甘蔗腋芽形成发育过程的转录组分析

doi:10.13560/j.cnki.biotech.bull.1985.2024-0755

摘要/Abstract

摘要：

目的发掘甘蔗腋芽形成发育关键代谢通路和调控基因，为甘蔗优良品种选育及遗传改良策略制定提供基因资源。方法以甘蔗品种‘新台糖22号（XTT22）’为材料，分别选取其幼嫩、半大、成型、成熟腋芽，以茎尖生长点为对照。首先通过RNA-seq获得甘蔗腋芽形成发育4个时期的转录组文库，然后使用DESeq2软件筛选差异表达基因（DEGs），并开展GO和KEGG功能富集分析，再通过RT-qPCR验证转录组测序结果的可靠性，最后通过WGCNA挖掘与甘蔗腋芽形成发育相关的核心基因。结果甘蔗腋芽形成发育4个时期共获得62 630个差异表达基因，KEGG分析主要富集在甘露糖型O-聚糖的生物合成、吲哚生物碱生物合成、油菜素内酯生物合成等通路；KEGG富集通路网络分析表明：植物激素信号转导、氰胺酸代谢以及苯丙烷类物质生物合成等通路是腋芽形成发育中共同富集的核心通路，而β-丙氨酸代谢和氮代谢是幼嫩腋芽发育期的特有核心通路；C-5支链二元酸代谢，色氨酸代谢和脂肪酸延生通路分别是成型芽和成熟芽特有富集核心通路。9个表达趋势变化明显的DEGs的RT-qPCR结果与RNA-seq 结果呈现相似的表达模式。WGCNA分析鉴定了UBR7、IRK和POLD等20个与甘蔗腋芽形成发育相关的核心基因。结论甘蔗腋芽形成发育过程中需要以甘露糖型O-聚糖、蔗糖、淀粉和氮素等作为物质和能量基础，同时还需要合成植物激素和次生代谢物来调控相关生长发育过程；UBR7、IRK以及POLD等基因可能在甘蔗腋芽形成发育中发挥正调控作用，而DGK1、PCaP1、LSD1等基因可能负调控甘蔗腋芽形成发育。

关键词: 甘蔗, 腋芽形成发育, 转录组测序, 代谢通路, 加权共表达网络分析

Abstract:

Objective The key metabolic pathways and regulatory genes of sugarcane axillary bud formation and development were explored to provide valuable genetic resources for the breeding of sugarcane varieties and the formulation of genetic improvement strategies. Method The tender, semi-large, young and mature axillary buds of ‘XTT22’ were selected as the material, and the growth points of stem apex were used as the control. First, transcriptome libraries of the four stages of axillary bud formation and development were obtained by RNA-seq. The DESeq2 software was used to screen differentially expressed genes (DEGs), as well as GO and KEGG functional enrichment analysis was carried out. Then real-time fluorescent quantitative PCR (RT-qPCR) was used to verify the reliability of transcriptome sequencing results. Finally, the core genes related to the formation and development of sugarcane axillary buds were excavated by weighted gene co-expression network analysis (WGCNA). Result A total of 62 630 DEGs were obtained during the formation and development of sugarcane axillary buds. KEGG enrichment analysis mainly concentrated in mannose-type O-glycan biosynthesis, indole alkaloid biosynthesis, brassinolide biosynthesis and other pathways. KEGG enrichment pathway network analysis showed that hormone signal transduction, cyanamide metabolism and phenylpropanoid biosynthesis are the core pathways of axillary bud formation and development, while β‍-alanine metabolism and nitrogen metabolism are the specific core pathways in the development of tender axillary buds. C-5 branched-chain dibasic acid metabolism, tryptophan metabolism and fatty acid progression pathway are the core enrichment pathways of young and mature axillary buds respectively. The RT-qPCR results of 9 DEGs showed similar expression patterns to those of RNA-seq results. The 20 core genes related to the formation and development of sugarcane axillary buds, including UBR7, IRK and POLD WGCNA analysis was identified. Conclusion During the formation and development of sugarcane axillary buds, mannose-type O-glycan, sucrose, starch and nitrogen are needed as the material and energy basis, and plant hormones and secondary metabolites are also needed to regulate the related growth and development process. UBR7, IRK and POLD genes may play a positive role in the formation and development of sugarcane axillary buds, while DGK1, PCaP1 and LSD1 may negatively regulate the formation and development of sugarcane axillary buds.

Key words: sugarcane (Saccharum spp.), axillary bud formation and development, RNA-seq, metabolic pathway, WGCNA

李旭娟, 李纯佳, 刘洪博, 徐超华, 林秀琴, 陆鑫, 刘新龙. 甘蔗腋芽形成发育过程的转录组分析[J]. 生物技术通报, 2025, 41(3): 202-218.

LI Xu-juan, LI Chun-jia, LIU Hong-bo, XU Chao-hua, LIN Xiu-qin, LU Xin, LIU Xin-long. Transcriptome Analysis of Axillary Bud Formation and Development in Sugarcane[J]. Biotechnology Bulletin, 2025, 41(3): 202-218.

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基因ID Gene ID	基因名 Gene name	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）
CL3565.Contig2_All	ARF7	TTCGGTTGGAACATTGCTGC	TGTACAGGAGGGCAGACTGA
CL1829.Contig12_All	HSP70	AGCTTGAGGGGATCTGCAAC	TGCAACACCACGTCTAACCA
Unigene43477_All	HSF-C2a	CTGTAGCACCGGAGACGAAG	CAGTTGGTGATGAGGGGCAA
CL6559.Contig7_All	PRP	CGTCCTCGACATGTGCTTCT	GTGATCATCAACCACGCACG
Unigene49447_All	SCL9	TGGTCAGTCTTCTCAACCGC	GGGATCTGGCCATTCGTGAT
CL526.Contig2_All	WRKY48	GCACTACCAGGAAGGCAGAG	CCTGCAGGTCCATTGGAGAG
CL11262.Contig6_All	MYB61	GCATGTAGCTCGACCTTTTTGT	CCCAAGAGCTACGGACAGAG
Unigene48620_All	ATLP3	TAGCACCGTCAACTTCGTCC	TGCACGCAGGCGTATAATCT
CL14664.Contig8_All	SAPK4	ACCGTTTGTTTGCACTCTGC	TGGAAGAAATGCACACCCGA
	GAPDH	CACGGCCACTGGAAGCA	TCCTCAGGGTTCCTGATGCC

基因ID Gene ID	基因名 Gene name	正向引物 Forward primer （5′-3′）	反向引物 Reverse primer （5′-3′）
CL3565.Contig2_All	ARF7	TTCGGTTGGAACATTGCTGC	TGTACAGGAGGGCAGACTGA
CL1829.Contig12_All	HSP70	AGCTTGAGGGGATCTGCAAC	TGCAACACCACGTCTAACCA
Unigene43477_All	HSF-C2a	CTGTAGCACCGGAGACGAAG	CAGTTGGTGATGAGGGGCAA
CL6559.Contig7_All	PRP	CGTCCTCGACATGTGCTTCT	GTGATCATCAACCACGCACG
Unigene49447_All	SCL9	TGGTCAGTCTTCTCAACCGC	GGGATCTGGCCATTCGTGAT
CL526.Contig2_All	WRKY48	GCACTACCAGGAAGGCAGAG	CCTGCAGGTCCATTGGAGAG
CL11262.Contig6_All	MYB61	GCATGTAGCTCGACCTTTTTGT	CCCAAGAGCTACGGACAGAG
Unigene48620_All	ATLP3	TAGCACCGTCAACTTCGTCC	TGCACGCAGGCGTATAATCT
CL14664.Contig8_All	SAPK4	ACCGTTTGTTTGCACTCTGC	TGGAAGAAATGCACACCCGA
	GAPDH	CACGGCCACTGGAAGCA	TCCTCAGGGTTCCTGATGCC

基因编号 Gene ID	基因名 Gene name	基因注释 Gene annotation
CL3565.Contig2_All	ARF7	XM_002453947.2：高粱生长素响应因子7，mRNA
CL1829.Contig12_All	HSP70	XP_002456611.1：高粱热激蛋白70 mRNA
Unigene43477_All	HSF-C2a	XM_002451780.2：高粱热胁迫转录因子C-2a，转录变体X2，mRNA
CL6559.Contig7_All	PRP	CAB65536.1：玉米富含脯氨酸蛋白，mRNA
Unigene49447_All	SCL9	XM_021446388.1：高粱SCL9蛋白（LOC110429790），转录变体X1，mRNA
Unigene48620_All	ATLP3	XM_002450322.2：高粱生长素转运类蛋白3，mRNA
CL526.Contig2_All	WRKY48	XM_002463811.2：高粱转录因子WRKY48 （LOC8086215），mRNA
CL11262.Contig6_All	MYB61	XM_002457641.2：高粱转录因子MYB61 （LOC8078133），转录变体X1，mRNA
CL14664.Contig8_All	SAPK4	XM_021447946.1：高粱丝氨酸/苏氨酸蛋白激酶SAPK4（LOC8058510），转录变体X3，mRNA

基因编号 Gene ID	基因名 Gene name	基因注释 Gene annotation
CL3565.Contig2_All	ARF7	XM_002453947.2：高粱生长素响应因子7，mRNA
CL1829.Contig12_All	HSP70	XP_002456611.1：高粱热激蛋白70 mRNA
Unigene43477_All	HSF-C2a	XM_002451780.2：高粱热胁迫转录因子C-2a，转录变体X2，mRNA
CL6559.Contig7_All	PRP	CAB65536.1：玉米富含脯氨酸蛋白，mRNA
Unigene49447_All	SCL9	XM_021446388.1：高粱SCL9蛋白（LOC110429790），转录变体X1，mRNA
Unigene48620_All	ATLP3	XM_002450322.2：高粱生长素转运类蛋白3，mRNA
CL526.Contig2_All	WRKY48	XM_002463811.2：高粱转录因子WRKY48 （LOC8086215），mRNA
CL11262.Contig6_All	MYB61	XM_002457641.2：高粱转录因子MYB61 （LOC8078133），转录变体X1，mRNA
CL14664.Contig8_All	SAPK4	XM_021447946.1：高粱丝氨酸/苏氨酸蛋白激酶SAPK4（LOC8058510），转录变体X3，mRNA

模块 Module	基因号 Gene ID	Nt功能注释 Nt Annotation
蓝色	CL11755.Contig1_All	XM_002437021.2：高粱E3泛素蛋白连接酶7 （LOC8072631），mRNA
	CL11416.Contig2_All	XM_002467860.2：高粱LRR受体类丝氨酸/苏氨酸蛋白激酶IRK （LOC8082337），mRNA
	CL9946.Contig1_All	XM_002459710.2：高粱聚［adp-核糖］聚合酶1 （LOC8057336），mRNA
	Unigene27412_All	XM_002451536.2：高粱DNA聚合酶δ催化亚基POLD （LOC8074668），mRNA
	CL414.Contig1_All	XM_002437978.2：高粱LRR受体样丝氨酸/苏氨酸蛋白激酶ERECTA （LOC8077321），mRNA
褐色	CL9713.Contig1_All	M86717.1：甘蔗核酮糖1，5-二磷酸羧化酶/加氧酶小亚基基因
	CL7506.Contig2_All	XM_021463606.1：高粱豌豆蛋白（LOC8064511），转录变体X2，mRNA
	CL1675.Contig6_All	XM_021461443.1：高粱LNK1-类蛋白（LOC110435648），mRNA
	CL10608.Contig2_All	NM_001153244.1：玉米热胁迫转录因子A-6b （cl30385_1），mRNA
	Unigene37307_All	XM_002437010.2：高粱转录因子WRKY19，mRNA
绿色	CL11922.Contig2_All	芒草ARM重复超家族蛋白（NCGR_LOCUS6946），mRNA
	CL4984.Contig2_All	XM_002456186.2：高粱单myb4组蛋白（LOC8069770），mRNA
	Unigene34707_All	XM_008679969.2：玉米VIN3-类蛋白（LOC103652991），mRNA
	Unigene7438_All	XM_002439022.2：高粱胼胝质合成酶3 （LOC8066386），mRNA
	CL6695.Contig6_All	XM_002462606.2：高粱adp核糖化因子gtpase激活蛋白AGD3 （LOC8054803），mRNA
黑色	CL471.Contig5_All	XM_002443369.2：高粱二酰基甘油激酶（LOC8074256），mRNA
	CL654.Contig6_All	KT891986.1：甘蔗质膜阳离子结合蛋白（pcap1），mRNA
	CL5540.Contig5_All	XM_002445052.2：高粱LSD1蛋白，XM_002445052.2，mRNA
	CL5050.Contig15_All	XM_002454463.2：高粱水通道蛋白PIP1-2，mRNA
	Unigene46867_All	XM_021450410.1：高粱δ（24）-类甾醇还原酶（LOC110431358），mRNA