深圳大学学报理工版

为研究菜心吸收和转运镉的机制,对镉胁迫前后菜心叶部和根部的转录组进行高通量测序及差异表达分析,共获得3 854个差异表达基因.GO(gene ontology)富集分析显示,差异表达基因主要富集在与次生代谢物合成、氧化还原反应、光合作用、铁离子稳态及木质素或木栓质的合成及代谢等有关的GO条目中.KEGG(kyoto encyclopedia of genes and genomes)富集分析结果表明,差异表达上调基因主要富集在植物病原菌互作、植物信号传导、木栓质等物质的生物合成和谷胱甘肽代谢等通路中; 差异表达下调基因主要富集在光合作用、核糖体、生物素代谢、脂肪酸的生物合成和芥子油苷的生物合成等通路中; 这些差异表达基因可能与菜心应对镉胁迫的生理生化反应相关.分析了菜心在镉胁迫下响应的主要通路及基因,为进一步探索菜心镉胁迫响应机制、培养低镉积累的菜心品种提供理论基础.

In order to investigate the mechanism of cadmium(Cd)uptake and transport of Choy-sum(Brassica rapa ssp. chinensis var. parachinensis), transcriptome sequencing is conducted on the leaves and roots of Choy-sum before and after Cd stress, and the differential gene expression is analyzed. Total 3 854 differentially expressed genes(DEGs)are annotated. The gene ontology(GO)enrichment analysis shows that most of the DEGs are predominantly enriched in the terms of those related to secondary metabolic process, photosynthesis, redox reaction, ion transport, suberin biosynthesis process, lignin catabolic process, etc. The KEGG enrichment analysis shows that the up-regulated DEGs are predominantly enriched in the pathways involved in plant-pathogen interaction, plant signal transduction, suberine biosynthesis and glutathione metabolism. The down-regulated DEGs are predominantly enriched in the pathways involved in photosynthesis, ribosome, biotin metabolism, fatty acid biosynthesis, glucosinolate biosynthesis and so on. The study reveals major genes and pathways involved in response to Cd stress of Choy-sum. It will provide theoretical basis and novel strategies for creating new varieties of choy-sum with low accumulation of Cd via molecular breeding methods.

引言
1 材料与方法
2 结果与分析
3 讨论
4 结语

表1 qRT-PCR验证所用引物序列<br/>Table 1 Primer sequences for qRT-PCR analysis

表1 qRT-PCR验证所用引物序列
Table 1 Primer sequences for qRT-PCR analysis

表2 转录组数据与大白菜参考基因组比对分析<br/>Table 2 Mapping quality analysis of RNA-seq data with the reference genome of Brassica rapa

表2 转录组数据与大白菜参考基因组比对分析
Table 2 Mapping quality analysis of RNA-seq data with the reference genome of Brassica rapa

图1 差异表达基因GO注释以及分类分析<br/>Fig.1 GO annotation and classification of DEGs

图1 差异表达基因GO注释以及分类分析
Fig.1 GO annotation and classification of DEGs

表3 差异表达基因GO富集分析<br/>Table 3 GO enrichment analysis of DEGs

表3 差异表达基因GO富集分析
Table 3 GO enrichment analysis of DEGs

图2 GO富集分析中部分GO亚分类的相关基因的表达趋势<br/>Fig.2 Gene expression trends of partial GO terms in GO significant enrichment analysis

图2 GO富集分析中部分GO亚分类的相关基因的表达趋势
Fig.2 Gene expression trends of partial GO terms in GO significant enrichment analysis

表4 差异表达上调基因KEGG富集分析<br/>Table 4 KEGG pathway enrichment analysis of up-regulated DEGs

表4 差异表达上调基因KEGG富集分析
Table 4 KEGG pathway enrichment analysis of up-regulated DEGs

表5 差异表达下调基因KEGG富集分析<br/>Table 5 KEGG pathway enrichment analysis of down-regulated DEGs

表5 差异表达下调基因KEGG富集分析
Table 5 KEGG pathway enrichment analysis of down-regulated DEGs

图3 转录组数据与qPCR验证的相关性分析<br/>Fig.3 Correlation analysis of qPCR and transcriptome(RNA-seq)results

图3 转录组数据与qPCR验证的相关性分析
Fig.3 Correlation analysis of qPCR and transcriptome(RNA-seq)results

[1] CAO Fangbin, CAI Yue, LIU Li, et al. Differences in photosynthesis, yield and grain cadmium accumulation as affected by exogenous cadmium and glutathione in the two rice genotypes[J]. Plant Growth Regulation, 2015, 75(3): 715-723.
[2] SANITÀ DI TOPPI L, GABBRIELLI R. Response to cadmium in higher plants[J]. Environmental and Experimental Botany, 1999,41(2):105-130.
[3] BENAVIDES M P, GALLEGO S M, TOMARO M L. Cadmium toxicity in plants[J]. Brazilian Journal of Plant Physiology,2005, 17(1): 21-34.
[4] HUANG Xinyuan, DENG Fenglin, YAMAJI N, et al. A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain[J]. Nature Communications, 2016, 7: 12138.
[5] SEMANE B, CUYPERS A, SMEETS K, et al. Cadmium responses in Arabidopsis thaliana: glutathione metabolism and antioxidative defence system[J]. Physiologia Plantarum, 2007, 129(3): 519-528.
[6] QIU Qiu, WANG Yutao, YANG Zhongyi, et al. Responses of different Chinese flowering cabbage(Brassica parachinensis L.)cultivars to cadmium and lead exposure: screening for Cd + Pb pollution-safe cultivars[J]. Clean-Soil Air Water, 2011, 39(11): 925-932.
[7] KIM D, LANGMEAD B, SALZBERG S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature Methods, 2015, 12(4): 357-360.
[8] WANG Xiaowu, WANG Hanzhong, WANG Jun, et al. The genome of the mesopolyploid crop species Brassica rapa[J]. Nature Genetics, 2011, 43(10): 1035-1039.
[9] CHEN Chengjie, XIA Rui, CHEN Hao, et al. TBtools, a toolkit for biologists integrating various HTS-data handling tools with a user-friendly interface[J/OL]. BioRxiv, 2018.(2018- 05-27)[2018- 07-25] https://www.biorxiv.org/content/early/2018/03/27/289660. doi: https://doi.org/10.1101/289660.
[10] ROBINSON M, MCCARTHY D, SMYTH G K. EdgeR: differential expression analysis of digital gene expression data[J]. Journal of Hospice & Palliative Nursing, 2010, 4(4): 206-207.
[11] ZHOU Qian, YANG Yuchen, SHEN Chuang, et al. Comparative analysis between low- and high-cadmium-accumulating cultivars of Brassica parachinensis to identify difference of cadmium-induced microRNA and their targets[J]. Plant and Soil, 2017,420(1/2):223-237.
[12] DOMERGUE F, VISHWANATH S J, JOUBES J A, et al. Three Arabidopsis fatty acyl-coenzyme a reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition[J]. Plant Physiology, 2010, 153(4): 1539-1554.
[13] 刘清泉,陈亚华,沈振国,等. 细胞壁在植物重金属耐性中的作用[J]. 植物生理学报, 2014(5): 605- 611.
[14] THOMINE S, WANG R C, WARD J M, et al. Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes[J]. Proceedings of the National Academy of Sciences of the United States of America, 2000, 97(9): 4991- 4996.
[15] CHENG Feng, SUN Rifei, HOU Xilin, et al. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea[J]. Nature Genetics, 2016, 48(10): 1218-1224.
[16] LIN C Y, TRINH N N, FU S F, et al. Comparison of early transcriptome responses to copper and cadmium in rice roots[J]. Plant Molecular Biology, 2013,81(4/5):507-522.
[17] PENG Hua, HE Xiujing, GAO Jian, et al. Transcriptomic changes during maize roots development responsive to cadmium(Cd)pollution using comparative RNAseq-based approach[J]. Biochemical and Biophysical Research Communications, 2015, 464(4): 1040-1047.
[18] SHI Xiang, SUN Haijing, CHEN Yitai, et al. Transcriptome sequencing and expression analysis of cadmium(Cd)transport and detoxification related genes in Cd-accumulating Salix integra[J]. Frontiers in Plant Science, 2016, 7: 1577.
[19] ZHOU Qian, GUO Jingjie, HE Chuntao, et al. Comparative transcriptome analysis between low- and high-cadmium-accumulating genotypes of Pakchoi(Brassica chinensis L.)in response to cadmium stress[J]. Environmental Science & Technology, 2016, 50(12): 6485-6494.
[20] LEE S B, JUNG S J, GO Y S, et al. Two Arabidopsis 3-ketoacyl CoA synthase genes, KCS20 and KCS2/DAISY, are functionally redundant in cuticular wax and root suberin biosynthesis, but differentially controlled by osmotic stress[J]. Plant Journal, 2009, 60(3): 462- 475.
[21] YADAV V, MOLINA I, RANATHUNGE K, et al. ABCG transporters are required for suberin and pollen wall extracellular barriers in Arabidopsis[J]. Plant Cell, 2014, 26(9): 3569-3588.
[22] ZHAO Qiao, NAKASHIMA J, CHEN Fang, et al. Laccase is necessary and nonredundant with peroxidase for lignin polymerization during vascular development in Arabidopsis[J]. Plant Cell, 2013, 25(10): 3976-3987.
[23] WANG Jinhui, FENG Juanjuan, JIA Weitao, et al. Lignin engineering through laccase modification: a promising field for energy plant improvement[J]. Biotechnology for Biofuels, 2015, 8(1): 145.
[24] WANG Congying, YU Yang, CHEN Yueqin, et al. MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis[J]. Plant Biotechnology Journal, 2014, 12(8): 1132-1142.
[25] XU Shanshan, LIN Sizu, LAI Zhongxiong. Cadmium impairs iron homeostasis in Arabidopsis thaliana by increasing the polysaccharide contents and the iron-binding capacity of root cell walls[J]. Plant and Soil, 2015, 392(1/2): 71-85.
[26] BOURNIER M, TISSOT N, MARI S, et al. Arabidopsis ferritin 1(AtFer1)gene regulation by the phosphate starvation response 1(AtPHR1)transcription factor reveals a direct molecular link between iron and phosphate homeostasis[J]. Journal of Biological Chemistry, 2013, 288(31): 22670-22680.

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2 结果与分析

3 讨论

4 结语

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