, 2000,124(3):1251-1264.
[29] JENSEN K, MOLLER B L . Plant NADPH-cytochrome P450 oxidoreductases. Phytochemistry, 2010,71(2-3):132-141.
[30] CASTORINA G, PERSICO M, ZILIO M, SANGIORGIO S, CARABELLI L, CONSONNI G . The maize lilliputian1 (lil1) gene, encoding a brassinosteroid cytochrome P450 C-6 oxidase, is involved in plant growth and drought response. Annals of Botany, 2018,122(2):227-238.
[31] GOLLDACK D, LUKING I, YANG O . Plant tolerance to drought and salinity: Stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Reports, 2011,30(8):1383-1391.
[1] LIN XinYing,WANG PengJie,YANG RuXing,ZHENG YuCheng,CHEN XiaoMin,ZHANG Lei,SHAO ShuXian,YE NaiXing. The Albino Mechanism of a New High Theanine Tea Cultivar Fuhuang 1 [J]. Scientia Agricultura Sinica, 2022, 55(9): 1831-1845.
[2] HU YaLi,NIE JingZhi,WU Xia,PAN Jiao,CAO Shan,YUE Jiao,LUO DengJie,WANG CaiJin,LI ZengQiang,ZHANG Hui,WU QiJing,CHEN Peng. Effect of Salicylic Acid Priming on Salt Tolerance of Kenaf Seedlings [J]. Scientia Agricultura Sinica, 2022, 55(14): 2696-2708.
[3] ZHU ChunYan,SONG JiaWei,BAI TianLiang,WANG Na,MA ShuaiGuo,PU ZhengFei,DONG Yan,LÜ JianDong,LI Jie,TIAN RongRong,LUO ChengKe,ZHANG YinXia,MA TianLi,LI PeiFu,TIAN Lei. Effects of NaCl Stress on the Chlorophyll Fluorescence Characteristics of Seedlings of Japonica Rice Germplasm with Different Salt Tolerances [J]. Scientia Agricultura Sinica, 2022, 55(13): 2509-2525.
[4] LIU Chuang,GAO Zhen,YAO YuXin,DU YuanPeng. Functional Identification of Grape Potassium Ion Transporter VviHKT1;7 Under Salt Stress [J]. Scientia Agricultura Sinica, 2021, 54(9): 1952-1963.
[5] ZHANG GuiYun,ZHU JingWen,SUN MingFa,YAN GuoHong,LIU Kai,WAN BaiJie,DAI JinYing,ZHU GuoYong. Analysis of Differential Metabolites in Grains of Rice Cultivar Changbai 10 Under Salt Stress [J]. Scientia Agricultura Sinica, 2021, 54(4): 675-683.
[6] WANG Jie,WU XiaoYu,YANG Liu,DUAN QiaoHong,HUANG JiaBao. Genome-Wide Identification and Expression Analysis of ACA Gene Family in Brassica rapa [J]. Scientia Agricultura Sinica, 2021, 54(22): 4851-4868.
[7] SHAO MeiQi,ZHAO WeiSong,SU ZhenHe,DONG LiHong,GUO QingGang,MA Ping. Effect of Bacillus subtilis NCD-2 on the Growth of Tomato and the Microbial Community Structure of Rhizosphere Soil Under Salt Stress [J]. Scientia Agricultura Sinica, 2021, 54(21): 4573-4584.
[8] WANG Na,ZHAO ZiBo,GAO Qiong,HE ShouPu,MA ChenHui,PENG Zhen,DU XiongMing. Cloning and Functional Analysis of Salt Stress Response Gene GhPEAMT1 in Upland Cotton [J]. Scientia Agricultura Sinica, 2021, 54(2): 248-260.
[9] KONG YaLi,ZHU ChunQuan,CAO XiaoChuang,ZHU LianFeng,JIN QianYu,HONG XiaoZhi,ZHANG JunHua. Research Progress of Soil Microbial Mechanisms in Mediating Plant Salt Resistance [J]. Scientia Agricultura Sinica, 2021, 54(10): 2073-2083.
[10] LI Hui,HAN ZhanPin,HE LiXia,YANG YaLing,YOU ShuYan,DENG Lin,WANG ChunGuo. Cloning and Functional Analysis of BraERF023a Under Salt and Drought Stresses in Cauliflower (Brassica oleracea L. var. botrytis) [J]. Scientia Agricultura Sinica, 2021, 54(1): 152-163.
[11] ShuJun MENG,XueHai ZHANG,QiYue WANG,Wen ZHANG,Li HUANG,Dong DING,JiHua TANG. Identification of miRNAs and tRFs in Response to Salt Stress in Rice Roots [J]. Scientia Agricultura Sinica, 2020, 53(4): 669-682.
[12] ZHOU Lian,XIONG YuHan,HONG XiangDe,ZHOU Jing,LIU ChaoXian,WANG JiuGuang,WANG GuoQiang,CAI YiLin. Functional Characterization of a Maize Plasma Membrane Intrinsic Protein ZmPIP2;6 Responses to Osmotic, Salt and Drought Stress [J]. Scientia Agricultura Sinica, 2020, 53(3): 461-473.
[13] SI XuYang,JIA XiaoWei,ZHANG HongYan,JIA YangYang,TIAN ShiJun,ZHANG Ke,PAN YanYun. Genomic Profiling and Expression Analysis of Phosphatidylinositol- specific PLC Gene Families Among Chinese Spring Wheat [J]. Scientia Agricultura Sinica, 2020, 53(24): 4969-4981.
[14] HAO ShuLin,CHEN HongWei,LIAO FangLi,LI Li,LIU ChangYan,LIU LiangJun,WAN ZhengHuang,SHA AiHua. Analysis of F-Box Gene Family Based on Salt-Stressed Transcriptome Sequencing in Vicia faba L. [J]. Scientia Agricultura Sinica, 2020, 53(17): 3443-3454.
[15] ChunHua PANG,Yuan ZHANG,YaNi LI. Effects of Soaking Seeds with Lanthanum Nitrate on Seed Germination and Seedling Growth of Quinoa Under Salt Stress [J]. Scientia Agricultura Sinica, 2019, 52(24): 4484-4492.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd