Transcriptome Screening and Functional Analysis of Dwarf Related Genes in Pear

doi:10.16420/j.issn.0513-353x.2024-0481

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (3): 545-560.doi: 10.16420/j.issn.0513-353x.2024-0481

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

Transcriptome Screening and Functional Analysis of Dwarf Related Genes in Pear

LIN Ruxue, WANG Fei, ZHANG Yanjie, MA Li, LIU Xiaofeng, LI Shuran, LIU Yalong, WANG Chen, JIANG Shuling^*(), OU Chunqing^*()

Key Laboratory of Biology and Genetic Improvement of Horticultural Crops，Germplasm Resources Utilization，Ministry of Agriculture and Rural Affairs，Research Institute of Pomology，Chinese Academy of Agricultural Sciences，Xingcheng，Liaoning 125100，China

Received:2024-07-09 Revised:2024-11-25 Online:2025-03-25 Published:2025-03-25
Contact: JIANG Shuling, OU Chunqing

Abstract

Abstract:

To screen the dwarf trait related genes，the shoot length and internode length of 12 pear varieties or selections with different plant architectures were measured during the new shoot growth period. The genes differentially expressed in the growth points，leaves and phloem among three pear varieties ‘Zaosu’（vigorous），‘Jinxiang’（semi-dwarf）and‘Zhongai 1’（dwarf）at different periods were screened by transcripome sequencing analysis. Combined with the expression verification in new shoot phloem of 12 varieties or selections，dwarf trait related candidate genes were obtained. One of the candidate genes PcGA2ox2 was overexpressed in tobacco to analyze its function. The results showed that the new shoot length of‘Zaosu’，‘Jinxiang’and‘Zhongai 1’had a slight difference in the early growth period，while showed a significant difference in the middle and late growth period of new shoot. The internode length of dwarf varieties were shorter than that of vigorous varieties in all test periods. The shoot length and internode length of six vigorous varieties were significantly longer than those of six dwarf or semi-dwarf varieties or selections in the middle and late growth period of new shoot. The number of differentially expressed genes between two samples ranged from 1 882 to 5 729 in different tissues，and periods of three varieties. Among them，51 differentially expressed genes showed an increase or decrease in expression levels with the decrease of new shoot length in both leaf and phloem. Nine differentially expressed genes in new shoot phloem of three varieties were selected to verify the expression levels by RT-qPCR in the phloem of 12 pear varieties or selections in the late growth period of new shoot. Among them，four genes showed a tendency of significant higher or lower expression in dwarf varieties or selections than that in vigorous varieties or selections，and were identified as candidate genes related to dwarf trait. One of the dwarf candidate genes was a member of GA2ox family genes. Total 15 members of the GA2ox gene family were further identified in the‘Zhongai 1’genome，and the expression of the candidate PcGA2ox2 gene was significantly higher in new shoot phloem of dwarf varieties or selections than that of vigorous varieties. Then PcGA2ox2 gene was overexpressed in tobacco，the transformed plants were significantly smaller than the control plants. In conclusion，PcGA2ox2 gene plays a key role in the dwarf trait of‘Zhongai 1’pear.

Key words: pear, dwarf, transcriptome analysis, gibberellin, PcGA2ox

LIN Ruxue, WANG Fei, ZHANG Yanjie, MA Li, LIU Xiaofeng, LI Shuran, LIU Yalong, WANG Chen, JIANG Shuling, OU Chunqing. Transcriptome Screening and Functional Analysis of Dwarf Related Genes in Pear[J]. Acta Horticulturae Sinica, 2025, 52(3): 545-560.

Figures/Tables 12

References 51

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基因ID Gene ID	正向引物（5′-3′）Forward primer	反向引物（5′-3′）Reverse primer
Pdr15g002180	CCCCTTGTGGCTCCCAATA	CCTGAAAGTATCCATTCCCAAAT
Pdr3g011110	TGCTCCATGTCCATTTCCTTC	ACTCGGTGTTTGATGCTCTTGTAT
New Gene_2402	GATCTCTTCCCTTATTTTTCATCAGTT	GTTCCTACCGTGCCCTTTGT
Pdr11g021900	CTCGGGTTTCTACTTCTACACTGG	AGGGCACAATTCACTGCTCTTA
Pdr14g004080	TGGCGGTTCGGCTTGG	GGGTTGACCATTGGATTGTCTC
Pdr13g000360	CAAAACGGAACACGCAAACC	TTACAAGGAAGCACAAGAGGACC
Pdr10g017040	AGGTTGTTGAAAATGGAGCAGC	GAGGCACCTGTGAAAGTTGTCC
Pdr17g005180	CTCCCAACTTTCGCCGTCT	AAAAAGGCTCGGTCCAGAAAT
Pdr7g012000	TCCGAAGATGTTGGGGACC	AACTGCTCACATGGCACGGT
PcActin （GU830958.1）	GGAATGGAAGCTGCTGGC	CGTCATACTCACCCTTGGAAATC
NtActin（NM_001325686.1）	CTACTTACTGAA GCACCCTTGAATCC	CCTGCCCA TCTGGTAACTCATAGC

基因ID Gene ID	正向引物（5′-3′）Forward primer	反向引物（5′-3′）Reverse primer
Pdr15g002180	CCCCTTGTGGCTCCCAATA	CCTGAAAGTATCCATTCCCAAAT
Pdr3g011110	TGCTCCATGTCCATTTCCTTC	ACTCGGTGTTTGATGCTCTTGTAT
New Gene_2402	GATCTCTTCCCTTATTTTTCATCAGTT	GTTCCTACCGTGCCCTTTGT
Pdr11g021900	CTCGGGTTTCTACTTCTACACTGG	AGGGCACAATTCACTGCTCTTA
Pdr14g004080	TGGCGGTTCGGCTTGG	GGGTTGACCATTGGATTGTCTC
Pdr13g000360	CAAAACGGAACACGCAAACC	TTACAAGGAAGCACAAGAGGACC
Pdr10g017040	AGGTTGTTGAAAATGGAGCAGC	GAGGCACCTGTGAAAGTTGTCC
Pdr17g005180	CTCCCAACTTTCGCCGTCT	AAAAAGGCTCGGTCCAGAAAT
Pdr7g012000	TCCGAAGATGTTGGGGACC	AACTGCTCACATGGCACGGT
PcActin （GU830958.1）	GGAATGGAAGCTGCTGGC	CGTCATACTCACCCTTGGAAATC
NtActin（NM_001325686.1）	CTACTTACTGAA GCACCCTTGAATCC	CCTGCCCA TCTGGTAACTCATAGC

编号 Code	采样时间/ （M-D） Sampling time	组织 Tissue	比对材料 Comparative materials	高表达 High expression	低表达 Low expression	合计 Total
1	04-28	生长点 Growing point	早酥 vs. 锦香 Zaosu vs. Jinxiang	1 723	1 244	2 967
2			早酥vs. 中矮1号Zaosu vs. Zhongai 1	1 158	724	1 882
3			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	1 269	1 111	2 380
			1 ~ 3合计 Total of 1-3	3 301	2 671	4 865
4	05-18	叶片Leaf	早酥 vs. 锦香 Zaosu vs. Jinxiang	2 503	2 244	4 747
5			早酥vs. 中矮1号Zaosu vs. Zhongai 1	3 450	2 049	5 499
6			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	2 482	1 292	3 774
7		韧皮部Phloem	早酥 vs. 锦香 Zaosu vs. Jinxiang	2 679	2 181	4 860
8			早酥vs. 中矮1号Zaosu vs. Zhongai 1	2 540	1 717	4 257
9			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	1 463	1 069	2 532
			4 ~ 9合计 Total of 4-9	7 878	6 252	11 741
10	06-15	叶片Leaf	早酥 vs. 锦香 Zaosu vs. Jinxiang	2 890	1 859	4 749
11			早酥vs. 中矮1号Zaosu vs. Zhongai 1	2 951	2 333	5 284
12			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	2 139	2 562	4 701
13		韧皮部Phloem	早酥 vs. 锦香 Zaosu vs. Jinxiang	3 043	2 686	5 729
14			早酥vs. 中矮1号Zaosu vs. Zhongai 1	2 606	1 956	4 562
15			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	1 596	1 167	2 763
			10 ~ 15合计 Total of 10-15	7 907	7 275	12 201
16	04-28	生长点 Growing point	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	6	3	9
17	05-18	叶片Leaf	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	124	72	196
18		韧皮部Phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	37	43	80
19	06-15	叶片Leaf	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	113	77	190
20		韧皮部Phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	51	46	97
			16 ~ 20合计 Total of 16-20	276	190	466
21	05-18， 06-15	叶片Leaf	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	18	20	38
22		韧皮部Phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	11	10	21
			21 ~ 22合计 Total of 21-22	26	25	51
23	05-18， 06-15	叶片和韧皮部 Leaf and phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	3	5	8

编号 Code	采样时间/ （M-D） Sampling time	组织 Tissue	比对材料 Comparative materials	高表达 High expression	低表达 Low expression	合计 Total
1	04-28	生长点 Growing point	早酥 vs. 锦香 Zaosu vs. Jinxiang	1 723	1 244	2 967
2			早酥vs. 中矮1号Zaosu vs. Zhongai 1	1 158	724	1 882
3			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	1 269	1 111	2 380
			1 ~ 3合计 Total of 1-3	3 301	2 671	4 865
4	05-18	叶片Leaf	早酥 vs. 锦香 Zaosu vs. Jinxiang	2 503	2 244	4 747
5			早酥vs. 中矮1号Zaosu vs. Zhongai 1	3 450	2 049	5 499
6			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	2 482	1 292	3 774
7		韧皮部Phloem	早酥 vs. 锦香 Zaosu vs. Jinxiang	2 679	2 181	4 860
8			早酥vs. 中矮1号Zaosu vs. Zhongai 1	2 540	1 717	4 257
9			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	1 463	1 069	2 532
			4 ~ 9合计 Total of 4-9	7 878	6 252	11 741
10	06-15	叶片Leaf	早酥 vs. 锦香 Zaosu vs. Jinxiang	2 890	1 859	4 749
11			早酥vs. 中矮1号Zaosu vs. Zhongai 1	2 951	2 333	5 284
12			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	2 139	2 562	4 701
13		韧皮部Phloem	早酥 vs. 锦香 Zaosu vs. Jinxiang	3 043	2 686	5 729
14			早酥vs. 中矮1号Zaosu vs. Zhongai 1	2 606	1 956	4 562
15			锦香vs. 中矮1号Jinxiang vs. Zhongai 1	1 596	1 167	2 763
			10 ~ 15合计 Total of 10-15	7 907	7 275	12 201
16	04-28	生长点 Growing point	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	6	3	9
17	05-18	叶片Leaf	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	124	72	196
18		韧皮部Phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	37	43	80
19	06-15	叶片Leaf	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	113	77	190
20		韧皮部Phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	51	46	97
			16 ~ 20合计 Total of 16-20	276	190	466
21	05-18， 06-15	叶片Leaf	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	18	20	38
22		韧皮部Phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	11	10	21
			21 ~ 22合计 Total of 21-22	26	25	51
23	05-18， 06-15	叶片和韧皮部 Leaf and phloem	早酥 vs. 锦香vs. 中矮1号Zaosu vs. Jinxiang vs. Zhongai 1	3	5	8

组织 Tissue	随新梢长度的缩短表达升高的基因 Genes that increase in expression with the decrease of new shoot length		随新梢长度的缩短表达降低的基因 Genes that decrease in expression with the decrease of new shoot length
组织 Tissue	ID	注释Annotation	ID	注释Annotation
叶片 Leaf	Pdr8g014740	Probable disease resistance protein At4g27220	Pdr16g015850	Protein SIEVE ELEMENT OCCLUSION B-like
		isoform X2	Pdr0g057320	Uncharacterized protein
	Pdr5g018850	G-type lectin S-receptor-like serine/threonine-protein kinase At4g27290 isoform X1	Pdr11g012240	Palmitoyl-monogalactosyldiacylglycerol delta-7 desaturase，chloroplastic-like
	Pdr11g021340	UDP-glycosyltransferase 87A1-like	Pdr17g003340	UDP-glycosyltransferase 83A1-like
	Pdr10g027130	Carbonic anhydrase 2-like isoform X1	Pdr17g001240	Putative glucose-6-phosphate 1-epimerase isoform X1
	Pdr7g014190	3-ketoacyl-CoA synthase 19-like	Pdr10g015920	Putative amidase C869.01 isoform X1
	Pdr0g030210	Probable serine/threonine-protein kinase	Pdr11g022920	Uncharacterized protein
		DDB_G0282963	Pdr16g009800	Geraniol 8-hydroxylase-like isoform X1
	Pdr11g002090	LEC14B protein-like isoform X1	Pdr0g061140	Succinate dehydrogenase subunit 5，mitochondrial-like
	Pdr9g003550	Uncharacterized protein At1g03900-like	Pdr11g004540	Probable leucine-rich repeat receptor-like
	Pdr4g000300	Serine carboxypeptidase-like 20		serine/threonine-protein kinase
	Pdr6g013710	-	Pdr9g003650	Uncharacterized protein
	Pdr10g000140	Early nodulin-like protein 2	Pdr9g006840	Acid phosphatase 1-like
	Pdr2g011040	TMV resistance protein N-like	Pdr3g014200	Uncharacterized protein
	NewGene_1645	-	Pdr9g000780	Disease resistance protein At4g27190-like isoform X2
	NewGene_492	Uncharacterized protein	NewGene_3128	40S ribosomal protein S29
	NewGene_7522	Uncharacterized protein
韧皮部	Pdr15g002180	Protein EXORDIUM-like	Pdr6g000360	Cinnamoyl-CoA reductase 2-like
Phloem	Pdr0g064490	Uncharacterized protein	Pdr16g022720	Uncharacterized protein
	Pdr9g009480	Uncharacterized protein	Pdr1g005260	Trans-resveratrol di-O-methyltransferase-like
	Pdr11g021900	Putative disease resistance protein RGA1 isoform	Pdr15g014540	BURP domain protein RD22-like
		X1	Pdr10g006620	CSC1-like protein ERD4
	Pdr1g005700	（+）-neomenthol dehydrogenase-like isoform X1
	Pdr10g000410	Ankyrin repeat-containing protein NPR4-like
	Pdr2g010870	Uncharacterized protein
	Pdr9g000720	DNA polymerase delta catalytic subunit
叶片和韧皮部 Leaf and phloem	Pdr9g008130	Ras-associated and pleckstrin homology domains-containing protein 1-like	Pdr16g008560	Non-functional NADPH-dependent codeinone reductase 2-like
	NewGene_2402	Topless-related protein 1-like isoform X1	Pdr11g007050	Putative disease resistance RPP13-like protein 1
	NewGene_4126	-	Pdr0g010770	Uncharacterized protein
			Pdr7g019110	TMV resistance protein N-like
			NewGene_4125	Uncharacterized protein

Transcriptome Screening and Functional Analysis of Dwarf Related Genes in Pear

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基因ID Gene ID	NR注释 NR annotation	基因ID Gene ID	NR注释 NR annotation
Pdr3g011110	Gibberellin 2-beta-dioxygenase 8-like	Pdr14g004080	Probable carboxylesterase 15
Pdr13g000360	Indole-3-acetic acid-induced protein ARG7-like	Pdr10g017040	Epidermal growth factor receptor substrate 15-like 1
Pdr17g005180	Myb-related protein Myb4-like	Pdr7g012000	WRKY transcription factor 46

基因ID Gene ID	命名 Name	染色体 Chromosome	编码蛋白序列长度/aa Length of coding protein sequence	注释 Annotation
Pdr1g012890	PcGA2ox1	Chr1	369	Gibberellin 2-beta-dioxygenase 2-like
Pdr3g011110	PcGA2ox2	Chr3	331	Gibberellin 2-beta-dioxygenase 8-like
Pdr3g019490	PcGA2ox3	Chr3	135	Gibberellin 2-beta-dioxygenase 8-like
Pdr3g019500	PcGA2ox4	Chr3	880	Gibberellin 2-beta-dioxygenase 8-like
Pdr5g017610	PcGA2ox5	Chr5	337	Gibberellin 2-beta-dioxygenase 1-like isoform X1
Pdr5g025480	PcGA2ox6	Chr5	343	Gibberellin 2-beta-dioxygenase 8
Pdr10g001990	PcGA2ox7	Chr10	341	Gibberellin 2-beta-dioxygenase 8-like
Pdr10g006080	PcGA2ox8	Chr10	342	Gibberellin 2-beta-dioxygenase-like
Pdr10g011570	PcGA2ox9	Chr10	337	Gibberellin 2-beta-dioxygenase 1-like
Pdr11g008580	PcGA2ox10	Chr11	337	Gibberellin 2-beta-dioxygenase 8-like
Pdr11g020650	PcGA2ox11	Chr11	330	Gibberellin 2-beta-dioxygenase 8
Pdr13g002200	PcGA2ox12	Chr13	346	Gibberellin 2-beta-dioxygenase 2-like
Pdr16g000310	PcGA2ox13	Chr16	335	Gibberellin 2-beta-dioxygenase 8-like
Pdr16g012050	PcGA2ox14	Chr16	345	Gibberellin 2-beta-dioxygenase 2-like
Pdr17g016870	PcGA2ox15	Chr17	358	Gibberellin 2-beta-dioxygenase 2

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