Transcriptome Analysis and Differential Gene Mining of Perennial-root Sugarcane

doi:10.13523/j.cb.2306028

China Biotechnology

2024, Vol. 44

Issue (2/3): 25-38 DOI: 10.13523/j.cb.2306028

Transcriptome Analysis and Differential Gene Mining of Perennial-root Sugarcane

CHENG Qin,LI Jiahui,TAN Qinliang,SONG Qiqi,ZHU Pengjin^**(

),OU Kewei,NONG Zemei,LU Yefei,LV Ping,ZHOU Quanguang,PANG Xinhua,PENG Xinyi^**(

)

Guangxi Institute of Subtropical Crops, Nanning 530001, China

Download:

HTML

PDF(3564KB) HTML
Export: BibTeX | EndNote (RIS)

Abstract

Sugarcane ratooning ability is directly related to its production cost and cultivation efficiency. Sugarcane ratooning productivity is influenced by variety, environment and cultivation measures, but variety is the most critical factor. There are few reports explaining the differences in sugarcane ratooning ability at the molecular biological level both domestically and internationally. In this paper, transcriptome sequencing was used to analyze the differences in gene expression between sugarcane GR2 and ROC22 of different root years. The results showed that 100 558 transcripts and 25 582 unigenes were obtained by transcriptome sequencing. By functional annotation of unigenes, including comparison with NR, Swiss-Prot, KEGG, COG, KOG, GO and Pfam databases, a total of 53 790 unigene annotation results were obtained. The GO functional annotation was divided into three categories and 51 subcategories. A total of 1 029 differential genes were annotated in six-year-old sugarcane, and 3 391 differential genes were annotated in three-year-old sugarcane. There are eight major KEGG metabolic pathways, which are mainly involved in plant hormone signal transduction, starch and sucrose metabolism, glycine, serine and threonine metabolism, phenylpropanoid biosynthesis, homologous recombination, DNA replication, mismatch repair and plant pathogen interaction. Six abscisic acid-related differentially identified genes are: abscisic acid-insensitive 5-like protein 2 (ABI2), putative bZIP transcription factor superfamily protein, protein abscisic acid-insensitive 5 (ABI5), aba responsive element-binding factor 1 (partial ABF1), G-box binding factor 4 (GBFs), and aba responsive element-binding factor 1 (ABF). The above differential genes will serve as reference genes for our later gene expression and function analysis, and further analyze the molecular mechanism affecting sugarcane ratooning ability by combining proteomics.

Key words： Saccharum hybirds Perennial root Transcriptome Abscisic acid

Received: 21 June 2023 Published: 03 April 2024

ZTFLH:

Q78

	Service
	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	Qin CHENG
	Jiahui LI
	Qinliang TAN
	Qiqi SONG
	Pengjin ZHU
	Kewei OU
	Zemei NONG
	Yefei LU
	Ping LV
	Quanguang ZHOU
	Xinhua PANG
	Xinyi PENG

Cite this article:

CHENG Qin, LI Jiahui, TAN Qinliang, SONG Qiqi, ZHU Pengjin, OU Kewei, NONG Zemei, LU Yefei, LV Ping, ZHOU Quanguang, PANG Xinhua, PENG Xinyi. Transcriptome Analysis and Differential Gene Mining of Perennial-root Sugarcane. China Biotechnology, 2024, 44(2/3): 25-38.

URL:

https://manu60.magtech.com.cn/biotech/10.13523/j.cb.2306028 OR https://manu60.magtech.com.cn/biotech/Y2024/V44/I2/3/25

Table 1 Analysis results of sugarcane young root transcriptome data

Table 2 The statistical table of assemble result

Table 3 Annotation statistics of Unigene

Fig.1 Species distribution of the BLASTX results coincided to NR database

Table 4 Statistical table of number of differentially expressed genes

Fig.2 Volcano map of differentially expressed genes of sugarcane varieties with different perennial root age

Table 5 Statistical table of the number of differentially expressed genes annotated

Fig.3 Gene ontology functional enrichment of sugarcane ratoon for six years

Fig.4 Gene ontology functional enrichment of sugarcane ratoon for three years

Fig.5 COG function classification of differentially expressed genes of sugarcane ratoon for six years

Fig.6 COG function classification of differentially expressed genes of sugarcane ratoon for three years A:RNA processing and modification;B:Chromatin structure and dynamic;C:Energy production and conversion;D:Cell cycle control, cell division, chromosome partitioning;E:Amino acid transport and metabolism;F:Nucleotide transport and metabolism;G:Carbohydrate transport and metabolism;H:Coenzyme transport and metabolism;I:Lipid transport and metabolism;J:Translation, ribosomal structure and biogenesis;K:Transcription;L:Replication, recombination and repair;M:Cell wall/membrane/envelope biogenesis;N:Cell motility;O:Posttranslational modification, protein turnover, chaperones;P:Inorganic ion transport and metabolism;Q:Secondary metabolites biosynthesis, transport and catabolism;R:General function prediction only;S:Function unknown;T:Signal transduction mechanisms;U:Intracellular trafficking, secretion, and vesicular transport;V:Defense mechanisms;W:Extracellular structures;X:Mobilome: prophages, transposons;Z:Cytoskeleton

Fig.7 KEGG annotation of differentially expressed gene of sugarcane ratoon for six years

Fig.8 KEGG annotation of differentially expressed gene of sugarcane ratoon for three years T-ROC_vs_T-GR.KEGG

Fig.9 T-ROC_vs_T-GR.KEGG enrichment factor

Fig.10 S-ROC_vs_S-GR.KEGG enrichment factor

Table 6 Notes on the main KEGG metabolic pathways

Table 7 Analysis of differential gene expression of abscisic acid


[1]	唐仕云, 杨丽涛, 李杨瑞. 低温胁迫下不同甘蔗品种的转录组比较分析. 生物技术通报, 2018, 34(12): 116-124. doi: 10.13560/j.cnki.biotech.bull.1985.2018-0522

[1]	Tang S Y, Yang L T, Li Y R. Comparative analysis on transcriptome among different sugarcane cultivars under low temperature stress. Biotechnology Bulletin, 2018, 34(12): 116-124. doi: 10.13560/j.cnki.biotech.bull.1985.2018-0522

[2]	李穆, 程志远, 石莹, 等. 基于RNA-seq技术的甘蔗参考转录组建立及分析. 分子植物育种, 2015, 13(2): 355-360.

[2]	Li M, Cheng Z Y, Shi Y, et al. Establishment and analysis on reference transcriptome of sugarcane based on RNA-seq technology. Molecular Plant Breeding, 2015, 13(2): 355-360.

[3]	苏亚春. 甘蔗应答黑穗病菌侵染的转录组与蛋白组研究及抗性相关基因挖掘. 福州: 福建农林大学, 2014.

[3]	Su Y C. Transcriptomics and proteomics of sugarcane response to Sporisorium scitamineum infection and mining of resistance-related genes. Fuzhou: Fujian Agriculture and Forestry University, 2014.

[4]	马丽, 苏火生, 刘新龙, 等. 国内甘蔗种质六年宿根蔗的产量评价. 中国糖料, 2012, 34(4): 29-32.

[4]	Ma L, Su H S, Liu X L, et al. Evaluating yield and sucrose content for the sixth year ratoot sugarcane in China. Sugar Crops of China, 2012, 34(4): 29-32.

[5]	覃伟, 吴才文, 曾千春, 等. 用新台糖甘蔗品种作母本培育强宿根后代的潜力评价. 湖南农业大学学报(自然科学版), 2012, 38(1): 1-7.

[5]	Qin W, Wu C W, Zeng Q C, et al. Ratooning traits in sugarcane progenies of ROC varieties as female parents. Journal of Hunan Agricultural University (Natural Sciences), 2012, 38(1): 1-7.

[6]	庞新华, 朱鹏锦, 周全光, 等. 广西蔗区引进甘蔗品种(系)的比较试验. 作物杂志, 2016(2): 73-78.

[6]	Pang X H, Zhu P J, Zhou Q G, et al. Comparative study of introduced sugarcane varieties(lines) in Guangxi. Crops, 2016(2): 73-78.

[7]	张玉叶. 甘蔗受黑穗病菌胁迫下microRNA差异表达及其靶基因功能分析. 福州: 福建农林大学, 2015.

[7]	Zhang Y Y. Differentially expressed microRNAs in sugarcane challenged by Sporisorium scitamineum and their target gene function identification. Fuzhou: Fujian Agriculture and Forestry University, 2015.

[8]	张培珠. 基于转录组测序技术的赖草根茎发育调控基因分析及应用研究. 济南: 济南大学, 2017.

[8]	Zhang P Z. Analysis and application of genes controlling rhizome development in Leymus secalinus based on transcriptome sequencing technique. Jinan: University of Jinan, 2017.

[9]	丘立杭, 罗含敏, 陈荣发, 等. 基于RNA-Seq的甘蔗主茎和分蘖茎转录组建立及初步分析. 基因组学与应用生物学, 2018, 37(3): 1271-1279.

[9]	Qiu L H, Luo H M, Chen R F, et al. Establishment and preliminary analysis on transcriptome of sugarcane between stalk and tiller based on RNA-seq technology. Genomics and Applied Biology, 2018, 37(3): 1271-1279.

[10]	Cardoso-Silva C B, Costa E A, Mancini M C, et al. De novo assembly and transcriptome analysis of contrasting sugarcane varieties. PLoS One, 2014, 9(2): e88462.

[11]	Zeng Q Y, Ling Q P, Fan L N, et al. Transcriptome profiling of sugarcane roots in response to low potassium stress. PLoS One, 2015, 10(5): e0126306.

[12]	Li M, Liang Z X, Zeng Y, et al. De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.). BMC Genomics, 2016, 17: 195. doi: 10.1186/s12864-016-2552-2

[13]	Ye Y P. Studies on the physiological and biochemical mechanism on ethephon promoting effective tillering in sugarcane. Nanning: Guangxi University, 2006.

[14]	丘立杭, 范业庚, 罗含敏, 等. 甘蔗分蘖发生及成茎的调控研究进展. 植物生理学报, 2018, 54(2): 192-202. doi: 10.1104/pp.54.2.192

[14]	Qiu L H, Fan Y G, Luo H M, et al. Advances of regulation study on tillering formation and stem forming from available tillers in sugarcane (Saccharum officinarum). Plant Physiology Journal, 2018, 54(2): 192-202. doi: 10.1104/pp.54.2.192

[15]	Pribil M, Ngo C, Wang L, et al. Altering sugarcane shoot architecture through genetic engineering: prospects for increasing cane and sugar yield. Proceedings of the Australian Society of Sugar Cane Technologist, 2007, 29:251-257.

[16]	Wang J, Wu B W, Lu K, et al. The amino acid permease 5 (OsAAP5) regulates tiller number and grain yield in rice. Plant Physiology, 2019, 180(2): 1031-1045. doi: 10.1104/pp.19.00034 pmid: 30890663

[17]	程琴, 谭秦亮, 李佳慧, 等. 不同宿根年限甘蔗品种内源激素及酶活性分析. 作物杂志, 2022(3): 181-186.

[17]	Cheng Q, Tan Q L, Li J H, et al. Endogenous hormones and enzyme activity analysis in sugarcane varieties with different perennial root ages. Crops, 2022(3): 181-186.

[18]	Fujii H, Chinnusamy V, Rodrigues A, et al. In vitro reconstitution of an abscisic acid signalling pathway. Nature, 2009, 462(7273): 660-664. doi: 10.1038/nature08599

[19]	Umezawa T, Nakashima K, Miyakawa T, et al. Molecular basis of the core regulatory network in ABA responses: sensing, signaling and transport. Plant and Cell Physiology, 2010, 51(11): 1821-1839. doi: 10.1093/pcp/pcq156 pmid: 20980270

[20]	Righetto G L, Sriranganadane D, Halabelian L, et al. The C-terminal domains SnRK 2 box and ABA box have a role in sugarcane SnRK2s auto-activation and activity. Frontiers in Plant Science, 2019, 10: 1105 doi: 10.3389/fpls.2019.01105

[21]	邢璐. 植物激素脱落酸的受体蛋白PYL8和PYL9通过结合转录因子MYB家族成员调控拟南芥的侧根生长. 合肥: 中国科学技术大学, 2016.

[21]	Xing L. ABA receptors PYL8 and PYL9 regulate plant lateral root growth via MYB transcription factors. Hefei: University of Science and Technology of China, 2016.

[22]	Koornneef M, Reuling G, Karssen C M. The isolation and characterization of abscisic acid-insensitive mutants of Arabidopsis thaliana. Physiologia Plantarum, 1984, 61(3): 377-383. doi: 10.1111/ppl.1984.61.issue-3

[23]	Finkelstein R R. Abscisic acid-insensitive mutations provide evidence for stage-specific signal pathways regulating expression of an Arabidopsis late embryo genesis-abundant (lea) gene. Molecular and General Genetics MGG, 1993, 238(3): 401-408. doi: 10.1007/BF00291999

[24]	Merlot S, Gosti F, Guerrier D, et al. The ABI1 and ABI 2 protein phosphatases 2C act in a negative feedback regulatory loop of the abscisic acid signalling pathway. The Plant Journal, 2001, 25(3): 295-303. doi: 10.1046/j.1365-313x.2001.00965.x

[25]	Leung J, Merlot S, Giraudat J. The Arabidopsis ABSCISIC ACID-INSENSITIVE2 (ABI2) and ABI1 genes encode homologous protein phosphatases 2C involved in abscisic acid signal transduction. The Plant Cell, 1997, 9(5): 759-771.

[26]	Antoni R, Rodriguez L, Gonzalez-Guzman M, et al. News on ABA transport, protein degradation, and ABFs/WRKYs in ABA signaling. Current Opinion in Plant Biology, 2011, 14(5): 547-553. doi: 10.1016/j.pbi.2011.06.004 pmid: 21742545

[27]	Lopez-Molina L, Mongrand S, McLachlin D T, et al. ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination. The Plant Journal, 2002, 32(3): 317-328. doi: 10.1046/j.1365-313X.2002.01430.x

[28]	Carles C, Bies-Etheve N, Aspart L, et al. Regulation of Arabidopsis thaliana Em genes: role of ABI5. The Plant Journal, 2002, 30(3): 373-383. doi: 10.1046/j.1365-313X.2002.01295.x

[29]	刘传光, 伍时照, 王雪梅, 等. 宿根性水稻的越冬机理初探. 作物研究, 1999, 13(4): 12-13.

[29]	Liu C G, Wu S Z, Wang X M, et al. Preliminary study on overwintering mechanism of perennial rice. Crop Research, 1999, 13(4): 12-13.

[30]	Schlögl P S, Nogueira F T S, Drummond R, et al. Identification of new ABA- and MEJA-activated sugarcane bZIP genes by data mining in the SUCEST database. Plant Cell Reports, 2008, 27(2): 335-345.

[31]	Xu F, Wang Z T, Lu G L, et al. Sugarcane ratooning ability: research status, shortcomings, and prospects. Biology, 2021, 10(10): 1052.

[32]	杨荣仲. 甘蔗宿根性与抗寒性初探. 甘蔗糖业, 1996(6): 13-17.

[32]	Yang R Z. The preliminary study on cold-resistance and ratooning ability of sugarcane. Sugarcane and Canesugar, 1996(6): 13-17.

[33]	Papini-Terzi F S, Rocha F R, Vêncio R Z N, et al. Sugarcane genes associated with sucrose content. BMC Genomics, 2009, 10: 120. doi: 10.1186/1471-2164-10-120 pmid: 19302712

[34]	Banerjee N, Siraree A, Yadav S, et al. Marker-trait association study for sucrose and yield contributing traits in sugarcane (Saccharum spp. hybrid). Euphytica, 2015, 205(1): 185-201. doi: 10.1007/s10681-015-1422-3

[35]	Wang H B. Genetic map construction and QTL mapping of main agronomic traits in sugarcane. Fuzhou: Fujian Agriculture and Forestry University, 2018.

[36]	Ukoskit K, Posudsavang G, Pongsiripat N, et al. Detection and validation of EST-SSR markers associated with sugar-related traits in sugarcane using linkage and association mapping. Genomics, 2019, 111(1): 1-9. doi: S0888-7543(18)30027-2 pmid: 29608956

[37]	Aljanabi S M, Parmessur Y, Kross H, et al. Identification of a major quantitative trait locus (QTL) for yellow spot (Mycovellosiella koepkei) disease resistance in sugarcane. Molecular Breeding, 2007, 19(1): 1-14. doi: 10.1007/s11032-006-9008-3

[1]	MA Cong, ZHANG Xiang-jun, YE Tong, LIU Feng-min, ZHANG Hao-jie, LIU Hui-yan, FANG Hai-tian. Transcriptomics-based Analysis of the Effect of purR Gene Deletion on Cytidine Anabolism in Escherichia coli[J]. China Biotechnology, 2023, 43(8): 52-62.

[2]	MA Li, CUI Hai-xing, LI Jin-ze. Analysis of Patent Trends for the Spatial Omics Technology[J]. China Biotechnology, 2023, 43(8): 111-117.

[3]	LU Nan-xun, Wang Li-wei, LIU Mei-xiu, ZHANG Zhong-hua, CHANG Jing-ling, LI Zhi-gang. Global Gene Transcriptome Analysis for Enhanced Cyclic Adenosine Monophosphate Fermentation Performance by Polyphosphates[J]. China Biotechnology, 2023, 43(4): 41-50.

[4]	HE Li-heng,ZHANG Yi,ZHANG Jie,REN Yu-chao,XIE Hong-e,TANG Rui-min,JIA Xiao-yun,WU Zong-xin. Construction of Gene Co-expression Network and Identification of Hub Genes Related to Anthocyanin Biosynthesis Based on RNA-seq and WGCNA in Sweetpotato[J]. China Biotechnology, 2021, 41(9): 27-36.

[5]	HE Guan-rong,HE Bi-zhu,WU Sha-sha,SHI Jing-shan,CHEN Ji-shuang,LAN Si-ren. Establishment of an Efficient Regeneration System in Goodyera foliosa and Comprehensive Analysis of Functionally Regulated Genes Involved in Developmental Regulatory Pathways Based on Transcriptome Analysis[J]. China Biotechnology, 2018, 38(12): 57-64.

[6]	SU Zhi-zhe, WANG Xue-hua, YANG Hua, SUN Huan, WEI Wei. Transcriptome Analysis of Cadmium Exposed Jatropha curcas[J]. China Biotechnology, 2016, 36(4): 69-77.

[7]	ZHOU Qian, ZHAO Hui-xin, LI Ping-ping, ZENG Wei-jun, LI Yan-hong, GE Feng-wei, ZHAO Jun-jie, ZHAO He-ping. De novo Characterization of the Seed Transcriptome of Lepidium apetalum Willd[J]. China Biotechnology, 2016, 36(1): 38-46.

[8]	AO Yan, MA Lv-yi, HAN Shu-wen, YANG Xiao-hui. *Transcriptome Analysis for Xanthoceras sorbifolia* Bunge Based on High-throughput Sequencing Technology**[J]. China Biotechnology, 2015, 35(7): 22-29.

[9]	LI Zhen, LIU Zhao-yu, XU Dan, CHEN Ting, MENG Zan, TANG Yong, PENG Yan. Astrocyte Promotes Oligodendrocyte Precursor Cell Proliferating through Connexion CX47[J]. China Biotechnology, 2015, 35(12): 21-29.

[10]	ZHANG Nan, SUN Gui-ling, DAI Jun-gui, YANG Yan-fang, LIU Hong-wei, QIU De-you. *Sequencing and Analysis of the Transcriptome of Ginkgo biloba* L. Cells**[J]. China Biotechnology, 2013, 33(5): 112-119.

[11]	LV Chang-yong, CHEN Chao-yin, GE Feng, LIU Di-qiu, KONG Xiang-jun. The New Development of the Research Method for Molecular Microbial Ecology[J]. China Biotechnology, 2012, 32(08): 111-118.

[12]	WANG Xing-chun, YANG Zhi-rong, WANG Min, LI Wei, LI Sheng-cai. High-throughput Sequencing Technology and Its Application[J]. China Biotechnology, 2012, 32(01): 109-114.

[13]	LIU Xin-xing, CHEN Chao. *De Novo Assembly of Allotetraploid Arabidopsis suecica* Transcriptome using Short Reads for Gene Discovery and Marker Identification**[J]. China Biotechnology, 2011, 31(7): 45-53.

[14]	. Regulatory role of Abscisic Acid in Plant Somatic Embryogenesis[J]. China Biotechnology, 2007, 27(11): 92-98.

Viewed

Full text

Abstract

Cited

Shared

Discussed