Genome wide association analysis of powdery mildew resistance of bottle gourd based on MAGIC population

doi:10.3969/j.issn.1004-1524.20221361

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (10): 2398-2407.DOI: 10.3969/j.issn.1004-1524.20221361

• Plant Protection • Previous Articles Next Articles

Genome wide association analysis of powdery mildew resistance of bottle gourd based on MAGIC population

ZHONG Liping¹(), WANG Jian², WU Xiaohua², WANG Ying², WU Xinyi², WANG Baogen², LU Zhongfu², WANG Huasen¹^,^*(), LI Guojing²^,^*()

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

Received:2022-09-20 Online:2023-10-25 Published:2023-10-31

Abstract

Abstract:

Powdery mildew is one of the common diseases of Cucurbitaceae crops, which seriously affects the yield and quality of bottle gourd. In this study, 203 MAGIC (multi-parent advanced generation inter cross) populations from the F₈ generation of 8 gourd parents were used to conduct genome wide association analysis (GWAS) based on 221 043 high-quality SNPs screened by gene re-sequencing filter using the disease resistant phenotype data in 2020 and 2021. In two years’ data, 46 SNPs were repeatedly detected to be significantly related to powdery mildew resistance, and 32 candidate genes were detected in the candidate regions associated with disease resistance, of which 12 genes were predicted to be related to the disease resistance function of bottle gourd. In this study, MAGIC population was constructed in Cucurbitaceae crops for the first time, and the powdery mildew resistance gene was mapped through GWAS analysis, which laid a foundation for cloning powdery mildew resistance related genes of bottle gourd, and also had important significance for in-depth understanding of powdery mildew resistance mechanism and assisting in breeding resistant varieties.

Key words: powdery mildew of bottle gourd, MAGIC group, genome wide association analysis, candidate gene

CLC Number:

S436.429

ZHONG Liping, WANG Jian, WU Xiaohua, WANG Ying, WU Xinyi, WANG Baogen, LU Zhongfu, WANG Huasen, LI Guojing. Genome wide association analysis of powdery mildew resistance of bottle gourd based on MAGIC population[J]. Acta Agriculturae Zhejiangensis, 2023, 35(10): 2398-2407.

Figures/Tables 9

References 31

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标记 Marker	染色体 Chromosome	物理位置 Position	等位变异 Allelic variation	2020		2021
标记 Marker	染色体 Chromosome	物理位置 Position	等位变异 Allelic variation	LOD	R²	LOD	R²
rs128943	4	16716155	T/C	4.37	0.10	4.44	0.11
rs133635	4	20719657	A/C	5.21	0.12	5.42	0.12
rs133636	4	20719660	T/C	4.24	0.09	4.45	0.10
rs133637	4	20719661	A/G	4.09	0.09	4.46	0.10
rs155165	5	11936046	A/T	4.93	0.12	4.15	0.10
rs209093	6	24723915	A/G	4.93	0.12	4.00	0.10
rs209142	6	24825291	C/T	4.84	0.12	4.07	0.10
rs209168	6	24876006	T/C	5.14	0.12	4.21	0.10
rs209230	6	25032014	G/A	5.14	0.12	4.08	0.10
rs209251	6	25066874	G/A	4.98	0.12	4.15	0.10
rs209271	6	25090297	T/A	4.52	0.13	4.07	0.11
rs209283	6	25102969	G/A	5.40	0.14	4.89	0.13
rs209284	6	25103852	C/T	4.73	0.12	4.28	0.11
rs209326	6	25189107	C/T	4.80	0.12	4.03	0.10
rs209351	6	25265209	G/A	6.20	0.16	5.52	0.14
rs209453	6	25488354	A/C	6.70	0.15	5.69	0.13
rs209468	6	25525766	C/A	5.48	0.13	4.30	0.10
rs209469	6	25527123	A/G	7.39	0.19	5.94	0.16
rs209471	6	25535101	T/C	6.95	0.17	5.68	0.14
rs209472	6	25537606	T/A	5.00	0.12	4.17	0.10
rs209474	6	25541933	T/C	5.34	0.14	4.16	0.11
rs209477	6	25544278	A/G	6.40	0.16	5.09	0.13
rs209490	6	25558414	A/C	6.75	0.15	5.74	0.13
rs209513	6	25602550	A/C	5.17	0.14	4.02	0.11
rs209517	6	25610710	C/T	4.94	0.14	4.01	0.11
rs209550	6	25673431	C/A	6.33	0.14	5.19	0.12
rs209581	6	25777110	G/A	6.17	0.17	4.67	0.13
rs209597	6	25809928	C/T	4.94	0.14	4.19	0.12
rs209612	6	25844215	A/C	5.25	0.12	4.03	0.10
rs209648	6	25886250	G/A	5.93	0.15	4.93	0.13
rs209651	6	25890262	A/T	6.06	0.16	4.66	0.13
rs209653	6	25892149	A/C	5.43	0.15	4.53	0.12
rs209684	6	25983533	C/A	6.41	0.18	5.22	0.15
rs209708	6	26030284	T/C	5.51	0.14	4.32	0.11
rs209712	6	26034201	G/A	6.29	0.16	4.96	0.12
rs209781	6	26188347	G/A	6.75	0.16	5.16	0.12
rs209805	6	26214788	C/T	6.39	0.16	4.91	0.13
rs209874	6	26364399	C/A	6.25	0.14	4.93	0.12
rs232529	7	18504253	C/T	6.16	0.15	4.17	0.10
rs233763	7	19428401	C/T	5.18	0.11	4.76	0.10
rs233981	7	19522446	T/C	4.72	0.12	4.15	0.11
rs242106	8	2443873	G/T	4.64	0.10	4.42	0.09
rs252061	8	11388148	A/G	4.25	0.09	4.72	0.10
rs307101	10	17188451	G/A	4.16	0.10	4.19	0.10
rs309292	10	18960817	T/C	4.78	0.12	4.35	0.11
rs316055	11	566683	A/T	4.22	0.11	4.16	0.11

标记 Marker	染色体 Chromosome	物理位置 Position	等位变异 Allelic variation	2020		2021
标记 Marker	染色体 Chromosome	物理位置 Position	等位变异 Allelic variation	LOD	R²	LOD	R²
rs128943	4	16716155	T/C	4.37	0.10	4.44	0.11
rs133635	4	20719657	A/C	5.21	0.12	5.42	0.12
rs133636	4	20719660	T/C	4.24	0.09	4.45	0.10
rs133637	4	20719661	A/G	4.09	0.09	4.46	0.10
rs155165	5	11936046	A/T	4.93	0.12	4.15	0.10
rs209093	6	24723915	A/G	4.93	0.12	4.00	0.10
rs209142	6	24825291	C/T	4.84	0.12	4.07	0.10
rs209168	6	24876006	T/C	5.14	0.12	4.21	0.10
rs209230	6	25032014	G/A	5.14	0.12	4.08	0.10
rs209251	6	25066874	G/A	4.98	0.12	4.15	0.10
rs209271	6	25090297	T/A	4.52	0.13	4.07	0.11
rs209283	6	25102969	G/A	5.40	0.14	4.89	0.13
rs209284	6	25103852	C/T	4.73	0.12	4.28	0.11
rs209326	6	25189107	C/T	4.80	0.12	4.03	0.10
rs209351	6	25265209	G/A	6.20	0.16	5.52	0.14
rs209453	6	25488354	A/C	6.70	0.15	5.69	0.13
rs209468	6	25525766	C/A	5.48	0.13	4.30	0.10
rs209469	6	25527123	A/G	7.39	0.19	5.94	0.16
rs209471	6	25535101	T/C	6.95	0.17	5.68	0.14
rs209472	6	25537606	T/A	5.00	0.12	4.17	0.10
rs209474	6	25541933	T/C	5.34	0.14	4.16	0.11
rs209477	6	25544278	A/G	6.40	0.16	5.09	0.13
rs209490	6	25558414	A/C	6.75	0.15	5.74	0.13
rs209513	6	25602550	A/C	5.17	0.14	4.02	0.11
rs209517	6	25610710	C/T	4.94	0.14	4.01	0.11
rs209550	6	25673431	C/A	6.33	0.14	5.19	0.12
rs209581	6	25777110	G/A	6.17	0.17	4.67	0.13
rs209597	6	25809928	C/T	4.94	0.14	4.19	0.12
rs209612	6	25844215	A/C	5.25	0.12	4.03	0.10
rs209648	6	25886250	G/A	5.93	0.15	4.93	0.13
rs209651	6	25890262	A/T	6.06	0.16	4.66	0.13
rs209653	6	25892149	A/C	5.43	0.15	4.53	0.12
rs209684	6	25983533	C/A	6.41	0.18	5.22	0.15
rs209708	6	26030284	T/C	5.51	0.14	4.32	0.11
rs209712	6	26034201	G/A	6.29	0.16	4.96	0.12
rs209781	6	26188347	G/A	6.75	0.16	5.16	0.12
rs209805	6	26214788	C/T	6.39	0.16	4.91	0.13
rs209874	6	26364399	C/A	6.25	0.14	4.93	0.12
rs232529	7	18504253	C/T	6.16	0.15	4.17	0.10
rs233763	7	19428401	C/T	5.18	0.11	4.76	0.10
rs233981	7	19522446	T/C	4.72	0.12	4.15	0.11
rs242106	8	2443873	G/T	4.64	0.10	4.42	0.09
rs252061	8	11388148	A/G	4.25	0.09	4.72	0.10
rs307101	10	17188451	G/A	4.16	0.10	4.19	0.10
rs309292	10	18960817	T/C	4.78	0.12	4.35	0.11
rs316055	11	566683	A/T	4.22	0.11	4.16	0.11

基因 Gene	染色体 Chromosome	起始位置 Start position	终止位置 Termination position	基因注释 Gene annotation
HG_GLEAN_10010653	6	24445461	24452650	PREDICTED: serine/threonine-protein kinase ATG1a isoform X4 [Cucumis melo]
HG_GLEAN_10010699	6	24954657	24959458	serine/threonine-protein kinase PBS1-like [Cucurbita maxima]
HG_GLEAN_10010836	6	26331125	26337328	MLO-like protein 1 [Cucumis melo]>gi\|261263490\|gb\|ACX55085.1\| Mlo1 [Cucumis melo]
HG_GLEAN_10010861	6	26570005	26571963	PREDICTED: receptor-like serine/threonine-protein kinase At2g45590 [Cucumis melo]
HG_GLEAN_10006490	7	19152316	19158212	PREDICTED: probable serine/threonine-protein kinase At1g54610 [Cucumis melo]
HG_GLEAN_10006502	7	19277449	19280693	PREDICTED: probable serine/threonine-protein kinase WNK9 [Cucumis melo]
HG_GLEAN_10006508	7	19371792	19377140	PREDICTED: serine/threonine-protein kinase Nek2-like isoform X1 [Cucumis melo]
HG_GLEAN_10006568	7	19920968	19922269	PREDICTED: CBL-interacting serine/threonine-protein kinase 6 [Cucumis sativus]
HG_GLEAN_10006594	7	20207830	20208111	cysteine-rich receptor-like protein kinase 4 isoform X2 [Cucurbita maxima]
HG_GLEAN_10008051	10	19112275	19116452	PREDICTED: CBL-interacting serine/threonine-protein kinase 24 isoform X1 [Cucumis melo]
HG_GLEAN_10001793	11	491462	494227	PREDICTED: serine/threonine-protein kinase-like protein ACR4 [Cucumis sativus]

基因 Gene	染色体 Chromosome	起始位置 Start position	终止位置 Termination position	基因注释 Gene annotation
HG_GLEAN_10010653	6	24445461	24452650	PREDICTED: serine/threonine-protein kinase ATG1a isoform X4 [Cucumis melo]
HG_GLEAN_10010699	6	24954657	24959458	serine/threonine-protein kinase PBS1-like [Cucurbita maxima]
HG_GLEAN_10010836	6	26331125	26337328	MLO-like protein 1 [Cucumis melo]>gi\|261263490\|gb\|ACX55085.1\| Mlo1 [Cucumis melo]
HG_GLEAN_10010861	6	26570005	26571963	PREDICTED: receptor-like serine/threonine-protein kinase At2g45590 [Cucumis melo]
HG_GLEAN_10006490	7	19152316	19158212	PREDICTED: probable serine/threonine-protein kinase At1g54610 [Cucumis melo]
HG_GLEAN_10006502	7	19277449	19280693	PREDICTED: probable serine/threonine-protein kinase WNK9 [Cucumis melo]
HG_GLEAN_10006508	7	19371792	19377140	PREDICTED: serine/threonine-protein kinase Nek2-like isoform X1 [Cucumis melo]
HG_GLEAN_10006568	7	19920968	19922269	PREDICTED: CBL-interacting serine/threonine-protein kinase 6 [Cucumis sativus]
HG_GLEAN_10006594	7	20207830	20208111	cysteine-rich receptor-like protein kinase 4 isoform X2 [Cucurbita maxima]
HG_GLEAN_10008051	10	19112275	19116452	PREDICTED: CBL-interacting serine/threonine-protein kinase 24 isoform X1 [Cucumis melo]
HG_GLEAN_10001793	11	491462	494227	PREDICTED: serine/threonine-protein kinase-like protein ACR4 [Cucumis sativus]

Genome wide association analysis of powdery mildew resistance of bottle gourd based on MAGIC population

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