山西小麦矮秆基因的鉴定及株高遗传位点挖掘

doi:10.3864/j.issn.0578-1752.2025.17.002

中国农业科学 ›› 2025, Vol. 58 ›› Issue (17): 3372-3388.doi: 10.3864/j.issn.0578-1752.2025.17.002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

山西小麦矮秆基因的鉴定及株高遗传位点挖掘

向爱慧¹^,²(), 白荣基²(), 郝宇琼¹, 赵佳佳¹, 武棒棒¹, 李晓华¹, 郑兴卫¹, 关攀锋³^,^*(), 郑军¹^,²^,^*()

¹ 山西农业大学小麦研究所/农业农村部有机旱作农业重点实验室（部省共建），山西临汾 041000
² 山西农业大学农学院，山西太谷 030801
³ 郑州大学农学院，郑州 450001

收稿日期:2025-03-06 接受日期:2025-05-01 出版日期:2025-09-01 发布日期:2025-09-02
通信作者:
郑军，E-mail：sxnkyzj@126.com。
郑军，E-mail：sxnkyzj@126.com。
联系方式: 向爱慧，E-mail：13278756912@163.com。白荣基，E-mail：bairongji1999@126.com。向爱慧和白荣基为同等贡献作者。
基金资助:
山西省科技重大专项计划揭榜挂帅项目(202201140601025-2); 山西省现代农业产业技术体系(2024CYJSTX02); 山西农业大学生物育种工程(YZGC013)

Identification of Dwarf Genes and Mining of Plant Height Genetic Loci in Shanxi Wheat

XIANG AiHui¹^,²(), BAI RongJi²(), HAO YuQiong¹, ZHAO JiaJia¹, WU BangBang¹, LI XiaoHua¹, ZHENG XingWei¹, GUAN PanFeng³^,^*(), ZHENG Jun¹^,²^,^*()

¹ Institute of Wheat Research, Shanxi Agriculture University/Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Linfen 041000, Shanxi
² College of Agriculture, Shanxi Agricultural University, Taigu 030801, Shanxi
³ School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001

Received:2025-03-06 Accepted:2025-05-01 Published:2025-09-01 Online:2025-09-02

摘要/Abstract

摘要：

【目的】矮秆基因是小麦遗传育种关注的重要基因，不同生态区和品种类型对小麦株高的要求不尽相同，因此，鉴定山西小麦品种矮秆基因的分布规律和特点，并挖掘株高相关遗传新位点，为小麦株高遗传改良提供参考。【方法】在株高及其相关性状准确鉴定的基础上，对306份山西小麦中11个已知的矮秆基因类型进行基因型检测，并结合16K SNP芯片进行全基因组关联分析，挖掘控制株高的新位点。【结果】除穗长外，山西小麦的株高和株高相关性状随育种年代逐渐降低，不同株高相关性状受到的选择压力不同。11个矮秆基因在山西小麦中的分布频率从高到低依次为Rht12、Rht24、Rht8、Rht26、Rht13、Rht25、Rht2、Rht5、Rht4、Rht1和Rht9，其中，Rht1、Rht2和Rht25在地方品种中尚未发现，除Rht2和Rht25在水地品种中远多于旱地品种外，其他基因在旱地品种和水地品种中的分布基本一致；共鉴定出125种不同矮秆基因组合，其中，分布频率最高的组合为Rht8+Rht12+Rht24。结合关联分析，在1A、2A和2B等14条染色体上共检测到26个稳定的遗传位点，其中，QPH-6D、QPH-7A和Q3rd IL-1D等8个位点未见报道；QPH-6D主要通过缩短第3节间和第4节间长度，使株高降低13.68%，QPH-7A则主要通过缩短第2节间和第3节间长度，使株高降低16.87%。【结论】山西小麦的株高逐年降低，不同株高相关性状受到的育种选择压力有差异；山西小麦的矮秆基因主要为Rht12、Rht24和Rht8；在1A、2A和2B等14条染色体上定位到26个稳定的遗传位点，其中，QPH-6D、QPH-7A和Q3rd IL-1D等8个位点可能是株高相关的新位点。

关键词: 山西小麦, 株高, 相关性状, 矮秆基因, 全基因组关联分析

Abstract:

【Objective】Dwarf genes play a crucial role in wheat genetics and breeding. Different ecological zones and wheat varieties have varying requirements for plant height. Therefore, understanding the distribution pattern and characteristics of dwarf genes in Shanxi wheat, as well as identifying novel genetic loci related to plant height will contribute to wheat genetic improvement.【Method】Based on the accurate identification of plant height and component traits, a total of 11 known dwarfing gene types were genotyped in 306 Shanxi wheat samples and integrated with a 16K SNP chip to conduct genome-wide association analysis aimed at identifying new loci controlling plant height.【Result】With the exception of spike length, both of the plant height and component traits of Shanxi wheat exhibited a gradual decline over the years of breeding and the various compositional traits associated with plant height were influenced by distinct selection pressures. The distribution frequency of 11 dwarfing genes in Shanxi wheat from high to low was Rht12, Rht24, Rht8, Rht26, Rht13, Rht25, Rht2, Rht5, Rht4, Rht1, and Rht9, among which Rht1, Rht2, and Rht25 have not been found in landraces. Except for Rht2 and Rht25 is more widely distributed in irrigated cultivars than in dryland cultivars, the distribution of other dwarfing genes is relatively similar in dryland cultivars and irrigated cultivars. A total of 125 different dwarf genes combination were identified, of which the combination with the highest distribution frequency was Rht8+Rht12+Rht24. Combined with association analysis, a total of 26 stable genetic loci were identified to be distributed on 14 chromosomes including 1A, 2A, and 2B. Notably, eight loci such as QPH-6D, QPH-7A, and Q3rd IL-1D have not been reported yet. Among these, QPH-6D mainly reduced plant height by shortening the length of the third and fourth internodes by approximately 13.68 %, while QPH-7A reduced the plant height by 16.87 % via shortening the length of the second and third internodes.【Conclusion】The main dwarf genes in Shanxi wheat were mainly Rht12, Rht24, and Rht8. 26 stable genetic loci were located on chromosomes 1A, 2A, and 2B, among which eight loci such as QPH-6D, QPH-7A, and Q3rd IL-1D may be novel loci related to plant height.

Key words: Shanxi wheat, plant height, compositional traits, dwarf gene, genome-wide association study

向爱慧, 白荣基, 郝宇琼, 赵佳佳, 武棒棒, 李晓华, 郑兴卫, 关攀锋, 郑军. 山西小麦矮秆基因的鉴定及株高遗传位点挖掘[J]. 中国农业科学, 2025, 58(17): 3372-3388.

XIANG AiHui, BAI RongJi, HAO YuQiong, ZHAO JiaJia, WU BangBang, LI XiaoHua, ZHENG XingWei, GUAN PanFeng, ZHENG Jun. Identification of Dwarf Genes and Mining of Plant Height Genetic Loci in Shanxi Wheat[J]. Scientia Agricultura Sinica, 2025, 58(17): 3372-3388.

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图/表 7

表1

表2

不同类型品种株高及相关性状的表型分析"

性状 Trait	环境 Env.	地方品种Landrace			育成品种<BOLD>C</BOLD>ultivar			旱地品种Dryland cultivar			水地品种Irrigated cultivar				总计Total
性状 Trait	环境 Env.	变幅 Range	均值 Mean	变异系数 CV (%)	变幅 Range	均值 Mean	变异系数 CV (%)	变幅 Range	均值 Mean	变异系数 CV (%)	变幅 Range	均值 Mean	变异系数 CV (%)		变幅 Range	均值 Mean	变异系数 CV (%)
株高 PH (cm)	E1	103.20-160.80	131.63	8.90	66.20-165.60	93.36**	17.82	66.94-165.60	98.44	17.73	66.20-139.60	88.76**		16.19	66.20-165.60	97.72		20.69
	E2	87.40-151.20	133.24	11.23	60.40-163.20	86.78**	20.24	62.18-163.20	91.63	19.94	60.40-138.60	82.41**		19.09	60.40-163.20	92.62		24.98
	E3	87.00-156.60	131.20	13.70	61.40-148.80	89.19**	20.85	61.90-148.80	93.21	20.88	61.40-148.40	85.47**		19.81	61.40-156.60	94.42		24.50
	E4	85.20-158.20	133.80	13.31	57.60-161.90	89.60**	20.10	68.46-161.90	94.86	19.48	57.60-147.00	84.84**		19.06	57.60-161.90	95.16		24.37
	BLUP	86.56-148.80	129.40	12.35	64.98-158.51	89.92**	18.50	68.27-158.51	94.61	18.25	64.98-140.51	85.73**		17.32	64.98-158.51	95.09		22.35
穗长 SL (cm)	E1	5.54-12.04	7.99	16.55	6.40-13.00	9.07**	12.29	6.40-12.48	9.21	11.56	6.46-13.00	8.95		12.85	5.54-13.00	8.95		13.29
	E2	4.56-15.38	8.66	24.71	5.64-12.72	8.78	12.76	6.74-11.74	8.93	11.56	5.64-12.72	8.64*		13.68	4.56-15.38	8.76		14.71
	E3	5.42-11.20	7.88	15.02	5.76-12.48	9.00**	12.35	6.12-12.04	9.13	12.00	5.76-12.48	8.89		12.54	5.42-12.48	8.87		13.30
	E4	5.24-14.54	8.23	20.58	6.36-13.18	8.83**	12.56	6.38-12.22	9.00	11.14	6.36-13.18	8.68*		13.67	5.24-14.54	8.76		13.84
	BLUP	5.90-14.08	8.38	18.75	6.34-12.17	8.93**	10.13	6.92-10.90	9.05	8.89	6.34-12.17	8.82*		11.08	5.90-14.08	8.86		11.63
穗叶距 DSL (cm)	E1	8.60-33.38	25.11	18.98	4.76-36.10	13.67**	37.04	5.86-27.42	14.77	36.16	4.76-36.10	12.68**		36.14	4.76-36.10	14.97		41.45
	E2	5.72-38.46	25.31	25.00	3.52-32.86	13.55**	42.11	4.78-30.04	14.76	40.50	3.52-32.86	12.47**		41.93	3.52-38.46	15.03		46.41
	E3	11.44-35.14	23.37	23.44	3.00-30.40	13.34**	41.27	3.00-30.4	14.52	39.30	3.24-28.24	12.24**		41.61	3.00-35.14	14.59		43.99
	E4	5.58-38.22	24.57	27.42	3.44-32.46	14.04**	40.71	4.60-29.68	15.38	38.10	3.44-32.46	12.86**		41.20	1.58-38.22	15.37		44.30
	BLUP	4.25-33.02	23.34	24.54	5.26-31.82	13.74**	36.64	5.63-26.82	14.88	35.15	5.26-31.82	12.74**		36.34	4.25-33.02	15.00		40.40
穗下节间长度 UIL (cm)	E1	30.68-52.66	45.49	10.79	19.80-55.90	31.84**	19.92	21.72-49.54	33.46	19.46	19.80-55.90	30.38**		19.11	19.80-55.90	33.40		22.65
	E2	32.72-59.58	43.85	14.01	18.16-54.88	30.53**	22.71	18.88-49.98	32.21	21.74	18.16-54.88	29.04**		22.47	18.16-59.58	32.21		25.26
	E3	28.32-56.80	43.33	14.37	18.74-53.44	31.45**	21.00	22.10-53.44	32.80	20.30	18.74-49.54	30.19**		20.89	18.74-56.80	32.93		23.19
	E4	29.02-58.18	43.85	15.21	19.06-53.22	31.60**	22.16	19.58-53.22	33.55	21.76	19.06-51.88	29.84**		20.80	19.06-58.18	33.14		24.30
	BLUP	31.25-52.19	42.87	12.33	20.44-50.54	31.46**	19.38	22.36-47.92	33.03	18.77	20.44-50.54	30.07**		18.79	20.44-52.19	32.95		21.61
第2节间长度 2nd IL	E1	22.48-38.78	33.49	10.81	14.56-39.74	23.87**	19.74	15.96-39.74	25.41	19.10	14.56-37.26	22.47**		18.32	14.56-39.74	24.97		22.12
	E2	21.44-41.34	32.82	16.60	14.74-38.08	22.66**	20.26	14.74-38.08	23.92	20.20	14.84-35.22	21.54**		18.84	14.74-41.34	23.94		24.16
	E3	20.78-41.82	34.59	14.49	9.48-38.78	22.96**	22.66	13.74-38.78	24.18	22.33	9.48-35.76	21.83**		21.78	9.48-41.82	24.41		26.40
	E4	20.26-45.88	34.59	18.25	13.06-41.44	23.07**	21.10	14.14-41.44	24.73	20.63	13.06-34.62	21.57**		19.01	13.06-45.88	24.52		25.88
	BLUP	20.94-40.41	32.80	15.29	15.39-37.35	23.19**	19.30	15.39-37.35	24.57	18.88	15.46-34.48	21.94**		17.90	15.39-40.41	24.44		22.83
第3节间长度 3rd IL (cm)	E1	14.88-26.32	21.84	14.67	8.02-31.58	13.69**	22.80	9.62-31.58	14.49	22.47	8.02-20.62	12.96**		21.71	8.02-31.58	14.62		27.78
	E2	13.46-25.56	20.75	17.63	7.46-32.20	12.39**	24.79	8.52-32.20	13.00	25.84	7.46-23.34	11.84**		22.66	7.46-32.20	13.44		31.21
	E3	11.22-30.78	22.44	22.15	5.44-26.55	13.05**	27.76	7.50-25.90	13.56	28.23	5.44-26.55	12.58*		26.74	5.44-30.78	14.22		34.54
	E4	11.72-30.08	21.43	21.24	6.32-31.20	13.13**	24.54	8.84-31.20	13.91	24.75	6.32-25.94	12.41**		22.81	6.32-31.20	14.17		30.93
	BLUP	12.88-26.12	21.77	14.15	8.88-29.44	13.12**	21.87	9.57-29.44	13.78	22.10	8.88-21.90	12.54**		20.55	8.88-29.44	14.25		28.83
第4节间长度 4th IL (cm)	E1	8.82-17.90	14.15	15.86	5.48-22.24	9.45**	25.94	6.00-22.24	10.02	25.70	5.48-15.68	8.92**		24.86	5.48-22.24	9.99		28.54
	E2	5.84-17.00	12.82	21.48	3.38-19.84	8.15**	28.37	4.54-19.84	8.64	29.04	3.38-14.00	7.70**		26.38	3.38-19.84	8.74		32.39
	E3	8.36-20.54	14.49	23.06	1.45-20.38	8.66**	31.42	4.36-16.94	9.11	30.76	1.45-20.38	8.24**		31.41	1.45-20.54	9.39		36.21
	E4	7.28-22.93	13.56	24.31	4.06-19.02	8.59**	26.92	4.06-19.02	9.15	27.58	4.34-15.70	8.07**		24.48	4.06-22.93	9.22		32.07
	BLUP	8.30-17.88	13.15	16.82	5.51-17.69	8.76**	22.65	6.45-17.69	9.24	22.53	5.51-14.91	8.33**		21.55	5.51-17.88	9.34		26.76
第5节间长度 5th IL (cm)	E1	4.42-14.16	8.93	25.47	1.23-14.76	5.15**	38.39	2.25-14.76	5.47	38.90	1.23-11.15	4.86*		36.74	1.23-14.76	5.58		42.01
	E2	2.07-11.78	7.38	30.75	1.50-13.98	4.18**	41.08	1.50-13.98	4.43	43.70	1.50-9.26	3.96*		37.14	1.50-13.98	4.59		45.50
	E3	3.70-14.44	9.14	33.32	0.35-15.08	4.43**	49.19	0.35-10.96	4.53	48.47	0.35-15.08	4.35*		49.67	0.35-15.08	5.03		55.44
	E4	2.66-15.68	7.69	40.19	1.15-12.74	4.48**	39.73	1.15-12.74	4.77	41.00	1.20-12.02	4.22*		37.12	1.15-15.68	4.89		46.18
	BLUP	3.94-11.93	7.64	23.84	2.13-11.08	4.61**	28.03	2.74-11.08	4.81	29.06	2.13-10.04	4.44*		26.24	2.13-11.93	5.01		34.12

表2

图1

图2

图3

表3

株高及相关性状QTL位点"

性状 Traits	QTL标记 QTL marker	染色体 Chr.	位置 Position (Mb)	标记 Marker	环境 Environment	P值 <BOLD>P</BOLD> value (×10^-5)	表型贡献率 R² (%)	参考文献 References
株高 PH	QPH-2A	2A	59.28-115.28	2A_87283474	E1, E2, E3, E4, BLUP	1.63-6.10	4.88-5.78	[52]
	QPH-2D	2D	29.47-36.47	2D_32970833	E2, E4, BLUP	0.76-4.70	4.96-6.40	Rht8^[6]
	QPH-4A	4A	618.36-670.86	4A_644613024	E2, E4, BLUP	2.18-6.18	4.85-5.47	[53]
	QPH-4B	4B	30.82-55.82	4B_48317177	E4	9.82	3.64	Rht1^[3]
	QPH-4D	4D	0.92-20.92	4D_10917137	E1	1.47	5.88	Rht2^[3]
	QPH-5A	5A	560.95-608.95	5A_608950417	E2, E3, E4, BLUP	1.14-4.30	5.12-6.21	Rht9^[43]
	QPH-6D	6D	387.78-392.08	6D_389928252	E2, E4, BLUP	1.72-7.30	3.56-6.75
	QPH-7A	7A	682.23-702.23	7A_692232694	E1, E3, E4, BLUP	2.59-7.75	4.63-7.58
穗长SL	QSL-1A	1A	12.22-16.72	1A_14467852	E2, E4, BLUP	0.80-5.88	5.18-6.34	[61]
穗叶距 DSL	QDSL-5A	5A	318.46-336.24	5A_324460015	E1, E4, BLUP	0.31-8.95	4.62-6.99	[55]
	QDSL-4D	4D	0.92-20.92	4D_10917137	E1	9.77	4.76	Rht2^[3]
	QDSL-6A	6A	76.49-129.49	6A_102993644	E3	1.04	5.22	Rht25^[18]
穗下节间长度UIL	QUIL-6A	6A	76.49-129.49	6A_102993644	E3	1.49	5.04	Rht25^[18]
第2节间长度 2nd IL	Q2nd IL-2D	2D	29.47-36.47	2D_32970833	E4	9.69	4.64	Rht8^[6]
	Q2nd IL-4B	4B	40.82-55.82	4B_48317177	E1, E2, E3, BLUP	1.10-3.92	4.26-4.99	Rht1^[3]
	Q2nd IL-7A	7A	682.23-702.23	7A_692232694	E1, E2, E3, E4, BLUP	1.17-6.66	4.76-6.17
第3节间长度 3rd IL	Q3rd IL-1D	1D	262.94-274.14	1D_268540306	E1, E2, E4, BLUP	0.29-8.27	4.55-7.00
	Q3rd IL-2A	2A	59.28-115.28	2A_87283474	E2, E4, BLUP	1.18-3.60	5.01-5.93	[46]
	Q3rd IL-2B	2B	197.11-202.11	2B_202107777	E1, E2, BLUP	3.01-7.68	5.42-6.08	[58]
	Q3rd IL-2D	2D	29.47-36.47	2D_32970833	E2, E4, BLUP	1.34-4.35	4.89-5.95	Rht8^[6]
	Q3rd IL-3B	3B	0-42.16	3B_10662726	E2	9.87	4.54	Rht5^[57]
	Q3rd IL-4B	4B	30.82-55.82	4B_48317177	E1, E4, BLUP	4.82-9.57	3.48-3.85	Rht1^[3]
	Q3rd IL-4D	4D	18.55-38.55	4D_28547729	E4	1.17	6.15	Rht2^[3]
	Q3rd IL.6A	6A	558.85-611.85	6A_585345446	E2, E4, BLUP	3.14-7.49	4.99-5.37	[59]
	Q3rd IL-6D	6D	387.78-392.08	6D_389928252	E1, E2, E3, BLUP	4.35-7.25	3.77-5.04
	Q3rd IL-7A	7A	682.23-702.23	7A_692232694	E2, E3, E4, BLUP	0.54-2.72	5.47-6.56
	Q3rd IL-7B	7B	233.63-245.13	7B_239379204	E1, E4, BLUP	0.84-8.93	4.48-6.34	[62]
第4节间长度 4th IL	Q4th IL-2A	2A	59.28-115.28	2A_87283474	E1, E2, BLUP	1.99-8.31	4.62-5.72	[46]
	Q4th IL-2D	2D	29.47-36.47	2D_32970833	E2, E3, E4, BLUP	0.18-2.65	5.33-7.41	Rht8^[6]
	Q4th IL-3B	3B	9.28-72.28	3B_40776268	E4	2.05	5.50	Rht5^[57]
	Q4th IL-4B	4B	30.82-55.82	4B_48317177	E4	7.02	3.60	Rht1^[3]
	Q4th IL-4D	4D	18.55-38.55	4D_28547729	E4	2.00	5.57	Rht2^[3]
	Q4th IL-6D	6D	387.78-392.08	6D_389928252	E1, E2, BLUP	2.77-8.08	4.75-5.35
第5节间长度 5th IL	Q5th IL-1B	1B	544.60-558.35	1B_546854696	E1, E4, BLUP	1.53-3.23	4.70-5.63	[60]
	Q5th IL-2B	2B	419.99-429.99	2B_424009984	E1, E2, E4	1.87-8.05	4.52-5.34
	Q5th IL-5A.2	5A	552.57-564.57	5A_558574163	E2	1.00	7.52	Rht9^[54]
	Q5th IL-5A.4	5A	687.64-699.64	5A_693635094	E3	8.38	5.02	Rht12^[56]
	Q5th IL-5D	5D	494.40-496.40	5D_495395359	E1, E2, E3, BLUP	0.05-2.11	5.24-5.67	[63]
	Q5th IL-7A	7A	212.95-232.95	7A_222945332	E1, E4, BLUP	1.84-2.10	4.18-5.35	[4]

表3

图4

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基因 Gene	标记 Marker	引物序列 Primer sequence (5′-3′)	参考文献 References
Rht4	WMS317-F	TGCTAGCAATGCTCCGGGTAAC	[32]
Rht4	WMS317-R	TCACGAAACCTTTTCCTCCTCC	[32]
Rht5	BARC102-F	GGAGAGGACCTGCTAAAATCGAAGACA	[33]
Rht5	BARC102-R	GCGTTTACGGATCAGTGTTGGAGA	[33]
Rht8	WMC503-F	GCAATAGTTCCCGCAAGAAAAG	[34]
Rht8	WMC503-R	ATCAACTACCTCCAGATCCCGT
Rht9	BARC151-F	TGAGGAAAATGTCTCTATAGCATCC
Rht9	BARC151-R	CGCATAAACACCTTCGCTCTTCCACTC
Rht12	WMS291-F	CATCCCTACGCCACTCTGC	[35]
Rht12	WMS291-R	AATGGTATCTATTCCGACCCG	[35]
Rht13	WMS577-F	ATGGCATAATTTGGTGAAATTG	[36]
Rht13	WMS577-R	TGTTTCAAGCCCAACTTCTATT	[36]
Rht25	PlzAR1	GAGGCAGCAAAAGTGGAAGG	[7]
Rht25	PlzAF2	CTGTATATGCATGTGTGTCTC	[7]
Rht26	KASP518-A	GAAGGTGACCAAGTTCATGCTAGTGCCCACTACCGGTTCG	[20]
	KASP518-B	GAAGGTCGGAGTCAACGGATTAGTGCCCACTACCGGTTCA
	KASP518-C	GGATTGGAAAAGTGACCCGC

山西小麦矮秆基因的鉴定及株高遗传位点挖掘

Identification of Dwarf Genes and Mining of Plant Height Genetic Loci in Shanxi Wheat

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