«上一篇/Previous Article|本期目录/Table of Contents|下一篇/Next Article»

《江苏农业科学》[ISSN:1002-1302/CN:32-1214/S]

卷:

第51卷

期数:

2023年第5期

页码:

1-11

栏目:

“转录组学” 专栏

出版日期:

2023-03-05

文章信息/Info

Title:

Study on transcriptome alternative splicing difference of two cotton varieties under high temperature stress

作者:

丁宇; 王马寅; 唐敏强; 李子阳; 谢尚潜

海南大学，海南海口 570228

Author(s):

Ding Yu; et al

关键词:

棉花; 高温胁迫; 全长转录组; 纳米孔测序; 可变剪切

Keywords:

-

分类号:

S562.01

DOI:

-

文献标志码:

A

摘要:

棉花(Gossypium hirsutum L.)是一种重要的经济作物，是世界上第二大的天然纺织纤维来源和重要的食用油来源。棉花对生物和非生物胁迫高度敏感，尤其是高温胁迫极易影响花粉的活力和花药的开裂。为了解析棉花在高温胁迫下基因转录水平的相应变化机制，开展了热敏和耐热2个棉花品种的全长转录组响应高温胁迫处理变化的研究。通过转录本的可变剪切分析发现，2个棉花品种在高温胁迫下可变剪切的总数显著增加。热敏品种Che61-72中发现了2 900个差异表达基因，并且差异基因在加热前样本(R0)和加热12 h后的样本(R12)中分别识别到了 13 251 个和25 296个可变剪切事件，其中内含子保留事件增加得最多，有3 837个。耐热品种新陆早36号中发现了 2 437 个差异表达基因，在加热前样本(T0)和加热12 h后的样本(T12)中鉴定到了11 248个和13 769个可变剪切事件，外显子跳跃事件变化得最大，增加了4 144个。富集分析发现，2个品种的差异基因都显著富集到了光系统Ⅰ的光捕获、叶绿体类囊体膜和光合作用-天线蛋白通路中，并筛选出5个关键基因(CPB3、A0A1U8IZF2、A0A1U8KCA2、A0A1U8NDW4和A0A1U8NI70)，均被注释为叶绿素a/b结合蛋白，它们参与了调控棉花光合作用动态平衡。本研究为棉花在高温胁迫的调节机制的深入研究提供了理论依据，为后续耐高温的种质改良及新品种培育提供了数据支持。

Abstract:

-

参考文献/References:

［1］Han Z，Wang C，Song X，et al. Characteristics，development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton ［J］. Theoretical and Applied Genetics，2006，112(3)：430-439.
［2］Grover A，Mittal D，Negi M，et al. Generating high temperature tolerant transgenic plants：achievements and challenges ［J］. Plant Science，2013，205：38-47.
［3］Zahid K R，Ali F，Shah F，et al. Response and tolerance mechanism of cotton Gossypium hirsutum L. to elevated temperature stress：a review ［J］. Frontiers in Plant Science，2016，7：937.
［4］Pettigrew W T. The effect of higher temperatures on cotton lint yield production and fiber quality ［J］. Crop Science，2008，48(1)：278-285.
［5］Burke J J，Wanjura D F. Plant responses to temperature extremes［M］//Physiology of cotton. Berlin：Springer，2010：123-128.
［6］Oosterhuis D M，Snider J L. High temperature stress on floral development and yield of cotton ［M］//Oosterhuis D M. Stress physiology in cotton. Cordova，Tennessee：The Cotton Foundation，2011：1-24.
［7］Reddy K R，Kakanl V G，Zhao D，et al. Interactive effects of ultraviolet-B radiation and temperature on cotton physiology，growth，development and hyperspectral reflectance ［J］. Photochemistry and Photobiology，2004，79(5)：416-427.
［8］Liang Y，Gong Z，Wang J，et al. Nanopore-based comparative transcriptome analysis reveals the potential mechanism of high-temperature tolerance in cotton (Gossypium hirsutum L.) ［J］. Plants，2021，10(11)：2517.
［9］Reddy K，Hodges H，Reddy V. Temperature effects on cotton fruit retention ［J］. Agronomy Journal，1992，84(1)：26-30.
［10］Reddy V，Reddy K，and Baker D. Temperature effect on growth and development of cotton during the fruiting period ［J］. Agronomy Journal，1991，83(1)：211-217.
［11］Soliz L M A，Oosterhuis D M，Coker D L，et al. Physiological response of cotton to high night temperature ［J］. Am J Plant Sci Biotechnol，2008，2：63-68.
［12］Barua D，Downs C A，Heckathorn S A. Variation in chloroplast small heat-shock protein function is a major determinant of variation in thermotolerance of photosynthetic electron transport among ecotypes of Chenopodium album［J］. Functional Plant Biology，2003，30(10)：1071-1079.
［13］Min L，Zhu L，Tu L，et al. Cotton Gh CKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase ［J］. The Plant Journal，2013，75(5)：823-835.
［14］Wang Q，Liu N，Yang X，et al. Small RNA-mediated responses to low-and high-temperature stresses in cotton ［J］. Scientific Reports，2016，6(1)：1-14.
［15］Ma Y，Min L，Wang J，et al. A combination of genome-wide and transcriptome-wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton ［J］. New Phytologist，2021，231(1)：165-181.
［16］Barash Y，Calarco J A，Gao W，et al. Deciphering the splicing code ［J］. Nature，2010，465(7294)：53-59.
［17］Zhao L，Zhang H，Kohnen M V，et al. Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and nanopore-based direct RNA sequencing ［J］. Frontiers in Genetics，2019，10：253.
［18］Abdel-Ghany S E，Hamilton M，Jacobi J L，et al. A survey of the sorghum transcriptome using single-molecule long reads ［J］. Nature Communications，2016，7(1)：1-11.
［19］Wang B，Tseng E，Regulski M，et al. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing ［J］. Nature communications，2016，7(1)：1-13.
［20］Wang Q，Rio D C. JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns ［J］. Proceedings of the National Academy of Sciences，2018，115(35)：EB181-EB190.
［21］Wang X，Xu Y，Zhang S，et al. Genomic analyses of primitive，wild and cultivated citrus provide insights into asexual reproduction ［J］. Nature Genetics，2017，49(5)：765-772.
［22］Li H. Minimap2：pairwise alignment for nucleotide sequences ［J］. Bioinformatics，2018，34(18)：3094-3100.
［23］Tardaguila M，de la Fuente L，Marti C，et al. SQANTI：extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification ［J］. Genome Research，2018，28(3)：396-411.
［24］Trincado J L，Entizne J C，Hysenaj G，et al. SUPPA2：fast，accurate，and uncertainty-aware differential splicing analysis across multiple conditions ［J］. Genome Biology，2018，19(1)：40.
［25］Patro R，Duggal G，Love M I，et al. Salmon provides fast and bias-aware quantification of transcript expression ［J］. Nature Methods，2017，14(4)：417-419.
［26］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.
［27］Cantalapiedra C P，Hernández-Plaza A，Letunic L，et al. eggNOG-mapper v2：functional annotation，orthology assignments，and domain prediction at the metagenomic scale ［J］. Molecular Biology and Evolution，2021，38(12)：5825-5829.
［28］Yu G，Wang L G，Han Y，et al. clusterProfiler：an R package for comparing biological themes among gene clusters ［J］. Omics，2012，16(5)：284-287.
［29］Xie C，Mao X，Huang J，et al. KOBAS 2.0：a web server for annotation and identification of enriched pathways and diseases ［J］. Nucleic Acids Res，2011，39(Web Server issue)：W316-W322.
［30］Chaudhary S，Jabre I，Reddy A S N，et al. Perspective on alternative splicing and proteome complexity in plants ［J］. Trends in Plant Science，2019，24(6)：496-506.
［31］Kim S，Kim T H. Alternative splicing for improving abiotic stress tolerance and agronomic traits in crop plants ［J］. Journal of Plant Biology，2020，63(6)：409-420.
［32］Laloum T，Martín G，Duque P. Alternative splicing control of abiotic stress responses ［J］. Trends in Plant Science，2018，23(2)：140-150.
［33］Cui J W，Shen N，Lu Z G，et al. Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome ［J］. Plant Methods，2020，16(1)：85.
［34］Ivanov A G，Velitchkova M Y，Allakhverdiev S I，et al. Heat stress-induced effects of photosystem Ⅰ：an overview of structural and functional responses ［J］. Photosynthesis Research，2017，133(1/2/3)：17-30.
［35］Allakhverdiev S I，Kreslavski V D，Klimov V V，et al. Heat stress：an overview of molecular responses in photosynthesis ［J］. Photosynthesis Research，2008，98(1/2/3)：541-550.
［36］Shakeel S N，Aman S，Haq N U，et al. Proteomic and transcriptomic analyses of Agave americana in response to heat stress ［J］. Plant Molecular Biology Reporter，2013，31(4)：840-851.
［37］Li W M，Wei Z W，Qiao Z H，et al. Proteomics analysis of alfalfa response to heat stress ［J］. PLoS One，2013，8(12)：e82725.
［38］Spence A K，Boddu J，Wang D F，et al. Transcriptional responses indicate maintenance of photosynthetic proteins as key to the exceptional chilling tolerance of C₄ photosynthesis in Miscanthus×giganteus［J］. Journal of Experimental Botany，2014，65(13)：3737-3747.

相似文献/References:

[1]沙向红,严建萍.低温胁迫对幼苗期棉花根系ADHa与BADH表达的影响[J].江苏农业科学,2013,41(08):37.
　Sha Xianghong,et al.Effect of low temperature stress on expression of ADHa and BADH gene in root of cotton seedlings[J].Jiangsu Agricultural Sciences,2013,41(5):37.
[2]池文泽,周斌,盛玮,等.保水剂在棉花生产上的应用[J].江苏农业科学,2013,41(05):73.
　Chi Wenze,et al.Study on application of water retention agent in cotton production[J].Jiangsu Agricultural Sciences,2013,41(5):73.
[3]杨富强,杨长琴,刘瑞显,等.不同生育期渍水对棉花恢复生长及产量的影响[J].江苏农业科学,2014,42(12):108.
　Yang Fuqiang,et al.Effects of waterlogging in different growth stages on recovery growth and yield of cotton[J].Jiangsu Agricultural Sciences,2014,42(5):108.
[4]李玉侠,李家运,李长敏,等.江苏丰县棉花生产变化及植棉技术优化[J].江苏农业科学,2014,42(12):111.
　Li Yuxia,et al.Changes of cotton production and optimization of cotton planting technology in Fengxian County，Jiangsu Province[J].Jiangsu Agricultural Sciences,2014,42(5):111.
[5]马晓梅,孙杰,李保成,等.新陆早51号棉花器官同伸关系及棉铃空间分布[J].江苏农业科学,2014,42(11):123.
　Ma Xiaomei,et al().Together growth of organs and cotton bolls spatial distribution of cotton cultivar “Xinluzao No.51”[J].Jiangsu Agricultural Sciences,2014,42(5):123.
[6]丁锦平.棉花病毒诱导基因沉默体系构建[J].江苏农业科学,2013,41(06):38.
　Ding Jinping.Establishment of virus induced gene silencing system in cotton[J].Jiangsu Agricultural Sciences,2013,41(5):38.
[7]王义霞,刘春生,苏彦华.新疆棉花品种新陆中51号在山东棉区的需钾特性[J].江苏农业科学,2014,42(10):80.
　Wang Yixia,et al.Potassium requirement characteristics of Xinjiang cotton cultivar “Xinluzhong No.51” in Shandong cotton region[J].Jiangsu Agricultural Sciences,2014,42(5):80.
[8]刘瑞显,张国伟,杨长琴,等.转变现代棉花生产技术研究理念的新视角——基于复杂性科学的思考[J].江苏农业科学,2014,42(10):1.
　Liu Ruixian,et al.A new perspective on ideological changes of cotton productive technological innovation-Based on reflections on complexity science[J].Jiangsu Agricultural Sciences,2014,42(5):1.
[9]陈向阳,陈丽萍,王思乐,等.粗糙集在棉花异性纤维图像去噪中的应用[J].江苏农业科学,2016,44(03):446.
　Chen Xiangyang,et al.Application of rough set in denoising of cotton fiber image[J].Jiangsu Agricultural Sciences,2016,44(5):446.
[10]姚琛,华春,周峰,等.盐碱滩涂植物资源筛选与利用[J].江苏农业科学,2013,41(10):357.
　Yao Chen,et al.Screening and utilization of plant resources cultivated on saline tidal flats[J].Jiangsu Agricultural Sciences,2013,41(5):357.

备注/Memo

备注/Memo:

收稿日期：2022-05-17
基金项目：国家自然科学基金(编号：32060149、31760316)；海南省自然科学基金(编号：320RC500、321RC469)。
作者简介：丁宇(1996—)，女，海南海口人，硕士研究生，主要从事转录组、基因组等生物信息学研究。E-mail：woshidingyuya@163.com。
通信作者：谢尚潜，博士，教授，主要从事生物信息学和基于三代测序的基因组学和转录组学研究。E-mail：sqianxie@foxmail.com。

常用功能

更新日期/Last Update: 2023-03-05