玉米抗倒伏相关性状QTL的关联和连锁分析

doi:10.3724/SP.J.1006.2022.03072

Abstract

Abstract:

Lodging is one of the main factors affecting the grain yield and mechanized harvesting in maize. Dissecting the genetic basis of lodging related traits can provide a theoretical basis for high yield and mechanized harvest breeding of maize. In this study, genome-wide association study (GWAS) and linkage analysis were combined to identify the significant loci interrelated with lodging related traits using 153 inbred lines from China and abroad. We detected 5, 14, 16, and 21 SNPs significant SNPs related to stem strength, plant height, ear height, and ear height-to-plant height ratio, respectively. Among these significant SNPs, the maximum effect value of a single site was 13.24. Twenty-one QTLs related to lodging related traits were identified by linkage analysis, which explaining the phenotypic variations of 3.86%-16.58% in F₅population constructed by KA105 and KB020. Further, we noticed that two QTL intervals were coincided with the candidate intervals of association analysis. Finally, GRMZM2G105391, GRMZM2G014119, and GRMZM2G341410 candidate genes related to cell wall biosynthesis, cell division and elongation were predicted by functional annotation for these candidate regions. These results can provide a new reference for further analysis of the genetic basis of lodging resistance in maize.

Key words: maize, lodging, association analysis, linkage analysis

YU Rui-Su, TIAN Xiao-Kang, LIU Bin-Bin, DUAN Ying-Xin, LI Ting, ZHANG Xiu-Ying, ZHANG Xing-Hua, HAO Yin-Chuan, LI Qin, XUE Ji-Quan, XU Shu-Tu. Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize[J].Acta Agronomica Sinica, 2022, 48(1): 138-150.

Figures/Tables 9

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Correlated SNP with lodging resistance related traits"

SNP序号	染色体	位置	候选区间	-log₁₀(P)	效应值	性状
SNP ID	Chr.	Position	Candidate interval	-log₁₀(P)	Effect	Trait
SNP372	1	7,693,562	7,493,562-7,893,562	4.29	10.08	19EH, 19PH
SNP524	1	10,449,649	10,249,649-10,649,649	3.41	4.87	18EH, 18PH
SNP3638	1	84,326,155	84,126,155-84,526,155	4.81	-1.48	18SS, SS-BLUP
SNP6691	1	205,781,890	205,581,890-205,981,890	3.73	-0.01	19EH/PH, EH/PH-BLUP
SNP8730	1	253,324,984	253,124,984-253,524,984	3.28	7.56	19PH, PH-BLUP
SNP11723	2	13,290,858	13,090,858-13,490,858	3.59	9.47	19EH, 19PH
SNP13557	2	53,646,990	53,446,990-53,846,990	3.06	-5.12	18EH, 19EH
SNP19390	2	233,508,755	233,308,755-233,708,755	3.31	8.17	18PH,19PH
SNP20574	3	18,803,909	18,603,909-19,003,909	3.58	-0.02	19EH/PH, EH/PH-BLUP
SNP20816	3	24,476,830	24,276,830-24,676,830	4.23	3.99	19SS, SS-BLUP
SNP24414	3	155,835,074	155,635,074-156,035,074	4.18	-0.02	19EH/PH,19EH
SNP28310	4	10,227,629	10,027,629-10,427,629	4.72	4.48	18PH, 19PH, PH-BLUP
SNP29286	4	33,460,646	33,260,646-33,660,646	3.07	-9.27	19PH, PH-BLUP
SNP29306	4	33,912,195	33,712,195-34,112,195	4.23	-13.25	19PH, 19EH
SNP29662	4	43,179,107	42,979,107-43,379,107	3.06	7.25	19PH, 19EH
SNP30918	4	107,290,607	107,090,607-107,490,607	3.82	-0.04	19EH/PH, EH/PH-BLUP
SNP36977	5	27,793,091	27,593,091-27,993,091	3.50	-0.01	19EH/PH, EH/PH-BLUP
SNP37167	5	32,584,178	32,384,178-32,784,178	3.26	-0.02	19EH/PH, EH/PH-BLUP
SNP38017	5	61,705,387	61,505,387-61,905,387	4.11	-0.02	19EH/PH, EH/PH-BLUP
SNP38046	5	62,710,291	62,510,291-62,910,291	3.28	-0.02	19EH/PH, EH/PH-BLUP
SNP38174	5	68,434,295	68,234,295-68,634,295	4.32	-0.01	19EH/PH, EH/PH-BLUP
SNP38176	5	68,449,337	68,249,337-68,649,337	4.37	-0.01	19EH/PH, EH/PH-BLUP
SNP38400	5	78,025,941	77,825,941-78,225,941	3.62	-0.01	19EH/PH, EH/PH-BLUP
SNP39705	5	141,210,709	141,010,709-141,410,709	3.20	0.01	19EH/PH, EH/PH-BLUP
SNP40214	5	157,008,514	156,808,514-157,208,514	3.38	2.89	19SS, SS-BLUP
SNP40603	5	167,979,920	167,779,920-168,179,920	3.44	-0.01	19EH/PH, EH/PH-BLUP
SNP44092	6	45,709,401	45,509,401-45,909,401	3.22	-4.54	18EH, 18PH
SNP45353	6	96,088,816	95,888,816-96,288,816	3.40	3.70	19EH, EH-BLUP
SNP48778	7	1,222,716	1,022,716-1,422,716	3.02	-8.07	19EH, 19PH
SNP49397	7	14,735,621	14,535,621-14,935,621	3.99	2.30	18SS, SS-BLUP
SNP50621	7	75,380,048	75,180,048-75,580,048	6.01	2.00	18SS, SS-BLUP
SNP54911	8	13,140,414	12,940,414-13,340,414	3.41	-0.01	19EH/PH, EH/PH-BLUP
SNP56153	8	70,742,498	70,542,498-70,942,498	4.30	-0.03	19EH/PH, EH/PH-BLUP
SNP57890	8	129,488,487	129,288,487-129,688,487	4.14	-9.73	18EH, 19EH, EH-BLUP
						18PH, 19PH, PH-BLUP
SNP58030	8	133,307,178	133,107,178-133,507,178	4.78	-6.36	18EH, 19EH, 19PH
SNP58106	8	135,487,306	135,287,306-135,687,306	3.46	0.01	19EH/PH, EH/PH-BLUP
SNP58751	8	152,898,327	152,698,327-153,098,327	4.62	0.02	18EH/PH, EH/PH-BLUP
SNP59767	8	172,230,824	172,030,824-172,430,824	3.83	4.61	19EH,19PH
SNP59786	8	172,434,870	172,234,870-172,634,870	3.23	0.01	18EH, EH/PH-BLUP
SNP62666	9	89,001,322	88,801,322-89,201,322	3.28	-0.01	19EH/PH, EH/PH-BLUP
SNP62670	9	89,192,523	88,992,523-89,392,523	3.46	-0.02	19EH/PH, EH/PH-BLUP
SNP62676	9	89,529,835	89,329,835-89,729,835	3.73	-0.01	19EH/PH, EH/PH-BLUP
SNP62844	9	93,667,191	93,467,191-93,867,191	3.13	4.19	18EH, 19EH
SNP64186	9	129,539,571	129,339,571-129,739,571	3.26	3.90	18EH, 19EH

Table 3

Table 4

Table 5

Fig. 3

Table 6

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性状 Trait	年份 Year	范围 Range	平均值±标准差 Mean±SD	偏度 Skewness	峰度 Kurtosis	变异系数 CV (%)
茎秆强度	2018	32.99-66.23	50.21±6.24	0.12	-0.01	12.43
SS	2019	33.34-72.28	53.3±7.57	-0.08	-0.17	14.20
	SS-BLUP	43.74-60.62	52.04±3.32	0.24	0.13	6.38
株高	2018	170.30-280.70	221.92±23.11	0.28	-0.37	10.41
PH	2019	143.00-252.20	200.99±21.56	0.13	-0.42	10.73
	PH-BLUP	160.99-277.91	212.22±20.14	0.41	0.12	9.49
穗位高	2018	48.00-108.30	79.73±12.58	-0.21	-0.28	15.78
EH	2019	49.00-108.30	70.95±9.69	0.3	0.79	13.66
	EH-BLUP	53.08-110.48	75.88±9.82	0.38	0.98	12.94
穗位系数	2018	0.26-0.53	0.40±0.05	0.31	0.98	12.41
EH/PH	2019	0.25-0.47	0.35±0.04	0.4	0.82	10.47
	EH/PH-BLUP	0.28-0.46	0.35±0.03	0.5	0.87	9.49

变异 Variation	茎秆强度SS		株高PH		穗位高EH		穗位系数EH/PH
变异 Variation	MS	F	MS	F	MS	F	MS	F
基因型Genotypes (G)	119.15	2.24^***	1756.59	16.72^***	401.50	10.49^***	0.005	8.90^***
年份Year	1430.55	26.24^***	65,572.72	624.12^***	12,290.33	321.08^***	0.007	12.06^***
基因型×年份G×Year	63.29	1.19	221.13	2.10^***	77.43	2.02^***	0.001	1.81^***
误差Error	53.14		105.06		38.28		0.001
遗传力H² (%)	72.62		92.77		89.26		86.96

性状 Trait	环境 Environment	亲本 Parents		RILs群体 RILs population
		KA105	KB020	范围 Range	平均数±标准差 Mean±SD	偏度 Skewness	峰度 Kurtosis	变异系数 CV (%)
		茎秆强度	YU	55.78 b	63.30 a	30.44-74.01	53.24±8.32	-0.20	0.02	15.62
SS	HZ	47.96	51.41	35.09-65.69	49.92±6.33	-0.11	-0.35	12.68
	BLUP	51.87 b	57.35 a	29.33-62.81	51.28±4.51	-0.14	-0.07	8.79
株高	YU	223.90	234.70	159.90-275.10	222.37±28.25	-0.23	-0.29	12.70
EH	HZ	201.10 b	254.44 a	145.20-300.00	217.86±24.03	-0.38	1.09	11.03
	BLUP	213.00 b	244.54 a	158.90-281.24	219.78±21.95	-0.16	-0.10	9.99
穗位高	YU	65.70	62.60	38.50-94.80	72.60±10.98	-0.11	-0.42	15.12
PH	HZ	58.80 b	76.67 a	42.50-96.50	68.15±11.51	-0.08	-0.39	16.88
	BLUP	62.25 b	69.82 a	49.63-90.21	70.30±9.05	-0.11	-0.54	12.88
穗位系数	YU	0.29	0.26	0.22-0.45	0.33±0.03	-0.01	0.92	10.17
EH/PH	HZ	0.29	0.30	0.20-0.43	0.31±0.03	0.01	0.55	12.35
	BLUP	0.29 b	0.27 a	0.23-0.42	0.31±0.03	0.09	0.79	8.50

变异	茎秆强度SS		株高PH		穗位高EH		穗位系数EH/PH
Variation	MS	F	MS	F	MS	F	MS	F
基因型 Genotype (G)	157.78	4.96^***	2429.31	11.75^***	431.22	11.75^***	0.004	2.64^***
环境 Environment (E)	3748.35	117.72^***	5380.57	26.03^***	4153.35	26.03^***	0.150	95.67^***
基因型×环境 G×E	46.94	1.47^***	274.35	1.33^**	64.73	1.32^*	0.003	1.85^***
误差 Error	31.84		206.70		52.48		0.002
遗传力 H² (%)	83.40		92.80		90.50		66.67

性状		QTL		染色体		左翼标记		右翼标记		环境		LOD		贡献率		加性效应
Trait		QTL		Chr.		Left marker		Right marker		Environment		LOD		R² (%)		Add
茎秆强度		qSS5-1		5		5_140763773		5_140763857		YU		4.22		9.12		2.46
SS		qSS5-2		5		5_156167500		5_157012388		BLUP		10.35		16.58		2.02
		qSS5-3		5		5_158723309		5_159130066		HZ		7.66		9.99		2.39
		qSS5-4		5		5_178122149		5_179051498		HZ		4.14		5.22		-1.73
		qSS5-5		5		5_144226809		5_181226757		BLUP		3.59		5.52		-1.19
		qSS5-6		5		5_199338390		5_199672364		HZ		4.38		5.53		1.81
		qSS6		6		6_67861806		6_68984948		YU		4.24		9.05		-2.47
										BLUP		3.43		5.05		-1.13
株高		qPH1-1		1		1_112646044		1_115306380		YU		24.56		9.40		18.83
PH		qPH1-2		1		1_120199828		1_160600750		YU		36.96		16.53		-25.07
										BLUP		6.25		5.31		-6.36
		qPH2-1		2		2_9013265		2_10394566		HZ		3.97		4.46		-5.66
		qPH2-2		2		2_18731394		2_19945073		BLUP		5.16		4.32		-5.70
性状	QTL		染色体		左翼标记		右翼标记		环境		LOD		贡献率		加性效应
Trait	QTL		Chr.		Left marker		Right marker		Environment		LOD		R² (%)		Add
	qPH5-1		5		5_135497925		5_135725252		BLUP		5.39		4.52		-5.80
	qPH5-2		5		5_164963962		5_166327830		BLUP		10.49		9.44		8.40
	qPH5-3		5		5_1683956		5_1727799		HZ		3.45		3.86		-5.27
	qPH6		6		6_68984948		6_128701322		HZ		5.16		7.94		-7.65
									YU		12.43		4.83		-13.55
									BLUP		11.76		11.63		-9.44
	qPH7		7		7_11482224		7_14968823		BLUP		4.78		4.04		5.50
穗位高	qEH1		1		1_107294393		1_109785426		HZ		4.88		9.07		-3.58
EH									YU		5.33		5.96		-3.06
									BLUP		7.16		10.16		-3.11
	qEH2		2		2_190284923		2_192872800		YU		4.81		5.39		-2.90
	qEH6-1		6		6_68984948		6_128701322		YU		7.56		11.33		-4.25
	qEH6-2		6		6_112247546		6_117497921		BLUP		3.65		5.00		-2.18
	qEH10		10		10_13473790		10_18247431		YU		4.02		4.49		2.66
									BLUP		3.65		5.05		2.20

Dissecting the genetic architecture of lodging related traits by genome-wide association study and linkage analysis in maize

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