Genome-wide association study and candidate gene prediction of pectin content of pumpkin (Cucurbita moschata)

doi:10.3969/j.issn.1004-1524.20240543

Acta Agriculturae Zhejiangensis ›› 2025, Vol. 37 ›› Issue (6): 1244-1251.DOI: 10.3969/j.issn.1004-1524.20240543

• Horticultural Science • Previous Articles Next Articles

Genome-wide association study and candidate gene prediction of pectin content of pumpkin (Cucurbita moschata)

TAO Peng¹(), DING Xiaoya¹^,², YUE Zhichen¹, ZHAO Yanting¹, LEI Juanli¹, HU Qizan¹, ZANG Yunxiang², LI Biyuan¹^,^*()

1. Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
2. College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China

Received:2024-06-24 Online:2025-06-25 Published:2025-07-08

Abstract

Abstract:

To investigate the genetic regulatory mechanisms of pectin content in pumpkin and identify key genes, and provide a theoretical basis for the genetic improvement of pumpkin fruit texture quality, pectin content of 208 pumpkin germplasm resources was determined using sulfuric acid-carbazole method, a genome-wide association study (GWAS) was conducted by integrating the pectin content data with single nucleotide polymorphisms (SNP) obtained from whole-genome resequencing, candidate gene screening and functional annotation were performed in the significantly associated genomic regions. The results revealed that pumpkin pectin content followed a normal distribution, 21 SNPs significantly associated with pumpkin pectin content were identified on chromosomes 2, 4, 12, and 20, with 13 significant SNPs located in 8330664-8436445 on chromosome 2. Totally, 40 candidate genes were screened, with three genes (gene ID were CmoCh02G014160, CmoCh02G014170 and CmoCh02G014260) annotated to be involved in sugar metabolism pathways. These three candidate genes had a large number of SNP and InDel variations in the pumpkin germplasm resources, and were expressed in pumpkin fruits, they may be involved in pectin biosynthesis in pumpkin fruits. This study can provides new molecular markers and candidate genes for optimizing pectin content and improving pumpkin quality through genetic breeding.

Key words: pumpkin, pectin, genome-wide association study, gene, sugar metabolism

CLC Number:

S642.1

TAO Peng, DING Xiaoya, YUE Zhichen, ZHAO Yanting, LEI Juanli, HU Qizan, ZANG Yunxiang, LI Biyuan. Genome-wide association study and candidate gene prediction of pectin content of pumpkin (Cucurbita moschata)[J]. Acta Agriculturae Zhejiangensis, 2025, 37(6): 1244-1251.

Figures/Tables 6

References 23

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SNP名称 SNP name	染色体 Chromosome	位置 Position	等位基因 Allelic	P值 P value/10^-7	-lgP值 -lgP value	表型变异解释率 PVE/%
Chr2-8330664	2	8330664	G/A	3.38	6.471	19.1
Chr2-8432314	2	8432314	T/C	8.96	6.048	13.2
Chr2-8432414	2	8432414	C/T	7.60	6.119	14.0
Chr2-8432432	2	8432432	A/T	4.69	6.328	14.3
Chr2-8432490	2	8432490	C/T	4.49	6.347	14.3
Chr2-8432870	2	8432870	T/C	8.55	6.068	14.7
Chr2-8432911	2	8432911	C/T	9.72	6.012	14.9
Chr2-8432944	2	8432944	T/A	2.30	6.639	16.3
Chr2-8436163	2	8436163	C/T	3.02	6.519	14.1
Chr2-8436367	2	8436367	A/G	3.42	6.466	14.1
Chr2-8436409	2	8436409	A/G	5.31	6.275	13.5
Chr2-8436428	2	8436428	T/G	2.25	6.648	14.4
Chr2-8436445	2	8436445	G/A	4.93	6.307	13.6
Chr4-12932869	4	12932869	C/T	6.66	6.176	12.6
Chr4-12942475	4	12942475	G/A	5.93	7.227	15.0
Chr4-12981263	4	12981263	G/A	3.59	6.445	12.6
Chr4-13041495	4	13041495	G/T	3.44	6.464	13.9
Chr4-14599018	4	14599018	G/C	4.81	6.318	14.7
Chr12-5902631	12	5902631	A/C	7.43	6.129	11.8
Chr12-6609511	12	6609511	T/A	12.1	7.919	15.1
Chr20-4190818	20	4190818	T/C	7.06	6.151	13.3

SNP名称 SNP name	染色体 Chromosome	位置 Position	等位基因 Allelic	P值 P value/10^-7	-lgP值 -lgP value	表型变异解释率 PVE/%
Chr2-8330664	2	8330664	G/A	3.38	6.471	19.1
Chr2-8432314	2	8432314	T/C	8.96	6.048	13.2
Chr2-8432414	2	8432414	C/T	7.60	6.119	14.0
Chr2-8432432	2	8432432	A/T	4.69	6.328	14.3
Chr2-8432490	2	8432490	C/T	4.49	6.347	14.3
Chr2-8432870	2	8432870	T/C	8.55	6.068	14.7
Chr2-8432911	2	8432911	C/T	9.72	6.012	14.9
Chr2-8432944	2	8432944	T/A	2.30	6.639	16.3
Chr2-8436163	2	8436163	C/T	3.02	6.519	14.1
Chr2-8436367	2	8436367	A/G	3.42	6.466	14.1
Chr2-8436409	2	8436409	A/G	5.31	6.275	13.5
Chr2-8436428	2	8436428	T/G	2.25	6.648	14.4
Chr2-8436445	2	8436445	G/A	4.93	6.307	13.6
Chr4-12932869	4	12932869	C/T	6.66	6.176	12.6
Chr4-12942475	4	12942475	G/A	5.93	7.227	15.0
Chr4-12981263	4	12981263	G/A	3.59	6.445	12.6
Chr4-13041495	4	13041495	G/T	3.44	6.464	13.9
Chr4-14599018	4	14599018	G/C	4.81	6.318	14.7
Chr12-5902631	12	5902631	A/C	7.43	6.129	11.8
Chr12-6609511	12	6609511	T/A	12.1	7.919	15.1
Chr20-4190818	20	4190818	T/C	7.06	6.151	13.3

基因号Gene ID	基因位置Gene position	基因注释Gene annotation
CmoCh02G014040	Chr02(-): 8325550~8335639	溶酶体Pro-X羧肽酶Lysosomal Pro-X carboxypeptidase
CmoCh02G014050	Chr02(-): 8335746~8339202	未知蛋白质Unknown protein
CmoCh02G014060	Chr02(+):8343868~8349768	含RING/FYVE/PHD型锌指结构域的酰基辅酶A
		N-酰基转移酶Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger domain
CmoCh02G014070	Chr02(+):8350376~8351998	细胞周期蛋白依赖性激酶调节亚基
		Cyclin-dependent kinases regulatory subunit
CmoCh02G014080	Chr02(-):8352475~8353128	丝氨酸/精氨酸重复基质蛋白1类似蛋白
		Serine/arginine repetitive matrix protein 1-like
CmoCh02G014090	Chr02(-):8357278~8358063	锌指蛋白ZAT5类似蛋白Zinc finger protein ZAT5-like
CmoCh02G014100	Chr02(-):8362767~8366474	超氧化物歧化酶[Cu-Zn] Superoxide dismutase[Cu-Zn]
CmoCh02G014110	Chr02(+):8367274~8374936	SMG8蛋白Protein SMG8
CmoCh02G014120	Chr02(-):8376820~8380071	UPSTREAM OF FLC异构体X1蛋白UPSTREAM OF FLC isoform X1 protein
CmoCh02G014130	Chr02(-):8380657~8381203	未知蛋白质Unknown protein
CmoCh02G014140	Chr02(+):8381617~8382519	未知蛋白质Unknown protein
CmoCh02G014150	Chr02(-):8383315~8384591	功能未知蛋白(DUF1635结构域)Protein of unknown function (DUF1635)
CmoCh02G014160	Chr02(+):8389007~8390973	次生细胞壁相关糖基转移酶家族47蛋白
		Secondary cell wall-related glycosyltransferase family 47
CmoCh02G014170	Chr02(-):8392267~8394030	木葡聚糖内糖基转移酶/水解酶Xyloglucan endotransglucosylase/hydrolase
CmoCh02G014180	Chr02(+):8393117~8394157	未知蛋白质Unknown protein
CmoCh02G014190	Chr02(+):8394181~8395242	未知蛋白质Unknown protein
CmoCh02G014200	Chr02(+):8397944~8400183	MYB转录因子MYB transcription factor
CmoCh02G014210	Chr02(-):8401784~8404963	未知蛋白质Unknown protein
CmoCh02G014220	Chr02(+):8403870~8404717	未知蛋白质Unknown protein
CmoCh02G014230	Chr02(+):8406957~8409232	重金属关联异戊二烯化植物蛋白3类似蛋白
		Heavy metal-associated isoprenylated plant protein 3-like
CmoCh02G014240	Chr02(+):8415597~8419352	ABC转运蛋白F家族成员1类似蛋白ABC transporter F family member 1-like
CmoCh02G014250	Chr02(-):8420202~8420603	生长素响应蛋白SAUR50类似蛋白Auxin-responsive protein SAUR50-like
CmoCh02G014260	Chr02(+):8423493~8425615	UDP-糖基转移酶超家族蛋白UDP-Glycosyltransferase superfamily protein
CmoCh02G014270	Chr02(-):8425474~8426228	SNF1相关蛋白激酶调节亚基β-3类似蛋白
		SNF1-related protein kinase regulatory subunit beta-3-like
CmoCh02G014280	Chr02(-):8431448~8436941	未知蛋白质Unknown protein
CmoCh04G020920	Chr04(-):12944306~12944713	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020930	Chr04(-):12948680~12949156	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020940	Chr04(-):12950807~12951151	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020950	Chr04(-):12954636~12954845	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020960	Chr04(-):13018338~13021396	病程相关蛋白1 Pathogenesis-related protein 1
CmoCh12G007880	Chr12(+):6613163~6617250	核糖体大亚基蛋白2 Rib large subunit 2
CmoCh12G007890	Chr12(+):6618055~6618522	未知蛋白质Unknown protein
CmoCh12G007900	Chr12(+):6618678~6619198	核糖体结构组分蛋白Structural constituent of ribosome
CmoCh12G007910	Chr12(+):6620547~6621080	核糖体小亚基蛋白3 Rib small subunit 3
CmoCh12G007920	Chr12(+):6621127~6621978	核糖体结构组分蛋白Structural constituent of ribosome
CmoCh20G008360	Chr20(+):4169755~4177633	SUMO激活酶2 SUMO-activating enzyme 2
CmoCh20G008370	Chr20(-):4178136~4187836	肌醇磷酸磷酸酶 Inositol-phosphate phosphatase
CmoCh20G008380	Chr20(-):4190500~4194167	未知蛋白质Unknown protein
CmoCh20G008390	Chr20(-):4199239~4201656	推断的跨膜蛋白Transmembrane protein, putative
CmoCh20G008400	Chr20(-):4206891~4211285	分子伴侣dnaJ 10类似蛋白Chaperone dnaJ 10-like protein

基因号Gene ID	基因位置Gene position	基因注释Gene annotation
CmoCh02G014040	Chr02(-): 8325550~8335639	溶酶体Pro-X羧肽酶Lysosomal Pro-X carboxypeptidase
CmoCh02G014050	Chr02(-): 8335746~8339202	未知蛋白质Unknown protein
CmoCh02G014060	Chr02(+):8343868~8349768	含RING/FYVE/PHD型锌指结构域的酰基辅酶A
		N-酰基转移酶Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger domain
CmoCh02G014070	Chr02(+):8350376~8351998	细胞周期蛋白依赖性激酶调节亚基
		Cyclin-dependent kinases regulatory subunit
CmoCh02G014080	Chr02(-):8352475~8353128	丝氨酸/精氨酸重复基质蛋白1类似蛋白
		Serine/arginine repetitive matrix protein 1-like
CmoCh02G014090	Chr02(-):8357278~8358063	锌指蛋白ZAT5类似蛋白Zinc finger protein ZAT5-like
CmoCh02G014100	Chr02(-):8362767~8366474	超氧化物歧化酶[Cu-Zn] Superoxide dismutase[Cu-Zn]
CmoCh02G014110	Chr02(+):8367274~8374936	SMG8蛋白Protein SMG8
CmoCh02G014120	Chr02(-):8376820~8380071	UPSTREAM OF FLC异构体X1蛋白UPSTREAM OF FLC isoform X1 protein
CmoCh02G014130	Chr02(-):8380657~8381203	未知蛋白质Unknown protein
CmoCh02G014140	Chr02(+):8381617~8382519	未知蛋白质Unknown protein
CmoCh02G014150	Chr02(-):8383315~8384591	功能未知蛋白(DUF1635结构域)Protein of unknown function (DUF1635)
CmoCh02G014160	Chr02(+):8389007~8390973	次生细胞壁相关糖基转移酶家族47蛋白
		Secondary cell wall-related glycosyltransferase family 47
CmoCh02G014170	Chr02(-):8392267~8394030	木葡聚糖内糖基转移酶/水解酶Xyloglucan endotransglucosylase/hydrolase
CmoCh02G014180	Chr02(+):8393117~8394157	未知蛋白质Unknown protein
CmoCh02G014190	Chr02(+):8394181~8395242	未知蛋白质Unknown protein
CmoCh02G014200	Chr02(+):8397944~8400183	MYB转录因子MYB transcription factor
CmoCh02G014210	Chr02(-):8401784~8404963	未知蛋白质Unknown protein
CmoCh02G014220	Chr02(+):8403870~8404717	未知蛋白质Unknown protein
CmoCh02G014230	Chr02(+):8406957~8409232	重金属关联异戊二烯化植物蛋白3类似蛋白
		Heavy metal-associated isoprenylated plant protein 3-like
CmoCh02G014240	Chr02(+):8415597~8419352	ABC转运蛋白F家族成员1类似蛋白ABC transporter F family member 1-like
CmoCh02G014250	Chr02(-):8420202~8420603	生长素响应蛋白SAUR50类似蛋白Auxin-responsive protein SAUR50-like
CmoCh02G014260	Chr02(+):8423493~8425615	UDP-糖基转移酶超家族蛋白UDP-Glycosyltransferase superfamily protein
CmoCh02G014270	Chr02(-):8425474~8426228	SNF1相关蛋白激酶调节亚基β-3类似蛋白
		SNF1-related protein kinase regulatory subunit beta-3-like
CmoCh02G014280	Chr02(-):8431448~8436941	未知蛋白质Unknown protein
CmoCh04G020920	Chr04(-):12944306~12944713	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020930	Chr04(-):12948680~12949156	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020940	Chr04(-):12950807~12951151	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020950	Chr04(-):12954636~12954845	病程相关蛋白1类似蛋白的碱性形式
		Basic form of pathogenesis-related protein 1-like
CmoCh04G020960	Chr04(-):13018338~13021396	病程相关蛋白1 Pathogenesis-related protein 1
CmoCh12G007880	Chr12(+):6613163~6617250	核糖体大亚基蛋白2 Rib large subunit 2
CmoCh12G007890	Chr12(+):6618055~6618522	未知蛋白质Unknown protein
CmoCh12G007900	Chr12(+):6618678~6619198	核糖体结构组分蛋白Structural constituent of ribosome
CmoCh12G007910	Chr12(+):6620547~6621080	核糖体小亚基蛋白3 Rib small subunit 3
CmoCh12G007920	Chr12(+):6621127~6621978	核糖体结构组分蛋白Structural constituent of ribosome
CmoCh20G008360	Chr20(+):4169755~4177633	SUMO激活酶2 SUMO-activating enzyme 2
CmoCh20G008370	Chr20(-):4178136~4187836	肌醇磷酸磷酸酶 Inositol-phosphate phosphatase
CmoCh20G008380	Chr20(-):4190500~4194167	未知蛋白质Unknown protein
CmoCh20G008390	Chr20(-):4199239~4201656	推断的跨膜蛋白Transmembrane protein, putative
CmoCh20G008400	Chr20(-):4206891~4211285	分子伴侣dnaJ 10类似蛋白Chaperone dnaJ 10-like protein

Genome-wide association study and candidate gene prediction of pectin content of pumpkin (Cucurbita moschata)

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References 23

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[2]	WANG Yidi, WANG Jinglei, HU Tianhua, XU Yunmin, BAO Chonglai. Development of molecular markers for clubroot resistance and their application in Brassicaceae breeding [J]. Acta Agriculturae Zhejiangensis, 2025, 37(6): 1272-1284.
[3]	YI Ming, SUN Hong, SHEN Qi, TANG Jiangwu. Research progress on ectopic fermentation system in treatment of fecal residue and waste water of livestock and poultry [J]. Acta Agriculturae Zhejiangensis, 2025, 37(6): 1390-1396.
[4]	MA Jing'e, WU Siqi, WAN Shumin, XIONG Xinwei, XU Jiguo, XU Jing, RAO Yousheng, ZHOU Min. Proteomic study of large and small testes in Ningdu Yellow chicken based on tandem mass tags(TMT) technology [J]. Acta Agriculturae Zhejiangensis, 2025, 37(5): 1029-1044.
[5]	PEI Damei, ZHAO Hongping, WANG Long, LI Huaxin, ZHAO Zhi, XIAO Lu. Mixed genetic model analysis of major gene + polygene of branch angle in Brassica rapa L. [J]. Acta Agriculturae Zhejiangensis, 2025, 37(4): 745-753.
[6]	NI Zheng, LU Lei, ZHU Yinchu, CHEN Liu, LI Xinji, YE Weicheng, YUN Tao, HUA Jionggang, FU Yuan, ZHANG Cun. Epidemiological investigation and evaluation of purification strategies for avian leukosis in local chicken breeds in Zhejiang Province of China [J]. Acta Agriculturae Zhejiangensis, 2025, 37(4): 790-799.
[7]	MA Yuan, HAO Luyao, ZHANG Yanni, Ll Qiannan, WANG Rui. Preparation, regeneration and genetic system construction of Pochonia chlamydosporia protoplasts [J]. Acta Agriculturae Zhejiangensis, 2025, 37(4): 800-807.
[8]	ZHAO Jiahao, XU Xing, ZHOU Weidong, YANG Hua, ZHAO Xihong, WANG Wen. Characteristics of bacteria community and antibiotic resistance genes in piggery wastewater and surrounding water environment [J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 621-632.
[9]	WANG Binbin, QI Keke, MEN Xiaoming, XU Ziwei. Application and perspect of genomic selection in pork quality breeding [J]. Acta Agriculturae Zhejiangensis, 2025, 37(3): 726-735.
[10]	ZHENG Ting, XIANG Jiang, WEI Lingzhu, WU Jiang, CHENG Jianhui. Analysis on the effects of CPPU and TDZ on the aroma of Tiangong Moyu grape using WGCNA and the exploration of the key genes [J]. Acta Agriculturae Zhejiangensis, 2025, 37(2): 311-320.
[11]	ZHANG Meiying, MO Qian, QI Xiushuang, TONG Ningning, KONG Fan, LIU Zheng’an, LYU Changping, PENG Liping. Cloning and expression analysis of peony PoLPAT2 gene [J]. Acta Agriculturae Zhejiangensis, 2025, 37(2): 321-328.
[12]	LI Can, YANG Ting, SUN Yiming, CHEN Hongliang, CUI Qi, SHEN Xiaoxia. Selection and evaluation of superior germplasm resources of Rubus chingii Hu [J]. Acta Agriculturae Zhejiangensis, 2025, 37(2): 349-364.
[13]	YANG Xiaoyu, MA Zhihui, WEI Qing, NIU Zhipeng, CHEN Anqi, HU Zhengchong, WANG Linsheng. Preliminary mapping of a wheat awn length gene and prediction of candidate genes [J]. Acta Agriculturae Zhejiangensis, 2025, 37(1): 14-23.
[14]	QIN Douwen, LIU Weiqiang, TIAN Jiting, JU Xiuting. Establishment of cpDNA-PCR reaction system and genetic diversity analysis of Tulipa iliensis [J]. Acta Agriculturae Zhejiangensis, 2025, 37(1): 78-89.
[15]	LI Xing, LIU Yan, GAO Jianzhou. Cloning and expression analysis of homologous FLOWERING LOCUS T(FT) genes from three species of Paeonia spp. [J]. Acta Agriculturae Zhejiangensis, 2025, 37(1): 90-102.