QTL mapping and candidate gene analysis of leaf area in maize （Zea mays） under different watering environments

doi:10.11686/cyxb2020295

Abstract

Abstract:

Leaf area （LA） and its distribution influences the efficiency of photosynthesis and transpiration rate， and is also closely related to drought tolerance， planting density， degree of lodging and grain yield in maize （Zea mays）. In-depth analysis of the molecular mechanisms controlling LA under different moisture levels at different growth stages is of great significance for the breeding of drought tolerant and high-yielding new maize varieties. In this study， composite interval mapping （CIM） and mixed linear model mapping based on composite interval mapping （MCIM） was carried out across two F_2∶3 populations under eight different ‘environments’. Specifically， experiments were set up in Gansu Province between 1508 and 1785 m altitude at Wuwei and Zhangye in 2014 and Gulang and Jingtai in 2015， and each of the four experiments had contrasting fully watered and moisture deficit treatments. Quantitative trait loci （QTLs） for LA （determined by measuring the 10th-12th leaves in late vegetative and three ear-leaves in early reproductive growth stages） were analyzed in single environments and across all environments. The candidate genes in the stable QTLs （sQTLs） were identified and the corresponding gene functions were determined using the reference genome B73 RefGen_v3. A total of seven QTLs were identified by CIM mapping cross vegetative and reproductive growth stages of the two F_2∶3 populations in all eight environments， five of these in fully watered treatments， five in moisture deficit treatments and three shared by both fully watered and moisture deficit treatments. These QTLs exhibited dominance （81.0%）， partial-dominance （14.3%）， and over-dominance （4.7%） effects. Six joint QTLs for LA were found among all environments by joint analysis with MCIM， three from each of the two populations. One QTL was involved in a significant QTL by environment interaction （QTL×E； Bin 2.08-2.09）， and one significant epistasis （Bin 1.08-1.10 and Bin 2.08-2.09） was mapped with an additive by additive （AA） effect. Combining CIM and MCIM methods for further analysis， six stable QTLs （sQTLs） were detected in Bin 1.08-1.10， Bin 2.08-2.09， Bin 4.08-4.09， Bin 6.05， Bin 8.03， and Bin 10.03， and 12 candidate genes that regulated leaf development in maize were located in these sQTL intervals. From bioinformatic data， 75 candidate genes related to leaf development were collected and their phylogenetic tree constructed. The phylogenetic tree of these 75 genes comprised three major evolutionary branches， and the 12 candidate genes identified above were distributed on the three branches. These results lay a foundation for systematic understanding of the molecular mechanisms governing LA in different environments at different plant growth stages. These detected sQTLs identify important genomic regions for LA improvement， and the detected candidate genes can provide reference sequences for further gene cloning， functional analysis， and other breeding applications.

Key words: Zea mays, leaf area, drought, QTL, candidate gene

Xiao-qiang ZHAO, Yuan ZHONG, Wen-qi ZHOU. QTL mapping and candidate gene analysis of leaf area in maize （Zea mays） under different watering environments[J]. Acta Prataculturae Sinica, 2021, 30(5): 103-120.

Figures/Tables 11

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时期Stage	环境 Environment	双亲Parents		F₁杂交种 F₁Hybrid （H_LT）	F_2∶3群体F_2∶3 Population (POP_LT，H²=59.76%~64.96%)
时期Stage	环境 Environment	廊黄 Langhuang	TS141	F₁杂交种 F₁Hybrid （H_LT）	均值 Mean	变幅 Range	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
V₁₈	E₁	301.84±16.84C	642.41±26.20B	912.05±36.13A	510.92±49.92	291.79~869.50	9.77	-0.624	-0.147
	E₂	285.20±20.17C	463.53±21.72B	668.23±31.11A	455.85±46.04	257.14~826.57	10.10	0.370	0.245
	E₃	319.29±20.33C	667.80±24.29B	964.37±32.28A	547.90±46.85	328.50~895.18	8.55	0.462	0.103
	E₄	289.95±18.16C	480.04±22.75B	763.19±30.40A	449.26±49.17	260.02~831.84	10.95	0.911	-0.069
R₁	E₁	510.06±30.42C	937.51±40.46AB	1191.58±41.62A	611.86±65.30	340.30~1024.12	10.67	0.273	0.515
	E₂	437.83±34.70B	540.78±43.22AB	852.82±39.68A	519.92±69.49	309.62~971.75	13.37	0.519	-0.722
	E₃	537.52±39.95C	1014.05±42.13B	1389.28±48.94A	658.65±62.64	373.85~1159.13	9.51	0.070	0.116
	E₄	479.83±40.12c	601.03±43.77b	952.71±45.05a	541.16±68.81	359.81~989.07	12.72	-0.114	0.531
时期Stage	环境 Environment	双亲Parents		F₁杂交种 F₁Hybrid （H_CT）	F_2∶3群体F_2∶3 Population (POP_CT, H²=64.06%~59.53%)
时期Stage	环境 Environment	昌7-2 Chang7-2	TS141	F₁杂交种 F₁Hybrid （H_CT）	均值 Mean	变幅 Range	变异系数CV (%)	偏度Skewness	峰度Kurtosis
V₁₈	E₅	321.20±20.17C	639.20±28.93B	900.68±41.00A	475.80±50.13	289.03~846.22	10.54	0.417	0.505
	E₆	300.59±23.10c	491.12±29.56b	697.30±38.86a	430.78±48.80	248.49~812.16	11.33	0.084	0.622
	E₇	326.42±24.52C	687.88±25.11B	930.63±45.25A	527.41±53.96	319.75~864.51	10.23	-0.336	-0.916
	E₈	296.96±26.39C	519.23±24.15AB	711.21±40.18A	452.80±47.24	250.58~830.77	10.43	0.614	-0.110
R₁	E₅	538.37±37.25B	1015.16±46.02A	1197.20±47.61A	585.84±68.90	337.95~977.32	11.76	0.622	0.494
	E₆	436.80±39.11c	643.80±41.05b	908.57±41.19a	507.44±63.25	315.48~969.04	12.46	-0.191	-1.002
	E₇	552.29±32.48B	1029.93±42.23A	1013.00±45.37A	631.42±69.74	394.12~1194.79	11.04	-0.438	0.389
	E₈	457.52±36.49c	671.95±47.80b	856.19±37.42a	530.20±68.06	347.88~1018.21	12.84	-0.714	-0.116

时期Stage	环境 Environment	双亲Parents		F₁杂交种 F₁Hybrid （H_LT）	F_2∶3群体F_2∶3 Population (POP_LT，H²=59.76%~64.96%)
时期Stage	环境 Environment	廊黄 Langhuang	TS141	F₁杂交种 F₁Hybrid （H_LT）	均值 Mean	变幅 Range	变异系数 CV (%)	偏度 Skewness	峰度 Kurtosis
V₁₈	E₁	301.84±16.84C	642.41±26.20B	912.05±36.13A	510.92±49.92	291.79~869.50	9.77	-0.624	-0.147
	E₂	285.20±20.17C	463.53±21.72B	668.23±31.11A	455.85±46.04	257.14~826.57	10.10	0.370	0.245
	E₃	319.29±20.33C	667.80±24.29B	964.37±32.28A	547.90±46.85	328.50~895.18	8.55	0.462	0.103
	E₄	289.95±18.16C	480.04±22.75B	763.19±30.40A	449.26±49.17	260.02~831.84	10.95	0.911	-0.069
R₁	E₁	510.06±30.42C	937.51±40.46AB	1191.58±41.62A	611.86±65.30	340.30~1024.12	10.67	0.273	0.515
	E₂	437.83±34.70B	540.78±43.22AB	852.82±39.68A	519.92±69.49	309.62~971.75	13.37	0.519	-0.722
	E₃	537.52±39.95C	1014.05±42.13B	1389.28±48.94A	658.65±62.64	373.85~1159.13	9.51	0.070	0.116
	E₄	479.83±40.12c	601.03±43.77b	952.71±45.05a	541.16±68.81	359.81~989.07	12.72	-0.114	0.531
时期Stage	环境 Environment	双亲Parents		F₁杂交种 F₁Hybrid （H_CT）	F_2∶3群体F_2∶3 Population (POP_CT, H²=64.06%~59.53%)
时期Stage	环境 Environment	昌7-2 Chang7-2	TS141	F₁杂交种 F₁Hybrid （H_CT）	均值 Mean	变幅 Range	变异系数CV (%)	偏度Skewness	峰度Kurtosis
V₁₈	E₅	321.20±20.17C	639.20±28.93B	900.68±41.00A	475.80±50.13	289.03~846.22	10.54	0.417	0.505
	E₆	300.59±23.10c	491.12±29.56b	697.30±38.86a	430.78±48.80	248.49~812.16	11.33	0.084	0.622
	E₇	326.42±24.52C	687.88±25.11B	930.63±45.25A	527.41±53.96	319.75~864.51	10.23	-0.336	-0.916
	E₈	296.96±26.39C	519.23±24.15AB	711.21±40.18A	452.80±47.24	250.58~830.77	10.43	0.614	-0.110
R₁	E₅	538.37±37.25B	1015.16±46.02A	1197.20±47.61A	585.84±68.90	337.95~977.32	11.76	0.622	0.494
	E₆	436.80±39.11c	643.80±41.05b	908.57±41.19a	507.44±63.25	315.48~969.04	12.46	-0.191	-1.002
	E₇	552.29±32.48B	1029.93±42.23A	1013.00±45.37A	631.42±69.74	394.12~1194.79	11.04	-0.438	0.389
	E₈	457.52±36.49c	671.95±47.80b	856.19±37.42a	530.20±68.06	347.88~1018.21	12.84	-0.714	-0.116

群体 Population (QTL)	染色体 Chromosome	时期 Stage	环境 Environment	QTL 位置 QTL position		LOD	遗传效应 Genetic effect		基因方式 Gene action		贡献率 Contribution rate (R²， %)
群体 Population (QTL)	染色体 Chromosome	时期 Stage	环境 Environment	图距Graph distance (cM)	区间 Interval	LOD	加性 Additive	显性 Dominance	\|d/a\|	类型 Type	贡献率 Contribution rate (R²， %)
POP_LT
qLA-Ch.1-1	1	V₁₈	E₂	109.6	mmc0041~phi308707	5.47	1.58	1.62	1.03	D	8.11
qLA-Ch.1-1	1	V₁₈	E₃	109.6	mmc0041~phi308707	5.90	-1.51	0.93	0.62	PD	9.79
qLA-Ch.1-1	1	R₁	E₁	109.1	mmc0041~phi308707	3.93	1.18	-1.20	1.02	D	7.00
qLA-Ch.1-1	1	R₁	E₂	109.1	mmc0041~phi308707	4.11	1.30	-1.24	0.95	D	7.13
qLA-Ch.1-1	1	R₁	E₄	109.6	mmc0041~phi308707	6.95	1.97	-2.00	1.02	D	10.40
qLA-Ch.2-1	2	V₁₈	E₃	44.7	bnlg1909~bnlg1613	3.89	-2.16	2.95	1.37	OD	5.60
qLA-Ch.4-1	4	V₁₈	E₂	180.6	umc2041~umc2287	3.03	0.27	0.12	0.44	PD	3.43
qLA-Ch.4-1	4	R₁	E₂	180.6	umc2041~umc2287	4.55	0.99	-0.47	0.47	PD	6.12
qLA-Ch.8-1	8	V₁₈	E₁	45.1	bnlg1863~umc2075	4.00	1.19	-1.25	1.05	D	6.94
qLA-Ch.8-1	8	V₁₈	E₂	46.0	bnlg1863~umc2075	4.32	1.49	1.61	1.08	D	7.22
qLA-Ch.8-1	8	R₁	E₁	45.2	bnlg1863~umc2075	3.75	1.22	1.14	0.93	D	7.38
qLA-Ch.8-1	8	R₁	E₂	46.0	bnlg1863~umc2075	4.49	1.37	1.51	1.10	D	8.41
qLA-Ch.10-1	10	V₁₈	E₃	47.2	bnlg1655~umc1345	3.84	-1.28	-1.15	0.89	D	7.51
qLA-Ch.10-1	10	R₁	E₃	47.2	bnlg1655~umc1345	6.10	-1.71	-1.77	1.04	D	11.84
POP_CT
qLA-Ch.1-1	1	V₁₈	E₆	156.1	mmc0041~phi308707	3.98	-1.96	-2.03	1.03	D	6.05
qLA-Ch.1-1	1	R₁	E₆	156.1	mmc0041~phi308707	5.00	-1.89	2.10	1.11	D	6.89
qLA-Ch.1-1	1	R₁	E₈	156.1	mmc0041~phi308707	4.13	-2.14	-2.18	1.02	D	6.21
qLA-Ch.6-1	6	V₁₈	E₇	90.4	umc2040~bnlg1174a	3.95	-2.00	-2.22	1.11	D	6.02
qLA-Ch.6-1	6	V₁₈	E₈	90.4	umc2040~bnlg1174a	4.49	2.28	2.13	0.93	D	6.49
qLA-Ch.6-1	6	R₁	E₆	90.4	umc2040~bnlg1174a	7.28	-1.80	-1.71	0.95	D	9.33
qLA-Ch.6-1	6	R₁	E₈	90.4	umc2040~bnlg1174a	8.00	-2.82	-2.49	0.88	D	11.94

群体 Population (QTL)	染色体 Chromosome	时期 Stage	环境 Environment	QTL 位置 QTL position		LOD	遗传效应 Genetic effect		基因方式 Gene action		贡献率 Contribution rate (R²， %)
群体 Population (QTL)	染色体 Chromosome	时期 Stage	环境 Environment	图距Graph distance (cM)	区间 Interval	LOD	加性 Additive	显性 Dominance	\|d/a\|	类型 Type	贡献率 Contribution rate (R²， %)
POP_LT
qLA-Ch.1-1	1	V₁₈	E₂	109.6	mmc0041~phi308707	5.47	1.58	1.62	1.03	D	8.11
qLA-Ch.1-1	1	V₁₈	E₃	109.6	mmc0041~phi308707	5.90	-1.51	0.93	0.62	PD	9.79
qLA-Ch.1-1	1	R₁	E₁	109.1	mmc0041~phi308707	3.93	1.18	-1.20	1.02	D	7.00
qLA-Ch.1-1	1	R₁	E₂	109.1	mmc0041~phi308707	4.11	1.30	-1.24	0.95	D	7.13
qLA-Ch.1-1	1	R₁	E₄	109.6	mmc0041~phi308707	6.95	1.97	-2.00	1.02	D	10.40
qLA-Ch.2-1	2	V₁₈	E₃	44.7	bnlg1909~bnlg1613	3.89	-2.16	2.95	1.37	OD	5.60
qLA-Ch.4-1	4	V₁₈	E₂	180.6	umc2041~umc2287	3.03	0.27	0.12	0.44	PD	3.43
qLA-Ch.4-1	4	R₁	E₂	180.6	umc2041~umc2287	4.55	0.99	-0.47	0.47	PD	6.12
qLA-Ch.8-1	8	V₁₈	E₁	45.1	bnlg1863~umc2075	4.00	1.19	-1.25	1.05	D	6.94
qLA-Ch.8-1	8	V₁₈	E₂	46.0	bnlg1863~umc2075	4.32	1.49	1.61	1.08	D	7.22
qLA-Ch.8-1	8	R₁	E₁	45.2	bnlg1863~umc2075	3.75	1.22	1.14	0.93	D	7.38
qLA-Ch.8-1	8	R₁	E₂	46.0	bnlg1863~umc2075	4.49	1.37	1.51	1.10	D	8.41
qLA-Ch.10-1	10	V₁₈	E₃	47.2	bnlg1655~umc1345	3.84	-1.28	-1.15	0.89	D	7.51
qLA-Ch.10-1	10	R₁	E₃	47.2	bnlg1655~umc1345	6.10	-1.71	-1.77	1.04	D	11.84
POP_CT
qLA-Ch.1-1	1	V₁₈	E₆	156.1	mmc0041~phi308707	3.98	-1.96	-2.03	1.03	D	6.05
qLA-Ch.1-1	1	R₁	E₆	156.1	mmc0041~phi308707	5.00	-1.89	2.10	1.11	D	6.89
qLA-Ch.1-1	1	R₁	E₈	156.1	mmc0041~phi308707	4.13	-2.14	-2.18	1.02	D	6.21
qLA-Ch.6-1	6	V₁₈	E₇	90.4	umc2040~bnlg1174a	3.95	-2.00	-2.22	1.11	D	6.02
qLA-Ch.6-1	6	V₁₈	E₈	90.4	umc2040~bnlg1174a	4.49	2.28	2.13	0.93	D	6.49
qLA-Ch.6-1	6	R₁	E₆	90.4	umc2040~bnlg1174a	7.28	-1.80	-1.71	0.95	D	9.33
qLA-Ch.6-1	6	R₁	E₈	90.4	umc2040~bnlg1174a	8.00	-2.82	-2.49	0.88	D	11.94

群体 Population	染色体 Chromosome	时期 Stage	QTL位置QTL position			A	AE₁/AE₅	AE₂/AE₆	AE₃/AE₇	AE₄/AE₈	h²(A) (%)	h²(AE) (%)
群体 Population	染色体 Chromosome	时期 Stage	图距 Graph distance (cM)	区间距离 Interval distance (Mb)	区间 Interval	A	AE₁/AE₅	AE₂/AE₆	AE₃/AE₇	AE₄/AE₈	h²(A) (%)	h²(AE) (%)
POP_LT
qLA-Ch.1-1	1	V₁₈	109.3	17.51	mmc0041~phi308707	0.99	-	-	-	-	6.58	-
qLA-Ch.1-1	1	R₁	109.5	17.51	mmc0041~phi308707	0.63	-	-	-	-	4.84	-
qLA-J2-1	2	R₁	77.8	14.79	bnlg1233~bnlg1520	-1.90	-	0.66	-	-	9.20	4.52
qLA-Ch.8-1	8	V₁₈	46.0	0.39	bnlg1863~umc2075	1.03	-	-	-	-	6.68	-
qLA-Ch.8-1	8	R₁	45.8	0.39	bnlg1863~umc2075	0.78	-	-	-	-	5.04	-
POP_CT
qLA-Ch.1-1	1	V₁₈	156.0	17.51	mmc0041~phi308707	-0.70	-	-	-	-	4.89	-
qLA-Ch.1-1	1	R₁	156.1	17.51	mmc0041~phi308707	-0.84	-	-	-	-	5.02	-
qLA-J2-1	2	R₁	116.8	14.79	bnlg1233~bnlg1520	-1.43	-	-	-	-	6.00	-
qLA-Ch.6-1	6	V₁₈	90.4	11.12	umc2040~bnlg1174a	-0.66	-	-	-	-	4.82	-
qLA-Ch.6-1	6	R₁	90.4	11.12	umc2040~bnlg1174a	-0.91	-	-	-	-	5.09	-