Analysis of Phenotypic Characteristics and Root Transcriptomics of Sugarcane with Different Genotypes

doi:10.13560/j.cnki.biotech.bull.1985.2025-0966

Abstract

Abstract:

Objective To clarify the phenotypic variation pattern of sugarcane germplasm resources and theregulatory mechanism of key genes, and provide molecular targets for the directional breeding of nitrogen-efficient varieties. Method Seventeen sugarcane genotype materials with clear genetic backgrounds were used as the research objects. Seven agronomic traits such as plant height, stem diameter, and single-stem weight were systematically measured to evaluate their genetic diversity. Phenotypic groups were divided by cluster analysis, and a total of six extreme materials from two groups were selected for root transcriptome sequencing. The DESeq2 software was used to screen differentially expressed genes (DEGs), and GO and KEGG functional enrichment analyses were performed. Weighted gene co-expression network analysis (WGCNA) was used to mine core genes related to group differentiation, and their expression patterns were verified by RT-qPCR. Furthermore, the differences in nitrogen absorption and utilization abilities of the two types of materials were verified through a ¹⁵N isotope absorption experiment. Result The phenotypic variation coefficients of 17 materials ranged from 0.10 to 0.84, and the genetic diversity indices were between 2.55 and 2.83. By cluster analysis they were divided into Group Ι (7 materials) and Group Ⅱ (10 materials). The two groups showed significant differences in traits such as stem diameter (1.12 cm vs. 1.39 cm), number of effective stems (28.0 vs 15.1), and brix (11.1 vs 14.9). Transcriptome analysis identified a total of 9 724 differentially expressed genes (DEGs), which were significantly enriched in pathways such as linoleic acid metabolism (ko00591), flavonoid biosynthesis (ko00941), α-linolenic acid metabolism (ko00592), glutathione metabolism (ko00480), glycolysis/gluconeogenesis (ko00010), glyoxylate and dicarboxylate metabolism (ko00630), starch and sucrose metabolism (ko00500), and ether lipid metabolism (ko00565). Via weighted gene co-expression network analysis (WGCNA) the 10 hub genes were identified significantly associated with phenotypes, including Sspon.02G0013210-1A (AP2 transcription factor), Sspon.02G0008140-1T (GTP-binding protein), etc. The ¹⁵N absorption experiment showed that the materials in Group II had a stronger nitrogen absorption capacity, while the materials in Group I presented higher nitrogen accumulation characteristics. Conclusion Wild species materials adapt to low-nitrogen environments by increasing the number of effective stems, while hybrid materials achieve biomass and sugar accumulation by enhancing nitrogen absorption and utilization efficiency. The coordinated regulation of carbon and nitrogen metabolism and redox balance by key genes is an important molecular basis for the formation of nitrogen efficiency in sugarcane.

Key words: sugarcane (Saccharum spp.), phenotypic diversity, transcriptome, nitrogen metabolism, WGCNA, nitrogen absorption and utilization, DEGs, hub genes

YANG Ting, YANG Zong-tao, AI Jing, WANG Yu-tong, LI Yan-ye, DENG jun, LIU Jia-yong, ZHAO Yong, ZHANG Yue-bin. Analysis of Phenotypic Characteristics and Root Transcriptomics of Sugarcane with Different Genotypes[J]. Biotechnology Bulletin, 2026, 42(4): 190-201.

Figures/Tables 12

References 39

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材料序号 Material number	材料编码 Material code	材料类型 Material type	亲本信息（母本×父本） Parental cross （female × male）
01	越南2号	野生种	-
02	云南82-1	野生种	-
03	2017-12-165	野生种	-
04	2017-22	野生种	-
05	云蔗0551	商品种	-
06	A1	杂交种	云南82-1×2017-22
07	A2	杂交种	云南82-1×2017-22
08	B1	杂交种	越南2号×2017-12-165
09	B2	杂交种	越南2号×2017-12-165
10	N1	杂交种	云蔗0551×2017-22
11	N2	杂交种	云蔗0551×越南2号
12	N3	杂交种	云蔗0551×A1
13	N4	杂交种	云蔗0551×B1
14	N5	杂交种	云蔗0551×AB6
15	N6	杂交种	云蔗0551×AB8
16	AB6	杂交种	A1×B1
17	AB8	杂交种	A1×B1

材料序号 Material number	材料编码 Material code	材料类型 Material type	亲本信息（母本×父本） Parental cross （female × male）
01	越南2号	野生种	-
02	云南82-1	野生种	-
03	2017-12-165	野生种	-
04	2017-22	野生种	-
05	云蔗0551	商品种	-
06	A1	杂交种	云南82-1×2017-22
07	A2	杂交种	云南82-1×2017-22
08	B1	杂交种	越南2号×2017-12-165
09	B2	杂交种	越南2号×2017-12-165
10	N1	杂交种	云蔗0551×2017-22
11	N2	杂交种	云蔗0551×越南2号
12	N3	杂交种	云蔗0551×A1
13	N4	杂交种	云蔗0551×B1
14	N5	杂交种	云蔗0551×AB6
15	N6	杂交种	云蔗0551×AB8
16	AB6	杂交种	A1×B1
17	AB8	杂交种	A1×B1

基因ID/内参名称 Gene ID/Internal reference name	正向引物 Forward primer （5′‒3′）	反向引物 Reverse primer （5′‒3′）
Sspon.02G0008140-1T	GCCCATGGTGGTGGAGAC	CAACAGCCACCGTTTGCC
Sspon.05G0002890-3D	TTACCAGTGGGCTTGCGG	GCAAGTGCAGCCACATCG
Sspon.02G0013210-1A	ACTCGTCACAGCCAACCG	CCCGTCGCGTCGAATACA
Sspon.07G0022280-2C	GCCAGCGACTCTGCATCT	TGCTGCTGTGCAAAAGGC
Sspon.04G0031010-1P	GAGTGCCCTGTGTCGCAT	GTCTGGCCGCTGAACCTT
Sspon.01G0014700-2B	GGCTCCGAGGTTGCAGTT	TCTGAGCTTCTGCCCCCA
25S rRNA1	CCTGAAGATCACCCTGTGCT	GCAGTCTCCAGCTCCTGTTC

基因ID/内参名称 Gene ID/Internal reference name	正向引物 Forward primer （5′‒3′）	反向引物 Reverse primer （5′‒3′）
Sspon.02G0008140-1T	GCCCATGGTGGTGGAGAC	CAACAGCCACCGTTTGCC
Sspon.05G0002890-3D	TTACCAGTGGGCTTGCGG	GCAAGTGCAGCCACATCG
Sspon.02G0013210-1A	ACTCGTCACAGCCAACCG	CCCGTCGCGTCGAATACA
Sspon.07G0022280-2C	GCCAGCGACTCTGCATCT	TGCTGCTGTGCAAAAGGC
Sspon.04G0031010-1P	GAGTGCCCTGTGTCGCAT	GTCTGGCCGCTGAACCTT
Sspon.01G0014700-2B	GGCTCCGAGGTTGCAGTT	TCTGAGCTTCTGCCCCCA
25S rRNA1	CCTGAAGATCACCCTGTGCT	GCAGTCTCCAGCTCCTGTTC

性状 Trait	最小值 Min	最大值 Max	平均值 Average	极差 Range	标准差 S	变异系数 CV	遗传多样性指数 H′
株高 PH （cm）	218.00	314.60	253.61	96.60	24.67	0.10	2.83
茎径 SD （cm）	0.74	2.51	1.28	1.77	0.48	0.37	2.77
茎节数 SNN （Nodes/m）	16.40	31.00	24.05	14.60	3.59	0.15	2.82
节间长度 STL （cm）	18.10	29.84	22.86	11.74	3.20	0.14	2.82
单茎重 SNW （kg）	0.09	1.26	0.36	1.17	0.31	0.84	2.55
有效茎数 ESN （Stem nodes/plant）	5.80	44.80	20.40	39.00	12.34	0.61	2.66