基于MAGIC群体瓠瓜白粉病抗性的全基因组关联分析

doi:10.3969/j.issn.1004-1524.20221361

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (10): 2398-2407.DOI: 10.3969/j.issn.1004-1524.20221361

基于MAGIC群体瓠瓜白粉病抗性的全基因组关联分析

钟丽萍¹(), 王尖², 吴晓花², 汪颖², 吴新义², 汪宝根², 鲁忠富², 王华森¹^,^*(), 李国景²^,^*()

1.浙江农林大学园艺科学学院,浙江杭州 311300
2.浙江省农业科学院蔬菜研究所,浙江杭州 310021

收稿日期:2022-09-20 出版日期:2023-10-25 发布日期:2023-10-31
作者简介:钟丽萍(1998—),女,福建龙岩人,硕士研究生,研究方向为蔬菜作物分子育种。E-mail:572597612@qq.com
通讯作者: ^*李国景,E-mail: ligj@zaas.ac.cn;王华森,E-mail: wanghs@zafu.edu.cn
基金资助:
浙江省重点研发计划(2021C02042);国家自然科学基金(31801865)

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

摘要/Abstract

摘要：

白粉病是葫芦科作物共有的病害之一,严重影响瓠瓜的产量和品质。本研究采用8个瓠瓜亲本F₈代的203个MAGIC(multi-parent advanced generation inter-cross)群体,利用2020和2021年两年的抗病表型数据,基于基因重测序过滤筛选得到的221 043个高质量SNPs进行全基因组关联分析(genome-wide association study, GWAS)。在两年数据中重复检测到46个SNPs位点与白粉病抗性显著相关,在与抗病相关联的候选区段内共检测到32个候选基因,其中有12个基因预测与瓠瓜抗病功能相关。本研究首次在葫芦科作物中构建了MAGIC群体,并通过GWAS分析进行白粉病抗病基因定位,为克隆瓠瓜抗白粉病相关基因奠定了基础,也对深入了解白粉病抗性机制、辅助培育抗病品种具有重要意义。

关键词: 瓠瓜白粉病, MAGIC群体, 全基因组关联分析, 候选基因

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

中图分类号:

S436.429

钟丽萍, 王尖, 吴晓花, 汪颖, 吴新义, 汪宝根, 鲁忠富, 王华森, 李国景. 基于MAGIC群体瓠瓜白粉病抗性的全基因组关联分析[J]. 浙江农业学报, 2023, 35(10): 2398-2407.

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.

图/表 9

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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]

基于MAGIC群体瓠瓜白粉病抗性的全基因组关联分析

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

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