Differential Expressed Analysis by Transcriptome Sequencing in Leaves of Different Ploidy Paeonia ostii‘Fengdan’

doi:10.16420/j.issn.0513-353x.2024-0781

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (12): 3288-3302.doi: 10.16420/j.issn.0513-353x.2024-0781

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Differential Expressed Analysis by Transcriptome Sequencing in Leaves of Different Ploidy Paeonia ostii‘Fengdan’

PENG Chaofeng¹^,², QI Shuaizheng², GENG Xining², YAO Pengqiang², XIE Lihua², ZHANG Yu²^,³, CHEN Minghui², SHI Jiang¹^,^*(), CHENG Shiping²^,^*()

¹ College of Agriculture/Tree Peony，Henan University of Science & Technology，Luoyang，Henan 471000，China
² Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant，School of Chemistry and Environmental Engineering，Pingdingshan University，Pingdingshan，Henan 467000，China
³ College of Agriculture/Tree Peony，Henan University of Science & Technology，Luoyang，Henan 471000，China

Received:2025-05-29 Revised:2025-09-26 Online:2025-12-25 Published:2025-12-20
Contact: SHI Jiang, CHENG Shiping

Abstract

Abstract:

In this study，the leaves from different ploidy Paeonia ostii‘Fengdan’at blooming and flower decay stage as test materials，the change of leaf phenotype，anatomical structure and transcriptome were analyed. The results showed that the order of leaf area size was triploid > tetraploid > diploid；the order of leaf blade thickness and vein diameter were tetraploid > triploid > diploid. Compared with diploid flowering leaves，19 genes such as SAUR23，SAUR32，ARR4，IPT3，and IPT5 were up-regulated expression in triploid leaves at blooming stage；18 genes，including SAUR78，CYCD3，ARP5，ZOG2，HEMD，and HEME，were up-regulated expression in tetraploid leaves at bloom stage. Up-regulated expression of 10 genes including ARF10，IPT9，and HEMB in triploid leaves at flower decay stage；13 genes，including AHP4，CKX7，ZOG，UGT83A1，PAO，and SGR，were up-regulated expression in tetraploid leaves at flower decay stage. The analysis of differential genes in the pathway of carbon fixation in photosynthetic organisms showed that the expression levels of GAPC and MDH genes were higher in triploid leaves at blooming stage. WGCNA analyses showed that 18 core genes，including TCTP，BTB，BRH1 and PsMYC2，were expressed at higher levels in triploid，and 15 core genes，such as GLY，NmrA-like and WAT1，were highly expressed in tetraploid. The result of qRT-PCR confirmed the reliability of the RNA-seq data. The differential expression of these genes affected the growth and development of polyploid P. ostii‘Fengdan’leaves.

Key words: Paeonia ostii, polyploid, transcriptome sequencing, WGCNA analysis

PENG Chaofeng, QI Shuaizheng, GENG Xining, YAO Pengqiang, XIE Lihua, ZHANG Yu, CHEN Minghui, SHI Jiang, CHENG Shiping. Differential Expressed Analysis by Transcriptome Sequencing in Leaves of Different Ploidy Paeonia ostii‘Fengdan’[J]. Acta Horticulturae Sinica, 2025, 52(12): 3288-3302.

Figures/Tables 10

Fig. 1 Schematic diagram of leaf sampling location a，b，and c indicate the sampling positions of the leaflets in the compound leaf of‘Fengdan’

Fig. 2 Phenotypes（A）and anatomical structures（B）of Paeonia ostii‘Fengdan’leaves of different ploidy and period

Table 1 Growth characteristics of different ploidy Paeonia ostii‘Fengdan’

倍性 Ploidy	叶长/cm Leaf length	叶宽/cm Leaf width	叶面积/cm² Leaf area	叶片厚度/μm Leaf thickness	叶脉直径/μm Vein diameter
二倍体 Diploid	9.56 ± 0.50 a	2.93 ± 0.25 b	23.38 ± 2.08 b	152.70 ± 15.34 c	828.08 ± 46.42 b
三倍体 Triploid	9.03 ± 0.85 a	5.80 ± 0.87 a	34.86 ± 5.76 a	206.76 ± 14.19 b	840.70 ± 34.38 b
四倍体 Tetraploid	7.23 ± 0.25 b	3.80 ± 0.50 b	25.01 ± 3.01 b	233.81 ± 18.95 a	976.92 ± 56.21 a

Table 2 Quality analysis of transcriptome sequencing data

样品倍性 Sample Ploidy		原始数据 Raw reads	质控数据 Clean reads	质控数据碱基数 Clean base（G）	Q20/%	Q30/%	GC含量/% GC Content
盛花期 Full flowering period	二倍体 Diploid	59 143 608	55 527 696	8.33	98.96	96.66	45.23
		53 698 588	50 179 058	7.53	98.82	96.25	45.10
		54 181 490	50 801 050	7.62	98.77	96.10	45.07
	三倍体 Triploid	43 391 280	41 104 402	6.17	98.85	96.31	45.15
		53 750 618	50 548 380	7.58	99.01	96.79	45.17
		50 647 764	47 605 318	7.14	98.98	96.73	45.17
	四倍体 Tetraploid	57 476 282	54 146 594	8.12	98.96	96.66	45.05
		43 140 704	40 339 548	6.05	98.92	96.54	44.98
		49 974 664	47 103 112	7.07	98.84	96.29	44.90
花衰败期 Flower decay period	二倍体 Diploid	57 079 036	53 328 478	8.00	99.01	96.81	44.77
		52 656 282	49 232 680	7.38	98.83	96.22	44.75
		52 691 956	49 349 472	7.40	98.79	96.10	44.82
	三倍体 Triploid	58 114 202	54 795 360	8.22	98.91	96.47	44.95
		48 957 976	45 976 076	6.90	98.90	96.43	44.95
		53 091 772	50 658 874	7.60	98.86	96.32	44.90
	四倍体 Tetraploid	57 574 644	55 121 600	8.27	98.76	96.04	44.88
		55 111 304	52 274 248	7.84	99.00	96.78	45.01
		54 178 576	50 654 914	7.60	99.00	96.79	45.03

Fig. 3 Differential expression genes（DEG）（A）and venn diagram（B）in the leaves Paeonia ostii‘Fengdan’under different ploidys and periods B2：Diploid during the blooming period；B3：Triploid during the blooming period；B4：Tetraploid during the blooming period；D2：Diploid during the decline period；D3：Triploid during the decline period；D4：Tetraploid during the decline period

Fig. 4 Heatmap of the DEG in auxin signaling transduction（A），cytokinin signaling transduction（B），zeatin biosynthesis（C）and chlorophyll metabolic pathways（D）during polyploid leaf of Paeonia ostii‘Fengdan’ B2：Diploid during the blooming period；B3：Triploid during the blooming period；B4：Tetraploid during the blooming period；D2：Diploid during the decline period；D3：Triploid during the decline period；D4：Tetraploid during the decline period. The same below

Fig. 5 Differential genes in thecarbon fixation in photosynthetic organismspathway of B3 vs. B2 and B4 vs. B2

Fig. 6 Gene clustering tree（A）and gene modules correlate with plant ploidy and period（B）

Fig. 7 Co-expression network of core genes

Fig. 8 The stability of transcriptome data was verified by qRT-PCR Different lowercase letters indicate significant differences（P < 0.05）

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Differential Expressed Analysis by Transcriptome Sequencing in Leaves of Different Ploidy Paeonia ostii‘Fengdan’

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