陆地棉动态株高与SSR标记的关联分析

doi:10.6048/j.issn.1001-4330.2023.12.005

新疆农业科学 ›› 2023, Vol. 60 ›› Issue (12): 2892-2901.DOI: 10.6048/j.issn.1001-4330.2023.12.005

• 作物遗传育种·种质资源·分子遗传学·土壤肥料 • 上一篇下一篇

陆地棉动态株高与SSR标记的关联分析

文佳(), 黄陈珏, 嵇子涵, 李黎贝, 冯震(), 喻树迅()

浙江农林大学现代农学院,浙江临安 311300

收稿日期:2023-04-08 出版日期:2023-12-20 发布日期:2024-01-03
通信作者: 喻树迅(1953-),男,湖北麻城人,中国工程院院士,教授,博士,博士生导师,研究方向为棉花育种,(E-mail)yushuxun@zafu.edu.cn;冯震(1982-),男,浙江临安人,实验师,硕士,研究方向为棉花育种,(E-mail)fengzhen@zafu.edu.cn
作者简介:文佳(1994-),女,湖南醴陵人,硕士研究生,研究方向为棉花育种,(E-mail)17773326468@163.com
基金资助:
浙江农林大学校科研发展基金项目(2021LFR005)

Association analysis of dynamic plant height trait using SSR marker in Gossypium hirsutum L.

WEN Jia(), HUANG Chenjue, JI Zihan, LI Libei, FENG Zhen(), YU Shuxun()

College of Modern Agriculture,Zhejiang A&F University,Lin'an Zhejiang 311300, China

Received:2023-04-08 Online:2023-12-20 Published:2024-01-03
Correspondence author: YU Shuxun (1953-), male, native place: Hubei Province. Academician of CAE, Member Professor, research field: Cotton breeding, (E-mail)yushuxun@zafu.edu.cn;FENG Zhen (1982-), male, native place: Zhejiang Province. Research filed: Cotton breeding, (E-mail)fengzhen@zafu.edu.cn
Supported by:
R & D Project of Zhejiang A&F University(2021LFR005)

摘要/Abstract

摘要：

【目的】分析185份陆地棉品种(系)的开花期株高(PH-ST₁)和吐絮期株高(PH-ST₂)关联度,发掘动态株高的优异等位变异,为进一步棉花高产分子辅助育种提供参考。【方法】利用185份陆地棉品种(系)的基因型,将137对简单重复序列(simple sequence repeat,SSR)多态性引物开发出的355个多态性位点,并结合5个环境下两个时期的株高表型数据,采用一般线性模型(general linear model,GLM)和混合线性模型(mixed linear model,MLM)进行关联分析。【结果】使用GLM模型和MLM模型,分别检测到54、12个与PH-ST₁显著相关的位点和62、12个与PH-ST₂显著相关的位点;其中,31个位点在3个或3个以上的环境都与株高显著相关。【结论】挖掘了多个可重复检测到的与陆地棉株高相关联的分子标记位点。定位到与株高性状相关的位点有24个。

关键词: 陆地棉; SSR; 株高; GLM; MLM

Abstract:

【Objective】To carry out association analysis of plant height of 185 upland cotton cultivars during the cotton flowering stage (PH-ST₁) and spikelike inflorescence period (PH-ST₂) to investigate the superior alleles variation of dynamic plant height. Which can provide a guidance for further high-yield molecular marker-assisted selection breeding of upland cotton.【Methods】355 polymorphism loci developed from 137 pairs of SSR polymorphism primers were combined with plant height phenotype data from two periods in five environments, and the general linear model (GLM) and mixed linear model (MLM) were used for association analysis by the genotypes of 185 upland cotton varieties.【Results】54 and 12 alleles in PH-ST₁ were detected by the GLM and MLM model, respectively. Meanwhile, 62 and 12 alleles in PH-ST₂ were detected by the GLM and MLM model. Among them, 31 loci were significantly related to plant height in 3 or more environments.【Conclusion】Through correlation analysis, multiple molecular markers that can be repeatedly detected and associated with the height of upland cotton were excavated.The 24 loci were reported.

Key words: Gossypium hirsutum L.; SSR; plant height; GLM; MLM

中图分类号:

S562
S188

文佳, 黄陈珏, 嵇子涵, 李黎贝, 冯震, 喻树迅. 陆地棉动态株高与SSR标记的关联分析[J]. 新疆农业科学, 2023, 60(12): 2892-2901.

WEN Jia, HUANG Chenjue, JI Zihan, LI Libei, FENG Zhen, YU Shuxun. Association analysis of dynamic plant height trait using SSR marker in Gossypium hirsutum L.[J]. Xinjiang Agricultural Sciences, 2023, 60(12): 2892-2901.

图/表 10

表1 185份陆地棉材料在不同环境下株高性状

Tab.1 Statistical analysis of plant height traits in 185 upland cotton cultivars under different environments

环境 Environment	时期 Stage	均值 Mean	极小值 Min	极大值 Max	标准差 SD	变异系数 CV(%)	G	G×E	遗传率 h²(%)
中国海南三亚(2020年) Sanya,Hainan,China(2020)	开花期	58.45	35.86	80.84	8.72	14.56	^***	^***	63.67
中国湖北黄冈(2021年) Huanggang,Hubei China(2021)	开花期	46.93	34.41	59.63	5.84	12.45
中国海南三亚(2021年) Sanya,Hainan,China(2021)	开花期	60.02	36.67	84.47	7.95	13.29
中国山东临清(2021年) Linqing,Shandong,China(2021)	开花期	59.92	38.94	76.48	7.49	12.82
中国海南三亚(2020年) Sanya,Hainan,China(2020)	吐絮期	66.21	40.07	98.73	11.14	16.83	^***	^***	85.66
中国湖北黄冈(2021年) Huanggang,Hubei China(2021)	吐絮期	98.05	56.15	136.85	18.07	18.43
中国海南三亚(2021年) Sanya,Hainan,China(2021)	吐絮期	71.66	43.50	106.78	10.61	14.81
中国山东临清(2021年) Linqing,Shandong,China(2021)	吐絮期	88.30	53.15	123.41	15.78	17.87

图1 185份陆地棉材料的群体结构

Fig.1 The population structure of 185 upland cotton accessions

表2 基于GLM模型在3个及以上环境的PH-ST1关联性

Tab.2 Association analysis results of PH-ST1 based on GLM model in 3 or more environments

位点 Locus	GLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
NAU828-418bp					2.35	4.16	3.14	5.56	2.67	4.41
DPL0524-3193bp	2.92	5.12			2.56	4.77	2.69	4.75	3.10	5.37
CGR5202-175bp	7.20	14.19			6.00	12.45			4.61	8.64
HAU2873-340bp	3.75	6.74			4.54	9.02	4.08	7.66	5.25	9.59
MGHES-73-352bp					2.34	4.26	5.68	10.92	3.60	6.36
HAU3318-310bp	4.41	7.98			5.24	10.51	4.96	9.43	5.97	10.95
HAU3318-308bp	5.07	9.30			4.81	9.60	5.92	11.36	6.69	12.33
PGML01548-281bp	3.60	6.48			3.15	6.00			4.15	7.50
NAU797-307bp	2.82	5.01			4.42	9.11			3.92	7.29
BNL2646-161bp	3.14	5.61	3.46	6.27	3.87	7.69	2.65	4.74	5.01	9.25
SWU0146-181bp			2.49	4.25	4.95	9.79	2.81	4.99	4.66	8.31
SWU0376-137bp			2.45	4.14	3.93	7.60			3.41	5.92
SWU0483-186bp					3.91	7.43	2.63	4.53	3.89	6.76
SWU0951-261bp	2.41	4.37	3.21	6.23	3.03	6.23			4.06	7.77
SWU1132-192bp	3.32	5.89			4.91	9.89			4.05	7.26
NAU2238-3			5.05	9.45	4.16	8.16	5.67	10.83	6.27	11.56
PGML01548-405bp	3.73	6.66	2.45	4.16					3.00	5.15
SWU0218-141bp			2.46	4.17			3.83	7.03	3.44	5.96
NAU4042-185bp	2.61	4.50					4.23	8.00	3.18	5.58

表2 基于GLM模型在3个及以上环境的PH-ST1关联性

Tab.2 Association analysis results of PH-ST1 based on GLM model in 3 or more environments

位点 Locus	GLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
NAU828-418bp					2.35	4.16	3.14	5.56	2.67	4.41
DPL0524-3193bp	2.92	5.12			2.56	4.77	2.69	4.75	3.10	5.37
CGR5202-175bp	7.20	14.19			6.00	12.45			4.61	8.64
HAU2873-340bp	3.75	6.74			4.54	9.02	4.08	7.66	5.25	9.59
MGHES-73-352bp					2.34	4.26	5.68	10.92	3.60	6.36
HAU3318-310bp	4.41	7.98			5.24	10.51	4.96	9.43	5.97	10.95
HAU3318-308bp	5.07	9.30			4.81	9.60	5.92	11.36	6.69	12.33
PGML01548-281bp	3.60	6.48			3.15	6.00			4.15	7.50
NAU797-307bp	2.82	5.01			4.42	9.11			3.92	7.29
BNL2646-161bp	3.14	5.61	3.46	6.27	3.87	7.69	2.65	4.74	5.01	9.25
SWU0146-181bp			2.49	4.25	4.95	9.79	2.81	4.99	4.66	8.31
SWU0376-137bp			2.45	4.14	3.93	7.60			3.41	5.92
SWU0483-186bp					3.91	7.43	2.63	4.53	3.89	6.76
SWU0951-261bp	2.41	4.37	3.21	6.23	3.03	6.23			4.06	7.77
SWU1132-192bp	3.32	5.89			4.91	9.89			4.05	7.26
NAU2238-3			5.05	9.45	4.16	8.16	5.67	10.83	6.27	11.56
PGML01548-405bp	3.73	6.66	2.45	4.16					3.00	5.15
SWU0218-141bp			2.46	4.17			3.83	7.03	3.44	5.96
NAU4042-185bp	2.61	4.50					4.23	8.00	3.18	5.58

表3 基于GLM模型在3个及以上环境的PH-ST2的关联性

Tab.3 Association analysis results of PH-ST2 based on GLM model in 3 or more environments

位点 Locus	GLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
PGML02558-395bp					3.75	6.03	3.27	5.29	3.25	5.13
NAU4042-185bp	2.68	4.59			5.87	9.95	5.88	10.09	5.17	8.63
NAU3913-415bp					3.14	5.04	2.73	4.34	2.80	4.38
NAU1042-351bp					3.12	4.90	2.43	3.70	2.91	4.47
NAU833-433bp					3.86	6.12	2.70	4.13	3.44	5.33
NAU828-418bp					4.45	7.15	3.21	5.04	3.93	6.19
DPL0524-199bp					3.24	5.21	3.39	5.57	2.66	4.12
DPL0524-3193bp	3.18	5.58			4.82	8.07	4.37	7.36	4.70	7.77
BNL1705-180bp					2.57	3.87	2.68	4.16	2.79	4.26
HAU2873-340bp	3.99	7.13	2.38	4.11	7.09	12.02	6.20	10.59	6.90	11.55
MGHES-73-352bp					4.12	6.77	5.35	9.07	4.45	7.28
MGHES-73-340bp	2.39	4.11			4.26	7.28	2.41	3.85	2.96	4.79
NAU1102-236bp					3.25	5.22	4.70	7.92	4.00	6.51
NAU1190-222bp					2.39	3.58	3.96	6.42	3.04	4.69
HAU3318-310bp	3.52	6.19			7.53	12.78	6.68	11.44	6.12	10.23
HAU3318-308bp	4.40	7.92			6.96	11.81	7.33	12.57	6.64	11.11
PGML01548-281bp	3.15	5.50			3.73	6.10	3.25	5.28	3.72	6.03
NAU797-307bp	2.98	5.30			3.38	5.66	3.30	5.61	3.47	5.79
BNL2646-161bp	3.15	5.57	3.43	6.31	6.01	10.30	4.36	7.40	6.08	10.29
SWU0146-195bp					4.81	7.91	3.37	5.43	3.48	5.50
SWU0146-181bp			2.71	4.75	4.51	7.38	3.65	5.90	4.62	7.46
SWU0163-191bp					4.52	7.42	2.95	4.67	3.72	5.91
SWU0140-175bp			2.45	4.20	5.90	9.79	7.91	13.35	6.93	11.45
SWU0483-373bp			2.36	4.03	2.71	4.16	3.50	5.64	3.76	5.97
SWU0483-186bp			2.43	4.10	3.09	4.76	2.82	4.33	3.64	5.69
SWU0951-261bp			3.14	6.10	3.49	5.95	2.33	3.74	3.86	6.51
SWU0987-206bp					3.60	5.80	3.70	6.07	4.01	6.45
NAU2679-2					4.02	6.94	3.64	6.27	3.13	5.18
NAU2238-3			5.63	10.75	8.68	14.63	6.60	11.26	8.45	14.17
NAU2173-3					3.16	4.97	2.60	3.99	2.35	3.50
NAU2132					4.47	7.44	4.06	6.78	3.64	5.90
NAU1269-3					4.52	7.33	4.20	6.85	3.79	6.01
NAU1255-2					4.14	6.71	3.80	6.17	3.51	5.56
NAU1230-2					4.37	7.17	4.35	7.21	3.72	5.96

表3 基于GLM模型在3个及以上环境的PH-ST2的关联性

Tab.3 Association analysis results of PH-ST2 based on GLM model in 3 or more environments

位点 Locus	GLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
PGML02558-395bp					3.75	6.03	3.27	5.29	3.25	5.13
NAU4042-185bp	2.68	4.59			5.87	9.95	5.88	10.09	5.17	8.63
NAU3913-415bp					3.14	5.04	2.73	4.34	2.80	4.38
NAU1042-351bp					3.12	4.90	2.43	3.70	2.91	4.47
NAU833-433bp					3.86	6.12	2.70	4.13	3.44	5.33
NAU828-418bp					4.45	7.15	3.21	5.04	3.93	6.19
DPL0524-199bp					3.24	5.21	3.39	5.57	2.66	4.12
DPL0524-3193bp	3.18	5.58			4.82	8.07	4.37	7.36	4.70	7.77
BNL1705-180bp					2.57	3.87	2.68	4.16	2.79	4.26
HAU2873-340bp	3.99	7.13	2.38	4.11	7.09	12.02	6.20	10.59	6.90	11.55
MGHES-73-352bp					4.12	6.77	5.35	9.07	4.45	7.28
MGHES-73-340bp	2.39	4.11			4.26	7.28	2.41	3.85	2.96	4.79
NAU1102-236bp					3.25	5.22	4.70	7.92	4.00	6.51
NAU1190-222bp					2.39	3.58	3.96	6.42	3.04	4.69
HAU3318-310bp	3.52	6.19			7.53	12.78	6.68	11.44	6.12	10.23
HAU3318-308bp	4.40	7.92			6.96	11.81	7.33	12.57	6.64	11.11
PGML01548-281bp	3.15	5.50			3.73	6.10	3.25	5.28	3.72	6.03
NAU797-307bp	2.98	5.30			3.38	5.66	3.30	5.61	3.47	5.79
BNL2646-161bp	3.15	5.57	3.43	6.31	6.01	10.30	4.36	7.40	6.08	10.29
SWU0146-195bp					4.81	7.91	3.37	5.43	3.48	5.50
SWU0146-181bp			2.71	4.75	4.51	7.38	3.65	5.90	4.62	7.46
SWU0163-191bp					4.52	7.42	2.95	4.67	3.72	5.91
SWU0140-175bp			2.45	4.20	5.90	9.79	7.91	13.35	6.93	11.45
SWU0483-373bp			2.36	4.03	2.71	4.16	3.50	5.64	3.76	5.97
SWU0483-186bp			2.43	4.10	3.09	4.76	2.82	4.33	3.64	5.69
SWU0951-261bp			3.14	6.10	3.49	5.95	2.33	3.74	3.86	6.51
SWU0987-206bp					3.60	5.80	3.70	6.07	4.01	6.45
NAU2679-2					4.02	6.94	3.64	6.27	3.13	5.18
NAU2238-3			5.63	10.75	8.68	14.63	6.60	11.26	8.45	14.17
NAU2173-3					3.16	4.97	2.60	3.99	2.35	3.50
NAU2132					4.47	7.44	4.06	6.78	3.64	5.90
NAU1269-3					4.52	7.33	4.20	6.85	3.79	6.01
NAU1255-2					4.14	6.71	3.80	6.17	3.51	5.56
NAU1230-2					4.37	7.17	4.35	7.21	3.72	5.96

表4 基于MLM模型在3个及以上环境的PH-ST1关联性

Tab.4 Association analysis results of PH-ST1 based on MLM model in 3 or more environments

位点 Locus	MLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
CGR5202-175bp	4.43	10.21			3.51	8.55			3.53	8.10
SWU0483-338bp	NA	0	NA	0	NA	0	NA	0	NA	0

表4 基于MLM模型在3个及以上环境的PH-ST1关联性

Tab.4 Association analysis results of PH-ST1 based on MLM model in 3 or more environments

位点 Locus	MLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
CGR5202-175bp	4.43	10.21			3.51	8.55			3.53	8.10
SWU0483-338bp	NA	0	NA	0	NA	0	NA	0	NA	0

表5 基于MLM模型在3个及以上的环境的PH-ST2的关联性

Tab.5 Association analysis results of PH-ST2 based on MLM model in 3 or more environments

位点 Locus	MLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
NAU2503-1			3.25	7.85			2.40	4.88	2.54	5.43
SWU0483-338bp	NA	0	NA	0	NA	0			NA	0

表5 基于MLM模型在3个及以上的环境的PH-ST2的关联性

Tab.5 Association analysis results of PH-ST2 based on MLM model in 3 or more environments

位点 Locus	MLM
	中国海南三亚 (2020年) Sanya,Hainan, China(2020)		中国海南三亚 (2021年) Sanya,Hainan, China(2021)		中国湖北黄冈 (2021年) Huanggang,Hubei China(2021)		中国山东临清 (2021年) Linqing,Shandong, China(2021)		BLUP值
	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)	lg( $P -$ )	R²(%)
NAU2503-1			3.25	7.85			2.40	4.88	2.54	5.43
SWU0483-338bp	NA	0	NA	0	NA	0			NA	0

图2 在GLM和MLM模型下不同时期株高的SSR位点韦恩图

Fig.2 Venn diagrams of SSR locus associated with plant height at different stages based on GLM and MLM model

图3 CGR5202-175bp位点的表型效应注:Hap 1:不含有CGR5202-175bp位点的材料;Hap 2:含CGR5202-175bp位点的材料

Fig.3 Phenotypic effects analysis of CGR5202-175bp locus Note:Hap 1:Material without the CGR5202-175bp locus;Hap 2:Material containing the CGR5202-175bp locus

图4 NAU2238-3位点的表型效应 Hap 1:不含有NAU2238-3位点的材料;Hap 2:含NAU2238-3位点的材料

Fig.4 Phenotypic effects analysis of NAU2238-3 locus Note:Hap 1:Material without NAU2238-3 locus;Hap 2:Material containing NAU2238-3 locus

图5 与前人研究报道的棉花株高QTL区间比较注:蓝色代表前人定位到的QTL,红色代表位于前人定位QTL 1Mb范围内的SSR位点

Fig.5 Comparison of the QTL for plant height in cotton between this study and previous reports Note:Blue represents QTL in previous studies,red represents SSR loci within 1 Mb of QTL mapped previously

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陆地棉动态株高与SSR标记的关联分析

Association analysis of dynamic plant height trait using SSR marker in Gossypium hirsutum L.

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