Transcriptome Analysis of Diploid and Autotetraploid in Cucumber Fruit

doi:10.13560/j.cnki.biotech.bull.1985.2022-0974

Abstract

Abstract:

Fruit shape and sugar content are important quality traits closely related to the appearance, nutrition and flavor of melon vegetables, respectively. To investigate the molecular mechanism of fruit shape and sugar content in cucumber caused by ploidy differences, the diploid（long fruit/low sugar）and autotetraploid（short fruit/high sugar）cucumber with significant differences of shape and sugar content were selected as the study materials, and RNA-seq analysis on the fruits at 0 and 9 d after flowering were performed. The results showed that a total of 1 874 differentially expressed genes（DEGs）were identified from diploid and autotetraploid at 9 d after flowering, including 818 up-regulated genes and 1 056 down-regulated genes. GO analysis demonstrated that the DEGs were significantly enriched in DNA replication（GO:0006260）, DNA metabolic process（GO:0006259）, protein-DNA complex（GO:0032993）, chromosome（GO:0005694）, and protein dimerization activity（GO:0046983）. KEGG analysis revealed that the DEGs were enriched in “plant hormone signal transduction”（csv04075）, “starch and sucrose metabolism”（csv00500）and other metabolic pathways. The up-regulated expressions of AUX1, DELLA, B-ARR and TCH4 and down-regulated expression of GH3, GID1, PP2C and CYCD3 related to “plant hormone signal transduction”, as well as the up-regulated expression of SPS and SUSY related to “starch and sucrose metabolism”, may correlate with fruit shape index decreasing shortening and sugar content increasing in the cucumber. Quantitative reverse transcription-PCR（RT-qPCR）analysis showed that the expression pattern of selected DEGs was consistent with the expression trend of RNA-Seq except for ARF4, among which SUSY was highly differentially expressed between diploid and autotetraploid cucumber fruits, suggesting that SUSY plays a critical role in regulating fruit shape and sugar content in cucumber autotetraploid.

Key words: cucumber, autotetraploid, transcriptome, differentially expressed genes

XIE Yang, XING Yu-meng, ZHOU Guo-yan, LIU Mei-yan, YIN Shan-shan, YAN Li-ying. Transcriptome Analysis of Diploid and Autotetraploid in Cucumber Fruit[J]. Biotechnology Bulletin, 2023, 39(3): 152-162.

Figures/Tables 9

References 34

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样品名称 Sample name	Raw reads/Mb	Clean reads/Mb	Unique map/Mb	Q30/%	GC/%
CK_S1_1	45.32	43.78	40.87	92.94	40.88
CK_S1_2	48.02	45.29	43.08	94.72	40.85
CK_S2_1	44.23	43.35	40.80	93.02	42.14
CK_S2_2	44.89	43.22	40.68	92.63	42.28
T_S1_1	46.21	43.69	40.35	92.56	40.82
T_S1_2	47.89	45.85	42.61	92.98	41.09
T_S2_1	45.83	44.53	42.08	92.9	42.43
T_S2_2	47.69	45.88	43.46	93.49	42.43

样品名称 Sample name	Raw reads/Mb	Clean reads/Mb	Unique map/Mb	Q30/%	GC/%
CK_S1_1	45.32	43.78	40.87	92.94	40.88
CK_S1_2	48.02	45.29	43.08	94.72	40.85
CK_S2_1	44.23	43.35	40.80	93.02	42.14
CK_S2_2	44.89	43.22	40.68	92.63	42.28
T_S1_1	46.21	43.69	40.35	92.56	40.82
T_S1_2	47.89	45.85	42.61	92.98	41.09
T_S2_1	45.83	44.53	42.08	92.9	42.43
T_S2_2	47.69	45.88	43.46	93.49	42.43

基因名称Gene name	基因 ID Gene ID	log₂FC	基因注释Gene annotation
AUX1	Csa_3G731880	0.511028525	Auxin influx carrier（AUX1 LAX family）
B-ARR	Csa_2G350290	1.199233905	Uncharacterized protein LOC101203501 isoform X1
DELLA	Csa_5G569350	0.641993478	DELLA protein
SIMKK	Csa_3G651720	0.521551332	Mitogen-activated protein kinase kinase 4/5
EIN2	Csa_6G445230	0.401357885	Ethylene-insensitive protein 2
EIN3	Csa_6G051520	0.672607401	Ethylene-insensitive protein 3
BRI1	Csa_6G486870	0.529640378	Protein brassinosteroid insensitive 1
BIN2	Csa_6G157100	0.536467357	Protein brassinosteroid insensitive 2
BZR1/2	Csa_2G361450	0.587660284	Brassinosteroid resistant 1/2
TCH4	Csa_1G422470	1.185601828	Xyloglucan:xyloglucosyl transferase TCH4
TGA	Csa_6G152350	1.955263915	Transcription factor TGA
GH3	Csa_6G493310	-0.840958686	Auxin responsive GH3 gene family
GID1	Csa_7G391240	-1.403103089	Gibberellin receptor GID1
PP2C	Csa_1G574880	-1.528004155	Protein phosphatase 2C
ETR	Csa_2G070880	-0.799320186	Ethylene receptor
BAK1	Csa_7G060160	-0.875573337	Brassinosteroid insensitive 1-associated receptor kinase 1
BKI1	Csa_2G359970	-1.610933985	BRI1 kinase inhibitor 1
CYCD3	Csa_6G491650	-1.00709524	Cyclin D3, plant
JAZ	Csa_1G042920	-0.913564833	Jasmonate ZIM domain-containing protein
AGLU1	Csa_1G716250	0.650665663	Alpha-glucosidase
SPS	Csa_2G401440	0.977042232	Sucrose-phosphate synthase
SUSY	Csa_5G322500	2.088838655	Sucrose synthase
FRK	Csa_3G345390	-0.650140834	Fuctokinase
AGPase	Csa_3G149890	-1.393581098	Glucose-1-phosphate adenylyltransferase
SS	Csa_6G497160	-0.899393235	Starch synthase
GTase	Csa_5G606600	-0.684711983	4-alpha-glucanotransferase
GBE1	Csa_7G213190	-1.304743764	1,4-alpha-glucan branching enzyme
BMY	Csa_3G017020	-3.271484788	Beta-amylase
TRE	Csa_5G149880	-1.411978481	Alpha,alpha-trehalase

基因名称Gene name	基因 ID Gene ID	log₂FC	基因注释Gene annotation
AUX1	Csa_3G731880	0.511028525	Auxin influx carrier（AUX1 LAX family）
B-ARR	Csa_2G350290	1.199233905	Uncharacterized protein LOC101203501 isoform X1
DELLA	Csa_5G569350	0.641993478	DELLA protein
SIMKK	Csa_3G651720	0.521551332	Mitogen-activated protein kinase kinase 4/5
EIN2	Csa_6G445230	0.401357885	Ethylene-insensitive protein 2
EIN3	Csa_6G051520	0.672607401	Ethylene-insensitive protein 3
BRI1	Csa_6G486870	0.529640378	Protein brassinosteroid insensitive 1
BIN2	Csa_6G157100	0.536467357	Protein brassinosteroid insensitive 2
BZR1/2	Csa_2G361450	0.587660284	Brassinosteroid resistant 1/2
TCH4	Csa_1G422470	1.185601828	Xyloglucan:xyloglucosyl transferase TCH4
TGA	Csa_6G152350	1.955263915	Transcription factor TGA
GH3	Csa_6G493310	-0.840958686	Auxin responsive GH3 gene family
GID1	Csa_7G391240	-1.403103089	Gibberellin receptor GID1
PP2C	Csa_1G574880	-1.528004155	Protein phosphatase 2C
ETR	Csa_2G070880	-0.799320186	Ethylene receptor
BAK1	Csa_7G060160	-0.875573337	Brassinosteroid insensitive 1-associated receptor kinase 1
BKI1	Csa_2G359970	-1.610933985	BRI1 kinase inhibitor 1
CYCD3	Csa_6G491650	-1.00709524	Cyclin D3, plant
JAZ	Csa_1G042920	-0.913564833	Jasmonate ZIM domain-containing protein
AGLU1	Csa_1G716250	0.650665663	Alpha-glucosidase
SPS	Csa_2G401440	0.977042232	Sucrose-phosphate synthase
SUSY	Csa_5G322500	2.088838655	Sucrose synthase
FRK	Csa_3G345390	-0.650140834	Fuctokinase
AGPase	Csa_3G149890	-1.393581098	Glucose-1-phosphate adenylyltransferase
SS	Csa_6G497160	-0.899393235	Starch synthase
GTase	Csa_5G606600	-0.684711983	4-alpha-glucanotransferase
GBE1	Csa_7G213190	-1.304743764	1,4-alpha-glucan branching enzyme
BMY	Csa_3G017020	-3.271484788	Beta-amylase
TRE	Csa_5G149880	-1.411978481	Alpha,alpha-trehalase

基因名称Gene name	注释Annotation	引物序列Primer sequence（5'-3'）
SUSY	蔗糖合酶 Sucrose synthase	F：TGAGAACGATGAGCATATAG
SUSY	蔗糖合酶 Sucrose synthase	R：TCCAACCACAACAAGATT
K-box	转录因子K-box Transcription factor K-box	F：CAAGAACAGGAAGAGGAA
K-box	转录因子K-box Transcription factor K-box	R：GAGGAGAAGACGATAAGAG
WUS	WUSCHEL相关homeobox WUSCHEL-related homeobox	F：GTGAGCCATTGATGACAT
WUS	WUSCHEL相关homeobox WUSCHEL-related homeobox	R：GGAACCAGTTATAGACATTAGA
SUT	蔗糖转运蛋白 Sucrose transporter	F：CTGAGACGGTTACTAAGAG
SUT	蔗糖转运蛋白 Sucrose transporter	R：TTGAATATAAGGAGTGAGAAGA
GLU8	葡萄糖转运蛋白8 Glucose transporter protein 8	F：CCTCACAACACTCAATCA
GLU8	葡萄糖转运蛋白8 Glucose transporter protein 8	R：CACAGACCAACAATCAGA
DNAH	DNA解旋酶 DNA helicase	F：GCTCAAGTCGTTACCATT
DNAH	DNA解旋酶 DNA helicase	R：CATCAACTGAACTCACCTT
ARF4	激素响应因子4 Auxin response factor 4	F：GTCTACCATACTCGTGTT
ARF4	激素响应因子4 Auxin response factor 4	R：CTAATGCCAGTGATTGTG
GIR	赤霉素调控蛋白 Gibberellin-regulated protein	F：TCCTCTCTTCTCGTTCTT
GIR	赤霉素调控蛋白 Gibberellin-regulated protein	R：GCTCCTCCACAATCAATA
LRK	蛋白激酶家族蛋白 Protein kinase family protein	F：CGGAGATGACTGTTGTAA
LRK	蛋白激酶家族蛋白 Protein kinase family protein	R：TCCAATCAGCAATAATAACG
CsActin	内参基因 Actin gene	F：ATTGTTCTCAGTGGTGGTTCTAC
CsActin	内参基因 Actin gene	R：CCTTTGAGATCCACATCTGCT