Transcriptome Analysis of Top Second Leaf Sheath of Rice Under Different Nitrogen Fertilizer Levels

doi:10.16819/j.1001-7216.2025.250306

Abstract

Abstract:

【Objective】 The leaf sheath is an important organ that simultaneously serves the functions of “source, sink, and transport”, playing a crucial role in the growth and development of rice plants. Identifying important genes in leaf sheaths in response to nitrogen will provide scientific evidence for the genetic improvement of nitrogen use efficiency in rice. 【Method】 The japonica rice cultivar Xiushui 134 was planted in percolation ponds at low nitrogen (LN), medium nitrogen (MN), and high nitrogen (HN) levels. The top second leaf sheaths were collected on the 10th day after heading for transcriptome sequencing analysis to identify important genes involved in the nitrogen response of rice leaf sheaths. 【Result】 Comparative analysis of the transcriptome data revealed 1,791 differentially expressed genes at the three nitrogen levels. The number of upregulated and downregulated genes between HN and MN, MN and LN, and HN and LN were 312 and 155, 263 and 160, and 1,059 and 542, respectively. The common upregulated and downregulated genes at the three nitrogen levels were 15 and 53, respectively, involved in physiological and biochemical processes such as nutrient element absorption and transport, responses to biotic and abiotic stresses, plant hormone responses, and light regulation. Based on GO enrichment analysis, KEGG metabolic pathway analysis, a total of 6 known functional genes related to nitrogen utilization and 4 genes related to photosynthesis, as well as 50 genes of unknown function, were identified. It is speculated that these genes play important roles in the nitrogen response of the second leaf sheath in rice. 【Conclusion】 The research results preliminarily clarify the important genes involved in the leaf sheath's response to different nitrogen levels, which may play significant roles in signal transduction pathways of nitrogen utilization.

Key words: rice, top second leaf sheath, nitrogen fertilizer, transcriptome analysis

摘要：

【目的】探明叶鞘对氮素响应的重要基因，为水稻氮素高效利用的遗传改良提供科学依据。【方法】将粳稻品种秀水134种植在低氮(LN)、中氮(MN)和高氮(HN)的渗漏池中，选取抽穗后第10天的倒二叶叶鞘进行转录组测序分析，以鉴定叶鞘对氮素响应的重要基因。【结果】转录组数据比较分析显示，三种氮素水平间存在1791个差异表达基因。其中HN与MN、MN与LN、以及HN与LN组间的上调和下调表达基因数分别为312个和155个，263个和160个，1059个和542个。三种施氮水平间的共有上调和下调差异表达基因分别为15个和53个，涉及营养元素吸收和转运、生物与非生物胁迫响应、植物激素响应以及光调控等生理生化过程。基于GO富集分析和KEGG代谢途经分析，最终鉴定出参与氮素利用及光合作用的已知功能基因分别为6个和4个，以及50个功能未知基因，推测这些基因在倒二叶叶鞘的氮素响应中发挥重要作用。【结论】研究结果初步明确了叶鞘对不同氮素水平响应的重要基因，这些基因在氮素利用的信号转导途径中发挥重要作用。

关键词: 水稻, 倒二叶叶鞘, 氮肥, 转录组分析

HUANG Fudeng, WU Chunyan, HAO Yuanyuan, HAN Yifei, ZHANG Xiaobin, SUN Huifeng, PAN Gang. Transcriptome Analysis of Top Second Leaf Sheath of Rice Under Different Nitrogen Fertilizer Levels[J]. Chinese Journal OF Rice Science, 2025, 39(4): 563-574.

黄福灯, 吴春艳, 郝媛媛, 韩一飞, 张小斌, 孙会锋, 潘刚. 不同氮肥水平下水稻倒二叶叶鞘的转录组分析[J]. 中国水稻科学, 2025, 39(4): 563-574.

Figures/Tables 11

References 31

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基因 ID	正向引物 Forward primer(5’-3’)	反向引物 Reverse primer(5’-3’)
LOC_Os07g48020	GCTCCAAGGTGAACTCCTAATT	CACCGTACCTATACTTGTGGTT
LOC_Os07g08160	GCCCTTCGTCAACGTCTAATTA	CCCTAGCTAGCTACCCAGTATA
LOC_Os11g25260	CAGTTACTTGCATTATGGGCTC	ATGTACCATTGAATTCGCGAAG
LOC_Os09g12290	AGTGGAAAGAGCTTCTACGAAA	TCATAATAGTGGCATGCTACGT
LOC_Os07g08150	GTACTTGCGTATGTACTGGGTA	CACTATCAAGCTTGCTACTTGC
LOC_Os01g14410	CTTCAATTCGATCCTCGCTAAG	CGCCATTGCAAATAACTCAAAC
LOC_Os10g01080	AAACACAAACACTGACGCC	GAGAAGCTACCGGACTTGTG
LOC_Os02g02120	GCCATAAAGCGCTCAAAGATTA	CTTCCACTTCTAAGCAACAACC
LOC_Os04g27670	CATTTTGAGTCTGTATGCGTGA	TGCTGCTTTTCTGTTTACTTCC

基因 ID	正向引物 Forward primer(5’-3’)	反向引物 Reverse primer(5’-3’)
LOC_Os07g48020	GCTCCAAGGTGAACTCCTAATT	CACCGTACCTATACTTGTGGTT
LOC_Os07g08160	GCCCTTCGTCAACGTCTAATTA	CCCTAGCTAGCTACCCAGTATA
LOC_Os11g25260	CAGTTACTTGCATTATGGGCTC	ATGTACCATTGAATTCGCGAAG
LOC_Os09g12290	AGTGGAAAGAGCTTCTACGAAA	TCATAATAGTGGCATGCTACGT
LOC_Os07g08150	GTACTTGCGTATGTACTGGGTA	CACTATCAAGCTTGCTACTTGC
LOC_Os01g14410	CTTCAATTCGATCCTCGCTAAG	CGCCATTGCAAATAACTCAAAC
LOC_Os10g01080	AAACACAAACACTGACGCC	GAGAAGCTACCGGACTTGTG
LOC_Os02g02120	GCCATAAAGCGCTCAAAGATTA	CTTCCACTTCTAAGCAACAACC
LOC_Os04g27670	CATTTTGAGTCTGTATGCGTGA	TGCTGCTTTTCTGTTTACTTCC

性状 Trait	低氮 LN	中氮 MN	高氮 HN
株高 Plant height(cm)	78.07±0.64 b	81.67±0.88 a	83.43±1.03 a
千粒重 1000-grain weight(g)	13.69±0.08 c	21.30±0.81 a	17.90±1.12 b
单株有效穗数 Effective pancle number	8.33±0.33 a	8.67±0.33 a	9.00±0.58 a
穗干质量 Panicle dry weight(g)	3.62±0.10 a	1.86±0.42 b	1.51±0.05 b
每穗总粒数 Grain number per panicle	99.67±1.45 c	152.00±1.15 b	166.67±1.76 a
结实率 Seed-setting rate(%)	77.27±9.87 b	92.40±2.00 a	93.08±1.34 a

性状 Trait	低氮 LN	中氮 MN	高氮 HN
株高 Plant height(cm)	78.07±0.64 b	81.67±0.88 a	83.43±1.03 a
千粒重 1000-grain weight(g)	13.69±0.08 c	21.30±0.81 a	17.90±1.12 b
单株有效穗数 Effective pancle number	8.33±0.33 a	8.67±0.33 a	9.00±0.58 a
穗干质量 Panicle dry weight(g)	3.62±0.10 a	1.86±0.42 b	1.51±0.05 b
每穗总粒数 Grain number per panicle	99.67±1.45 c	152.00±1.15 b	166.67±1.76 a
结实率 Seed-setting rate(%)	77.27±9.87 b	92.40±2.00 a	93.08±1.34 a

基因 ID	基因注释 Gene annotation	FPKM
基因 ID	基因注释 Gene annotation	LN	MN	HN
LOC_Os07g08150	早期光诱导蛋白Early light-induced protein Early light-induced protein	300.51	95.23	11.46
LOC_Os01g14410	早期光诱导蛋白Early light-induced protein	372.04	143.45	24.47
LOC_Os10g01080	SOR/SNZ家族蛋白SOR/SNZ family protein	163.38	70.66	22.57
LOC_Os07g08160	早期光诱导蛋白Early light-induced protein	268.08	103.47	14.41
LOC_Os11g01210	PPR蛋白Pentatricopeptide repeat protein	23.31	14.53	5.44
LOC_Os12g01210	PPR蛋白Pentatricopeptide repeat protein	18.86	11.60	4.45
LOC_Os01g45110	花青素-3-O-β-葡萄糖苷转移酶Anthocyanin 3-O-beta-glucosyltransferase	4.93	1.72	0.75
LOC_Os01g53330	花青素-5,3-O-糖苷转移酶Anthocyanidin 5,3-O-glucosyltransferase	16.97	7.89	2.66
LOC_Os09g26580	表达蛋白Expressed protein	21.29	15.22	6.63
LOC_Os07g06800	3-酮-5-α-类固醇-4-脱氢酶3-oxo-5-alpha-steroid 4-dehydrogenase	17.75	5.66	2.04
LOC_Os03g17460	IN2-1蛋白	2.37	1.20	0.42
LOC_Os07g44110	细胞色素P450 72A1 Cytochrome P450 72A1	1.37	0.51	0.34
LOC_Os07g04820	蛋白激酶Protein kinase	1.37	0.76	0.21
LOC_Os08g07730	转移酶家族蛋白Transferase family protein	4.16	2.26	0.74
LOC_Os08g10010	酰基去饱和酶Acyl-desaturase	0.79	0.60	0.10