Research Progress of Multi-omics Technologies in Plant Response to Abiotic Stress

doi:10.11924/j.issn.1000-6850.casb2023-0059

Abstract

Abstract:

In order to elucidate the mechanism of plant response to abiotic stress and accelerate the improvement of plant breeding, the application of genomics, transcriptomics, proteomics, metabolomics and phenomics in plant response to abiotic stress was summarized. The characteristics, advantages and disadvantages of genomics, transcriptomics, proteomics, metabolomics and phenomics technologies were analyzed. The research progresses of multi-omics technologies such as genomics, transcriptomics, proteomics, metabolomics, and phenomics in plant response to abiotic stress in recent years were generalized by key points in this paper. It was pointed out that there were some problems in the application of multi-omics technology in plants, such as weak correlation, insufficient data mining and so on. The overall mechanism of plant response to abiotic stress should be fully elucidated by using multi-omics technology. It was suggested that multi-omics techniques should be integrated, and bioinformatics analysis methods should be strengthened.

Key words: plant, abiotic stress, multi-omics, genomics, transcriptomics, proteomics, metabolomics

JI Yuan, YU Bing, CHEN Sixue. Research Progress of Multi-omics Technologies in Plant Response to Abiotic Stress[J]. Chinese Agricultural Science Bulletin, 2023, 39(23): 1-7.

Figures/Tables 4

References 46

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技术	基因芯片技术	表达序列标签技术	RNA-Seq技术	单细胞转录组测序技术
优点	①高通量 ②微型化 ③自动化 ④成本低 ⑤防污染	①由于没有内含子的存在，因此在cDNA及基因组模板中PCR产物的大小相同 ②与编码区具有很强的保守性不同，3’UTR序列的保守性较差，因此很容易将单个基因与编码序列关系非常紧密的相似基因家族成员分开	①通量高 ②准确性高 ③检测范围广 ④成本低	①高度的准确性和特异性 ②能以最小的样本起始量开展无偏差的高通量研究
缺点	①无法应用到还未完成全基因组测序以及基因注释信息不完善的物种上 ②低丰度表达基因不易获得	①ESTs很短，没有给出完整的表达序列 ②低丰度表达基因不易获得 ③错误率高	无法揭示单个细胞间表达的异质性	①只分析带poly(A)的RNA ②对样本质量要求高

技术	基因芯片技术	表达序列标签技术	RNA-Seq技术	单细胞转录组测序技术
优点	①高通量 ②微型化 ③自动化 ④成本低 ⑤防污染	①由于没有内含子的存在，因此在cDNA及基因组模板中PCR产物的大小相同 ②与编码区具有很强的保守性不同，3’UTR序列的保守性较差，因此很容易将单个基因与编码序列关系非常紧密的相似基因家族成员分开	①通量高 ②准确性高 ③检测范围广 ④成本低	①高度的准确性和特异性 ②能以最小的样本起始量开展无偏差的高通量研究
缺点	①无法应用到还未完成全基因组测序以及基因注释信息不完善的物种上 ②低丰度表达基因不易获得	①ESTs很短，没有给出完整的表达序列 ②低丰度表达基因不易获得 ③错误率高	无法揭示单个细胞间表达的异质性	①只分析带poly(A)的RNA ②对样本质量要求高

技术	双向凝胶电泳技术	双向荧光差异凝胶电泳技术	同位素亲和标签技术	同位素相对标记与绝对定量技术	无标记蛋白质组学定量技术
优点	①通量高 ②分辨率和重复性好 ③可与质谱联用	精确、标准化、重复性、高效、简化、可靠	①分离在肽段水平上进行，解决膜蛋白溶解性问题，可对膜蛋白进行鉴定和定量 ②可以鉴定和定量含有多个半胱氨酸的肽段 ③能够直接测量和鉴定低丰度蛋白质	①定量精确、灵敏度高 ②检测样本多样化，能对组织、细胞、血清、唾液、泪液等多种样本进行分析 ③可以检测出低丰度蛋白、强碱性蛋白	①成本更低 ②省去了胶染色和稳定同位素标记定量方法的繁杂样品处理过程
缺点	①只能分析可溶性蛋白 ②工作量大 ③需要蛋白样品量大	①在极端等电点、分子量的蛋白质的分离、低丰度和疏水蛋白质鉴定方面存在缺陷 ②荧光染料灵敏度低 ③使用荧光染料的过程需要严格避光，给操作带来不便	①ICAT的分子量约为500 Da，会影响小肽段的鉴定 ②无法分析不含Cys的蛋白质 ③不能准确反映细胞内蛋白质真正含量	成本较高	①过程准确性较低 ②对质谱实验的重现性有很大的依赖性

技术	双向凝胶电泳技术	双向荧光差异凝胶电泳技术	同位素亲和标签技术	同位素相对标记与绝对定量技术	无标记蛋白质组学定量技术
优点	①通量高 ②分辨率和重复性好 ③可与质谱联用	精确、标准化、重复性、高效、简化、可靠	①分离在肽段水平上进行，解决膜蛋白溶解性问题，可对膜蛋白进行鉴定和定量 ②可以鉴定和定量含有多个半胱氨酸的肽段 ③能够直接测量和鉴定低丰度蛋白质	①定量精确、灵敏度高 ②检测样本多样化，能对组织、细胞、血清、唾液、泪液等多种样本进行分析 ③可以检测出低丰度蛋白、强碱性蛋白	①成本更低 ②省去了胶染色和稳定同位素标记定量方法的繁杂样品处理过程
缺点	①只能分析可溶性蛋白 ②工作量大 ③需要蛋白样品量大	①在极端等电点、分子量的蛋白质的分离、低丰度和疏水蛋白质鉴定方面存在缺陷 ②荧光染料灵敏度低 ③使用荧光染料的过程需要严格避光，给操作带来不便	①ICAT的分子量约为500 Da，会影响小肽段的鉴定 ②无法分析不含Cys的蛋白质 ③不能准确反映细胞内蛋白质真正含量	成本较高	①过程准确性较低 ②对质谱实验的重现性有很大的依赖性

技术	GC-MS	LC-MS	NMR	CE-MS
检测对象	易挥发、能气化或小分子的化合物	高沸点、不易挥发、不易衍生化、大分子的化合物	代谢物中大多数的化合物	微量、复杂的样品
优点	①高分辨 ②高灵敏度 ③质谱库信息量大 ④价格经济 ⑤可进行化合物的结构鉴定	①分离效率高 ②分析速度快 ③可以分离相似结构的化合物	①样品用量少 ②无需样品前处理	①样品用量少 ②代谢物覆盖范围更广
缺点	①无法分离大分子 ②不能检测不能气化的物质 ③衍生化预处理费时	①不同柱材料都无法适应所有代谢物 ②分析代谢物种类有限 ③数据库含有数据量有限	①灵敏度与分辨率较低 ②对样品制备的要求高 ③动态范围有限 ④硬件投资大	①分离重现性差 ②定量分析时线性范围较窄